Journal Article
. 2013 Sep; 45(10):1127-33.
doi: 10.1038/ng.2762.

Emerging landscape of oncogenic signatures across human cancers

Giovanni Ciriello 1 Martin L Miller  Bülent Arman Aksoy  Yasin Senbabaoglu  Nikolaus Schultz  Chris Sander  
Affiliations
  • PMID: 24071851
  •     34 References
  •     566 citations

Abstract

Cancer therapy is challenged by the diversity of molecular implementations of oncogenic processes and by the resulting variation in therapeutic responses. Projects such as The Cancer Genome Atlas (TCGA) provide molecular tumor maps in unprecedented detail. The interpretation of these maps remains a major challenge. Here we distilled thousands of genetic and epigenetic features altered in cancers to ∼500 selected functional events (SFEs). Using this simplified description, we derived a hierarchical classification of 3,299 TCGA tumors from 12 cancer types. The top classes are dominated by either mutations (M class) or copy number changes (C class). This distinction is clearest at the extremes of genomic instability, indicating the presence of different oncogenic processes. The full hierarchy shows functional event patterns characteristic of multiple cross-tissue groups of tumors, termed oncogenic signature classes. Targetable functional events in a tumor class are suggestive of class-specific combination therapy. These results may assist in the definition of clinical trials to match actionable oncogenic signatures with personalized therapies.

Lessons from the cancer genome.
Levi A Garraway, Eric S Lander.
Cell, 2013 Apr 02; 153(1). PMID: 23540688
Highly Cited. Review.
Tumor-associated zinc finger mutations in the CTCF transcription factor selectively alter tts DNA-binding specificity.
Galina N Filippova, Chen-Feng Qi, +19 authors, Victor V Lobanenkov.
Cancer Res, 2002 Jan 10; 62(1). PMID: 11782357
Module identification in bipartite and directed networks.
Roger Guimerà, Marta Sales-Pardo, Luís A Nunes Amaral.
Phys Rev E Stat Nonlin Soft Matter Phys, 2007 Oct 13; 76(3 Pt 2). PMID: 17930301    Free PMC article.
International network of cancer genome projects.
International Cancer Genome Consortium, Thomas J Hudson, +413 authors, Huanming Yang.
Nature, 2010 Apr 16; 464(7291). PMID: 20393554    Free PMC article.
Highly Cited.
Precision oncology: an overview.
Levi A Garraway, Jaap Verweij, Karla V Ballman.
J Clin Oncol, 2013 Apr 17; 31(15). PMID: 23589545
Highly Cited.
Increase of ZASC1 gene copy number in recurrent oral carcinoma.
W-F Chiang, P-S Hung, +5 authors, S-C Lin.
Oral Dis, 2010 Jul 22; 17(1). PMID: 20646234
Integrated genomic analyses of ovarian carcinoma.
Cancer Genome Atlas Research Network.
Nature, 2011 Jul 02; 474(7353). PMID: 21720365    Free PMC article.
Highly Cited.
Patterns of somatic mutation in human cancer genomes.
Christopher Greenman, Philip Stephens, +63 authors, Michael R Stratton.
Nature, 2007 Mar 09; 446(7132). PMID: 17344846    Free PMC article.
Highly Cited.
Identification of ZASC1 encoding a Krüppel-like zinc finger protein as a novel target for 3q26 amplification in esophageal squamous cell carcinomas.
Issei Imoto, Yasuhiro Yuki, +4 authors, Johji Inazawa.
Cancer Res, 2003 Oct 03; 63(18). PMID: 14522885
An exceptionally conserved transcriptional repressor, CTCF, employs different combinations of zinc fingers to bind diverged promoter sequences of avian and mammalian c-myc oncogenes.
G N Filippova, S Fagerlie, +6 authors, V V Lobanenkov.
Mol Cell Biol, 1996 Jun 01; 16(6). PMID: 8649389    Free PMC article.
Highly Cited.
Sequence analysis of mutations and translocations across breast cancer subtypes.
Shantanu Banerji, Kristian Cibulskis, +44 authors, Matthew Meyerson.
Nature, 2012 Jun 23; 486(7403). PMID: 22722202    Free PMC article.
Highly Cited.
Blockbuster dreams for Pfizer's CDK inhibitor.
Malini Guha.
Nat Biotechnol, 2013 Mar 09; 31(3). PMID: 23471056
Genomics-driven oncology: framework for an emerging paradigm.
Levi A Garraway.
J Clin Oncol, 2013 Apr 17; 31(15). PMID: 23589557
Highly Cited. Review.
Epigenetic gene silencing in cancer: the DNA hypermethylome.
Manel Esteller.
Hum Mol Genet, 2007 Sep 26; 16 Spec No 1. PMID: 17613547
Highly Cited. Review.
Cyclin D as a therapeutic target in cancer.
Elizabeth A Musgrove, C Elizabeth Caldon, +2 authors, Robert L Sutherland.
Nat Rev Cancer, 2011 Jul 08; 11(8). PMID: 21734724
Highly Cited. Review.
Fast algorithm for detecting community structure in networks.
M E J Newman.
Phys Rev E Stat Nonlin Soft Matter Phys, 2004 Jul 13; 69(6 Pt 2). PMID: 15244693
Highly Cited.
ARID1A mutations in cancer: another epigenetic tumor suppressor?
Jennifer N Wu, Charles W M Roberts.
Cancer Discov, 2012 Dec 05; 3(1). PMID: 23208470    Free PMC article.
Highly Cited. Review.
Comprehensive genomic characterization defines human glioblastoma genes and core pathways.
Cancer Genome Atlas Research Network.
Nature, 2008 Sep 06; 455(7216). PMID: 18772890    Free PMC article.
Highly Cited.
Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia.
Cancer Genome Atlas Research Network, Timothy J Ley, +98 authors, Greg Eley.
N Engl J Med, 2013 May 03; 368(22). PMID: 23634996    Free PMC article.
Highly Cited.
Comprehensive molecular portraits of human breast tumours.
Cancer Genome Atlas Network.
Nature, 2012 Sep 25; 490(7418). PMID: 23000897    Free PMC article.
Highly Cited.
Resolution limit in community detection.
Santo Fortunato, Marc Barthélemy.
Proc Natl Acad Sci U S A, 2006 Dec 28; 104(1). PMID: 17190818    Free PMC article.
Highly Cited.
The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.
Ethan Cerami, Jianjiong Gao, +12 authors, Nikolaus Schultz.
Cancer Discov, 2012 May 17; 2(5). PMID: 22588877    Free PMC article.
Highly Cited.
Integrated genomic characterization of endometrial carcinoma.
Cancer Genome Atlas Research Network, Cyriac Kandoth, +16 authors, Douglas A Levine.
Nature, 2013 May 03; 497(7447). PMID: 23636398    Free PMC article.
Highly Cited.
Differential effect of zinc finger deletions on the binding of CTCF to the promoter of the amyloid precursor protein gene.
W W Quitschke, M J Taheny, L J Fochtmann, A A Vostrov.
Nucleic Acids Res, 2000 Aug 23; 28(17). PMID: 10954607    Free PMC article.
MuSiC: identifying mutational significance in cancer genomes.
Nathan D Dees, Qunyuan Zhang, +9 authors, Li Ding.
Genome Res, 2012 Jul 05; 22(8). PMID: 22759861    Free PMC article.
Highly Cited.
Cancer genome landscapes.
Bert Vogelstein, Nickolas Papadopoulos, +3 authors, Kenneth W Kinzler.
Science, 2013 Mar 30; 339(6127). PMID: 23539594    Free PMC article.
Highly Cited. Review.
PI3K/AKT/mTOR inhibitors in patients with breast and gynecologic malignancies harboring PIK3CA mutations.
Filip Janku, Jennifer J Wheler, +11 authors, Razelle Kurzrock.
J Clin Oncol, 2012 Jan 25; 30(8). PMID: 22271473    Free PMC article.
Highly Cited.
Modularity and community structure in networks.
M E J Newman.
Proc Natl Acad Sci U S A, 2006 May 26; 103(23). PMID: 16723398    Free PMC article.
Highly Cited.
Expression of p270 (ARID1A), a component of human SWI/SNF complexes, in human tumors.
Xiaomei Wang, Norman G Nagl, +3 authors, Elizabeth Moran.
Int J Cancer, 2004 Sep 24; 112(4). PMID: 15382044
Efficient modularity optimization by multistep greedy algorithm and vertex mover refinement.
Philipp Schuetz, Amedeo Caflisch.
Phys Rev E Stat Nonlin Soft Matter Phys, 2008 Jun 04; 77(4 Pt 2). PMID: 18517695
Comprehensive molecular characterization of human colon and rectal cancer.
Cancer Genome Atlas Network.
Nature, 2012 Jul 20; 487(7407). PMID: 22810696    Free PMC article.
Highly Cited.
Comprehensive genomic characterization of squamous cell lung cancers.
Cancer Genome Atlas Research Network.
Nature, 2012 Sep 11; 489(7417). PMID: 22960745    Free PMC article.
Highly Cited.
Modularity and community detection in bipartite networks.
Michael J Barber.
Phys Rev E Stat Nonlin Soft Matter Phys, 2008 Feb 01; 76(6 Pt 2). PMID: 18233893
Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma.
Rameen Beroukhim, Gad Getz, +28 authors, William R Sellers.
Proc Natl Acad Sci U S A, 2007 Dec 14; 104(50). PMID: 18077431    Free PMC article.
Highly Cited.
Genetics: genomic alteration profiles across different cancer types.
Vanessa Marchesi.
Nat Rev Clin Oncol, 2013 Oct 09; 10(12). PMID: 24101122
Cancer genomics: A panoramic view of cancer.
Magdalena Skipper.
Nat Rev Genet, 2013 Oct 19; 14(11). PMID: 24136505
Cancer genomics: A panoramic view of cancer.
Magdalena Skipper.
Nat Rev Cancer, 2013 Oct 25; 13(11). PMID: 24154715
Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine.
Benjamin J Raphael, Jason R Dobson, Layla Oesper, Fabio Vandin.
Genome Med, 2014 Feb 01; 6(1). PMID: 24479672    Free PMC article.
Highly Cited. Review.
Patterns and processes of somatic mutations in nine major cancers.
Peilin Jia, William Pao, Zhongming Zhao.
BMC Med Genomics, 2014 Feb 21; 7. PMID: 24552141    Free PMC article.
Collection, integration and analysis of cancer genomic profiles: from data to insight.
Jianjiong Gao, Giovanni Ciriello, Chris Sander, Nikolaus Schultz.
Curr Opin Genet Dev, 2014 Mar 04; 24. PMID: 24584084    Free PMC article.
Review.
Reversing Platinum Resistance in High-Grade Serous Ovarian Carcinoma: Targeting BRCA and the Homologous Recombination System.
W Ruprecht Wiedemeyer, Jessica A Beach, Beth Y Karlan.
Front Oncol, 2014 Mar 14; 4. PMID: 24624361    Free PMC article.
Review.
Hypomethylation of the CTCFL/BORIS promoter and aberrant expression during endometrial cancer progression suggests a role as an Epi-driver gene.
Erling A Hoivik, Kanthida Kusonmano, +10 authors, Helga B Salvesen.
Oncotarget, 2014 Mar 25; 5(4). PMID: 24658009    Free PMC article.
Modeling mutual exclusivity of cancer mutations.
Ewa Szczurek, Niko Beerenwinkel.
PLoS Comput Biol, 2014 Mar 29; 10(3). PMID: 24675718    Free PMC article.
The genomic landscape of mantle cell lymphoma is related to the epigenetically determined chromatin state of normal B cells.
Jenny Zhang, Dereje Jima, +15 authors, Sandeep S Dave.
Blood, 2014 Apr 01; 123(19). PMID: 24682267    Free PMC article.
Highly Cited.
Mechanisms of base substitution mutagenesis in cancer genomes.
Albino Bacolla, David N Cooper, Karen M Vasquez.
Genes (Basel), 2014 Apr 08; 5(1). PMID: 24705290    Free PMC article.
Tumor heterogeneity confounds and illuminates: assessing the implications.
Maria Kleppe, Ross L Levine.
Nat Med, 2014 Apr 09; 20(4). PMID: 24710377
Principles and methods of integrative genomic analyses in cancer.
Vessela N Kristensen, Ole Christian Lingjærde, +3 authors, Anne-Lise Børresen-Dale.
Nat Rev Cancer, 2014 Apr 25; 14(5). PMID: 24759209
Highly Cited. Review.
A fine-scale dissection of the DNA double-strand break repair machinery and its implications for breast cancer therapy.
Chao Liu, Sriganesh Srihari, +4 authors, Kum Kum Khanna.
Nucleic Acids Res, 2014 May 06; 42(10). PMID: 24792170    Free PMC article.
Review.
Clonal heterogeneity of lymphoid malignancies correlates with poor prognosis.
Miyuki Suguro, Noriaki Yoshida, +13 authors, Masao Seto.
Cancer Sci, 2014 May 13; 105(7). PMID: 24815991    Free PMC article.
Characterization of the genomic architecture and mutational spectrum of a small cell prostate carcinoma.
Alan F Scott, David W Mohr, +3 authors, Gregory S Liptak.
Genes (Basel), 2014 May 16; 5(2). PMID: 24823478    Free PMC article.
Use of RNAi screens to uncover resistance mechanisms in cancer cells and identify synthetic lethal interactions.
Paul Diehl, Donato Tedesco, Alex Chenchik.
Drug Discov Today Technol, 2014 May 23; 11. PMID: 24847648    Free PMC article.
Review.
mTORC2 in the center of cancer metabolic reprogramming.
Kenta Masui, Webster K Cavenee, Paul S Mischel.
Trends Endocrinol Metab, 2014 May 27; 25(7). PMID: 24856037    Free PMC article.
Multi-marker Solid Tumor Panels Using Next-generation Sequencing to Direct Molecularly Targeted Therapies.
Michael Marrone, Kelly K Filipski, +2 authors, Andrew N Freedman.
PLoS Curr, 2014 Jun 07; 6. PMID: 24904755    Free PMC article.
Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction.
Hilary S Parker, Jeffrey T Leek, +5 authors, Elana J Fertig.
Bioinformatics, 2014 Jun 08; 30(19). PMID: 24907368    Free PMC article.
JARID1B is a luminal lineage-driving oncogene in breast cancer.
Shoji Yamamoto, Zhenhua Wu, +19 authors, Kornelia Polyak.
Cancer Cell, 2014 Jun 18; 25(6). PMID: 24937458    Free PMC article.
Highly Cited.
The MAPK pathway across different malignancies: a new perspective.
Mauricio Burotto, Victoria L Chiou, Jung-Min Lee, Elise C Kohn.
Cancer, 2014 Jun 21; 120(22). PMID: 24948110    Free PMC article.
Highly Cited. Review.
CDK4/6 and IGF1 receptor inhibitors synergize to suppress the growth of p16INK4A-deficient pancreatic cancers.
Andreas M Heilmann, Rushika M Perera, +4 authors, Nicholas J Dyson.
Cancer Res, 2014 Jul 06; 74(14). PMID: 24986516    Free PMC article.
Mei-P26 mediates tissue-specific responses to the Brat tumor suppressor and the dMyc proto-oncogene in Drosophila.
Ana Ferreira, Laura Boulan, Lidia Perez, Marco Milán.
Genetics, 2014 Jul 06; 198(1). PMID: 24990993    Free PMC article.
e-Driver: a novel method to identify protein regions driving cancer.
Eduard Porta-Pardo, Adam Godzik.
Bioinformatics, 2014 Jul 30; 30(21). PMID: 25064568    Free PMC article.
Toward a systematic understanding of cancers: a survey of the pan-cancer study.
Zhaoqi Liu, Shihua Zhang.
Front Genet, 2014 Jul 30; 5. PMID: 25071824    Free PMC article.
Review.
Neurofibromatosis type 1 molecular diagnosis: what can NGS do for you when you have a large gene with loss of function mutations?
Eric Pasmant, Béatrice Parfait, +9 authors, Dominique Vidaud.
Eur J Hum Genet, 2014 Jul 31; 23(5). PMID: 25074460    Free PMC article.
Cancer: Directions for the drivers.
Greg Gibson.
Nature, 2014 Aug 01; 512(7512). PMID: 25079332
Comparison of gene expression patterns across 12 tumor types identifies a cancer supercluster characterized by TP53 mutations and cell cycle defects.
E Martínez, K Yoshihara, +3 authors, R G W Verhaak.
Oncogene, 2014 Aug 05; 34(21). PMID: 25088195    Free PMC article.
SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution.
Christopher A Miller, Brian S White, +14 authors, Li Ding.
PLoS Comput Biol, 2014 Aug 08; 10(8). PMID: 25102416    Free PMC article.
Highly Cited.
Development and translational imaging of a TP53 porcine tumorigenesis model.
Jessica C Sieren, David K Meyerholz, +15 authors, Christopher S Rogers.
J Clin Invest, 2014 Aug 12; 124(9). PMID: 25105366    Free PMC article.
Lessons learned from the study of 10,000 patients with soft tissue sarcoma.
Murray F Brennan, Cristina R Antonescu, Nicole Moraco, Samuel Singer.
Ann Surg, 2014 Aug 15; 260(3). PMID: 25115417    Free PMC article.
Elevated APOBEC3B correlates with poor outcomes for estrogen-receptor-positive breast cancers.
Anieta M Sieuwerts, Scooter Willis, +11 authors, John W M Martens.
Horm Cancer, 2014 Aug 16; 5(6). PMID: 25123150    Free PMC article.
Highly Cited.
Surveying Recent Themes in Translational Bioinformatics: Big Data in EHRs, Omics for Drugs, and Personal Genomics.
J C Denny.
Yearb Med Inform, 2014 Aug 16; 9. PMID: 25123743    Free PMC article.
Review.
Reporting tumor molecular heterogeneity in histopathological diagnosis.
Andrea Mafficini, Eliana Amato, +14 authors, Aldo Scarpa.
PLoS One, 2014 Aug 16; 9(8). PMID: 25127237    Free PMC article.
MYC and EGR1 synergize to trigger tumor cell death by controlling NOXA and BIM transcription upon treatment with the proteasome inhibitor bortezomib.
Matthias Wirth, Natasa Stojanovic, +7 authors, Günter Schneider.
Nucleic Acids Res, 2014 Aug 26; 42(16). PMID: 25147211    Free PMC article.
Genome-driven integrated classification of breast cancer validated in over 7,500 samples.
H Raza Ali, Oscar M Rueda, +4 authors, Carlos Caldas.
Genome Biol, 2014 Aug 29; 15(8). PMID: 25164602    Free PMC article.
Highly Cited.
A systematic approach to identify novel cancer drug targets using machine learning, inhibitor design and high-throughput screening.
Jouhyun Jeon, Satra Nim, +5 authors, Philip M Kim.
Genome Med, 2014 Aug 29; 6(7). PMID: 25165489    Free PMC article.
ATR inhibition preferentially targets homologous recombination-deficient tumor cells.
M Krajewska, R S N Fehrmann, +4 authors, M A T M van Vugt.
Oncogene, 2014 Sep 02; 34(26). PMID: 25174396
RTCGAToolbox: a new tool for exporting TCGA Firehose data.
Mehmet Kemal Samur.
PLoS One, 2014 Sep 03; 9(9). PMID: 25181531    Free PMC article.
Highly Cited.
Cancer systems biology: embracing complexity to develop better anticancer therapeutic strategies.
W Du, O Elemento.
Oncogene, 2014 Sep 16; 34(25). PMID: 25220419
Review.
Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication.
Eve Shinbrot, Erin E Henninger, +10 authors, David A Wheeler.
Genome Res, 2014 Sep 18; 24(11). PMID: 25228659    Free PMC article.
Highly Cited.
Human germline and pan-cancer variomes and their distinct functional profiles.
Yang Pan, Konstantinos Karagiannis, +5 authors, Raja Mazumder.
Nucleic Acids Res, 2014 Sep 19; 42(18). PMID: 25232094    Free PMC article.
Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis.
Simon Kebede Merid, Daria Goranskaya, Andrey Alexeyenko.
BMC Bioinformatics, 2014 Sep 23; 15. PMID: 25236784    Free PMC article.
Mutational profiling of kinases in glioblastoma.
Fonnet E Bleeker, Simona Lamba, +8 authors, Alberto Bardelli.
BMC Cancer, 2014 Sep 27; 14. PMID: 25256166    Free PMC article.
Integrative analysis of cancer imaging readouts by networks.
Marco Dominietto, Nicholas Tsinoremas, Enrico Capobianco.
Mol Oncol, 2014 Sep 30; 9(1). PMID: 25263240    Free PMC article.
Review.
Tug-of-war between driver and passenger mutations in cancer and other adaptive processes.
Christopher D McFarland, Leonid A Mirny, Kirill S Korolev.
Proc Natl Acad Sci U S A, 2014 Oct 04; 111(42). PMID: 25277973    Free PMC article.
Next generation sequencing and tumor mutation profiling: are we ready for routine use in the oncology clinic?
Debu Tripathy, Kathleen Harnden, Kimberly Blackwell, Mark Robson.
BMC Med, 2014 Oct 07; 12. PMID: 25286031    Free PMC article.
The dream and reality of histology agnostic cancer clinical trials.
Denis Lacombe, Susen Burock, +3 authors, Roger Stupp.
Mol Oncol, 2014 Oct 29; 8(6). PMID: 25349876    Free PMC article.
Mutant PIK3CA controls DUSP1-dependent ERK 1/2 activity to confer response to AKT target therapy.
A Sathe, F Guerth, +5 authors, R Nawroth.
Br J Cancer, 2014 Oct 29; 111(11). PMID: 25349966    Free PMC article.
The mutational landscapes of genetic and chemical models of Kras-driven lung cancer.
Peter M K Westcott, Kyle D Halliwill, +11 authors, Allan Balmain.
Nature, 2014 Nov 05; 517(7535). PMID: 25363767    Free PMC article.
Highly Cited.
Amplification of Chromosome 1q Genes Encoding the Phosphoinositide Signalling Enzymes PI4KB, AKT3, PIP5K1A and PI3KC2B in Breast Cancer.
Mark G Waugh.
J Cancer, 2014 Nov 05; 5(9). PMID: 25368680    Free PMC article.
Case-only exome sequencing and complex disease susceptibility gene discovery: study design considerations.
Lang Wu, Daniel J Schaid, +3 authors, Gloria M Petersen.
J Med Genet, 2014 Nov 06; 52(1). PMID: 25371537    Free PMC article.
Review.
A pan-cancer modular regulatory network analysis to identify common and cancer-specific network components.
Sara A Knaack, Alireza Fotuhi Siahpirani, Sushmita Roy.
Cancer Inform, 2014 Nov 07; 13(Suppl 5). PMID: 25374456    Free PMC article.
Cancer3D: understanding cancer mutations through protein structures.
Eduard Porta-Pardo, Thomas Hrabe, Adam Godzik.
Nucleic Acids Res, 2014 Nov 14; 43(Database issue). PMID: 25392415    Free PMC article.
[Mutational tumor profiles beyond organ and tissue specificity: implications for diagnostics and clinical study design].
F Klauschen.
Pathologe, 2014 Nov 15; 35 Suppl 2. PMID: 25394977
Review.
Pan-cancer patterns of DNA methylation.
Tania Witte, Christoph Plass, Clarissa Gerhauser.
Genome Med, 2014 Dec 05; 6(8). PMID: 25473433    Free PMC article.
A global assessment of cancer genomic alterations in epigenetic mechanisms.
Muhammad A Shah, Emily L Denton, +2 authors, Matthieu Schapira.
Epigenetics Chromatin, 2014 Dec 09; 7(1). PMID: 25484917    Free PMC article.
Copy number gain of hsa-miR-569 at 3q26.2 leads to loss of TP53INP1 and aggressiveness of epithelial cancers.
Pradeep Chaluvally-Raghavan, Fan Zhang, +28 authors, Gordon B Mills.
Cancer Cell, 2014 Dec 10; 26(6). PMID: 25490449    Free PMC article.
Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes.
Mark D M Leiserson, Fabio Vandin, +16 authors, Benjamin J Raphael.
Nat Genet, 2014 Dec 17; 47(2). PMID: 25501392    Free PMC article.
Highly Cited.
An in-tumor genetic screen reveals that the BET bromodomain protein, BRD4, is a potential therapeutic target in ovarian carcinoma.
Maria Giuseppina Baratta, Anna C Schinzel, +13 authors, David M Livingston.
Proc Natl Acad Sci U S A, 2014 Dec 24; 112(1). PMID: 25535366    Free PMC article.
Highly Cited.
Copy number variation analysis based on AluScan sequences.
Jian-Feng Yang, Xiao-Fan Ding, +22 authors, Hong Xue.
J Clin Bioinforma, 2015 Jan 06; 4(1). PMID: 25558350    Free PMC article.
Hypermutation in human cancer genomes: footprints and mechanisms.
Steven A Roberts, Dmitry A Gordenin.
Nat Rev Cancer, 2015 Jan 09; 14(12). PMID: 25568919    Free PMC article.
Highly Cited. Review.
Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma.
Kjong-Van Lehmann, André Kahles, +4 authors, Gunnar Rätsch.
Pac Symp Biocomput, 2015 Jan 17;. PMID: 25592567    Free PMC article.
The combinatorial complexity of cancer precision medicine.
Frederick Klauschen, Michael Andreeff, +2 authors, Albrecht Stenzinger.
Oncoscience, 2015 Jan 17; 1(7). PMID: 25594052    Free PMC article.
Epigenetic and genetic dispositions of ovarian carcinomas.
Ken Yamaguchi, Noriomi Matsumura, +3 authors, Susan K Murphy.
Oncoscience, 2015 Jan 17; 1(9). PMID: 25594067    Free PMC article.
The landscape of long noncoding RNAs in the human transcriptome.
Matthew K Iyer, Yashar S Niknafs, +16 authors, Arul M Chinnaiyan.
Nat Genet, 2015 Jan 20; 47(3). PMID: 25599403    Free PMC article.
Highly Cited.
The mutational landscape of endometrial cancer.
Bo Hong, Matthieu Le Gallo, Daphne W Bell.
Curr Opin Genet Dev, 2015 Jan 27; 30. PMID: 25622247    Free PMC article.
Review.
Comprehensive genomic characterization of head and neck squamous cell carcinomas.
Cancer Genome Atlas Network.
Nature, 2015 Jan 30; 517(7536). PMID: 25631445    Free PMC article.
Highly Cited.
Molecular pathways: novel approaches for improved therapeutic targeting of Hedgehog signaling in cancer stem cells.
Verline Justilien, Alan P Fields.
Clin Cancer Res, 2015 Feb 04; 21(3). PMID: 25646180    Free PMC article.
Highly Cited. Review.
Molecular profiling and targeted therapy for advanced thoracic malignancies: a biomarker-derived, multiarm, multihistology phase II basket trial.
Ariel Lopez-Chavez, Anish Thomas, +22 authors, Giuseppe Giaccone.
J Clin Oncol, 2015 Feb 11; 33(9). PMID: 25667274    Free PMC article.
Highly Cited.
Intra-tumor genetic heterogeneity and mortality in head and neck cancer: analysis of data from the Cancer Genome Atlas.
Edmund A Mroz, Aaron D Tward, +3 authors, James W Rocco.
PLoS Med, 2015 Feb 11; 12(2). PMID: 25668320    Free PMC article.
Highly Cited.
Role of chromosomal aberrations in clonal diversity and progression of acute myeloid leukemia.
T Bochtler, S Fröhling, A Krämer.
Leukemia, 2015 Feb 13; 29(6). PMID: 25673237
Review.
The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge.
Katarzyna Tomczak, Patrycja Czerwińska, Maciej Wiznerowicz.
Contemp Oncol (Pozn), 2015 Feb 19; 19(1A). PMID: 25691825    Free PMC article.
Highly Cited. Review.
Personalized cancer medicine: next steps in the genomic era.
S Derks, B Diosdado.
Cell Oncol (Dordr), 2015 Feb 28; 38(1). PMID: 25720594    Free PMC article.
A versatile modular vector system for rapid combinatorial mammalian genetics.
Joachim Albers, Claudia Danzer, +11 authors, Ian J Frew.
J Clin Invest, 2015 Mar 10; 125(4). PMID: 25751063    Free PMC article.
Protein domain-level landscape of cancer-type-specific somatic mutations.
Fan Yang, Evangelia Petsalaki, +3 authors, Frederick P Roth.
PLoS Comput Biol, 2015 Mar 21; 11(3). PMID: 25794154    Free PMC article.
Novel candidate key drivers in the integrative network of genes, microRNAs, methylations, and copy number variations in squamous cell lung carcinoma.
Tao Huang, Jing Yang, Yu-Dong Cai.
Biomed Res Int, 2015 Mar 25; 2015. PMID: 25802847    Free PMC article.
A thesaurus of genetic variation for interrogation of repetitive genomic regions.
Claudia Kerzendorfer, Tomasz Konopka, Sebastian M B Nijman.
Nucleic Acids Res, 2015 Mar 31; 43(10). PMID: 25820428    Free PMC article.
Cross-laboratory validation of the OncoScan® FFPE Assay, a multiplex tool for whole genome tumour profiling.
Joseph M Foster, Assa Oumie, +14 authors, Fiona Brew.
BMC Med Genomics, 2015 Apr 19; 8. PMID: 25889064    Free PMC article.
Molecular analysis of gastric cancer identifies subtypes associated with distinct clinical outcomes.
Razvan Cristescu, Jeeyun Lee, +31 authors, Amit Aggarwal.
Nat Med, 2015 Apr 22; 21(5). PMID: 25894828
Highly Cited.
SomInaClust: detection of cancer genes based on somatic mutation patterns of inactivation and clustering.
Jimmy Van den Eynden, Ana Carolina Fierro, Lieven P C Verbeke, Kathleen Marchal.
BMC Bioinformatics, 2015 Apr 24; 16. PMID: 25903787    Free PMC article.
Challenges in initiating and conducting personalized cancer therapy trials: perspectives from WINTHER, a Worldwide Innovative Network (WIN) Consortium trial.
J Rodon, J C Soria, +12 authors, R Kurzrock.
Ann Oncol, 2015 Apr 25; 26(8). PMID: 25908602    Free PMC article.
TP53 mutations, tetraploidy and homologous recombination repair defects in early stage high-grade serous ovarian cancer.
Jeremy Chien, Hugues Sicotte, +27 authors, Ellen L Goode.
Nucleic Acids Res, 2015 Apr 29; 43(14). PMID: 25916844    Free PMC article.
Genetic Basis of Common Human Disease: Insight into the Role of Missense SNPs from Genome-Wide Association Studies.
Lipika R Pal, John Moult.
J Mol Biol, 2015 May 06; 427(13). PMID: 25937569    Free PMC article.
Oligodendroglioma: pathology, molecular mechanisms and markers.
Pieter Wesseling, Martin van den Bent, Arie Perry.
Acta Neuropathol, 2015 May 07; 129(6). PMID: 25943885    Free PMC article.
Review.
Chromosomal instability as a prognostic marker in cervical cancer.
Christine How, Jeff Bruce, +9 authors, Fei-Fei Liu.
BMC Cancer, 2015 May 07; 15. PMID: 25944123    Free PMC article.
Identification of variants in primary and recurrent glioblastoma using a cancer-specific gene panel and whole exome sequencing.
Selene M Virk, Richard M Gibson, Miguel E Quinones-Mateu, Jill S Barnholtz-Sloan.
PLoS One, 2015 May 08; 10(5). PMID: 25950952    Free PMC article.
Pan-cancer stratification of solid human epithelial tumors and cancer cell lines reveals commonalities and tissue-specific features of the CpG island methylator phenotype.
Francisco Sánchez-Vega, Valer Gotea, Gennady Margolin, Laura Elnitski.
Epigenetics Chromatin, 2015 May 12; 8. PMID: 25960768    Free PMC article.
Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.
Adam D Ewing, Kathleen E Houlahan, +16 authors, Paul C Boutros.
Nat Methods, 2015 May 20; 12(7). PMID: 25984700    Free PMC article.
Highly Cited.
Scanning the human genome and the horizon: the potential and pitfalls of pharmacogenetics and stratified medicine.
Barbara A Jennings, Tom Shakespeare, Yoon K Loke.
Br J Gen Pract, 2015 May 27; 65(635). PMID: 26009508    Free PMC article.
Pan-cancer analysis of genomic scar signatures associated with homologous recombination deficiency suggests novel indications for existing cancer drugs.
Andrea M Marquard, Aron C Eklund, +7 authors, Nicolai J Birkbak.
Biomark Res, 2015 May 28; 3. PMID: 26015868    Free PMC article.
Whole-genome characterization of chemoresistant ovarian cancer.
Ann-Marie Patch, Elizabeth L Christie, +80 authors, David D L Bowtell.
Nature, 2015 May 29; 521(7553). PMID: 26017449
Highly Cited.
TP53: an oncogene in disguise.
T Soussi, K G Wiman.
Cell Death Differ, 2015 May 30; 22(8). PMID: 26024390    Free PMC article.
Highly Cited. Review.
Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism.
Francesco Gatto, Heike Miess, Almut Schulze, Jens Nielsen.
Sci Rep, 2015 Jun 05; 5. PMID: 26040780    Free PMC article.
Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.
Cancer Genome Atlas Research Network, Daniel J Brat, +305 authors, Jianan Zhang.
N Engl J Med, 2015 Jun 11; 372(26). PMID: 26061751    Free PMC article.
Highly Cited.
Appraisal of the technologies and review of the genomic landscape of ductal carcinoma in situ of the breast.
Jia-Min B Pang, Kylie L Gorringe, +3 authors, Stephen B Fox.
Breast Cancer Res, 2015 Jun 17; 17. PMID: 26078038    Free PMC article.
Review.
An integrated approach to reveal miRNAs' impacts on the functional consequence of copy number alterations in cancer.
Kening Li, Yongjing Liu, +7 authors, Yan Xu.
Sci Rep, 2015 Jun 24; 5. PMID: 26099552    Free PMC article.
Dysregulated transcription across diverse cancer types reveals the importance of RNA-binding protein in carcinogenesis.
Jing Wang, Qi Liu, Yu Shyr.
BMC Genomics, 2015 Jun 24; 16 Suppl 7. PMID: 26100984    Free PMC article.
Bioinformatics analysis of thousands of TCGA tumors to determine the involvement of epigenetic regulators in human cancer.
Florian Gnad, Sophia Doll, +2 authors, Zemin Zhang.
BMC Genomics, 2015 Jun 26; 16 Suppl 8. PMID: 26110843    Free PMC article.
Computational methods and resources for the interpretation of genomic variants in cancer.
Rui Tian, Malay K Basu, Emidio Capriotti.
BMC Genomics, 2015 Jun 26; 16 Suppl 8. PMID: 26111056    Free PMC article.
Review.
MYC in pancreatic cancer: novel mechanistic insights and their translation into therapeutic strategies.
E Hessmann, G Schneider, V Ellenrieder, J T Siveke.
Oncogene, 2015 Jun 30; 35(13). PMID: 26119937
Review.
Assessment of Esophageal Adenocarcinoma Risk Using Somatic Chromosome Alterations in Longitudinal Samples in Barrett's Esophagus.
Xiaohong Li, Thomas G Paulson, +8 authors, Patricia L Blount.
Cancer Prev Res (Phila), 2015 Jul 02; 8(9). PMID: 26130253    Free PMC article.
An improved understanding of cancer genomics through massively parallel sequencing.
Jamie K Teer.
Transl Cancer Res, 2015 Jul 07; 3(3). PMID: 26146607    Free PMC article.
Tumor characterization and stratification by integrated molecular profiles reveals essential pan-cancer features.
Zhaoqi Liu, Shihua Zhang.
BMC Genomics, 2015 Jul 08; 16. PMID: 26148869    Free PMC article.
Concordance of copy number alterations using a common analytic pipeline for genome-wide analysis of Illumina and Affymetrix genotyping data: a report from the Children's Oncology Group.
Marijana Vujkovic, Edward F Attiyeh, +11 authors, Richard Aplenc.
Cancer Genet, 2015 Jul 15; 208(7-8). PMID: 26163103    Free PMC article.
Not All Next Generation Sequencing Diagnostics are Created Equal: Understanding the Nuances of Solid Tumor Assay Design for Somatic Mutation Detection.
Phillip N Gray, Charles L M Dunlop, Aaron M Elliott.
Cancers (Basel), 2015 Jul 21; 7(3). PMID: 26193321    Free PMC article.
Review.
BayesPI-BAR: a new biophysical model for characterization of regulatory sequence variations.
Junbai Wang, Kirill Batmanov.
Nucleic Acids Res, 2015 Jul 24; 43(21). PMID: 26202972    Free PMC article.
Genetic Insights in Barrett's Esophagus and Esophageal Adenocarcinoma.
Brian J Reid, Thomas G Paulson, Xiaohong Li.
Gastroenterology, 2015 Jul 26; 149(5). PMID: 26208895    Free PMC article.
Review.
Model-Based Design of a Decision Tree for Treating HER2+ Cancers Based on Genetic and Protein Biomarkers.
D C Kirouac, J Lahdenranta, +4 authors, C F McDonagh.
CPT Pharmacometrics Syst Pharmacol, 2015 Aug 01; 4(3). PMID: 26225238    Free PMC article.
Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models.
Richard R Stein, Debora S Marks, Chris Sander.
PLoS Comput Biol, 2015 Aug 01; 11(7). PMID: 26225866    Free PMC article.
Review.
Cancer type-dependent genetic interactions between cancer driver alterations indicate plasticity of epistasis across cell types.
Solip Park, Ben Lehner.
Mol Syst Biol, 2015 Aug 01; 11(7). PMID: 26227665    Free PMC article.
Genetic determinants of FOXM1 overexpression in epithelial ovarian cancer and functional contribution to cell cycle progression.
Carter J Barger, Wa Zhang, +5 authors, Adam R Karpf.
Oncotarget, 2015 Aug 06; 6(29). PMID: 26243836    Free PMC article.
Integrated analysis of numerous heterogeneous gene expression profiles for detecting robust disease-specific biomarkers and proposing drug targets.
David Amar, Tom Hait, Shai Izraeli, Ron Shamir.
Nucleic Acids Res, 2015 Aug 12; 43(16). PMID: 26261215    Free PMC article.
Deciphering the Correlation between Breast Tumor Samples and Cell Lines by Integrating Copy Number Changes and Gene Expression Profiles.
Yi Sun, Qi Liu.
Biomed Res Int, 2015 Aug 15; 2015. PMID: 26273658    Free PMC article.
Harmful somatic amino acid substitutions affect key pathways in cancers.
Abhishek Niroula, Mauno Vihinen.
BMC Med Genomics, 2015 Aug 19; 8. PMID: 26282678    Free PMC article.
Perturbation biology nominates upstream-downstream drug combinations in RAF inhibitor resistant melanoma cells.
Anil Korkut, Weiqing Wang, +9 authors, Chris Sander.
Elife, 2015 Aug 19; 4. PMID: 26284497    Free PMC article.
Next-generation sequencing: hype and hope for development of personalized radiation therapy?
Ingeborg Tinhofer, Franziska Niehr, +6 authors, Volker Budach.
Radiat Oncol, 2015 Sep 01; 10. PMID: 26316159    Free PMC article.
Review.
Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling.
Åsmund Flobak, Anaïs Baudot, +4 authors, Astrid Lægreid.
PLoS Comput Biol, 2015 Sep 01; 11(8). PMID: 26317215    Free PMC article.
The sum of gains and losses of genes encoding the protein tyrosine kinase targets predicts response to multi-kinase inhibitor treatment: Characterization, validation, and prognostic value.
Xiaojun Jiang, Daniel Pissaloux, +17 authors, Jean-Yves Blay.
Oncotarget, 2015 Sep 01; 6(28). PMID: 26317543    Free PMC article.
Copy number analysis of ductal carcinoma in situ with and without recurrence.
Kylie L Gorringe, Sally M Hunter, +9 authors, Ian G Campbell.
Mod Pathol, 2015 Sep 01; 28(9). PMID: 26321097
Inferred miRNA activity identifies miRNA-mediated regulatory networks underlying multiple cancers.
Eunjee Lee, Koichi Ito, +3 authors, Jun Zhu.
Bioinformatics, 2015 Sep 12; 32(1). PMID: 26358730    Free PMC article.
DNA methylation changes in epithelial ovarian cancer histotypes.
Madalene A Earp, Julie M Cunningham.
Genomics, 2015 Sep 13; 106(6). PMID: 26363302    Free PMC article.
Review.
MYC: connecting selective transcriptional control to global RNA production.
Theresia R Kress, Arianna Sabò, Bruno Amati.
Nat Rev Cancer, 2015 Sep 19; 15(10). PMID: 26383138
Highly Cited. Review.
MYC Disrupts the Circadian Clock and Metabolism in Cancer Cells.
Brian J Altman, Annie L Hsieh, +17 authors, Chi V Dang.
Cell Metab, 2015 Sep 22; 22(6). PMID: 26387865    Free PMC article.
Highly Cited.
The Relationship of Immune Cell Signatures to Patient Survival Varies within and between Tumor Types.
Peter S Linsley, Damien Chaussabel, Cate Speake.
PLoS One, 2015 Sep 24; 10(9). PMID: 26398410    Free PMC article.
A Patient-Derived, Pan-Cancer EMT Signature Identifies Global Molecular Alterations and Immune Target Enrichment Following Epithelial-to-Mesenchymal Transition.
Milena P Mak, Pan Tong, +12 authors, Lauren Averett Byers.
Clin Cancer Res, 2015 Oct 01; 22(3). PMID: 26420858    Free PMC article.
Highly Cited.
Systematic analysis of somatic mutations impacting gene expression in 12 tumour types.
Jiarui Ding, Melissa K McConechy, +11 authors, Sohrab P Shah.
Nat Commun, 2015 Oct 06; 6. PMID: 26436532    Free PMC article.
From drug response profiling to target addiction scoring in cancer cell models.
Bhagwan Yadav, Peddinti Gopalacharyulu, +5 authors, Tero Aittokallio.
Dis Model Mech, 2015 Oct 07; 8(10). PMID: 26438695    Free PMC article.
Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer.
Giovanni Ciriello, Michael L Gatza, +30 authors, Charles M Perou.
Cell, 2015 Oct 10; 163(2). PMID: 26451490    Free PMC article.
Highly Cited.
EGFR Mutation Promotes Glioblastoma through Epigenome and Transcription Factor Network Remodeling.
Feng Liu, Gary C Hon, +21 authors, Paul S Mischel.
Mol Cell, 2015 Oct 13; 60(2). PMID: 26455392    Free PMC article.
Highly Cited.
Challenges of deciphering gastric cancer heterogeneity.
Petra Hudler.
World J Gastroenterol, 2015 Oct 13; 21(37). PMID: 26457012    Free PMC article.
Review.
Integrin α5β1 and p53 convergent pathways in the control of anti-apoptotic proteins PEA-15 and survivin in high-grade glioma.
G Renner, H Janouskova, +14 authors, M Dontenwill.
Cell Death Differ, 2015 Oct 17; 23(4). PMID: 26470725    Free PMC article.
A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces.
Eduard Porta-Pardo, Luz Garcia-Alonso, +2 authors, Adam Godzik.
PLoS Comput Biol, 2015 Oct 21; 11(10). PMID: 26485003    Free PMC article.
Identification of Novel Epigenetic Markers of Prostate Cancer by NotI-Microarray Analysis.
Alexey A Dmitriev, Eugenia E Rosenberg, +15 authors, Vladimir I Kashuba.
Dis Markers, 2015 Oct 23; 2015. PMID: 26491211    Free PMC article.
Rethinking ovarian cancer II: reducing mortality from high-grade serous ovarian cancer.
David D Bowtell, Steffen Böhm, +38 authors, Frances R Balkwill.
Nat Rev Cancer, 2015 Oct 24; 15(11). PMID: 26493647    Free PMC article.
Highly Cited. Review.
Detection of Clonal and Subclonal Copy-Number Variants in Cell-Free DNA from Patients with Breast Cancer Using a Massively Multiplexed PCR Methodology.
Eser Kirkizlar, Bernhard Zimmermann, +12 authors, Matthew Hill.
Transl Oncol, 2015 Oct 27; 8(5). PMID: 26500031    Free PMC article.
The Tip of the Iceberg: Clinical Implications of Genomic Sequencing Projects in Head and Neck Cancer.
Andrew C Birkeland, Megan L Ludwig, +2 authors, Mark E Prince.
Cancers (Basel), 2015 Oct 28; 7(4). PMID: 26506389    Free PMC article.
Review.
Evolution of metastasis revealed by mutational landscapes of chemically induced skin cancers.
Melissa Q McCreery, Kyle D Halliwill, +7 authors, Allan Balmain.
Nat Med, 2015 Nov 03; 21(12). PMID: 26523969    Free PMC article.
Translating cancer genomes and transcriptomes for precision oncology.
Sameek Roychowdhury, Arul M Chinnaiyan.
CA Cancer J Clin, 2015 Nov 04; 66(1). PMID: 26528881    Free PMC article.
Review.
Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models.
Dmitry Svetlichnyy, Hana Imrichova, +2 authors, Stein Aerts.
PLoS Comput Biol, 2015 Nov 13; 11(11). PMID: 26562774    Free PMC article.
Coping with cancer genes altered by copy number.
Natalie K Wolf, David A Largaespada, Branden S Moriarity.
Oncotarget, 2015 Nov 19; 6(34). PMID: 26577648    Free PMC article.
MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer.
Nicholas Paul Gauthier, Ed Reznik, +4 authors, Martin L Miller.
Nucleic Acids Res, 2015 Nov 22; 44(D1). PMID: 26590264    Free PMC article.
Treatment Algorithms Based on Tumor Molecular Profiling: The Essence of Precision Medicine Trials.
Christophe Le Tourneau, Maud Kamal, +11 authors, Ivan Bièche.
J Natl Cancer Inst, 2015 Nov 26; 108(4). PMID: 26598514    Free PMC article.
Review.
Impact of Pre-Analytical Variables on Cancer Targeted Gene Sequencing Efficiency.
Luiz H Araujo, Cynthia Timmers, +11 authors, David P Carbone.
PLoS One, 2015 Nov 26; 10(11). PMID: 26605948    Free PMC article.
Pan-cancer analysis of the extent and consequences of intratumor heterogeneity.
Noemi Andor, Trevor A Graham, +5 authors, Carlo C Maley.
Nat Med, 2015 Dec 01; 22(1). PMID: 26618723    Free PMC article.
Highly Cited.
β1 Integrins as Therapeutic Targets to Disrupt Hallmarks of Cancer.
Anne-Florence Blandin, Guillaume Renner, +3 authors, Monique Dontenwill.
Front Pharmacol, 2015 Dec 05; 6. PMID: 26635609    Free PMC article.
Review.
On the Sample Complexity of Cancer Pathways Identification.
Fabio Vandin, Benjamin J Raphael, Eli Upfal.
J Comput Biol, 2015 Dec 10; 23(1). PMID: 26645471    Free PMC article.
The chromosome 3q26 OncCassette: A multigenic driver of human cancer.
Alan P Fields, Verline Justilien, Nicole R Murray.
Adv Biol Regul, 2016 Jan 13; 60. PMID: 26754874    Free PMC article.
Genomic complexity of urothelial bladder cancer revealed in urinary cfDNA.
Fiona S Togneri, Douglas G Ward, +15 authors, Richard T Bryan.
Eur J Hum Genet, 2016 Jan 14; 24(8). PMID: 26757983    Free PMC article.
Distinct mutation accumulation rates among tissues determine the variation in cancer risk.
Dapeng Hao, Li Wang, Li-jun Di.
Sci Rep, 2016 Jan 21; 6. PMID: 26785814    Free PMC article.
Somatic Copy Number Alterations at Oncogenic Loci Show Diverse Correlations with Gene Expression.
Jason Roszik, Chang-Jiun Wu, +4 authors, Lawrence N Kwong.
Sci Rep, 2016 Jan 21; 6. PMID: 26787600    Free PMC article.
Genomic and epigenomic heterogeneity in molecular subtypes of gastric cancer.
Byungho Lim, Jong-Hwan Kim, Mirang Kim, Seon-Young Kim.
World J Gastroenterol, 2016 Jan 27; 22(3). PMID: 26811657    Free PMC article.
Review.
Transcriptional profiling analysis and functional prediction of long noncoding RNAs in cancer.
Jiao Yuan, Haiyan Yue, +14 authors, Runsheng Chen.
Oncotarget, 2016 Jan 27; 7(7). PMID: 26812883    Free PMC article.
Reply: Co-occurrence of MYC amplification and TP53 mutations in human cancer.
Mark D M Leiserson, Fabio Vandin, Hsin-Ta Wu, Benjamin J Raphael.
Nat Genet, 2016 Jan 28; 48(2). PMID: 26813760
Pan-cancer analysis of intratumor heterogeneity as a prognostic determinant of survival.
Luc G T Morris, Nadeem Riaz, +5 authors, Timothy A Chan.
Oncotarget, 2016 Feb 04; 7(9). PMID: 26840267    Free PMC article.
Highly Cited.
Web-TCGA: an online platform for integrated analysis of molecular cancer data sets.
Mario Deng, Johannes Brägelmann, Joachim L Schultze, Sven Perner.
BMC Bioinformatics, 2016 Feb 08; 17. PMID: 26852330    Free PMC article.
Ioncopy: a novel method for calling copy number alterations in amplicon sequencing data including significance assessment.
Jan Budczies, Nicole Pfarr, +10 authors, Carsten Denkert.
Oncotarget, 2016 Feb 26; 7(11). PMID: 26910888    Free PMC article.
An Atlas of the Human Kinome Reveals the Mutational Landscape Underlying Dysregulated Phosphorylation Cascades in Cancer.
Aleksandra Olow, Zhongzhong Chen, +7 authors, Jean-Philippe Coppé.
Cancer Res, 2016 Feb 28; 76(7). PMID: 26921330    Free PMC article.
A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers.
Yasin Şenbabaoğlu, Selçuk Onur Sümer, +4 authors, Chris Sander.
PLoS Comput Biol, 2016 Mar 02; 12(2). PMID: 26928298    Free PMC article.
Quantitative Trait Loci Identify Functional Noncoding Variation in Cancer.
Holger Heyn.
PLoS Genet, 2016 Mar 05; 12(3). PMID: 26938653    Free PMC article.
Review.
Genomic landscape of DNA repair genes in cancer.
Young Kwang Chae, Jonathan F Anker, +6 authors, Francis J Giles.
Oncotarget, 2016 Mar 24; 7(17). PMID: 27004405    Free PMC article.
Highly Cited.
Amplification of WHSC1L1 regulates expression and estrogen-independent activation of ERα in SUM-44 breast cancer cells and is associated with ERα over-expression in breast cancer.
Jonathan C Irish, Jamie N Mills, +7 authors, Stephen P Ethier.
Mol Oncol, 2016 Mar 24; 10(6). PMID: 27005559    Free PMC article.
Two classes of intrahepatic cholangiocarcinoma defined by relative abundance of mutations and copy number alterations.
Young-Ho Kim, Eun-Kyung Hong, +6 authors, Tae-Min Kim.
Oncotarget, 2016 Mar 25; 7(17). PMID: 27009864    Free PMC article.
An extensive program of periodic alternative splicing linked to cell cycle progression.
Daniel Dominguez, Yi-Hsuan Tsai, +3 authors, Zefeng Wang.
Elife, 2016 Mar 26; 5. PMID: 27015110    Free PMC article.
MDM2 oligomers: antagonizers of the guardian of the genome.
P L Leslie, Y Zhang.
Oncogene, 2016 Apr 05; 35(48). PMID: 27041565    Free PMC article.
Review.
A pan-cancer analysis of prognostic genes.
Jordan Anaya, Brian Reon, +2 authors, Anindya Dutta.
PeerJ, 2015 Jan 01; 3. PMID: 27047702    Free PMC article.
Genetically-defined novel oral squamous cell carcinoma cell lines for the development of molecular therapies.
Muhammad Zaki Hidayatullah Fadlullah, Ivy Kim-Ni Chiang, +18 authors, Sok Ching Cheong.
Oncotarget, 2016 Apr 07; 7(19). PMID: 27050151    Free PMC article.
Genomic Characterization of Esophageal Squamous Cell Carcinoma Reveals Critical Genes Underlying Tumorigenesis and Poor Prognosis.
Hai-De Qin, Xiao-Yu Liao, +17 authors, Wei-Hua Jia.
Am J Hum Genet, 2016 Apr 09; 98(4). PMID: 27058444    Free PMC article.
Highly Cited.
Epigenetic and genetic burden measures are associated with tumor characteristics in invasive breast carcinoma.
Dylan E O'Sullivan, Kevin C Johnson, +2 authors, Brock C Christensen.
Epigenetics, 2016 Apr 14; 11(5). PMID: 27070496    Free PMC article.
A genetic network that suppresses genome rearrangements in Saccharomyces cerevisiae and contains defects in cancers.
Christopher D Putnam, Anjana Srivatsan, +8 authors, Richard D Kolodner.
Nat Commun, 2016 Apr 14; 7. PMID: 27071721    Free PMC article.
Genomic aberrations frequently alter chromatin regulatory genes in chordoma.
Lu Wang, Ahmet Zehir, +11 authors, Meera Hameed.
Genes Chromosomes Cancer, 2016 Apr 14; 55(7). PMID: 27072194    Free PMC article.
Morphological and molecular approach to synchronous non-small cell lung carcinomas: impact on staging.
Frank Schneider, Veronica Derrick, +3 authors, Sanja Dacic.
Mod Pathol, 2016 Apr 16; 29(7). PMID: 27080983
A new molecular signature method for prediction of driver cancer pathways from transcriptional data.
Dmitry Rykunov, Noam D Beckmann, +3 authors, Boris Reva.
Nucleic Acids Res, 2016 Apr 22; 44(11). PMID: 27098033    Free PMC article.
Omics Profiling in Precision Oncology.
Kun-Hsing Yu, Michael Snyder.
Mol Cell Proteomics, 2016 Apr 22; 15(8). PMID: 27099341    Free PMC article.
Review.
Pan-cancer subtyping in a 2D-map shows substructures that are driven by specific combinations of molecular characteristics.
Erdogan Taskesen, Sjoerd M H Huisman, +6 authors, Marcel J T Reinders.
Sci Rep, 2016 Apr 26; 6. PMID: 27109935    Free PMC article.
Integrative analysis reveals clinical phenotypes and oncogenic potentials of long non-coding RNAs across 15 cancer types.
Ze-Lin Wang, Bin Li, +5 authors, Liang-Hu Qu.
Oncotarget, 2016 May 06; 7(23). PMID: 27147563    Free PMC article.
Immunomediated Pan-cancer Regulation Networks are Dominant Fingerprints After Treatment of Cell Lines with Demethylation.
Mariama El Baroudi, Caterina Cinti, Enrico Capobianco.
Cancer Inform, 2016 May 06; 15. PMID: 27147816    Free PMC article.
EGFR Activation Leads to Cell Death Independent of PI3K/AKT/mTOR in an AD293 Cell Line.
Cezary Treda, Marta Popeda, +6 authors, Piotr Rieske.
PLoS One, 2016 May 07; 11(5). PMID: 27153109    Free PMC article.
Identification of cancer-driver genes in focal genomic alterations from whole genome sequencing data.
Ho Jang, Youngmi Hur, Hyunju Lee.
Sci Rep, 2016 May 10; 6. PMID: 27156852    Free PMC article.
The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes.
Bernard Pereira, Suet-Feung Chin, +31 authors, Carlos Caldas.
Nat Commun, 2016 May 11; 7. PMID: 27161491    Free PMC article.
Highly Cited.
Genomic Approaches to Zebrafish Cancer.
Richard M White.
Adv Exp Med Biol, 2016 May 12; 916. PMID: 27165352    Free PMC article.
Review.
Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma.
Siyuan Zheng, Andrew D Cherniack, +41 authors, Roel G W Verhaak.
Cancer Cell, 2016 May 12; 29(5). PMID: 27165744    Free PMC article.
Highly Cited.
Reprogrammable CRISPR/Cas9-based system for inducing site-specific DNA methylation.
James I McDonald, Hamza Celik, +7 authors, Grant A Challen.
Biol Open, 2016 May 14; 5(6). PMID: 27170255    Free PMC article.
Highly Cited.
A nCounter CNV Assay to Detect HER2 Amplification: A Correlation Study with Immunohistochemistry and In Situ Hybridization in Advanced Gastric Cancer.
Soomin Ahn, Mineui Hong, +9 authors, Kyoung-Mee Kim.
Mol Diagn Ther, 2016 May 18; 20(4). PMID: 27179810
Triple-negative breast cancer: challenges and opportunities of a heterogeneous disease.
Giampaolo Bianchini, Justin M Balko, +2 authors, Luca Gianni.
Nat Rev Clin Oncol, 2016 Oct 19; 13(11). PMID: 27184417    Free PMC article.
Highly Cited. Review.
Low Mutation Burden in Ovarian Cancer May Limit the Utility of Neoantigen-Targeted Vaccines.
Spencer D Martin, Scott D Brown, +5 authors, Brad H Nelson.
PLoS One, 2016 May 19; 11(5). PMID: 27192170    Free PMC article.
Highly Cited.
Dual mTORC1/2 Inhibition as a Novel Strategy for the Resensitization and Treatment of Platinum-Resistant Ovarian Cancer.
Fernanda Musa, Amandine Alard, +3 authors, Robert J Schneider.
Mol Cancer Ther, 2016 May 20; 15(7). PMID: 27196780    Free PMC article.
Genomic Characterization of High-Grade Serous Ovarian Cancer: Dissecting Its Molecular Heterogeneity as a Road Towards Effective Therapeutic Strategies.
Lorenza Mittempergher.
Curr Oncol Rep, 2016 Jun 01; 18(7). PMID: 27241520
Review.
The Brazilian Hereditary Cancer Network: historical aspects and challenges for clinical cancer genetics in the public health care system in Brazil.
Patricia Ashton-Prolla, Hector N Seuanez.
Genet Mol Biol, 2016 Jun 09; 39(2). PMID: 27275665    Free PMC article.
A microscopic landscape of the invasive breast cancer genome.
Zheng Ping, Yuchao Xia, +8 authors, Dejun Shen.
Sci Rep, 2016 Jun 11; 6. PMID: 27283966    Free PMC article.
Extracting a low-dimensional description of multiple gene expression datasets reveals a potential driver for tumor-associated stroma in ovarian cancer.
Safiye Celik, Benjamin A Logsdon, +4 authors, Su-In Lee.
Genome Med, 2016 Jun 12; 8(1). PMID: 27287041    Free PMC article.
Cancer metabolism as a central driving force of glioma pathogenesis.
Kenta Masui, Webster K Cavenee, Paul S Mischel.
Brain Tumor Pathol, 2016 Jun 14; 33(3). PMID: 27295313    Free PMC article.
Review.
Trial Watch: Targeting ATM-CHK2 and ATR-CHK1 pathways for anticancer therapy.
Gwenola Manic, Florine Obrist, Antonella Sistigu, Ilio Vitale.
Mol Cell Oncol, 2016 Jun 17; 2(4). PMID: 27308506    Free PMC article.
Highly Cited. Review.
PKCι regulates nuclear YAP1 localization and ovarian cancer tumorigenesis.
Y Wang, V Justilien, +3 authors, A P Fields.
Oncogene, 2016 Jun 21; 36(4). PMID: 27321186    Free PMC article.
Diagnostic Potential of lncRNAs in Cancer.
Chi Han Li, Yangchao Chen.
EBioMedicine, 2016 Jun 21; 7. PMID: 27322445    Free PMC article.
PRAME expression and promoter hypomethylation in epithelial ovarian cancer.
Wa Zhang, Carter J Barger, +6 authors, Adam R Karpf.
Oncotarget, 2016 Jun 21; 7(29). PMID: 27322684    Free PMC article.
Suppression of ABHD2, identified through a functional genomics screen, causes anoikis resistance, chemoresistance and poor prognosis in ovarian cancer.
Koji Yamanoi, Noriomi Matsumura, +7 authors, Masaki Mandai.
Oncotarget, 2016 Jun 21; 7(30). PMID: 27323405    Free PMC article.
Divergent viral presentation among human tumors and adjacent normal tissues.
Song Cao, Michael C Wendl, +14 authors, Li Ding.
Sci Rep, 2016 Jun 25; 6. PMID: 27339696    Free PMC article.
Comprehensive assessment of the expression of the SWI/SNF complex defines two distinct prognostic subtypes of ovarian clear cell carcinoma.
Hisham Abou-Taleb, Ken Yamaguchi, +13 authors, Masaki Mandai.
Oncotarget, 2016 Jun 25; 7(34). PMID: 27340867    Free PMC article.
The genomic landscape and evolution of endometrial carcinoma progression and abdominopelvic metastasis.
William J Gibson, Erling A Hoivik, +25 authors, Helga B Salvesen.
Nat Genet, 2016 Jun 28; 48(8). PMID: 27348297    Free PMC article.
Highly Cited.
Hotspot mutations delineating diverse mutational signatures and biological utilities across cancer types.
Tenghui Chen, Zixing Wang, +4 authors, Ken Chen.
BMC Genomics, 2016 Jul 01; 17 Suppl 2. PMID: 27356755    Free PMC article.
Genomic alterations underlie a pan-cancer metabolic shift associated with tumour hypoxia.
Syed Haider, Alan McIntyre, +4 authors, Francesca M Buffa.
Genome Biol, 2016 Jul 01; 17(1). PMID: 27358048    Free PMC article.
A high-resolution transcriptome map of cell cycle reveals novel connections between periodic genes and cancer.
Daniel Dominguez, Yi-Hsuan Tsai, +3 authors, Zefeng Wang.
Cell Res, 2016 Jul 02; 26(8). PMID: 27364684    Free PMC article.
A Landscape of Pharmacogenomic Interactions in Cancer.
Francesco Iorio, Theo A Knijnenburg, +36 authors, Mathew J Garnett.
Cell, 2016 Jul 12; 166(3). PMID: 27397505    Free PMC article.
Highly Cited.
RB1: a prototype tumor suppressor and an enigma.
Nicholas J Dyson.
Genes Dev, 2016 Jul 13; 30(13). PMID: 27401552    Free PMC article.
Highly Cited. Review.
Clinical Genomics: Challenges and Opportunities.
Priyanka Vijay, Alexa B R McIntyre, +2 authors, Sheng Li.
Crit Rev Eukaryot Gene Expr, 2016 Aug 03; 26(2). PMID: 27480773    Free PMC article.
Review.
Identification of therapeutic targets applicable to clinical strategies in ovarian cancer.
Marianne K Kim, Natasha Caplen, +5 authors, Christina M Annunziata.
BMC Cancer, 2016 Aug 26; 16. PMID: 27558154    Free PMC article.
Multi-omics analysis of primary glioblastoma cell lines shows recapitulation of pivotal molecular features of parental tumors.
Shai Rosenberg, Maïté Verreault, +11 authors, Ahmed Idbaih.
Neuro Oncol, 2016 Aug 31; 19(2). PMID: 27571888    Free PMC article.
Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance.
Maria Secrier, Xiaodun Li, +24 authors, Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium.
Nat Genet, 2016 Sep 07; 48(10). PMID: 27595477    Free PMC article.
Highly Cited.
Overcome tumor heterogeneity-imposed therapeutic barriers through convergent genomic biomarker discovery: A braided cancer river model of kidney cancer.
James J Hsieh, Brandon J Manley, +3 authors, Emily H Cheng.
Semin Cell Dev Biol, 2016 Sep 13; 64. PMID: 27615548    Free PMC article.
Review.
Aurora kinase-A overexpression in mouse mammary epithelium induces mammary adenocarcinomas harboring genetic alterations shared with human breast cancer.
Warapen Treekitkarnmongkol, Hiroshi Katayama, +9 authors, Subrata Sen.
Carcinogenesis, 2016 Sep 15; 37(12). PMID: 27624071    Free PMC article.
TumorNext: A comprehensive tumor profiling assay that incorporates high resolution copy number analysis and germline status to improve testing accuracy.
Phillip N Gray, Huy Vuong, +18 authors, Aaron Elliott.
Oncotarget, 2016 Sep 15; 7(42). PMID: 27626691    Free PMC article.
An integrative and comparative study of pan-cancer transcriptomes reveals distinct cancer common and specific signatures.
Zhen Cao, Shihua Zhang.
Sci Rep, 2016 Sep 17; 6. PMID: 27633916    Free PMC article.
Tumor Infiltrating Lymphocytes Affect the Outcome of Patients with Operable Triple-Negative Breast Cancer in Combination with Mutated Amino Acid Classes.
Vassiliki Kotoula, Sotiris Lakis, +18 authors, George Fountzilas.
PLoS One, 2016 Sep 30; 11(9). PMID: 27685159    Free PMC article.
Importance of rare gene copy number alterations for personalized tumor characterization and survival analysis.
Michael Seifert, Betty Friedrich, Andreas Beyer.
Genome Biol, 2016 Oct 08; 17(1). PMID: 27716417    Free PMC article.
Targeted therapies: What have we learned from SHIVA?
Christophe Le Tourneau, Razelle Kurzrock.
Nat Rev Clin Oncol, 2016 Nov 03; 13(12). PMID: 27725677
Review.
Narrowing the focus: a toolkit to systematically connect oncogenic signaling pathways with cancer phenotypes.
Katherine R Singleton, Kris C Wood.
Genes Cancer, 2016 Oct 16; 7(7-8). PMID: 27738492    Free PMC article.
Review.
Using Pharmacogenomic Databases for Discovering Patient-Target Genes and Small Molecule Candidates to Cancer Therapy.
José E Belizário, Beatriz A Sangiuliano, +2 authors, Dayson F Moreira.
Front Pharmacol, 2016 Oct 18; 7. PMID: 27746730    Free PMC article.
Review.
Low-frequency KRAS mutations are prevalent in lung adenocarcinomas.
Meagan B Myers, Karen L McKim, Fanxue Meng, Barbara L Parsons.
Per Med, 2015 Mar 01; 12(2). PMID: 27795727    Free PMC article.
Rawcopy: Improved copy number analysis with Affymetrix arrays.
Markus Mayrhofer, Björn Viklund, Anders Isaksson.
Sci Rep, 2016 Nov 01; 6. PMID: 27796336    Free PMC article.
Efficient and simple approach to in vitro culture of primary epithelial cancer cells.
Karolina Janik, Marta Popeda, +6 authors, Magdalena Ksiazkiewicz.
Biosci Rep, 2016 Nov 03; 36(6). PMID: 27803125    Free PMC article.
ERBB2 mutation is associated with a worse prognosis in patients with CDH1 altered invasive lobular cancer of the breast.
Zheng Ping, Gene P Siegal, +10 authors, Dejun Shen.
Oncotarget, 2016 Nov 05; 7(49). PMID: 27811364    Free PMC article.
The rise of genomic profiling in ovarian cancer.
Rebecca A Previs, Anil K Sood, Gordon B Mills, Shannon N Westin.
Expert Rev Mol Diagn, 2016 Nov 10; 16(12). PMID: 27828713    Free PMC article.
Review.
A network of epigenetic modifiers and DNA repair genes controls tissue-specific copy number alteration preference.
Dina Cramer, Luis Serrano, Martin H Schaefer.
Elife, 2016 Nov 11; 5. PMID: 27831464    Free PMC article.
Structural basis of N-Myc binding by Aurora-A and its destabilization by kinase inhibitors.
Mark W Richards, Selena G Burgess, +4 authors, Richard Bayliss.
Proc Natl Acad Sci U S A, 2016 Nov 12; 113(48). PMID: 27837025    Free PMC article.
Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue.
Tanjina Kader, David L Goode, +9 authors, Kylie L Gorringe.
Genome Med, 2016 Nov 17; 8(1). PMID: 27846907    Free PMC article.
Genomics of Ovarian Cancer Progression Reveals Diverse Metastatic Trajectories Including Intraepithelial Metastasis to the Fallopian Tube.
Mark A Eckert, Shawn Pan, +9 authors, Ernst Lengyel.
Cancer Discov, 2016 Nov 20; 6(12). PMID: 27856443    Free PMC article.
Highly Cited.
Computational approaches for the identification of cancer genes and pathways.
Christos M Dimitrakopoulos, Niko Beerenwinkel.
Wiley Interdiscip Rev Syst Biol Med, 2016 Nov 20; 9(1). PMID: 27863091    Free PMC article.
Review.
Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking.
Joachim Weischenfeldt, Taronish Dubash, +29 authors, Jan O Korbel.
Nat Genet, 2016 Nov 22; 49(1). PMID: 27869826    Free PMC article.
Highly Cited.
The Emergence of Pan-Cancer CIMP and Its Elusive Interpretation.
Brendan F Miller, Francisco Sánchez-Vega, Laura Elnitski.
Biomolecules, 2016 Nov 24; 6(4). PMID: 27879658    Free PMC article.
Review.
p53 coordinates DNA repair with nucleotide synthesis by suppressing PFKFB3 expression and promoting the pentose phosphate pathway.
Derek A Franklin, Yizhou He, +4 authors, Yanping Zhang.
Sci Rep, 2016 Dec 03; 6. PMID: 27901115    Free PMC article.
Trans-acting epigenetic effects of chromosomal aneuploidies: lessons from Down syndrome and mouse models.
Catherine Do, Zhuo Xing, Y Eugene Yu, Benjamin Tycko.
Epigenomics, 2016 Dec 03; 9(2). PMID: 27911079    Free PMC article.
Review.
Whole-exome sequencing predicted cancer epitope trees of 23 early cervical cancers in Chinese women.
Xia Li, Hailiang Huang, +5 authors, Zhi-Ying Chen.
Cancer Med, 2016 Dec 21; 6(1). PMID: 27998038    Free PMC article.
Identifying the clonal origin of synchronous multifocal tumors in the hepatobiliary and pancreatic system using multi-omic platforms.
Weiqin Jiang, Yongfeng Ding, +9 authors, Weilin Wang.
Oncotarget, 2016 Dec 23; 8(3). PMID: 28008139    Free PMC article.
Somatic Mutation Patterns in Hemizygous Genomic Regions Unveil Purifying Selection during Tumor Evolution.
Jimmy Van den Eynden, Swaraj Basu, Erik Larsson.
PLoS Genet, 2016 Dec 28; 12(12). PMID: 28027311    Free PMC article.
Genomic Analysis of Uterine Lavage Fluid Detects Early Endometrial Cancers and Reveals a Prevalent Landscape of Driver Mutations in Women without Histopathologic Evidence of Cancer: A Prospective Cross-Sectional Study.
Navya Nair, Olga Camacho-Vanegas, +15 authors, John A Martignetti.
PLoS Med, 2016 Dec 28; 13(12). PMID: 28027320    Free PMC article.
Integrative genomic and transcriptomic analysis for pinpointing recurrent alterations of plant homeodomain genes and their clinical significance in breast cancer.
Huimei Yu, Yuanyuan Jiang, +4 authors, Zeng-Quan Yang.
Oncotarget, 2017 Jan 06; 8(8). PMID: 28055972    Free PMC article.
The Cellular Origin and Evolution of Breast Cancer.
Mei Zhang, Adrian V Lee, Jeffrey M Rosen.
Cold Spring Harb Perspect Med, 2017 Jan 08; 7(3). PMID: 28062556    Free PMC article.
Review.
Germline BRCA2 mutations drive prostate cancers with distinct evolutionary trajectories.
Renea A Taylor, Michael Fraser, +25 authors, Robert G Bristow.
Nat Commun, 2017 Jan 10; 8. PMID: 28067867    Free PMC article.
Highly Cited.
Genomic hallmarks of localized, non-indolent prostate cancer.
Michael Fraser, Veronica Y Sabelnykova, +67 authors, Paul C Boutros.
Nature, 2017 Jan 10; 541(7637). PMID: 28068672
Highly Cited.
Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy.
Teresa Davoli, Hajime Uno, Eric C Wooten, Stephen J Elledge.
Science, 2017 Jan 21; 355(6322). PMID: 28104840    Free PMC article.
Highly Cited.
Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks.
Fabian Fröhlich, Barbara Kaltenbacher, Fabian J Theis, Jan Hasenauer.
PLoS Comput Biol, 2017 Jan 24; 13(1). PMID: 28114351    Free PMC article.
Reconstructing metastatic seeding patterns of human cancers.
Johannes G Reiter, Alvin P Makohon-Moore, +5 authors, Martin A Nowak.
Nat Commun, 2017 Feb 01; 8. PMID: 28139641    Free PMC article.
Highly Cited.
Discovery of cancer common and specific driver gene sets.
Junhua Zhang, Shihua Zhang.
Nucleic Acids Res, 2017 Feb 09; 45(10). PMID: 28168295    Free PMC article.
Optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data.
Ítalo Faria do Valle, Enrico Giampieri, +11 authors, Gastone Castellani.
BMC Bioinformatics, 2017 Feb 12; 17(Suppl 12). PMID: 28185561    Free PMC article.
Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer.
Hannah Carter, Rachel Marty, +13 authors, Trey Ideker.
Cancer Discov, 2017 Feb 12; 7(4). PMID: 28188128    Free PMC article.
Highly Cited.
Haploinsufficiency networks identify targetable patterns of allelic deficiency in low mutation ovarian cancer.
Joe Ryan Delaney, Chandni B Patel, +15 authors, Dwayne G Stupack.
Nat Commun, 2017 Feb 16; 8. PMID: 28198375    Free PMC article.
Recurrent patterns of DNA copy number alterations in tumors reflect metabolic selection pressures.
Nicholas A Graham, Aspram Minasyan, +23 authors, Thomas G Graeber.
Mol Syst Biol, 2017 Feb 17; 13(2). PMID: 28202506    Free PMC article.
Multiple Roles of MYC in Integrating Regulatory Networks of Pluripotent Stem Cells.
Luca Fagnocchi, Alessio Zippo.
Front Cell Dev Biol, 2017 Feb 22; 5. PMID: 28217689    Free PMC article.
Review.
High mTORC1 activity drives glycolysis addiction and sensitivity to G6PD inhibition in acute myeloid leukemia cells.
L Poulain, P Sujobert, +23 authors, N Chapuis.
Leukemia, 2017 Mar 11; 31(11). PMID: 28280275
The metabolic waste ammonium regulates mTORC2 and mTORC1 signaling.
Ahmad Merhi, Paul Delrée, Anna Maria Marini.
Sci Rep, 2017 Mar 18; 7. PMID: 28303961    Free PMC article.
Comparing mutation calls in fixed tumour samples between the affymetrix OncoScan® array and PCR based next-generation sequencing.
Henry M Wood, Joseph M Foster, +7 authors, Philip Quirke.
BMC Med Genomics, 2017 Mar 21; 10(1). PMID: 28315634    Free PMC article.
Pan-cancer analysis distinguishes transcriptional changes of aneuploidy from proliferation.
Christopher Buccitelli, Lorena Salgueiro, +3 authors, Jan O Korbel.
Genome Res, 2017 Mar 23; 27(4). PMID: 28320919    Free PMC article.
Prospective phase II trial of everolimus in PIK3CA amplification/mutation and/or PTEN loss patients with advanced solid tumors refractory to standard therapy.
Seung Tae Kim, Jeeyun Lee, +4 authors, Ho Yeong Lim.
BMC Cancer, 2017 Mar 24; 17(1). PMID: 28330462    Free PMC article.
Functional variomics and network perturbation: connecting genotype to phenotype in cancer.
Song Yi, Shengda Lin, +3 authors, Nidhi Sahni.
Nat Rev Genet, 2017 Mar 28; 18(7). PMID: 28344341    Free PMC article.
Review.
CpG island methylator phenotype in adenocarcinomas from the digestive tract: Methods, conclusions, and controversies.
Francisco Sánchez-Vega, Valer Gotea, Yun-Ching Chen, Laura Elnitski.
World J Gastrointest Oncol, 2017 Mar 28; 9(3). PMID: 28344746    Free PMC article.
Revealing cancer subtypes with higher-order correlations applied to imaging and omics data.
Kiley Graim, Tiffany Ting Liu, +7 authors, Joshua M Stuart.
BMC Med Genomics, 2017 Apr 01; 10(1). PMID: 28359308    Free PMC article.
The temporal dynamics of chromosome instability in ovarian cancer cell lines and primary patient samples.
Signe Penner-Goeke, Zelda Lichtensztejn, +4 authors, Kirk J McManus.
PLoS Genet, 2017 Apr 05; 13(4). PMID: 28376088    Free PMC article.
High-confidence coding and noncoding transcriptome maps.
Bo-Hyun You, Sang-Ho Yoon, Jin-Wu Nam.
Genome Res, 2017 Apr 12; 27(6). PMID: 28396519    Free PMC article.
Reprogramming induced by isoliquiritigenin diminishes melanoma cachexia through mTORC2-AKT-GSK3β signaling.
Xiao-Yu Chen, De-Fang Li, +8 authors, Qiu-Sheng Zheng.
Oncotarget, 2017 Apr 15; 8(21). PMID: 28410220    Free PMC article.
p16 controls epithelial cell growth and suppresses carcinogenesis through mechanisms that do not require RB1 function.
M Sen, N Akeno, +3 authors, K A Wikenheiser-Brokamp.
Oncogenesis, 2017 Apr 18; 6(4). PMID: 28414317    Free PMC article.
Identification of DBCCR1 as a suppressor in the development of lung cancer that is associated with increased DNA methyltransferase 1.
Guoren Zhou, Jinjun Ye, +4 authors, Jifeng Feng.
Oncotarget, 2017 Apr 22; 8(20). PMID: 28427182    Free PMC article.
Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients.
Ahmet Zehir, Ryma Benayed, +97 authors, Michael F Berger.
Nat Med, 2017 May 10; 23(6). PMID: 28481359    Free PMC article.
Highly Cited.
Oncogenic activity of amplified miniature chromosome maintenance 8 in human malignancies.
D-M He, B-G Ren, +5 authors, J-H Luo.
Oncogene, 2017 May 10; 36(25). PMID: 28481876    Free PMC article.
Targeting Intracellular Calcium Signaling ([Ca2+]i) to Overcome Acquired Multidrug Resistance of Cancer Cells: A Mini-Overview.
Dietrich Büsselberg, Ana-Maria Florea.
Cancers (Basel), 2017 May 10; 9(5). PMID: 28486397    Free PMC article.
Review.
Single-cell sequencing deciphers a convergent evolution of copy number alterations from primary to circulating tumor cells.
Yan Gao, Xiaohui Ni, +13 authors, Ning Zhang.
Genome Res, 2017 May 11; 27(8). PMID: 28487279    Free PMC article.
Transcriptional response profiles of paired tumor-normal samples offer novel perspectives in pan-cancer analysis.
Shuofeng Hu, Hanyu Yuan, +7 authors, Xiaomin Ying.
Oncotarget, 2017 May 11; 8(25). PMID: 28489584    Free PMC article.
Single-cell template strand sequencing by Strand-seq enables the characterization of individual homologs.
Ashley D Sanders, Ester Falconer, +2 authors, Peter M Lansdorp.
Nat Protoc, 2017 May 12; 12(6). PMID: 28492527
Adhesion- and stress-related adaptation of glioma radiochemoresistance is circumvented by β1 integrin/JNK co-targeting.
Anne Vehlow, Erik Klapproth, +6 authors, Nils Cordes.
Oncotarget, 2017 May 18; 8(30). PMID: 28514757    Free PMC article.
Complexity and algorithms for copy-number evolution problems.
Mohammed El-Kebir, Benjamin J Raphael, +4 authors, Ron Zeira.
Algorithms Mol Biol, 2017 May 19; 12. PMID: 28515774    Free PMC article.
CVE: an R package for interactive variant prioritisation in precision oncology.
Andreas Mock, Suzanne Murphy, +3 authors, Charlie Massie.
BMC Med Genomics, 2017 May 27; 10(1). PMID: 28545463    Free PMC article.
A DNA methylation map of human cancer at single base-pair resolution.
E Vidal, S Sayols, +9 authors, M Esteller.
Oncogene, 2017 Jun 06; 36(40). PMID: 28581523    Free PMC article.
MYC Deregulation in Primary Human Cancers.
Manpreet Kalkat, Jason De Melo, +6 authors, Linda Z Penn.
Genes (Basel), 2017 Jun 08; 8(6). PMID: 28587062    Free PMC article.
Highly Cited. Review.
Selection of Nucleic Acid Aptamers Targeting Tumor Cell-Surface Protein Biomarkers.
Marie-Cécile Mercier, Monique Dontenwill, Laurence Choulier.
Cancers (Basel), 2017 Jun 22; 9(6). PMID: 28635657    Free PMC article.
Review.
Intra-tumor heterogeneity in head and neck cancer and its clinical implications.
Edmund A Mroz, James W Rocco.
World J Otorhinolaryngol Head Neck Surg, 2017 Jun 24; 2(2). PMID: 28642939    Free PMC article.
Breast cancers are rare diseases-and must be treated as such.
John M S Bartlett, Wendy Parelukar.
NPJ Breast Cancer, 2017 Jun 27; 3. PMID: 28649651    Free PMC article.
Computational Methods for Characterizing Cancer Mutational Heterogeneity.
Fabio Vandin.
Front Genet, 2017 Jul 01; 8. PMID: 28659971    Free PMC article.
Review.
A comprehensive genomic pan-cancer classification using The Cancer Genome Atlas gene expression data.
Yuanyuan Li, Kai Kang, +4 authors, Leping Li.
BMC Genomics, 2017 Jul 05; 18(1). PMID: 28673244    Free PMC article.
Epistasis in genomic and survival data of cancer patients.
Dariusz Matlak, Ewa Szczurek.
PLoS Comput Biol, 2017 Jul 06; 13(7). PMID: 28678836    Free PMC article.
Pilot study of sirolimus in patients with PIK3CA mutant/amplified refractory solid cancer.
Ki Sun Jung, Jeeyun Lee, +5 authors, Seung Tae Kim.
Mol Clin Oncol, 2017 Jul 08; 7(1). PMID: 28685070    Free PMC article.
Assessment of circulating copy number variant detection for cancer screening.
Bhuvan Molparia, Eshaan Nichani, Ali Torkamani.
PLoS One, 2017 Jul 08; 12(7). PMID: 28686671    Free PMC article.
Whole exome sequencing identified genetic variations in Chinese hemangioblastoma patients.
Dexuan Ma, Jingyun Yang, +3 authors, Liangfu Zhou.
Am J Med Genet A, 2017 Jul 26; 173(10). PMID: 28742274    Free PMC article.
Variation in organ-specific PIK3CA and KRAS mutant levels in normal human tissues correlates with mutation prevalence in corresponding carcinomas.
Barbara L Parsons, Karen L McKim, Meagan B Myers.
Environ Mol Mutagen, 2017 Jul 30; 58(7). PMID: 28755461    Free PMC article.
High-depth, high-accuracy microsatellite genotyping enables precision lung cancer risk classification.
K R Velmurugan, R T Varghese, N C Fonville, H R Garner.
Oncogene, 2017 Aug 02; 36(46). PMID: 28759038    Free PMC article.
HIT'nDRIVE: patient-specific multidriver gene prioritization for precision oncology.
Raunak Shrestha, Ermin Hodzic, +8 authors, S Cenk Sahinalp.
Genome Res, 2017 Aug 05; 27(9). PMID: 28768687    Free PMC article.
Epigenetics in ovarian cancer.
Yanina Natanzon, Ellen L Goode, Julie M Cunningham.
Semin Cancer Biol, 2017 Aug 08; 51. PMID: 28782606    Free PMC article.
Review.
TMPRSS2-ERG fusion co-opts master transcription factors and activates NOTCH signaling in primary prostate cancer.
Ken J Kron, Alexander Murison, +8 authors, Mathieu Lupien.
Nat Genet, 2017 Aug 08; 49(9). PMID: 28783165
Highly Cited.
Long non-coding RNAs and prostate cancer.
Aya Misawa, Ken-Ichi Takayama, Satoshi Inoue.
Cancer Sci, 2017 Aug 11; 108(11). PMID: 28796922    Free PMC article.
Review.
Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks.
Zeynep Kalender Atak, Hana Imrichova, +5 authors, Stein Aerts.
Genome Med, 2017 Sep 01; 9(1). PMID: 28854983    Free PMC article.
Crossed wires: 3D genome misfolding in human disease.
Heidi K Norton, Jennifer E Phillips-Cremins.
J Cell Biol, 2017 Sep 01; 216(11). PMID: 28855250    Free PMC article.
Review.
Intersection of retinoblastoma tumor suppressor function, stem cells, metabolism, and inflammation.
Shunsuke Kitajima, Chiaki Takahashi.
Cancer Sci, 2017 Sep 03; 108(9). PMID: 28865172    Free PMC article.
Review.
Putting p53 in Context.
Edward R Kastenhuber, Scott W Lowe.
Cell, 2017 Sep 09; 170(6). PMID: 28886379    Free PMC article.
Highly Cited. Review.
Precision Oncology: The Road Ahead.
Daniela Senft, Mark D M Leiserson, Eytan Ruppin, Ze'ev A Ronai.
Trends Mol Med, 2017 Sep 10; 23(10). PMID: 28887051    Free PMC article.
Review.
Involvement of DPP9 in gene fusions in serous ovarian carcinoma.
Marianne Lislerud Smebye, Antonio Agostini, +6 authors, Francesca Micci.
BMC Cancer, 2017 Sep 13; 17(1). PMID: 28893231    Free PMC article.
XCAVATOR: accurate detection and genotyping of copy number variants from second and third generation whole-genome sequencing experiments.
Alberto Magi, Tommaso Pippucci, Carlo Sidore.
BMC Genomics, 2017 Sep 25; 18(1). PMID: 28934930    Free PMC article.
The number of key carcinogenic events can be predicted from cancer incidence.
Aleksey V Belikov.
Sci Rep, 2017 Sep 25; 7(1). PMID: 28939880    Free PMC article.
miR-206 inhibits the growth of hepatocellular carcinoma cells via targeting CDK9.
Chi Pang, Gang Huang, +5 authors, Wangwei Cai.
Cancer Med, 2017 Sep 25; 6(10). PMID: 28940993    Free PMC article.
Network-Based Coverage of Mutational Profiles Reveals Cancer Genes.
Borislav H Hristov, Mona Singh.
Cell Syst, 2017 Sep 29; 5(3). PMID: 28957656    Free PMC article.
Somatic Superenhancer Duplications and Hotspot Mutations Lead to Oncogenic Activation of the KLF5 Transcription Factor.
Xiaoyang Zhang, Peter S Choi, +16 authors, Matthew Meyerson.
Cancer Discov, 2017 Oct 01; 8(1). PMID: 28963353    Free PMC article.
Perspective on the dynamics of cancer.
Youcef Derbal.
Theor Biol Med Model, 2017 Oct 04; 14(1). PMID: 28969664    Free PMC article.
Review.
A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines.
Mehmet Gönen, Barbara A Weir, +43 authors, Adam A Margolin.
Cell Syst, 2017 Oct 11; 5(5). PMID: 28988802    Free PMC article.
Genomic insights into head and neck cancer.
Tim N Beck, Erica A Golemis.
Cancers Head Neck, 2016 Jan 01; 1. PMID: 29034103    Free PMC article.
TissGDB: tissue-specific gene database in cancer.
Pora Kim, Aekyung Park, +3 authors, Zhongming Zhao.
Nucleic Acids Res, 2017 Oct 17; 46(D1). PMID: 29036590    Free PMC article.
Precision Medicine: Where have we reached and where are we headed?
Ikram A Burney, Ritu Lakhtakia.
Sultan Qaboos Univ Med J, 2017 Oct 25; 17(3). PMID: 29062546    Free PMC article.
mRNAs containing NMD-competent premature termination codons are stabilized and translated under UPF1 depletion.
Won Kyu Kim, SeongJu Yun, +4 authors, Hoguen Kim.
Sci Rep, 2017 Nov 22; 7(1). PMID: 29158530    Free PMC article.
Therapeutic Implications of the Genetic Landscape of Head and Neck Cancer.
Janice Cho, Daniel E Johnson, Jennifer R Grandis.
Semin Radiat Oncol, 2017 Nov 28; 28(1). PMID: 29173752    Free PMC article.
Review.
Screening drug effects in patient-derived cancer cells links organoid responses to genome alterations.
Julia Jabs, Franziska M Zickgraf, +14 authors, Christian Conrad.
Mol Syst Biol, 2017 Nov 29; 13(11). PMID: 29180611    Free PMC article.
Predicting cancer type from tumour DNA signatures.
Kee Pang Soh, Ewa Szczurek, Thomas Sakoparnig, Niko Beerenwinkel.
Genome Med, 2017 Dec 01; 9(1). PMID: 29183400    Free PMC article.
Characterizing the heterogeneity of tumor tissues from spatially resolved molecular measures.
John F Graf, Maria I Zavodszky.
PLoS One, 2017 Dec 01; 12(11). PMID: 29190747    Free PMC article.
CRISPR/Cas9-derived models of ovarian high grade serous carcinoma targeting Brca1, Pten and Nf1, and correlation with platinum sensitivity.
Josephine B Walton, Malcolm Farquharson, +10 authors, Iain A McNeish.
Sci Rep, 2017 Dec 06; 7(1). PMID: 29203787    Free PMC article.
Network dynamics-based cancer panel stratification for systemic prediction of anticancer drug response.
Minsoo Choi, Jue Shi, +2 authors, Kwang-Hyun Cho.
Nat Commun, 2017 Dec 07; 8(1). PMID: 29208897    Free PMC article.
PanCancer insights from The Cancer Genome Atlas: the pathologist's perspective.
Lee Ad Cooper, Elizabeth G Demicco, +3 authors, Alexander J Lazar.
J Pathol, 2017 Dec 31; 244(5). PMID: 29288495    Free PMC article.
Review.
Phenotypic characteristics of colorectal cancer in BRCA1/2 mutation carriers.
Albert Grinshpun, Naama Halpern, +7 authors, Tamar Peretz.
Eur J Hum Genet, 2018 Jan 13; 26(3). PMID: 29321669    Free PMC article.
Genomic analysis of head and neck cancer cases from two high incidence regions.
Sandra Perdomo, Devasena Anantharaman, +16 authors, Paul Brennan.
PLoS One, 2018 Jan 30; 13(1). PMID: 29377909    Free PMC article.
A Landscape of Metabolic Variation across Tumor Types.
Ed Reznik, Augustin Luna, +6 authors, Chris Sander.
Cell Syst, 2018 Feb 06; 6(3). PMID: 29396322    Free PMC article.
Highly Cited.
Promoter methylation of DNA damage repair (DDR) genes in human tumor entities: RBBP8/CtIP is almost exclusively methylated in bladder cancer.
Jolein Mijnes, Jürgen Veeck, +8 authors, Michael Rose.
Clin Epigenetics, 2018 Feb 16; 10. PMID: 29445424    Free PMC article.
Genomic Analysis Revealed New Oncogenic Signatures in TP53-Mutant Hepatocellular Carcinoma.
Venkatesh Kancherla, Samir Abdullazade, +7 authors, Salvatore Piscuoglio.
Front Genet, 2018 Feb 20; 9. PMID: 29456550    Free PMC article.
Combination Approach for Detecting Different Types of Alterations in Circulating Tumor DNA in Leiomyosarcoma.
Joanna Przybyl, Jacob J Chabon, +10 authors, Matt van de Rijn.
Clin Cancer Res, 2018 Feb 22; 24(11). PMID: 29463554    Free PMC article.
Reconstruction of kidney renal clear cell carcinoma evolution across pathological stages.
Shichao Pang, Yidi Sun, +4 authors, Yixue Li.
Sci Rep, 2018 Feb 22; 8(1). PMID: 29463849    Free PMC article.
The landscape of genomic alterations across childhood cancers.
Susanne N Gröbner, Barbara C Worst, +83 authors, Stefan M Pfister.
Nature, 2018 Mar 01; 555(7696). PMID: 29489754
Highly Cited.
Mapping a functional cancer genome atlas of tumor suppressors in mouse liver using AAV-CRISPR-mediated direct in vivo screening.
Guangchuan Wang, Ryan D Chow, +7 authors, Sidi Chen.
Sci Adv, 2018 Mar 06; 4(2). PMID: 29503867    Free PMC article.
Integrated genomics and functional validation identifies malignant cell specific dependencies in triple negative breast cancer.
Nirmesh Patel, Daniel Weekes, +18 authors, Andrew N J Tutt.
Nat Commun, 2018 Mar 15; 9(1). PMID: 29535384    Free PMC article.
A mechanistic pan-cancer pathway model informed by multi-omics data interprets stochastic cell fate responses to drugs and mitogens.
Mehdi Bouhaddou, Anne Marie Barrette, +7 authors, Marc R Birtwistle.
PLoS Comput Biol, 2018 Mar 27; 14(3). PMID: 29579036    Free PMC article.
Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas.
Franz X Schaub, Varsha Dhankani, +14 authors, Cancer Genome Atlas Network.
Cell Syst, 2018 Mar 30; 6(3). PMID: 29596783    Free PMC article.
Highly Cited.
Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers.
Suet-Feung Chin, Angela Santonja, +12 authors, Carlos Caldas.
Exp Mol Pathol, 2018 Apr 03; 104(3). PMID: 29608913    Free PMC article.
Multi-omics analysis reveals neoantigen-independent immune cell infiltration in copy-number driven cancers.
Daniel J McGrail, Lorenzo Federico, +6 authors, Nidhi Sahni.
Nat Commun, 2018 Apr 05; 9(1). PMID: 29615613    Free PMC article.
Epigenetic alterations to Polycomb targets precede malignant transition in a mouse model of breast cancer.
Ying Cai, Jhih-Rong Lin, +3 authors, Zhengdong D Zhang.
Sci Rep, 2018 Apr 05; 8(1). PMID: 29615825    Free PMC article.
Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas.
Theo A Knijnenburg, Linghua Wang, +36 authors, Chen Wang.
Cell Rep, 2018 Apr 05; 23(1). PMID: 29617664    Free PMC article.
Highly Cited.
Genomic and Functional Approaches to Understanding Cancer Aneuploidy.
Alison M Taylor, Juliann Shih, +12 authors, Matthew Meyerson.
Cancer Cell, 2018 Apr 07; 33(4). PMID: 29622463    Free PMC article.
Highly Cited.
A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers.
Ashton C Berger, Anil Korkut, +46 authors, Rehan Akbani.
Cancer Cell, 2018 Apr 07; 33(4). PMID: 29622464    Free PMC article.
Highly Cited.
Oncogenic Signaling Pathways in The Cancer Genome Atlas.
Francisco Sanchez-Vega, Marco Mina, +52 authors, Nikolaus Schultz.
Cell, 2018 Apr 07; 173(2). PMID: 29625050    Free PMC article.
Highly Cited.
A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples.
Han Chen, Chunyan Li, +4 authors, Han Liang.
Cell, 2018 Apr 07; 173(2). PMID: 29625054    Free PMC article.
Highly Cited.
Targeted therapy according to next generation sequencing-based panel sequencing.
Motonobu Saito, Tomoyuki Momma, Koji Kono.
Fukushima J Med Sci, 2018 Apr 10; 64(1). PMID: 29628467    Free PMC article.
High throughput discovery of protein variants using proteomics informed by transcriptomics.
Shyamasree Saha, David A Matthews, Conrad Bessant.
Nucleic Acids Res, 2018 May 03; 46(10). PMID: 29718325    Free PMC article.
Budget impact model for oncopharmacogenetics from the perspective of mandatory basic health insurance in Switzerland using the example of breast cancer.
Thomas D Szucs, Kevin P Szillat, Eva Blozik.
Pharmgenomics Pers Med, 2018 May 08; 11. PMID: 29731658    Free PMC article.
A feasibility study of colorectal cancer diagnosis via circulating tumor DNA derived CNV detection.
Bhuvan Molparia, Glenn Oliveira, +2 authors, Ali Torkamani.
PLoS One, 2018 May 24; 13(5). PMID: 29791457    Free PMC article.
Simultaneous identification of clinically relevant single nucleotide variants, copy number alterations and gene fusions in solid tumors by targeted next-generation sequencing.
Duarte Mendes Oliveira, Teresa Mirante, +8 authors, Antonia Rizzuto.
Oncotarget, 2018 Jun 02; 9(32). PMID: 29854313    Free PMC article.
Network-based machine learning and graph theory algorithms for precision oncology.
Wei Zhang, Jeremy Chien, Jeongsik Yong, Rui Kuang.
NPJ Precis Oncol, 2018 Jun 07; 1(1). PMID: 29872707    Free PMC article.
Review.
Identification of novel mutational drivers reveals oncogene dependencies in multiple myeloma.
Brian A Walker, Konstantinos Mavrommatis, +36 authors, Gareth J Morgan.
Blood, 2018 Jun 10; 132(6). PMID: 29884741    Free PMC article.
Highly Cited.
Genomic Landscapes of EBV-Associated Nasopharyngeal Carcinoma vs. HPV-Associated Head and Neck Cancer.
Hoi-Lam Ngan, Lan Wang, Kwok-Wai Lo, Vivian Wai Yan Lui.
Cancers (Basel), 2018 Jun 24; 10(7). PMID: 29933636    Free PMC article.
Review.
Autotaxin in Pathophysiology and Pulmonary Fibrosis.
Ioanna Ninou, Christiana Magkrioti, Vassilis Aidinis.
Front Med (Lausanne), 2018 Jun 29; 5. PMID: 29951481    Free PMC article.
Review.
Mutational landscape of a chemically-induced mouse model of liver cancer.
Frances Connor, Tim F Rayner, +4 authors, Duncan T Odom.
J Hepatol, 2018 Jul 01; 69(4). PMID: 29958939    Free PMC article.
Mechanistic Insights into Colorectal Cancer Phenomics from Fundamental and Organotypic Model Studies.
Frederick C Campbell, Maurice Bernard Loughrey, +3 authors, Lisa Rainey.
Am J Pathol, 2018 Jul 22; 188(9). PMID: 30028958    Free PMC article.
Review.
On statistical modeling of sequencing noise in high depth data to assess tumor evolution.
Raul Rabadan, Gyan Bhanot, +3 authors, Hossein Khiabanian.
J Stat Phys, 2018 Jul 24; 172(1). PMID: 30034030    Free PMC article.
SHP2 Inhibition Prevents Adaptive Resistance to MEK Inhibitors in Multiple Cancer Models.
Carmine Fedele, Hao Ran, +9 authors, Kwan Ho Tang.
Cancer Discov, 2018 Jul 27; 8(10). PMID: 30045908    Free PMC article.
Highly Cited.
Gene editing in the context of an increasingly complex genome.
K Blighe, L DeDionisio, +11 authors, C B T Moore.
BMC Genomics, 2018 Aug 09; 19(1). PMID: 30086710    Free PMC article.
Review.
A Survey of Molecular Heterogeneity in Hepatocellular Carcinoma.
Juan Jovel, Zhen Lin, +8 authors, Andrew L Mason.
Hepatol Commun, 2018 Aug 11; 2(8). PMID: 30094405    Free PMC article.
Homeobox oncogene activation by pan-cancer DNA hypermethylation.
Jianzhong Su, Yung-Hsin Huang, +9 authors, Wei Li.
Genome Biol, 2018 Aug 12; 19(1). PMID: 30097071    Free PMC article.
Copy number signatures and mutational processes in ovarian carcinoma.
Geoff Macintyre, Teodora E Goranova, +36 authors, James D Brenton.
Nat Genet, 2018 Aug 15; 50(9). PMID: 30104763    Free PMC article.
Highly Cited.
Improving Cancer Detection and Treatment with Liquid Biopsies and ptDNA.
Michael D Kessler, Nisha R Pawar, +2 authors, Timothy D O'Connor.
Trends Cancer, 2018 Aug 29; 4(9). PMID: 30149882    Free PMC article.
Review.
Emergence of Intrahepatic Cholangiocarcinoma: How High-Throughput Technologies Expedite the Solutions for a Rare Cancer Type.
Meng-Shin Shiao, Khajeelak Chiablaem, +2 authors, Natini Jinawath.
Front Genet, 2018 Aug 31; 9. PMID: 30158952    Free PMC article.
Review.
Effective normalization for copy number variation in Hi-C data.
Nicolas Servant, Nelle Varoquaux, +2 authors, Jean-Philippe Vert.
BMC Bioinformatics, 2018 Sep 08; 19(1). PMID: 30189838    Free PMC article.
Pan-cancer inference of intra-tumor heterogeneity reveals associations with different forms of genomic instability.
Franck Raynaud, Marco Mina, Daniele Tavernari, Giovanni Ciriello.
PLoS Genet, 2018 Sep 14; 14(9). PMID: 30212491    Free PMC article.
When More Is Less: Dual Phosphorylation Protects Signaling Off State against Overexpression.
Franziska Witzel, Nils Blüthgen.
Biophys J, 2018 Sep 16; 115(7). PMID: 30217381    Free PMC article.
Multi-level Proteomics Identifies CT45 as a Chemosensitivity Mediator and Immunotherapy Target in Ovarian Cancer.
Fabian Coscia, Ernst Lengyel, +12 authors, Marion Curtis.
Cell, 2018 Sep 23; 175(1). PMID: 30241606    Free PMC article.
Association Analysis of Somatic Copy Number Alteration Burden With Breast Cancer Survival.
Linfan Zhang, Nikta Feizi, Chen Chi, Pingzhao Hu.
Front Genet, 2018 Oct 20; 9. PMID: 30337938    Free PMC article.
Mutational interactions define novel cancer subgroups.
Jack Kuipers, Thomas Thurnherr, +5 authors, Niko Beerenwinkel.
Nat Commun, 2018 Oct 21; 9(1). PMID: 30341300    Free PMC article.
Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival.
Daniele Ramazzotti, Avantika Lal, +2 authors, Arend Sidow.
Nat Commun, 2018 Oct 28; 9(1). PMID: 30367051    Free PMC article.
Network integration of multi-tumour omics data suggests novel targeting strategies.
Ítalo Faria do Valle, Giulia Menichetti, +7 authors, Daniel Remondini.
Nat Commun, 2018 Oct 31; 9(1). PMID: 30375513    Free PMC article.
Development of biomarkers for real precision medicine.
Masahiro Shibata, Mohammad Obaidul Hoque.
Transl Lung Cancer Res, 2018 Nov 06; 7(Suppl 3). PMID: 30393609    Free PMC article.
Pathway-based subnetworks enable cross-disease biomarker discovery.
Syed Haider, Cindy Q Yao, +22 authors, Paul C Boutros.
Nat Commun, 2018 Nov 14; 9(1). PMID: 30420699    Free PMC article.
Computational analysis reveals histotype-dependent molecular profile and actionable mutation effects across cancers.
Daniel Heim, Grégoire Montavon, +2 authors, Frederick Klauschen.
Genome Med, 2018 Nov 18; 10(1). PMID: 30442178    Free PMC article.
Identifying Epistasis in Cancer Genomes: A Delicate Affair.
Joris van de Haar, Sander Canisius, +3 authors, Trey Ideker.
Cell, 2019 Jun 01; 177(6). PMID: 31150618    Free PMC article.
Review.
Focal Recurrent Copy Number Alterations Characterize Disease Relapse in High Grade Serous Ovarian Cancer Patients with Good Clinical Prognosis: A Pilot Study.
Matteo Dugo, Andrea Devecchi, +4 authors, Marina Bagnoli.
Genes (Basel), 2019 Sep 08; 10(9). PMID: 31491988    Free PMC article.
Association of Tumor Protein p53 and Ataxia-Telangiectasia Mutated Comutation With Response to Immune Checkpoint Inhibitors and Mortality in Patients With Non-Small Cell Lung Cancer.
Yu Chen, Gang Chen, +14 authors, Jian-Ji Pan.
JAMA Netw Open, 2019 Sep 21; 2(9). PMID: 31539077    Free PMC article.
Olfactory receptor gene abundance in invasive breast carcinoma.
Shirin Masjedi, Laurence J Zwiebel, Todd D Giorgio.
Sci Rep, 2019 Sep 26; 9(1). PMID: 31551495    Free PMC article.
Illuminating biological pathways for drug targeting in head and neck squamous cell carcinoma.
Gabrielle Choonoo, Aurora S Blucher, +13 authors, Ted Laderas.
PLoS One, 2019 Oct 10; 14(10). PMID: 31596908    Free PMC article.
STATegra, a comprehensive multi-omics dataset of B-cell differentiation in mouse.
David Gomez-Cabrero, Sonia Tarazona, +27 authors, Ana Conesa.
Sci Data, 2019 Nov 02; 6(1). PMID: 31672995    Free PMC article.
Tumor diversity and the trade-off between universal cancer tasks.
Jean Hausser, Pablo Szekely, +4 authors, Uri Alon.
Nat Commun, 2019 Nov 30; 10(1). PMID: 31780652    Free PMC article.
Effects of culture condition on epigenomic profiles of brain tumor cells.
Megan C Cox, Chengyu Deng, +2 authors, Scott S Verbridge.
ACS Biomater Sci Eng, 2019 Dec 05; 5(3). PMID: 31799379    Free PMC article.
Genomic Alteration Burden in Advanced Prostate Cancer and Therapeutic Implications.
Matthew J Ryan, Rohit Bose.
Front Oncol, 2019 Dec 12; 9. PMID: 31824860    Free PMC article.
Review.
Identification of Common and Subtype-Specific Mutated Sub-Pathways for a Cancer.
Haidan Yan, Xusheng Deng, +8 authors, Zheng Guo.
Front Genet, 2019 Dec 19; 10. PMID: 31850075    Free PMC article.
From genome to phenome: Predicting multiple cancer phenotypes based on somatic genomic alterations via the genomic impact transformer.
Yifeng Tao, Chunhui Cai, William W Cohen, Xinghua Lu.
Pac Symp Biocomput, 2019 Dec 05; 25. PMID: 31797588    Free PMC article.
Integrative proteogenomic analyses of human tumours identifies ADNP as a novel oncogenic mediator of cell cycle progression in high-grade serous ovarian cancer with poor prognosis.
Kubra Karagoz, Gaurav A Mehta, +2 authors, Michael L Gatza.
EBioMedicine, 2019 Nov 27; 50. PMID: 31767542    Free PMC article.
ADNP (Activity Dependent Neuroprotector Homeobox): A novel oncogene driving poor prognosis in high-grade serous carcinoma.
Gulisa Turashvili.
EBioMedicine, 2020 Jan 07; 51. PMID: 31901854    Free PMC article.
Relevance of arm somatic copy number alterations for oncologic outcomes and tumor immune microenvironment in clear cell renal cell carcinoma.
Ying Xiong, Yu Qi, +3 authors, Jianming Guo.
Ann Transl Med, 2020 Jan 14; 7(22). PMID: 31930047    Free PMC article.
Associating lncRNAs with small molecules via bilevel optimization reveals cancer-related lncRNAs.
Yongcui Wang, Shilong Chen, Luonan Chen, Yong Wang.
PLoS Comput Biol, 2019 Dec 27; 15(12). PMID: 31877126    Free PMC article.
Expression of LAMP3 and its correlation with clinicopathologic characteristics and prognosis in hepatocellular carcinoma.
Yang Gui, Wen-Bin Liu, +2 authors, Jian-Sheng Li.
Int J Clin Exp Pathol, 2018 Jan 01; 11(1). PMID: 31938120    Free PMC article.
A multiomics comparison between endometrial cancer and serous ovarian cancer.
Hui Zhong, Huiyu Chen, +2 authors, Zhihui Wu.
PeerJ, 2020 Jan 17; 8. PMID: 31942259    Free PMC article.
Fibroblast Growth Factor Receptor 1 (FGFR1) Amplification Detected by Droplet Digital Polymerase Chain Reaction (ddPCR) Is a Prognostic Factor in Colorectal Cancers.
Jeong Mo Bae, Xianyu Wen, +4 authors, Gyeong Hoon Kang.
Cancer Res Treat, 2019 May 18; 52(1). PMID: 31096734    Free PMC article.
Comprehensive identification and characterization of somatic copy number alterations in triple‑negative breast cancer.
Zaibing Li, Xiao Zhang, +6 authors, Ning Huang.
Int J Oncol, 2020 Jan 03; 56(2). PMID: 31894314    Free PMC article.
Unraveling cancer lineage drivers in squamous cell carcinomas.
Yinglu Guan, Guan Wang, +2 authors, Yejing Ge.
Pharmacol Ther, 2019 Dec 15; 206. PMID: 31836455    Free PMC article.
Review.
Identification of Distinct Immune Subtypes in Colorectal Cancer Based on the Stromal Compartment.
Rongfang Shen, Ping Li, +3 authors, Shujun Cheng.
Front Oncol, 2020 Jan 31; 9. PMID: 31998649    Free PMC article.
Genomic subtyping of liver cancers with prognostic application.
Zhenggang Wu, Xi Long, +5 authors, Hong Xue.
BMC Cancer, 2020 Feb 02; 20(1). PMID: 32005109    Free PMC article.
Transcriptional effects of copy number alterations in a large set of human cancers.
Arkajyoti Bhattacharya, Rico D Bense, +3 authors, Rudolf S N Fehrmann.
Nat Commun, 2020 Feb 07; 11(1). PMID: 32024838    Free PMC article.
A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns.
Wei Jiao, Gurnit Atwal, +12 authors, PCAWG Consortium.
Nat Commun, 2020 Feb 07; 11(1). PMID: 32024849    Free PMC article.
Pan-cancer analysis of whole genomes.
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium.
Nature, 2020 Feb 07; 578(7793). PMID: 32025007    Free PMC article.
Highly Cited.
A living biobank of ovarian cancer ex vivo models reveals profound mitotic heterogeneity.
Louisa Nelson, Anthony Tighe, +19 authors, Stephen S Taylor.
Nat Commun, 2020 Feb 15; 11(1). PMID: 32054838    Free PMC article.
DNA double-strand break repair pathway choice - from basic biology to clinical exploitation.
Ron D Jachimowicz, Jonas Goergens, H Christian Reinhardt.
Cell Cycle, 2019 May 23; 18(13). PMID: 31116084    Free PMC article.
Review.
SOX4: The unappreciated oncogene.
Carlos S Moreno.
Semin Cancer Biol, 2019 Aug 25; 67(Pt 1). PMID: 31445218    Free PMC article.
Review.
Genomic and transcriptomic profiling expands precision cancer medicine: the WINTHER trial.
Jordi Rodon, Jean-Charles Soria, +22 authors, Razelle Kurzrock.
Nat Med, 2019 Apr 24; 25(5). PMID: 31011205    Free PMC article.
Highly Cited.
Epigenetic activation of POTE genes in ovarian cancer.
Ashok Sharma, Mustafa Albahrani, +5 authors, Adam R Karpf.
Epigenetics, 2019 Feb 16; 14(2). PMID: 30764732    Free PMC article.
Comparison of TCGA and GENIE genomic datasets for the detection of clinically actionable alterations in breast cancer.
Pushpinder Kaur, Tania B Porras, +2 authors, Julie E Lang.
Sci Rep, 2019 Feb 08; 9(1). PMID: 30728399    Free PMC article.
Mutant p53 regulates LPA signaling through lysophosphatidic acid phosphatase type 6.
Agnieszka Chryplewicz, Samantha M Tienda, +3 authors, Mark A Eckert.
Sci Rep, 2019 Mar 28; 9(1). PMID: 30914657    Free PMC article.
Prognostic role of ARID1A negative expression in gastric cancer.
Mai Ashizawa, Motonobu Saito, +12 authors, Koji Kono.
Sci Rep, 2019 May 03; 9(1). PMID: 31043675    Free PMC article.
VCF2CNA: A tool for efficiently detecting copy-number alterations in VCF genotype data and tumor purity.
Daniel K Putnam, Xiaotu Ma, +4 authors, Xiang Chen.
Sci Rep, 2019 Jul 19; 9(1). PMID: 31316100    Free PMC article.
Tumour-specific Causal Inference Discovers Distinct Disease Mechanisms Underlying Cancer Subtypes.
Yifan Xue, Gregory Cooper, +4 authors, Xinghua Lu.
Sci Rep, 2019 Sep 15; 9(1). PMID: 31519988    Free PMC article.
Machine Learning for Better Prognostic Stratification and Driver Gene Identification Using Somatic Copy Number Variations in Anaplastic Oligodendroglioma.
Shai Rosenberg, Francois Ducray, +11 authors, POLA Network.
Oncologist, 2018 Jul 19; 23(12). PMID: 30018130    Free PMC article.
Genomic profiling of multiple breast cancer reveals inter-lesional heterogeneity.
Soomin Ahn, Hyun Jeong Kim, +5 authors, So Yeon Park.
Br J Cancer, 2020 Jan 14; 122(5). PMID: 31929516    Free PMC article.
Machine learning and feature selection for drug response prediction in precision oncology applications.
Mehreen Ali, Tero Aittokallio.
Biophys Rev, 2018 Aug 12; 11(1). PMID: 30097794    Free PMC article.
Review.
Frequent ESR1 and CDK Pathway Copy-Number Alterations in Metastatic Breast Cancer.
Ahmed Basudan, Nolan Priedigkeit, +16 authors, Steffi Oesterreich.
Mol Cancer Res, 2018 Oct 26; 17(2). PMID: 30355675    Free PMC article.
Development of tumor mutation burden as an immunotherapy biomarker: utility for the oncology clinic.
T A Chan, M Yarchoan, +4 authors, S Peters.
Ann Oncol, 2018 Nov 06; 30(1). PMID: 30395155    Free PMC article.
Highly Cited. Review.
Comparison of the genomic background of MET-altered carcinomas of the lung: biological differences and analogies.
Roberta Castiglione, Christina Alidousty, +11 authors, Anne Maria Schultheis.
Mod Pathol, 2018 Nov 22; 32(5). PMID: 30459450    Free PMC article.
Bayesian hierarchical classification and information sharing for clinical trials with subgroups and binary outcomes.
Nan Chen, J Jack Lee.
Biom J, 2018 Dec 07; 61(5). PMID: 30506747    Free PMC article.
Breaking point: the genesis and impact of structural variation in tumours.
Ailith Ewing, Colin Semple.
F1000Res, 2018 Dec 07; 7. PMID: 30519450    Free PMC article.
Review.
Exploring drivers of gene expression in the Cancer Genome Atlas.
Andrea Rau, Michael Flister, Hallgeir Rui, Paul L Auer.
Bioinformatics, 2018 Dec 19; 35(1). PMID: 30561551    Free PMC article.
Expression of the human antimicrobial peptide β-defensin-1 is repressed by the EGFR-ERK-MYC axis in colonic epithelial cells.
Clément Bonamy, Emmanuel Sechet, +5 authors, Brice Sperandio.
Sci Rep, 2018 Dec 24; 8(1). PMID: 30575780    Free PMC article.
Hybrid sequencing-based personal full-length transcriptomic analysis implicates proteostatic stress in metastatic ovarian cancer.
Ying Jing, Yi Zhang, +15 authors, Guanglei Zhuang.
Oncogene, 2019 Jan 09; 38(16). PMID: 30617306
Comparative oncogenomics identifies combinations of driver genes and drug targets in BRCA1-mutated breast cancer.
Stefano Annunziato, Julian R de Ruiter, +16 authors, Jos Jonkers.
Nat Commun, 2019 Jan 25; 10(1). PMID: 30674894    Free PMC article.
Shared heritability and functional enrichment across six solid cancers.
Xia Jiang, Hilary K Finucane, +330 authors, Sara Lindström.
Nat Commun, 2019 Jan 27; 10(1). PMID: 30683880    Free PMC article.
The landscape of selection in 551 esophageal adenocarcinomas defines genomic biomarkers for the clinic.
Alexander M Frankell, SriGanesh Jammula, +15 authors, Rebecca C Fitzgerald.
Nat Genet, 2019 Feb 06; 51(3). PMID: 30718927    Free PMC article.
Highly Cited.
Modeling double strand break susceptibility to interrogate structural variation in cancer.
Tracy J Ballinger, Britta A M Bouwman, +3 authors, Colin A Semple.
Genome Biol, 2019 Feb 10; 20(1). PMID: 30736820    Free PMC article.
NRF2 Activation in Cancer: From DNA to Protein.
Erica W Cloer, Dennis Goldfarb, +2 authors, Michael B Major.
Cancer Res, 2019 Feb 15; 79(5). PMID: 30760522    Free PMC article.
Highly Cited. Review.
Somatic mutations in early metazoan genes disrupt regulatory links between unicellular and multicellular genes in cancer.
Anna S Trigos, Richard B Pearson, Anthony T Papenfuss, David L Goode.
Elife, 2019 Feb 26; 8. PMID: 30803482    Free PMC article.
Estimating the number of genetic mutations (hits) required for carcinogenesis based on the distribution of somatic mutations.
Ramu Anandakrishnan, Robin T Varghese, Nicholas A Kinney, Harold R Garner.
PLoS Comput Biol, 2019 Mar 08; 15(3). PMID: 30845172    Free PMC article.
Molecular profiling of cancer patients enables personalized combination therapy: the I-PREDICT study.
Jason K Sicklick, Shumei Kato, +16 authors, Razelle Kurzrock.
Nat Med, 2019 Apr 24; 25(5). PMID: 31011206    Free PMC article.
Highly Cited.
Determinants of nutrient limitation in cancer.
Mark R Sullivan, Matthew G Vander Heiden.
Crit Rev Biochem Mol Biol, 2019 Jun 05; 54(3). PMID: 31162937    Free PMC article.
Review.
Regulated Phosphosignaling Associated with Breast Cancer Subtypes and Druggability.
Kuan-Lin Huang, Yige Wu, +23 authors, Li Ding.
Mol Cell Proteomics, 2019 Jun 15; 18(8). PMID: 31196969    Free PMC article.
Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference.
Chunhui Cai, Gregory F Cooper, +15 authors, Xinghua Lu.
PLoS Comput Biol, 2019 Jul 06; 15(7). PMID: 31276486    Free PMC article.
Claudin-low-like mouse mammary tumors show distinct transcriptomic patterns uncoupled from genomic drivers.
Christian Fougner, Helga Bergholtz, +2 authors, Therese Sørlie.
Breast Cancer Res, 2019 Aug 02; 21(1). PMID: 31366361    Free PMC article.
Profiling molecular regulators of recurrence in chemorefractory triple-negative breast cancers.
Bradley A Hancock, Yu-Hsiang Chen, +14 authors, Milan Radovich.
Breast Cancer Res, 2019 Aug 07; 21(1). PMID: 31383035    Free PMC article.
Defining Signatures of Arm-Wise Copy Number Change and Their Associated Drivers in Kidney Cancers.
Graeme Benstead-Hume, Sarah K Wooller, Jessica A Downs, Frances M G Pearl.
Int J Mol Sci, 2019 Nov 21; 20(22). PMID: 31744086    Free PMC article.
Control of p53-dependent transcription and enhancer activity by the p53 family member p63.
Gizem Karsli Uzunbas, Faraz Ahmed, Morgan A Sammons.
J Biol Chem, 2019 May 23; 294(27). PMID: 31113863    Free PMC article.
The Genomic and Immune Landscapes of Lethal Metastatic Breast Cancer.
Leticia De Mattos-Arruda, Stephen-John Sammut, +31 authors, Carlos Caldas.
Cell Rep, 2019 May 30; 27(9). PMID: 31141692    Free PMC article.
Highly Cited.
Dissecting Molecular Features of Gliomas: Genetic Loci and Validated Biomarkers.
Antonietta Arcella, Fiona Limanaqi, +6 authors, Francesco Fornai.
Int J Mol Sci, 2020 Jan 24; 21(2). PMID: 31968687    Free PMC article.
Review.
Interplay between DNA damage repair and apoptosis shapes cancer evolution through aneuploidy and microsatellite instability.
Noam Auslander, Yuri I Wolf, Eugene V Koonin.
Nat Commun, 2020 Mar 08; 11(1). PMID: 32144251    Free PMC article.
Prognosis, Biology, and Targeting of TP53 Dysregulation in Multiple Myeloma.
Erin Flynt, Kamlesh Bisht, +3 authors, Anjan Thakurta.
Cells, 2020 Jan 30; 9(2). PMID: 31991614    Free PMC article.
Review.
p53 CRISPR Deletion Affects DNA Structure and Nuclear Architecture.
Aline Rangel-Pozzo, Samuel Booth, +3 authors, Sabine Mai.
J Clin Med, 2020 Feb 27; 9(2). PMID: 32098416    Free PMC article.
Measuring DNA Copy Number Variation Using High-Density Methylation Microarrays.
Soonweng Cho, Hyun-Seok Kim, +2 authors, Leslie M Cope.
J Comput Biol, 2019 Feb 23; 26(4). PMID: 30789293    Free PMC article.
The Landscape of Somatic Copy Number Alterations in Head and Neck Squamous Cell Carcinoma.
Jian Yang, Yi Chen, Hong Luo, Haoyang Cai.
Front Oncol, 2020 Apr 01; 10. PMID: 32226775    Free PMC article.
Genome-Informed Targeted Therapy for Osteosarcoma.
Leanne C Sayles, Marcus R Breese, +18 authors, E Alejandro Sweet-Cordero.
Cancer Discov, 2018 Sep 30; 9(1). PMID: 30266815    Free PMC article.
Highly Cited.
Order and disorder: abnormal 3D chromatin organization in human disease.
Chiara Anania, Darío G Lupiáñez.
Brief Funct Genomics, 2020 Feb 07; 19(2). PMID: 32025693    Free PMC article.
Global DNA Hypomethylation in Epithelial Ovarian Cancer: Passive Demethylation and Association with Genomic Instability.
Wa Zhang, David Klinkebiel, +6 authors, Adam R Karpf.
Cancers (Basel), 2020 Mar 28; 12(3). PMID: 32213861    Free PMC article.
The role of bone marrow-derived cells in the origin of liver cancer revealed by single-cell sequencing.
Lu Chen, Xianfu Yi, +10 authors, Ning Zhang.
Cancer Biol Med, 2020 Apr 17; 17(1). PMID: 32296582    Free PMC article.
RDM1 promotes critical processes in breast cancer tumorigenesis.
Yajun Chen, Zhengwang Sun, Tianying Zhong.
J Cell Mol Med, 2019 Jun 22; 23(8). PMID: 31222930    Free PMC article.
Breast Cancer: A Molecularly Heterogenous Disease Needing Subtype-Specific Treatments.
Ugo Testa, Germana Castelli, Elvira Pelosi.
Med Sci (Basel), 2020 Mar 27; 8(1). PMID: 32210163    Free PMC article.
Review.
MicroRNAs Targeting MYC Expression: Trace of Hope for Pancreatic Cancer Therapy. A Systematic Review.
Roshanak Shams, Hamid Asadzadeh Aghdaei, +4 authors, José M Padrón.
Cancer Manag Res, 2020 Apr 21; 12. PMID: 32308478    Free PMC article.
Review.
Alternatively activated macrophage-derived secretome stimulates ovarian cancer spheroid spreading through a JAK2/STAT3 pathway.
Kaitlin C Fogg, Will R Olson, +5 authors, Pamela K Kreeger.
Cancer Lett, 2019 May 28; 458. PMID: 31129149    Free PMC article.
Three-dimensional genome: developmental technologies and applications in precision medicine.
Yingqi Li, Tao Tao, Likun Du, Xiao Zhu.
J Hum Genet, 2020 Mar 11; 65(6). PMID: 32152365
MEXPRESS update 2019.
Alexander Koch, Jana Jeschke, +2 authors, Tim De Meyer.
Nucleic Acids Res, 2019 May 23; 47(W1). PMID: 31114869    Free PMC article.
Highly Cited.
A Protein in the Yeast Saccharomyces cerevisiae Presents DNA Binding Homology to the p53 Checkpoint Protein and Tumor Suppressor.
Kanwal Farooqi, Marjan Ghazvini, +5 authors, Carol Wood Moore.
Biomolecules, 2020 Mar 12; 10(3). PMID: 32156076    Free PMC article.
Tumor Milieu Controlled by RB Tumor Suppressor.
Shunsuke Kitajima, Fengkai Li, Chiaki Takahashi.
Int J Mol Sci, 2020 Apr 05; 21(7). PMID: 32244804    Free PMC article.
Review.
Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences.
Sushant Kumar, Jonathan Warrell, +16 authors, Mark B Gerstein.
Cell, 2020 Feb 23; 180(5). PMID: 32084333    Free PMC article.
Mucinous Histology, BRCA1/2 Mutations, and Elevated Tumor Mutational Burden in Colorectal Cancer.
Noa Harpaz, Yair Eli Gatt, +3 authors, Albert Grinshpun.
J Oncol, 2020 May 08; 2020. PMID: 32377194    Free PMC article.
Chromatin regulators mediate anthracycline sensitivity in breast cancer.
Jose A Seoane, Jacob G Kirkland, +2 authors, Christina Curtis.
Nat Med, 2019 Nov 09; 25(11). PMID: 31700186    Free PMC article.
Metagenomic characterization of lysine acetyltransferases in human cancer and their association with clinicopathologic features.
Yuanyuan Jiang, Xuhui Guo, +4 authors, Zeng-Quan Yang.
Cancer Sci, 2020 Mar 13; 111(5). PMID: 32162442    Free PMC article.
Amplification of 3q26.2, 5q14.3, 8q24.3, 8q22.3, and 14q32.33 Are Possible Common Genetic Alterations in Oral Cancer Patients.
Melvin A Ambele, Andre van Zyl, +2 authors, Willie F P van Heerden.
Front Oncol, 2020 May 20; 10. PMID: 32426287    Free PMC article.
Impact of accumulated alterations in driver and passenger genes on response to radiation therapy.
Yuji Seo, Keisuke Tamari, +5 authors, Kazuhiko Ogawa.
Br J Radiol, 2020 Feb 08; 93(1109). PMID: 32031414    Free PMC article.
Biological Interpretation of Complex Genomic Data.
Kathleen M Fisch.
Methods Mol Biol, 2019 Jan 17; 1908. PMID: 30649721    Free PMC article.
Assessing the origin of high-grade serous ovarian cancer using CRISPR-modification of mouse organoids.
Kadi Lõhmussaar, Oded Kopper, +4 authors, Hans Clevers.
Nat Commun, 2020 May 29; 11(1). PMID: 32461556    Free PMC article.
Origins and characterization of variants shared between databases of somatic and germline human mutations.
William Meyerson, John Leisman, Fabio C P Navarro, Mark Gerstein.
BMC Bioinformatics, 2020 Jun 06; 21(1). PMID: 32498674    Free PMC article.
Computational algorithms for in silico profiling of activating mutations in cancer.
E Joseph Jordan, Keshav Patil, +4 authors, Ravi Radhakrishnan.
Cell Mol Life Sci, 2019 Apr 15; 76(14). PMID: 30982079    Free PMC article.
Review.
Colorectal Adenomas-Genetics and Searching for New Molecular Screening Biomarkers.
Anna Siskova, Klara Cervena, +3 authors, Veronika Vymetalkova.
Int J Mol Sci, 2020 May 10; 21(9). PMID: 32380676    Free PMC article.
Review.
Multifactorial Deep Learning Reveals Pan-Cancer Genomic Tumor Clusters with Distinct Immunogenomic Landscape and Response to Immunotherapy.
Feng Xie, Jianjun Zhang, +25 authors, Tian Xia.
Clin Cancer Res, 2020 Jan 09; 26(12). PMID: 31911545    Free PMC article.
RNF8 induces β-catenin-mediated c-Myc expression and promotes colon cancer proliferation.
Ling Ren, Tingting Zhou, +20 authors, Chengzhong Xing.
Int J Biol Sci, 2020 Jun 19; 16(12). PMID: 32549753    Free PMC article.
In vivo modeling of metastatic human high-grade serous ovarian cancer in mice.
Olga Kim, Eun Young Park, +25 authors, Jaeyeon Kim.
PLoS Genet, 2020 Jun 05; 16(6). PMID: 32497036    Free PMC article.
Somatic genetic aberrations in benign breast disease and the risk of subsequent breast cancer.
Zexian Zeng, Andy Vo, +7 authors, Susan E Clare.
NPJ Breast Cancer, 2020 Jun 23; 6. PMID: 32566745    Free PMC article.
Somatic Tissue Engineering in Mouse Models Reveals an Actionable Role for WNT Pathway Alterations in Prostate Cancer Metastasis.
Josef Leibold, Marcus Ruscetti, +22 authors, Scott W Lowe.
Cancer Discov, 2020 May 08; 10(7). PMID: 32376773    Free PMC article.
Multi-cancer analysis of clonality and the timing of systemic spread in paired primary tumors and metastases.
Zheng Hu, Zan Li, Zhicheng Ma, Christina Curtis.
Nat Genet, 2020 May 20; 52(7). PMID: 32424352    Free PMC article.
Somatic copy number profiling from hepatocellular carcinoma circulating tumor cells.
Colin M Court, Shuang Hou, +16 authors, Vatche G Agopian.
NPJ Precis Oncol, 2020 Jul 09; 4. PMID: 32637655    Free PMC article.
Oncotator: cancer variant annotation tool.
Alex H Ramos, Lee Lichtenstein, +5 authors, Gad Getz.
Hum Mutat, 2015 Feb 24; 36(4). PMID: 25703262    Free PMC article.
Highly Cited.
Copy number evolution with weighted aberrations in cancer.
Ron Zeira, Benjamin J Raphael.
Bioinformatics, 2020 Jul 14; 36(Suppl_1). PMID: 32657354    Free PMC article.
Characterization of Tumor-Suppressor Gene Inactivation Events in 33 Cancer Types.
Peilin Jia, Zhongming Zhao.
Cell Rep, 2019 Jan 10; 26(2). PMID: 30625331    Free PMC article.
Machine learning in oncology: a review.
Cecilia Nardini.
Ecancermedicalscience, 2020 Jul 31; 14. PMID: 32728381    Free PMC article.
Review.
The frequency and inter-relationship of PD-L1 expression and tumour mutational burden across multiple types of advanced solid tumours in China.
Yanhui Chen, Yating Wang, +5 authors, Henghui Zhang.
Exp Hematol Oncol, 2020 Aug 11; 9. PMID: 32775040    Free PMC article.
TMBIM6/BI-1 contributes to cancer progression through assembly with mTORC2 and AKT activation.
Hyun-Kyoung Kim, Kashi Raj Bhattarai, +8 authors, Han-Jung Chae.
Nat Commun, 2020 Aug 13; 11(1). PMID: 32782388    Free PMC article.
The TP53 mutation rate differs in breast cancers that arise in women with high or low mammographic density.
Dane Cheasley, Lisa Devereux, +16 authors, Ian G Campbell.
NPJ Breast Cancer, 2020 Aug 18; 6. PMID: 32802943    Free PMC article.
Integrative radiogenomics for virtual biopsy and treatment monitoring in ovarian cancer.
Paula Martin-Gonzalez, Mireia Crispin-Ortuzar, +9 authors, Evis Sala.
Insights Imaging, 2020 Aug 18; 11(1). PMID: 32804260    Free PMC article.
Review.
Clinically Integrated Sequencing Alters Therapy in Children and Young Adults With High-Risk Glial Brain Tumors.
Carl Koschmann, Yi-Mi Wu, +26 authors, Rajen Mody.
JCO Precis Oncol, 2018 Jan 01; 2. PMID: 32832832    Free PMC article.
A Deep Learning Framework to Predict Tumor Tissue-of-Origin Based on Copy Number Alteration.
Ying Liang, Haifeng Wang, +6 authors, Yinglong Wang.
Front Bioeng Biotechnol, 2020 Aug 28; 8. PMID: 32850687    Free PMC article.
Malignant Transformation and Associated Biomarkers of Ovarian Endometriosis: A Narrative Review.
Liudmila M Mikhaleva, Aleksandr I Davydov, +7 authors, Gjumrakch Aliev.
Adv Ther, 2020 May 10; 37(6). PMID: 32385745    Free PMC article.
Review.
Genomic Analysis of Localized High-Risk Prostate Cancer Circulating Tumor Cells at the Single-Cell Level.
Aline Rangel-Pozzo, Songyan Liu, +5 authors, Sabine Mai.
Cells, 2020 Aug 14; 9(8). PMID: 32784507    Free PMC article.
Exploitation of Precision Medicine Trials Data: Examples of Long Responders From the SHIVA01 Trial.
Clémence Basse, Claire Morel, +22 authors, Christophe Le Tourneau.
JCO Precis Oncol, 2018 Oct 19; 2. PMID: 32914004    Free PMC article.
Genomic Instability and TP53 Genomic Alterations Associate With Poor Antiproliferative Response and Intrinsic Resistance to Aromatase Inhibitor Treatment.
Eugene F Schuster, Pascal Gellert, +9 authors, POETIC Trial Management Group and Trialists.
JCO Precis Oncol, 2019 Jun 12; 3. PMID: 32914010    Free PMC article.
Identification of Actionable Genomic Alterations Using Circulating Cell-Free DNA.
Nora S Sánchez, Michael P Kahle, +13 authors, Funda Meric-Bernstam.
JCO Precis Oncol, 2020 Sep 15; 3. PMID: 32923868    Free PMC article.
Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data.
Simone Zaccaria, Benjamin J Raphael.
Nat Commun, 2020 Sep 04; 11(1). PMID: 32879317    Free PMC article.
Precision medicine review: rare driver mutations and their biophysical classification.
Ruth Nussinov, Hyunbum Jang, Chung-Jung Tsai, Feixiong Cheng.
Biophys Rev, 2019 Jan 06; 11(1). PMID: 30610579    Free PMC article.
Review.
Genetic Factors Associated with a Poor Outcome in Head and Neck Cancer Patients Receiving Definitive Chemoradiotherapy.
David M Vossen, Caroline V M Verhagen, +6 authors, Conchita Vens.
Cancers (Basel), 2019 Apr 03; 11(4). PMID: 30934880    Free PMC article.
A STATISTICAL FRAMEWORK FOR DATA INTEGRATION THROUGH GRAPHICAL MODELS WITH APPLICATION TO CANCER GENOMICS.
Yuping Zhang, Zhengqing Ouyang, Hongyu Zhao.
Ann Appl Stat, 2017 Mar 01; 11(1). PMID: 30956747    Free PMC article.
Differentially mutated subnetworks discovery.
Morteza Chalabi Hajkarim, Eli Upfal, Fabio Vandin.
Algorithms Mol Biol, 2019 Apr 13; 14. PMID: 30976291    Free PMC article.
The role of circadian clock genes in tumors.
Han-Xue Li.
Onco Targets Ther, 2019 Jun 14; 12. PMID: 31190867    Free PMC article.
Review.
Integrative analysis of common genes and driver mutations implicated in hormone stimulation for four cancers in women.
Salma Begum Bhyan, YongKiat Wee, +2 authors, Min Zhao.
PeerJ, 2019 Jun 18; 7. PMID: 31205821    Free PMC article.
RNA Aptamers Targeting Integrin α5β1 as Probes for Cyto- and Histofluorescence in Glioblastoma.
Pierre Fechter, Elisabete Cruz Da Silva, +11 authors, Laurence Choulier.
Mol Ther Nucleic Acids, 2019 Jun 22; 17. PMID: 31226519    Free PMC article.
Precision oncology in Latin America: current situation, challenges and perspectives.
Ali Calderón-Aparicio, Andrea Orue.
Ecancermedicalscience, 2019 Jul 10; 13. PMID: 31281417    Free PMC article.
Pan-Cancer and Single-Cell Modeling of Genomic Alterations Through Gene Expression.
Daniele Mercatelli, Forest Ray, Federico M Giorgi.
Front Genet, 2019 Aug 06; 10. PMID: 31379928    Free PMC article.
Hierarchical Classification of Cancers of Unknown Primary Using Multi-Omics Data.
Elham Bavafaye Haghighi, Michael Knudsen, Britt Elmedal Laursen, Søren Besenbacher.
Cancer Inform, 2019 Sep 14; 18. PMID: 31516310    Free PMC article.
A WEE1 family business: regulation of mitosis, cancer progression, and therapeutic target.
Andrea Ghelli Luserna di Rorà, Claudio Cerchione, Giovanni Martinelli, Giorgia Simonetti.
J Hematol Oncol, 2020 Sep 23; 13(1). PMID: 32958072    Free PMC article.
Review.
Identification of New Therapeutic Targets for Gastric Cancer With Bioinformatics.
Yang Li, Jin-Shen Wang, +2 authors, Le-Ping Li.
Front Genet, 2020 Oct 06; 11. PMID: 33014013    Free PMC article.
Whole-exome sequencing of long-term, never relapse exceptional responders of trastuzumab-treated HER2+ metastatic breast cancer.
Naomi Walsh, Charlotte Andrieu, +5 authors, John Crown.
Br J Cancer, 2020 Jul 28; 123(8). PMID: 32713940    Free PMC article.
Somatic structural variation targets neurodevelopmental genes and identifies SHANK2 as a tumor suppressor in neuroblastoma.
Gonzalo Lopez, Karina L Conkrite, +15 authors, Sharon J Diskin.
Genome Res, 2020 Aug 17; 30(9). PMID: 32796005    Free PMC article.
Leukoplakia and Immunology: New Chemoprevention Landscapes?
Roberto Grigolato, Maria Eleonora Bizzoca, +3 authors, Lorenzo Lo Muzio.
Int J Mol Sci, 2020 Sep 24; 21(18). PMID: 32961682    Free PMC article.
Review.
Multiomic Analysis of Subtype Evolution and Heterogeneity in High-Grade Serous Ovarian Carcinoma.
Ludwig Geistlinger, Sehyun Oh, +18 authors, Levi Waldron.
Cancer Res, 2020 Aug 05; 80(20). PMID: 32747365    Free PMC article.
Non-invasive detection of biliary tract cancer by low-coverage whole genome sequencing from plasma cell-free DNA: A prospective cohort study.
Xiang Wang, Xiao-Hui Fu, +7 authors, Wen-Long Yu.
Transl Oncol, 2020 Oct 16; 14(1). PMID: 33059123    Free PMC article.
Isolation and Characterization of Two Novel Colorectal Cancer Cell Lines, Containing a Subpopulation with Potential Stem-Like Properties: Treatment Options by MYC/NMYC Inhibition.
Jan Schulte Am Schulte Am Esch, Beatrice Ariane Windmöller, +6 authors, Christian Kaltschmidt.
Cancers (Basel), 2020 Sep 16; 12(9). PMID: 32927768    Free PMC article.
Genome-wide CRISPR screens of oral squamous cell carcinoma reveal fitness genes in the Hippo pathway.
Annie Wai Yeeng Chai, Pei San Yee, +11 authors, Sok Ching Cheong.
Elife, 2020 Sep 30; 9. PMID: 32990596    Free PMC article.
Targeting DNA Repair, Cell Cycle, and Tumor Microenvironment in B Cell Lymphoma.
Paul J Bröckelmann, Mathilde R W de Jong, Ron D Jachimowicz.
Cells, 2020 Oct 18; 9(10). PMID: 33066395    Free PMC article.
Review.
SHP2 inhibition diminishes KRASG12C cycling and promotes tumor microenvironment remodeling.
Carmine Fedele, Shuai Li, +20 authors, Benjamin G Neel.
J Exp Med, 2020 Oct 13; 218(1). PMID: 33045063    Free PMC article.
A Circle RNA Regulatory Axis Promotes Lung Squamous Metastasis via CDR1-Mediated Regulation of Golgi Trafficking.
Emily B Harrison, Alessandro Porrello, +20 authors, Chad V Pecot.
Cancer Res, 2020 Sep 27; 80(22). PMID: 32978168    Free PMC article.
Identification of a 6-gene signature for the survival prediction of breast cancer patients based on integrated multi-omics data analysis.
Wenju Mo, Yuqin Ding, +2 authors, Xiaowen Ding.
PLoS One, 2020 Nov 11; 15(11). PMID: 33170908    Free PMC article.
Identification of the HECT E3 ligase UBR5 as a regulator of MYC degradation using a CRISPR/Cas9 screen.
Lina Schukur, Tamara Zimmermann, +13 authors, Claudio R Thoma.
Sci Rep, 2020 Nov 20; 10(1). PMID: 33208877    Free PMC article.
Systems medicine in colorectal cancer: from a mathematical model toward a new type of clinical trial.
Nicoletta Castagnino, Massimo Maffei, +7 authors, Silvio Parodi.
Wiley Interdiscip Rev Syst Biol Med, 2016 May 31; 8(4). PMID: 27240214    Free PMC article.
Review.
TP53 Mutations in Breast and Ovarian Cancer.
Laxmi Silwal-Pandit, Anita Langerød, Anne-Lise Børresen-Dale.
Cold Spring Harb Perspect Med, 2016 Nov 07; 7(1). PMID: 27815305    Free PMC article.
Review.
Genomic perturbations reveal distinct regulatory networks in intrahepatic cholangiocarcinoma.
Chirag Nepal, Colm J O'Rourke, +11 authors, Jesper B Andersen.
Hepatology, 2017 Dec 27; 68(3). PMID: 29278425    Free PMC article.
TPX2/Aurora kinase A signaling as a potential therapeutic target in genomically unstable cancer cells.
Stephanie E van Gijn, Elles Wierenga, +6 authors, Rudolf S N Fehrmann.
Oncogene, 2018 Sep 05; 38(6). PMID: 30177840    Free PMC article.
CTCF Expression is Essential for Somatic Cell Viability and Protection Against Cancer.
Charles G Bailey, Cynthia Metierre, +6 authors, John Ej Rasko.
Int J Mol Sci, 2018 Dec 06; 19(12). PMID: 30513694    Free PMC article.
Systems proteogenomics for precision oncology.
Frederick Klauschen.
Oncotarget, 2019 Feb 19; 10(7). PMID: 30774770    Free PMC article.
Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers.
Ruth Nussinov, Hyunbum Jang, Chung-Jung Tsai, Feixiong Cheng.
PLoS Comput Biol, 2019 Mar 29; 15(3). PMID: 30921324    Free PMC article.
Highly Cited. Review.
Genes' Interactions: A Major Contributor to the Malignant Transformation of Endometriosis.
Konstantinos Sapalidis, Nikolaos Machairiotis, +12 authors, Isaak Kesisoglou.
Int J Mol Sci, 2019 Apr 25; 20(8). PMID: 31013963    Free PMC article.
Review.
Portrait of a cancer: mutational signature analyses for cancer diagnostics.
Arne Van Hoeck, Niels H Tjoonk, Ruben van Boxtel, Edwin Cuppen.
BMC Cancer, 2019 May 17; 19(1). PMID: 31092228    Free PMC article.
Review.
P53 and Apoptosis in the Drosophila Model.
Lei Zhou.
Adv Exp Med Biol, 2019 Sep 15; 1167. PMID: 31520351
Review.
Genome instability in multiple myeloma.
Carl Jannes Neuse, Oliver C Lomas, +4 authors, Irene M Ghobrial.
Leukemia, 2020 Jul 12; 34(11). PMID: 32651540
Review.
Evolving insights: how DNA repair pathways impact cancer evolution.
Jiadong Zhou, Xiao Albert Zhou, Ning Zhang, Jiadong Wang.
Cancer Biol Med, 2020 Dec 11; 17(4). PMID: 33299637    Free PMC article.
Review.
Single-cell analysis of structural variations and complex rearrangements with tri-channel processing.
Ashley D Sanders, Sascha Meiers, +20 authors, Jan O Korbel.
Nat Biotechnol, 2019 Dec 25; 38(3). PMID: 31873213
NRF2 Regulation by Noncoding RNAs in Cancers: The Present Knowledge and the Way Forward.
Federico Pio Fabrizio, Angelo Sparaneo, Lucia Anna Muscarella.
Cancers (Basel), 2020 Dec 09; 12(12). PMID: 33287295    Free PMC article.
Review.
The molecular landscape of Asian breast cancers reveals clinically relevant population-specific differences.
Jia-Wern Pan, Muhammad Mamduh Ahmad Zabidi, +10 authors, Soo-Hwang Teo.
Nat Commun, 2020 Dec 24; 11(1). PMID: 33353943    Free PMC article.
Defining the clinical genomic landscape for real-world precision oncology.
Philip A Beer, Susanna L Cooke, David K Chang, Andrew V Biankin.
Genomics, 2020 Nov 05; 112(6). PMID: 33144218    Free PMC article.
Nanomedicine of tyrosine kinase inhibitors.
Veronika Smidova, Petr Michalek, +4 authors, Zbynek Heger.
Theranostics, 2021 Jan 08; 11(4). PMID: 33408767    Free PMC article.
Review.
Targeting Loss of Heterozygosity: A Novel Paradigm for Cancer Therapy.
Xiaonan Zhang, Tobias Sjöblom.
Pharmaceuticals (Basel), 2021 Jan 17; 14(1). PMID: 33450833    Free PMC article.
Review.
Systematic analysis of enhancer regulatory circuit perturbation driven by copy number variations in malignant glioma.
Jun Xiao, Xiaoyan Jin, +6 authors, Yongsheng Li.
Theranostics, 2021 Feb 05; 11(7). PMID: 33537074    Free PMC article.
Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL.
Simone Zaccaria, Benjamin J Raphael.
Nat Biotechnol, 2020 Sep 04; 39(2). PMID: 32879467
Genome-wide analysis of copy number alterations led to the characterisation of PDCD10 as oncogene in ovarian cancer.
Carmela De Marco, Pietro Zoppoli, +15 authors, Giuseppe Viglietto.
Transl Oncol, 2021 Jan 31; 14(3). PMID: 33516089    Free PMC article.
Survival outcomes are associated with genomic instability in luminal breast cancers.
Lydia King, Andrew Flaus, Emma Holian, Aaron Golden.
PLoS One, 2021 Feb 04; 16(2). PMID: 33534788    Free PMC article.

;. PMID: 33574272

;. PMID: 33579974
ANKLE1 as New Hotspot Mutation for Breast Cancer in Indian Population and Has a Role in DNA Damage and Repair in Mammalian Cells.
Divya Bakshi, Archana Katoch, +9 authors, Rakesh Kumar.
Front Genet, 2021 Feb 16; 11. PMID: 33584808    Free PMC article.

;. PMID: 33594215
Mutations in long-lived epithelial stem cells and their clonal progeny in pre-malignant lesions and in oral squamous cell carcinoma.
Marta Melis, Tuo Zhang, Theresa Scognamiglio, Lorraine J Gudas.
Carcinogenesis, 2020 Mar 03; 41(11). PMID: 32115621    Free PMC article.
Oncoprotein HBXIP promotes tumorigenesis through MAPK/ERK pathway activation in non-small cell lung cancer.
Jun Zhang, Bei Sun, +5 authors, Ming Gao.
Cancer Biol Med, 2021 Feb 26; 18(1). PMID: 33628588    Free PMC article.
Recent Advances in Integrative Multi-Omics Research in Breast and Ovarian Cancer.
Christen A Khella, Gaurav A Mehta, Rushabh N Mehta, Michael L Gatza.
J Pers Med, 2021 Mar 07; 11(2). PMID: 33669749    Free PMC article.
Review.
Frequent Subgraph Mining of Functional Interaction Patterns Across Multiple Cancers.
Arda Durmaz, Tim A D Henderson, Gurkan Bebek.
Pac Symp Biocomput, 2021 Mar 11; 26. PMID: 33691023    Free PMC article.
Profiling of circulating tumor DNA and tumor tissue for treatment selection in patients with advanced and refractory carcinoma: a prospective, two-stage phase II Individualized Cancer Treatment trial.
Jakob M Riedl, Samantha O Hasenleithner, +13 authors, Armin Gerger.
Ther Adv Med Oncol, 2021 Mar 16; 13. PMID: 33717225    Free PMC article.
Identification of a druggable protein-protein interaction site between mutant p53 and its stabilizing chaperone DNAJA1.
Xin Tong, Dandan Xu, +5 authors, Guang-Yu Yang.
J Biol Chem, 2020 Nov 20; 296. PMID: 33208462    Free PMC article.
ZBTB2 represses HIV-1 transcription and is regulated by HIV-1 Vpr and cellular DNA damage responses.
James W Bruce, Megan Bracken, +2 authors, Paul Ahlquist.
PLoS Pathog, 2021 Feb 27; 17(2). PMID: 33635925    Free PMC article.
IGF2BP1 is a targetable SRC/MAPK-dependent driver of invasive growth in ovarian cancer.
Nadine Bley, Annekatrin Schott, +14 authors, Stefan Hüttelmaier.
RNA Biol, 2020 Sep 03; 18(3). PMID: 32876513    Free PMC article.
Identifying modules of cooperating cancer drivers.
Michael I Klein, Vincent L Cannataro, +3 authors, Hongyu Zhao.
Mol Syst Biol, 2021 Mar 27; 17(3). PMID: 33769711    Free PMC article.
Detection of Genomically Aberrant Cells within Circulating Tumor Microemboli (CTMs) Isolated from Early-Stage Breast Cancer Patients.
Marco Silvestri, Carolina Reduzzi, +12 authors, Vera Cappelletti.
Cancers (Basel), 2021 Apr 04; 13(6). PMID: 33808748    Free PMC article.
Horizons in Veterinary Precision Oncology: Fundamentals of Cancer Genomics and Applications of Liquid Biopsy for the Detection, Characterization, and Management of Cancer in Dogs.
Jason Chibuk, Andi Flory, +16 authors, Daniel S Grosu.
Front Vet Sci, 2021 Apr 10; 8. PMID: 33834049    Free PMC article.
Review.
Transposon Mutagenesis-Guided CRISPR/Cas9 Screening Strongly Implicates Dysregulation of Hippo/YAP Signaling in Malignant Peripheral Nerve Sheath Tumor Development.
Germán L Vélez-Reyes, Nicholas Koes, +8 authors, David A Largaespada.
Cancers (Basel), 2021 Apr 04; 13(7). PMID: 33808166    Free PMC article.
Comprehensive omic characterization of breast cancer in Mexican-Hispanic women.
Sandra L Romero-Cordoba, Ivan Salido-Guadarrama, +8 authors, Alfredo Hidalgo-Miranda.
Nat Commun, 2021 Apr 16; 12(1). PMID: 33854067    Free PMC article.
Concurrent mutations associated with trastuzumab-resistance revealed by single cell sequencing.
Yan Gao, Ning Wu, +3 authors, Bo Xu.
Breast Cancer Res Treat, 2021 Apr 28; 187(3). PMID: 33905021
T-Cell Receptor Therapy in the Treatment of Ovarian Cancer: A Mini Review.
Jessica W Y Wu, Sudiksha Dand, +4 authors, Joshua D Ooi.
Front Immunol, 2021 May 01; 12. PMID: 33927729    Free PMC article.
Review.
A High-Throughput Chromatin Immunoprecipitation Sequencing Approach to Study the Role of MYC on the Epigenetic Landscape.
Luca Fagnocchi, Alessio Zippo.
Methods Mol Biol, 2021 May 22; 2318. PMID: 34019291
Chromogenic In Situ Hybridization (CISH) as a Method for Detection of C-Myc Amplification in Formalin-Fixed Paraffin-Embedded Tumor Tissue: An Update.
Nataša Todorović-Raković.
Methods Mol Biol, 2021 May 22; 2318. PMID: 34019299
Developing neoantigen-targeted T cell-based treatments for solid tumors.
Tori N Yamamoto, Rigel J Kishton, Nicholas P Restifo.
Nat Med, 2019 Oct 09; 25(10). PMID: 31591590
Highly Cited. Review.
Recurrent Somatic MAP2K1 Mutations in Papillary Thyroid Cancer and Colorectal Cancer.
Rong Bu, Abdul K Siraj, +10 authors, Khawla S Al-Kuraya.
Front Oncol, 2021 May 29; 11. PMID: 34046359    Free PMC article.
Signatures of Discriminative Copy Number Aberrations in 31 Cancer Subtypes.
Bo Gao, Michael Baudis.
Front Genet, 2021 Jun 01; 12. PMID: 34054918    Free PMC article.
Tumor fraction-guided cell-free DNA profiling in metastatic solid tumor patients.
Dana W Y Tsui, Michael L Cheng, +34 authors, David B Solit.
Genome Med, 2021 Jun 02; 13(1). PMID: 34059130    Free PMC article.
Structural Variants at the BRCA1/2 Loci are a Common Source of Homologous Repair Deficiency in High-grade Serous Ovarian Carcinoma.
Ailith Ewing, Alison Meynert, +28 authors, Colin A Semple.
Clin Cancer Res, 2021 Mar 21; 27(11). PMID: 33741650    Free PMC article.
Frontline Maintenance Treatment for Ovarian Cancer.
Osnat Elyashiv, Yien Ning Sophia Wong, Jonathan A Ledermann.
Curr Oncol Rep, 2021 Jun 15; 23(8). PMID: 34125335    Free PMC article.
Review.
Opposed Interplay between IDH1 Mutations and the WNT/β-Catenin Pathway: Added Information for Glioma Classification.
Alexandre Vallée, Yves Lecarpentier, Jean-Noël Vallée.
Biomedicines, 2021 Jun 03; 9(6). PMID: 34070746    Free PMC article.
Review.
p85β alters response to EGFR inhibitor in ovarian cancer through p38 MAPK-mediated regulation of DNA repair.
Victor Cy Mak, Xinran Li, +3 authors, Lydia Wt Cheung.
Neoplasia, 2021 Jun 19; 23(7). PMID: 34144267    Free PMC article.
MYC Releases Early Reprogrammed Human Cells from Proliferation Pause via Retinoblastoma Protein Inhibition.
Tim A Rand, Kenta Sutou, +11 authors, Kazutoshi Takahashi.
Cell Rep, 2018 Apr 12; 23(2). PMID: 29641997    Free PMC article.
Deletion of Jdp2 enhances Slc7a11 expression in Atoh-1 positive cerebellum granule cell progenitors in vivo.
Chia-Chen Ku, Kenly Wuputra, +13 authors, Kazunari K Yokoyama.
Stem Cell Res Ther, 2021 Jul 01; 12(1). PMID: 34187574    Free PMC article.
SMOOTH-seq: single-cell genome sequencing of human cells on a third-generation sequencing platform.
Xiaoying Fan, Cheng Yang, +5 authors, Fuchou Tang.
Genome Biol, 2021 Jul 02; 22(1). PMID: 34193237    Free PMC article.
Understanding the tumor microenvironment for effective immunotherapy.
Habib Sadeghi Rad, James Monkman, +4 authors, Arutha Kulasinghe.
Med Res Rev, 2020 Dec 06; 41(3). PMID: 33277742    Free PMC article.
Review.
FOXM1: A Multifunctional Oncoprotein and Emerging Therapeutic Target in Ovarian Cancer.
Cassie Liu, Carter J Barger, Adam R Karpf.
Cancers (Basel), 2021 Jul 03; 13(12). PMID: 34205406    Free PMC article.
Review.
Non-coding driver mutations in human cancer.
Kerryn Elliott, Erik Larsson.
Nat Rev Cancer, 2021 Jul 08; 21(8). PMID: 34230647
Review.
Evaluating the utility of tumour mutational signatures for identifying hereditary colorectal cancer and polyposis syndrome carriers.
Peter Georgeson, Bernard J Pope, +20 authors, Daniel D Buchanan.
Gut, 2021 Jan 09;. PMID: 33414168    Free PMC article.
High-grade serous tubo-ovarian cancer refined with single-cell RNA sequencing: specific cell subtypes influence survival and determine molecular subtype classification.
Siel Olbrecht, Pieter Busschaert, +10 authors, Ignace Vergote.
Genome Med, 2021 Jul 10; 13(1). PMID: 34238352    Free PMC article.
Blood-Based Liquid Biopsy for Comprehensive Cancer Genomic Profiling Using Next-Generation Sequencing: An Emerging Paradigm for Non-invasive Cancer Detection and Management in Dogs.
Kristina M Kruglyak, Jason Chibuk, +10 authors, Andi Flory.
Front Vet Sci, 2021 Jul 27; 8. PMID: 34307538    Free PMC article.
Genomic Analysis of Response to Neoadjuvant Chemotherapy in Esophageal Adenocarcinoma.
Fereshteh Izadi, Benjamin P Sharpe, +11 authors, On Behalf Of Occams.
Cancers (Basel), 2021 Jul 25; 13(14). PMID: 34298611    Free PMC article.
Identification of putative actionable alterations in clinically relevant genes in breast cancer.
Pushpinder Kaur, Tania B Porras, +4 authors, Julie E Lang.
Br J Cancer, 2021 Aug 30;. PMID: 34455425
Transcriptomic rationale for synthetic lethality-targeting ERCC1 and CDKN1A in chronic myelomonocytic leukaemia.
Ana M Hurtado, Gines Luengo-Gil, +18 authors, Andres Jerez.
Br J Haematol, 2018 May 26; 182(3). PMID: 29797327    Free PMC article.
Acquisition of aneuploidy drives mutant p53-associated gain-of-function phenotypes.
Lindsay N Redman-Rivera, Timothy M Shaver, +8 authors, Jennifer A Pietenpol.
Nat Commun, 2021 Sep 02; 12(1). PMID: 34465782
Distinct transcriptional programs stratify ovarian cancer cell lines into the five major histological subtypes.
Bethany M Barnes, Louisa Nelson, +6 authors, Stephen S Taylor.
Genome Med, 2021 Sep 03; 13(1). PMID: 34470661