Journal Article
. 2011 Nov; 29(12):1120-7.
doi: 10.1038/nbt.2038.

Single-cell dissection of transcriptional heterogeneity in human colon tumors

Piero Dalerba 1 Tomer Kalisky  Debashis Sahoo  Pradeep S Rajendran  Michael E Rothenberg  Anne A Leyrat  Sopheak Sim  Jennifer Okamoto  Darius M Johnston  Dalong Qian  Maider Zabala  Janet Bueno  Norma F Neff  Jianbin Wang  Andrew A Shelton  Brendan Visser  Shigeo Hisamori  Yohei Shimono  Marc van de Wetering  Hans Clevers  Michael F Clarke  Stephen R Quake  
Affiliations
  • PMID: 22081019
  •     50 References
  •     339 citations

Abstract

Cancer is often viewed as a caricature of normal developmental processes, but the extent to which its cellular heterogeneity truly recapitulates multilineage differentiation processes of normal tissues remains unknown. Here we implement single-cell PCR gene-expression analysis to dissect the cellular composition of primary human normal colon and colon cancer epithelia. We show that human colon cancer tissues contain distinct cell populations whose transcriptional identities mirror those of the different cellular lineages of normal colon. By creating monoclonal tumor xenografts from injection of a single (n = 1) cell, we demonstrate that the transcriptional diversity of cancer tissues is largely explained by in vivo multilineage differentiation and not only by clonal genetic heterogeneity. Finally, we show that the different gene-expression programs linked to multilineage differentiation are strongly associated with patient survival. We develop two-gene classifier systems (KRT20 versus CA1, MS4A12, CD177, SLC26A3) that predict clinical outcomes with hazard ratios superior to those of pathological grade and comparable to those of microarray-derived multigene expression signatures.

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BMC Genomics, 2014 Mar 14; 15. PMID: 24621249    Free PMC article.
Highly Cited.
Single-cell analysis of the transcriptome and its application in the characterization of stem cells and early embryos.
Na Liu, Lin Liu, Xinghua Pan.
Cell Mol Life Sci, 2014 Mar 22; 71(14). PMID: 24652479
Review.
Discriminating cellular heterogeneity using microwell-based RNA cytometry.
Ivan K Dimov, Rong Lu, +5 authors, Luke P Lee.
Nat Commun, 2014 Mar 29; 5. PMID: 24667995    Free PMC article.
Cancer cell dormancy in novel mouse models for reversible pancreatic cancer: a lingering challenge in the development of targeted therapies.
Wan-Chi Lin, Nirakar Rajbhandari, Kay-Uwe Wagner.
Cancer Res, 2014 Mar 29; 74(8). PMID: 24670819    Free PMC article.
Review.
High-dimensional single-cell cancer biology.
Jonathan M Irish, Deon B Doxie.
Curr Top Microbiol Immunol, 2014 Mar 29; 377. PMID: 24671264    Free PMC article.
Review.
Silencing of the EPHB3 tumor-suppressor gene in human colorectal cancer through decommissioning of a transcriptional enhancer.
Sabine Jägle, Kerstin Rönsch, +11 authors, Andreas Hecht.
Proc Natl Acad Sci U S A, 2014 Apr 08; 111(13). PMID: 24707046    Free PMC article.
Redirection of Human Cancer Cells upon the Interaction with the Regenerating Mouse Mammary Gland Microenvironment.
Sonia M Rosenfield, Gilbert H Smith.
Cells, 2013 Jan 01; 2(1). PMID: 24709643    Free PMC article.
Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq.
Barbara Treutlein, Doug G Brownfield, +6 authors, Stephen R Quake.
Nature, 2014 Apr 18; 509(7500). PMID: 24739965    Free PMC article.
Highly Cited.
Heterogeneity in immune responses: from populations to single cells.
Rahul Satija, Alex K Shalek.
Trends Immunol, 2014 Apr 22; 35(5). PMID: 24746883    Free PMC article.
Review.
Microfluidic single-cell whole-transcriptome sequencing.
Aaron M Streets, Xiannian Zhang, +8 authors, Yanyi Huang.
Proc Natl Acad Sci U S A, 2014 May 02; 111(19). PMID: 24782542    Free PMC article.
Highly Cited.
The human gastrointestinal tract-specific transcriptome and proteome as defined by RNA sequencing and antibody-based profiling.
Gabriela Gremel, Alkwin Wanders, +6 authors, Fredrik Pontén.
J Gastroenterol, 2014 May 03; 50(1). PMID: 24789573
Regulation and roles of bicarbonate transporters in cancer.
Andrej Gorbatenko, Christina W Olesen, Ebbe Boedtkjer, Stine F Pedersen.
Front Physiol, 2014 May 06; 5. PMID: 24795638    Free PMC article.
Bayesian approach to single-cell differential expression analysis.
Peter V Kharchenko, Lev Silberstein, David T Scadden.
Nat Methods, 2014 May 20; 11(7). PMID: 24836921    Free PMC article.
Highly Cited.
Single-cell western blotting.
Alex J Hughes, Dawn P Spelke, +3 authors, Amy E Herr.
Nat Methods, 2014 Jun 02; 11(7). PMID: 24880876    Free PMC article.
Highly Cited.
Atomic force microscopic detection enabling multiplexed low-cycle-number quantitative polymerase chain reaction for biomarker assays.
Andrey Mikheikin, Anita Olsen, +3 authors, Jason Reed.
Anal Chem, 2014 Jun 12; 86(13). PMID: 24918650    Free PMC article.
Stem cell dynamics in homeostasis and cancer of the intestine.
Louis Vermeulen, Hugo J Snippert.
Nat Rev Cancer, 2014 Jun 13; 14(7). PMID: 24920463
Highly Cited. Review.
The transcription factor GATA6 enables self-renewal of colon adenoma stem cells by repressing BMP gene expression.
Gavin Whissell, Elisa Montagni, +14 authors, Eduard Batlle.
Nat Cell Biol, 2014 Jun 24; 16(7). PMID: 24952462
Single cell transcriptional analysis reveals novel innate immune cell types.
Linda E Kippner, Jinhee Kim, Greg Gibson, Melissa L Kemp.
PeerJ, 2014 Jul 16; 2. PMID: 25024920    Free PMC article.
Single-cell RNA-seq: advances and future challenges.
Antoine-Emmanuel Saliba, Alexander J Westermann, Stanislaw A Gorski, Jörg Vogel.
Nucleic Acids Res, 2014 Jul 24; 42(14). PMID: 25053837    Free PMC article.
Highly Cited. Review.
Mining TCGA data using Boolean implications.
Subarna Sinha, Emily K Tsang, +2 authors, David L Dill.
PLoS One, 2014 Jul 24; 9(7). PMID: 25054200    Free PMC article.
Lytic gene expression is frequent in HSV-1 latent infection and correlates with the engagement of a cell-intrinsic transcriptional response.
Joel Z Ma, Tiffany A Russell, +2 authors, David C Tscharke.
PLoS Pathog, 2014 Jul 25; 10(7). PMID: 25058429    Free PMC article.
Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex.
Alex A Pollen, Tomasz J Nowakowski, +27 authors, Jay A A West.
Nat Biotechnol, 2014 Aug 05; 32(10). PMID: 25086649    Free PMC article.
Highly Cited.
Bioinformatic approaches to augment study of epithelial-to-mesenchymal transition in lung cancer.
Tim N Beck, Adaeze J Chikwem, Nehal R Solanki, Erica A Golemis.
Physiol Genomics, 2014 Aug 07; 46(19). PMID: 25096367    Free PMC article.
Review.
Single-cell gene expression signatures reveal melanoma cell heterogeneity.
M Ennen, C Keime, +4 authors, I Davidson.
Oncogene, 2014 Aug 19; 34(25). PMID: 25132268
Deep sequencing of the X chromosome reveals the proliferation history of colorectal adenomas.
Anna De Grassi, Fabio Iannelli, +7 authors, Francesca D Ciccarelli.
Genome Biol, 2014 Sep 02; 15(8). PMID: 25175524    Free PMC article.
Patient-derived xenograft models: an emerging platform for translational cancer research.
Manuel Hidalgo, Frederic Amant, +11 authors, Alberto Villanueva.
Cancer Discov, 2014 Sep 04; 4(9). PMID: 25185190    Free PMC article.
Highly Cited. Review.
Cancer systems biology: embracing complexity to develop better anticancer therapeutic strategies.
W Du, O Elemento.
Oncogene, 2014 Sep 16; 34(25). PMID: 25220419
Review.
Cancer genomics: one cell at a time.
Nicholas E Navin.
Genome Biol, 2014 Sep 16; 15(8). PMID: 25222669    Free PMC article.
Highly Cited. Review.
Conceptualizing cancer drugs as classifiers.
Patrick Nathan Lawlor, Tomer Kalisky, +2 authors, Konrad Paul Kording.
PLoS One, 2014 Sep 24; 9(9). PMID: 25248130    Free PMC article.
Classification of subpopulations of cells within human primary brain tumors by single cell gene expression profiling.
Elin Möllerström, Bertil Rydenhag, +7 authors, Milos Pekny.
Neurochem Res, 2014 Sep 25; 40(2). PMID: 25249434
Review.
Genome-wide and single-cell analyses reveal a context dependent relationship between CBP recruitment and gene expression.
Lawryn H Kasper, Chunxu Qu, +2 authors, Paul K Brindle.
Nucleic Acids Res, 2014 Sep 25; 42(18). PMID: 25249627    Free PMC article.
SNAIL1 combines competitive displacement of ASCL2 and epigenetic mechanisms to rapidly silence the EPHB3 tumor suppressor in colorectal cancer.
Kerstin Rönsch, Sabine Jägle, +10 authors, Andreas Hecht.
Mol Oncol, 2014 Oct 04; 9(2). PMID: 25277775    Free PMC article.
Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing.
Mei-Chong Wendy Lee, Fernando J Lopez-Diaz, +7 authors, Nader Pourmand.
Proc Natl Acad Sci U S A, 2014 Oct 24; 111(44). PMID: 25339441    Free PMC article.
Noise in multiple sclerosis: unwanted and necessary.
Isabella Bordi, Vito A G Ricigliano, +5 authors, Marco Salvetti.
Ann Clin Transl Neurol, 2014 Oct 31; 1(7). PMID: 25356421    Free PMC article.
Predictive gene signatures: molecular markers distinguishing colon adenomatous polyp and carcinoma.
Janice E Drew, Andrew J Farquharson, +4 authors, Francis A Carey.
PLoS One, 2014 Nov 26; 9(11). PMID: 25423035    Free PMC article.
Granulocyte colony-stimulating factor prevents loss of spermatogenesis after sterilizing busulfan chemotherapy.
Roberto Benavides-Garcia, Rose Joachim, +3 authors, Brian P Hermann.
Fertil Steril, 2014 Dec 03; 103(1). PMID: 25439845    Free PMC article.
An integrated microfluidic chip system for single-cell secretion profiling of rare circulating tumor cells.
Yuliang Deng, Yu Zhang, +8 authors, Qihui Shi.
Sci Rep, 2014 Dec 17; 4. PMID: 25511131    Free PMC article.
Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape.
Eugenio Marco, Robert L Karp, +4 authors, Guo-Cheng Yuan.
Proc Natl Acad Sci U S A, 2014 Dec 17; 111(52). PMID: 25512504    Free PMC article.
Highly Cited.
Cell type specific gene expression analysis of prostate needle biopsies resolves tumor tissue heterogeneity.
Malte Krönig, Max Walter, +8 authors, Roland Schüle.
Oncotarget, 2014 Dec 17; 6(2). PMID: 25514598    Free PMC article.
Characterizing heterogeneity in leukemic cells using single-cell gene expression analysis.
Assieh Saadatpour, Guoji Guo, Stuart H Orkin, Guo-Cheng Yuan.
Genome Biol, 2014 Dec 18; 15(12). PMID: 25517911    Free PMC article.
Transcriptional and translational heterogeneity among neonatal mouse spermatogonia.
Brian P Hermann, Kazadi N Mutoji, +4 authors, John R McCarrey.
Biol Reprod, 2015 Jan 09; 92(2). PMID: 25568304    Free PMC article.
MALDI Imaging mass spectrometry: current frontiers and perspectives in pathology research and practice.
Michaela Aichler, Axel Walch.
Lab Invest, 2015 Jan 27; 95(4). PMID: 25621874
Highly Cited. Review.
Identification of cardiovascular lineage descendants at single-cell resolution.
Guang Li, Karolina Plonowska, +2 authors, Sean M Wu.
Development, 2015 Jan 31; 142(5). PMID: 25633351    Free PMC article.
3D computational reconstruction of tissues with hollow spherical morphologies using single-cell gene expression data.
Robert Durruthy-Durruthy, Assaf Gottlieb, Stefan Heller.
Nat Protoc, 2015 Feb 13; 10(3). PMID: 25675210    Free PMC article.
The CD20 homologue MS4A4 directs trafficking of KIT toward clathrin-independent endocytosis pathways and thus regulates receptor signaling and recycling.
Glenn Cruse, Michael A Beaven, +3 authors, Dean D Metcalfe.
Mol Biol Cell, 2015 Feb 27; 26(9). PMID: 25717186    Free PMC article.
The cancer stem cell niche: how essential is the niche in regulating stemness of tumor cells?
Vicki Plaks, Niwen Kong, Zena Werb.
Cell Stem Cell, 2015 Mar 10; 16(3). PMID: 25748930    Free PMC article.
Highly Cited. Review.
Single-cell printing based on impedance detection.
J Schoendube, D Wright, R Zengerle, P Koltay.
Biomicrofluidics, 2015 Mar 12; 9(1). PMID: 25759750    Free PMC article.
Single cell transcriptomics: methods and applications.
Itamar Kanter, Tomer Kalisky.
Front Oncol, 2015 Mar 26; 5. PMID: 25806353    Free PMC article.
Review.
Printing 2-dimentional droplet array for single-cell reverse transcription quantitative PCR assay with a microfluidic robot.
Ying Zhu, Yun-Xia Zhang, +3 authors, Bo Yao.
Sci Rep, 2015 Apr 02; 5. PMID: 25828383    Free PMC article.
Regulation of VDR Expression in Apc-Mutant Mice, Human Colon Cancers and Adenomas.
Charles Giardina, Masako Nakanishi, +4 authors, Daniel W Rosenberg.
Cancer Prev Res (Phila), 2015 Apr 16; 8(5). PMID: 25873367    Free PMC article.
Single-cell analysis of lung adenocarcinoma cell lines reveals diverse expression patterns of individual cells invoked by a molecular target drug treatment.
Ayako Suzuki, Koutatsu Matsushima, +4 authors, Yutaka Suzuki.
Genome Biol, 2015 Apr 19; 16. PMID: 25887790    Free PMC article.
KIT Signaling Promotes Growth of Colon Xenograft Tumors in Mice and Is Up-Regulated in a Subset of Human Colon Cancers.
Evan C Chen, Taylor A Karl, +7 authors, Michael E Rothenberg.
Gastroenterology, 2015 Jun 01; 149(3). PMID: 26026391    Free PMC article.
Scalable microfluidics for single-cell RNA printing and sequencing.
Sayantan Bose, Zhenmao Wan, +4 authors, Peter A Sims.
Genome Biol, 2015 Jun 07; 16. PMID: 26047807    Free PMC article.
Colorectal Cancer Classification and Cell Heterogeneity: A Systems Oncology Approach.
Moisés Blanco-Calvo, Ángel Concha, +2 authors, Manuel Valladares-Ayerbes.
Int J Mol Sci, 2015 Jun 18; 16(6). PMID: 26084042    Free PMC article.
Review.
Apc Restoration Promotes Cellular Differentiation and Reestablishes Crypt Homeostasis in Colorectal Cancer.
Lukas E Dow, Kevin P O'Rourke, +4 authors, Scott W Lowe.
Cell, 2015 Jun 20; 161(7). PMID: 26091037    Free PMC article.
Highly Cited.
Application of single-cell genomics in cancer: promise and challenges.
Quin F Wills, Adam J Mead.
Hum Mol Genet, 2015 Jun 27; 24(R1). PMID: 26113645    Free PMC article.
Review.
Mesenchymal stem cells: A new diagnostic tool?
Maria Teresa Valenti, Antonio Mori, Giovanni Malerba, Luca Dalle Carbonare.
World J Stem Cells, 2015 Jul 02; 7(5). PMID: 26131309    Free PMC article.
Properties of targeted preamplification in DNA and cDNA quantification.
Daniel Andersson, Nina Akrap, +4 authors, Anders Ståhlberg.
Expert Rev Mol Diagn, 2015 Jul 02; 15(8). PMID: 26132215    Free PMC article.
Congenital chloride-losing diarrhea in a Mexican child with the novel homozygous SLC26A3 mutation G393W.
Fabian R Reimold, Savithri Balasubramanian, +9 authors, Seth L Alper.
Front Physiol, 2015 Jul 15; 6. PMID: 26157392    Free PMC article.
Geometry of the Gene Expression Space of Individual Cells.
Yael Korem, Pablo Szekely, +6 authors, Uri Alon.
PLoS Comput Biol, 2015 Jul 15; 11(7). PMID: 26161936    Free PMC article.
Single cell measurement of telomerase expression and splicing using microfluidic emulsion cultures.
Richard Novak, Kristina Hart, Richard A Mathies.
Nucleic Acids Res, 2015 Jul 24; 43(16). PMID: 26202962    Free PMC article.
Clusterin, a gene enriched in intestinal stem cells, is required for L1-mediated colon cancer metastasis.
Beny Shapiro, Piera Tocci, +2 authors, Avri Ben-Ze'ev.
Oncotarget, 2015 Sep 25; 6(33). PMID: 26399194    Free PMC article.
Single-cell analysis reveals a stem-cell program in human metastatic breast cancer cells.
Devon A Lawson, Nirav R Bhakta, +10 authors, Zena Werb.
Nature, 2015 Sep 30; 526(7571). PMID: 26416748    Free PMC article.
Highly Cited.
Single-Cell Analysis in Cancer Genomics.
Assieh Saadatpour, Shujing Lai, Guoji Guo, Guo-Cheng Yuan.
Trends Genet, 2015 Oct 10; 31(10). PMID: 26450340    Free PMC article.
Review.
Asymmetric Cell Division in T Lymphocyte Fate Diversification.
Janilyn Arsenio, Patrick J Metz, John T Chang.
Trends Immunol, 2015 Oct 18; 36(11). PMID: 26474675    Free PMC article.
Review.
Circulating cancer stem cells: the importance to select.
Ming-Hsin Yang, Ahmet Imrali, Christopher Heeschen.
Chin J Cancer Res, 2015 Nov 07; 27(5). PMID: 26543330    Free PMC article.
Review.
Combined ultra-low input mRNA and whole-genome sequencing of human embryonic stem cells.
Florian Mertes, Björn Lichtner, +6 authors, James Adjaye.
BMC Genomics, 2015 Nov 14; 16. PMID: 26564201    Free PMC article.
Adult Human Mesenchymal Stem Cell Differentiation at the Cell Population and Single-Cell Levels Under Alternating Electric Current.
Marissa E Wechsler, Brian P Hermann, Rena Bizios.
Tissue Eng Part C Methods, 2015 Nov 18; 22(2). PMID: 26573771    Free PMC article.
Processing, visualising and reconstructing network models from single-cell data.
Steven Woodhouse, Victoria Moignard, Berthold Göttgens, Jasmin Fisher.
Immunol Cell Biol, 2015 Nov 19; 94(3). PMID: 26577213
Review.
Nanotechnologies for biomedical science and translational medicine.
James R Heath.
Proc Natl Acad Sci U S A, 2015 Nov 26; 112(47). PMID: 26598663    Free PMC article.
Review.
The niche in single-cell technologies.
Giacomo Donati.
Immunol Cell Biol, 2015 Dec 02; 94(3). PMID: 26620629
Review.
A Single-Cell Gene-Expression Profile Reveals Inter-Cellular Heterogeneity within Human Monocyte Subsets.
Susanne T Gren, Thomas B Rasmussen, +3 authors, Olof Grip.
PLoS One, 2015 Dec 10; 10(12). PMID: 26650546    Free PMC article.
Single-cell analysis tools for drug discovery and development.
James R Heath, Antoni Ribas, Paul S Mischel.
Nat Rev Drug Discov, 2015 Dec 17; 15(3). PMID: 26669673    Free PMC article.
Highly Cited. Review.
Simultaneous Multiplexed Measurement of RNA and Proteins in Single Cells.
Spyros Darmanis, Caroline Julie Gallant, +9 authors, Ulf Landegren.
Cell Rep, 2016 Jan 11; 14(2). PMID: 26748716    Free PMC article.
Highly Cited.
CFTR is a tumor suppressor gene in murine and human intestinal cancer.
B L N Than, J F Linnekamp, +18 authors, R T Cormier.
Oncogene, 2016 Jan 12; 35(32). PMID: 26751771    Free PMC article.
Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis.
Jean Fan, Neeraj Salathia, +8 authors, Peter V Kharchenko.
Nat Methods, 2016 Jan 19; 13(3). PMID: 26780092    Free PMC article.
Highly Cited.
CDX2 as a Prognostic Biomarker in Stage II and Stage III Colon Cancer.
Piero Dalerba, Debashis Sahoo, +15 authors, Michael F Clarke.
N Engl J Med, 2016 Jan 21; 374(3). PMID: 26789870    Free PMC article.
Highly Cited.
Serum-Based Culture Conditions Provoke Gene Expression Variability in Mouse Embryonic Stem Cells as Revealed by Single-Cell Analysis.
Guoji Guo, Luca Pinello, +6 authors, Stuart H Orkin.
Cell Rep, 2016 Jan 26; 14(4). PMID: 26804902    Free PMC article.
BCL9/9L-β-catenin Signaling is Associated With Poor Outcome in Colorectal Cancer.
Andreas E Moor, Pascale Anderle, +12 authors, Michel Aguet.
EBioMedicine, 2016 Feb 05; 2(12). PMID: 26844272    Free PMC article.
Defining a stem cell hierarchy in the intestine: markers, caveats and controversies.
Nicholas R Smith, Alexandra C Gallagher, Melissa H Wong.
J Physiol, 2016 Feb 13; 594(17). PMID: 26864260    Free PMC article.
Review.
Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas.
Yu Hou, Huahu Guo, +8 authors, Jirun Peng.
Cell Res, 2016 Feb 24; 26(3). PMID: 26902283    Free PMC article.
Highly Cited.
The Emerging Function and Mechanism of ceRNAs in Cancer.
Yunfei Wang, Jiakai Hou, +4 authors, Yiwen Chen.
Trends Genet, 2016 Feb 29; 32(4). PMID: 26922301    Free PMC article.
Review.
Tumour Cell Heterogeneity.
Laura Gay, Ann-Marie Baker, Trevor A Graham.
F1000Res, 2016 Mar 15; 5. PMID: 26973786    Free PMC article.
Review.
Single-cell sequencing in stem cell biology.
Lu Wen, Fuchou Tang.
Genome Biol, 2016 Apr 17; 17. PMID: 27083874    Free PMC article.
Review.
Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity.
Stephen J Clark, Heather J Lee, +2 authors, Wolf Reik.
Genome Biol, 2016 Apr 20; 17. PMID: 27091476    Free PMC article.
Highly Cited. Review.
Wnt signaling in cancer stem cells and colon cancer metastasis.
Sayon Basu, Gal Haase, Avri Ben-Ze'ev.
F1000Res, 2016 May 03; 5. PMID: 27134739    Free PMC article.
Highly Cited. Review.
Floating Droplet Array: An Ultrahigh-Throughput Device for Droplet Trapping, Real-time Analysis and Recovery.
Louai Labanieh, Thi N Nguyen, Weian Zhao, Dong-Ku Kang.
Micromachines (Basel), 2016 May 03; 6(10). PMID: 27134760    Free PMC article.
TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis.
Zhicheng Ji, Hongkai Ji.
Nucleic Acids Res, 2016 May 15; 44(13). PMID: 27179027    Free PMC article.
Highly Cited.
Comprehensive characterization of the patient-derived xenograft and the paralleled primary hepatocellular carcinoma cell line.
Phyllis F Y Cheung, Chi Wai Yip, +5 authors, Siu Tim Cheung.
Cancer Cell Int, 2016 Jun 10; 16. PMID: 27279800    Free PMC article.
UCN-01 enhances cytotoxicity of irinotecan in colorectal cancer stem-like cells by impairing DNA damage response.
Michele Signore, Mariachiara Buccarelli, +7 authors, Lucia Ricci-Vitiani.
Oncotarget, 2016 Jun 11; 7(28). PMID: 27286453    Free PMC article.
Microfluidic single-cell transcriptional analysis rationally identifies novel surface marker profiles to enhance cell-based therapies.
Robert C Rennert, Michael Januszyk, +12 authors, Geoffrey C Gurtner.
Nat Commun, 2016 Jun 22; 7. PMID: 27324848    Free PMC article.
Targeting signal transduction pathways of cancer stem cells for therapeutic opportunities of metastasis.
Waqas Iqbal, Saleh Alkarim, +2 authors, Kulvinder S Saini.
Oncotarget, 2016 Aug 04; 7(46). PMID: 27486983    Free PMC article.
Review.
Evaluating the Effect of Cell Culture on Gene Expression in Primary Tissue Samples Using Microfluidic-Based Single Cell Transcriptional Analysis.
Michael Januszyk, Robert C Rennert, +6 authors, Geoffrey C Gurtner.
Microarrays (Basel), 2015 Jan 01; 4(4). PMID: 27600239    Free PMC article.
Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction.
Alex S Genshaft, Shuqiang Li, +10 authors, Alex K Shalek.
Genome Biol, 2016 Sep 20; 17(1). PMID: 27640647    Free PMC article.
An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq.
Jinzhou Yuan, Peter A Sims.
Sci Rep, 2016 Sep 28; 6. PMID: 27670648    Free PMC article.
The linker histone H1.0 generates epigenetic and functional intratumor heterogeneity.
Cristina Morales Torres, Alva Biran, +13 authors, Paola Scaffidi.
Science, 2016 Oct 07; 353(6307). PMID: 27708074    Free PMC article.
Impaired coordination between signaling pathways is revealed in human colorectal cancer using single-cell mass cytometry of archival tissue blocks.
Alan J Simmons, Cherié R Scurrah, +5 authors, Ken S Lau.
Sci Signal, 2016 Oct 13; 9(449). PMID: 27729552    Free PMC article.
Next-generation molecular diagnosis: single-cell sequencing from bench to bedside.
Wanjun Zhu, Xiao-Yan Zhang, +4 authors, Xinghua Pan.
Cell Mol Life Sci, 2016 Oct 16; 74(5). PMID: 27738745
Review.
Massive and parallel expression profiling using microarrayed single-cell sequencing.
Sanja Vickovic, Patrik L Ståhl, +10 authors, Joakim Lundeberg.
Nat Commun, 2016 Oct 16; 7. PMID: 27739429    Free PMC article.
Precision targeted therapy of ovarian cancer.
Justin Sapiezynski, Oleh Taratula, Lorna Rodriguez-Rodriguez, Tamara Minko.
J Control Release, 2016 Nov 05; 243. PMID: 27746277    Free PMC article.
Review.
Data-driven identification of prognostic tumor subpopulations using spatially mapped t-SNE of mass spectrometry imaging data.
Walid M Abdelmoula, Benjamin Balluff, +5 authors, Boudewijn P F Lelieveldt.
Proc Natl Acad Sci U S A, 2016 Oct 30; 113(43). PMID: 27791011    Free PMC article.
Cancer heterogeneity is not compatible with one unique cancer cell metabolic map.
A Strickaert, M Saiselet, +5 authors, C Maenhaut.
Oncogene, 2016 Nov 01; 36(19). PMID: 27797377    Free PMC article.
Review.
Rapidly cycling Lgr5+ stem cells are exquisitely sensitive to extrinsic dietary factors that modulate colon cancer risk.
Eunjoo Kim, Laurie A Davidson, +9 authors, Robert S Chapkin.
Cell Death Dis, 2016 Nov 11; 7(11). PMID: 27831561    Free PMC article.
Tackling Cancer Stem Cells via Inhibition of EMT Transcription Factors.
Megan Mladinich, Diane Ruan, Chia-Hsin Chan.
Stem Cells Int, 2016 Nov 15; 2016. PMID: 27840647    Free PMC article.
Review.
Quantitating drug-target engagement in single cells in vitro and in vivo.
J Matthew Dubach, Eunha Kim, +5 authors, Ralph Weissleder.
Nat Chem Biol, 2016 Dec 06; 13(2). PMID: 27918558    Free PMC article.
Quantitative proteomic profiling of paired cancerous and normal colon epithelial cells isolated freshly from colorectal cancer patients.
Chengjian Tu, Wilfrido Mojica, +7 authors, Jun Qu.
Proteomics Clin Appl, 2016 Dec 13; 11(5-6). PMID: 27943637    Free PMC article.
A Quiescent Bcl11b High Stem Cell Population Is Required for Maintenance of the Mammary Gland.
Shang Cai, Tomer Kalisky, +18 authors, Michael F Clarke.
Cell Stem Cell, 2017 Jan 04; 20(2). PMID: 28041896    Free PMC article.
Determinants of metastatic competency in colorectal cancer.
Daniele V F Tauriello, Alexandre Calon, Enza Lonardo, Eduard Batlle.
Mol Oncol, 2017 Jan 14; 11(1). PMID: 28085225    Free PMC article.
Review.
Recent progress in single-cell cancer genomics.
Daphne Tsoucas, Guo-Cheng Yuan.
Curr Opin Genet Dev, 2017 Jan 28; 42. PMID: 28126650    Free PMC article.
Review.
Transcriptional heterogeneity in the lactase gene within cell-type is linked to the epigenome.
Edward Oh, Richie Jeremian, +7 authors, Viviane Labrie.
Sci Rep, 2017 Feb 01; 7. PMID: 28139744    Free PMC article.
Single-neuron identification of chemical constituents, physiological changes, and metabolism using mass spectrometry.
Hongying Zhu, Guichang Zou, +3 authors, Guangming Huang.
Proc Natl Acad Sci U S A, 2017 Feb 23; 114(10). PMID: 28223513    Free PMC article.
Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors.
Huipeng Li, Elise T Courtois, +14 authors, Shyam Prabhakar.
Nat Genet, 2017 Mar 21; 49(5). PMID: 28319088
Highly Cited.
Visualization and targeting of LGR5+ human colon cancer stem cells.
Mariko Shimokawa, Yuki Ohta, +7 authors, Toshiro Sato.
Nature, 2017 Mar 30; 545(7653). PMID: 28355176
Highly Cited.
A Modified Method for Purifying Gallbladder Epithelial Cells Using Fluorescence-activated Cell Sorting.
Hajime Imamura, Tomohiko Adachi, +9 authors, Susumu Eguchi.
In Vivo, 2017 Mar 31; 31(2). PMID: 28358696    Free PMC article.
Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq.
Andrew S Venteicher, Itay Tirosh, +31 authors, Mario L Suvà.
Science, 2017 Apr 01; 355(6332). PMID: 28360267    Free PMC article.
Highly Cited.
CHK1-targeted therapy to deplete DNA replication-stressed, p53-deficient, hyperdiploid colorectal cancer stem cells.
Gwenola Manic, Michele Signore, +23 authors, Ruggero De Maria.
Gut, 2017 Apr 09; 67(5). PMID: 28389531    Free PMC article.
Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices.
Sanjay M Prakadan, Alex K Shalek, David A Weitz.
Nat Rev Genet, 2017 Apr 11; 18(6). PMID: 28392571    Free PMC article.
Highly Cited. Review.
Metallothionein 1G promotes the differentiation of HT-29 human colorectal cancer cells.
Juan Martín Arriaga, Alicia Inés Bravo, José Mordoh, Michele Bianchini.
Oncol Rep, 2017 Apr 11; 37(5). PMID: 28393194    Free PMC article.
Microfluidics for genome-wide studies involving next generation sequencing.
Sai Ma, Travis W Murphy, Chang Lu.
Biomicrofluidics, 2017 Apr 12; 11(2). PMID: 28396707    Free PMC article.
Review.
Strategies for the acquisition of transcriptional and epigenetic information in single cells.
Guang Li, Elda Dzilic, +2 authors, Sean M Wu.
J Thorac Dis, 2017 Apr 28; 9(Suppl 1). PMID: 28446964    Free PMC article.
Review.
Evidence of drug-response heterogeneity rapidly generated from a single cancer cell.
Rong Wang, Chengmeng Jin, Xun Hu.
Oncotarget, 2017 May 04; 8(25). PMID: 28467802    Free PMC article.
A genome editing approach to study cancer stem cells in human tumors.
Carme Cortina, Gemma Turon, +8 authors, Eduard Batlle.
EMBO Mol Med, 2017 May 05; 9(7). PMID: 28468934    Free PMC article.
Generation of pure GABAergic neurons by transcription factor programming.
Nan Yang, Soham Chanda, +15 authors, Marius Wernig.
Nat Methods, 2017 May 16; 14(6). PMID: 28504679    Free PMC article.
Highly Cited.
Evidence of In Vitro Preservation of Human Nephrogenesis at the Single-Cell Level.
Naomi Pode-Shakked, Rotem Gershon, +8 authors, Benjamin Dekel.
Stem Cell Reports, 2017 May 30; 9(1). PMID: 28552604    Free PMC article.
Single-cell protein-mRNA correlation analysis enabled by multiplexed dual-analyte co-detection.
Haibiao Gong, Xiaohui Wang, +7 authors, Ramesh Ramakrishnan.
Sci Rep, 2017 Jun 07; 7(1). PMID: 28584233    Free PMC article.
AA-NAT, MT1 and MT2 Correlates with Cancer Stem-Like Cell Markers in Colorectal Cancer: Study of the Influence of Stage and p53 Status of Tumors.
Jorge Casado, Almudena Iñigo-Chaves, +7 authors, Josefa León.
Int J Mol Sci, 2017 Jun 13; 18(6). PMID: 28604612    Free PMC article.
PHF21B overexpression promotes cancer stem cell-like traits in prostate cancer cells by activating the Wnt/β-catenin signaling pathway.
Qiji Li, Liping Ye, +3 authors, Xinsheng Peng.
J Exp Clin Cancer Res, 2017 Jun 25; 36(1). PMID: 28645312    Free PMC article.
Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia.
Lili Wang, Jean Fan, +18 authors, Catherine J Wu.
Genome Res, 2017 Jul 07; 27(8). PMID: 28679620    Free PMC article.
Epigenetics and Cancer Stem Cells: Unleashing, Hijacking, and Restricting Cellular Plasticity.
Elanor N Wainwright, Paola Scaffidi.
Trends Cancer, 2017 Jul 19; 3(5). PMID: 28718414    Free PMC article.
Highly Cited. Review.
High-dimension single-cell analysis applied to cancer.
Lili Wang, Kenneth J Livak, Catherine J Wu.
Mol Aspects Med, 2017 Aug 22; 59. PMID: 28823596    Free PMC article.
Review.
Heterogeneity among Lgr5-positive colon stem cells.
Daisuke Shiokawa, Koji Okamoto.
Mol Cell Oncol, 2017 Sep 05; 4(4). PMID: 28868346    Free PMC article.
Advances in single-cell RNA sequencing and its applications in cancer research.
Sibo Zhu, Tao Qing, +2 authors, Leming Shi.
Oncotarget, 2017 Sep 09; 8(32). PMID: 28881849    Free PMC article.
Review.
Cancer stem cells revisited.
Eduard Batlle, Hans Clevers.
Nat Med, 2017 Oct 07; 23(10). PMID: 28985214
Highly Cited. Review.
Roles of microRNAs and RNA-Binding Proteins in the Regulation of Colorectal Cancer Stem Cells.
Junko Mukohyama, Yohei Shimono, +2 authors, Akira Suzuki.
Cancers (Basel), 2017 Oct 25; 9(10). PMID: 29064439    Free PMC article.
Review.
IL-17A-Induced PLET1 Expression Contributes to Tissue Repair and Colon Tumorigenesis.
Jarod A Zepp, Junjie Zhao, +16 authors, Xiaoxia Li.
J Immunol, 2017 Oct 27; 199(11). PMID: 29070673    Free PMC article.
The non-invasive exfoliated transcriptome (exfoliome) reflects the tissue-level transcriptome in a mouse model of NSAID enteropathy.
Canaan M Whitfield-Cargile, Noah D Cohen, +6 authors, Robert S Chapkin.
Sci Rep, 2017 Nov 02; 7(1). PMID: 29089621    Free PMC article.
Cancer Metabolism and Tumor Heterogeneity: Imaging Perspectives Using MR Imaging and Spectroscopy.
Gigin Lin, Kayvan R Keshari, Jae Mo Park.
Contrast Media Mol Imaging, 2017 Nov 09; 2017. PMID: 29114178    Free PMC article.
Review.
A sparse differential clustering algorithm for tracing cell type changes via single-cell RNA-sequencing data.
Martin Barron, Siyuan Zhang, Jun Li.
Nucleic Acids Res, 2017 Nov 16; 46(3). PMID: 29140455    Free PMC article.
Role of epithelial to mesenchymal transition associated genes in mammary gland regeneration and breast tumorigenesis.
Shaheen S Sikandar, Angera H Kuo, +11 authors, Michael F Clarke.
Nat Commun, 2017 Nov 23; 8(1). PMID: 29162812    Free PMC article.
Recent advances in the use of microfluidic technologies for single cell analysis.
Travis W Murphy, Qiang Zhang, +2 authors, Chang Lu.
Analyst, 2017 Nov 25; 143(1). PMID: 29170786    Free PMC article.
Review.
High-throughput full-length single-cell mRNA-seq of rare cells.
Chin Chun Ooi, Gary L Mantalas, +8 authors, Shan X Wang.
PLoS One, 2017 Dec 01; 12(11). PMID: 29186152    Free PMC article.
The Human Cell Atlas.
Aviv Regev, Sarah A Teichmann, +59 authors, Human Cell Atlas Meeting Participants.
Elife, 2017 Dec 06; 6. PMID: 29206104    Free PMC article.
Highly Cited.
The impact of non-genetic heterogeneity on cancer cell death.
Zintis Inde, Scott J Dixon.
Crit Rev Biochem Mol Biol, 2017 Dec 19; 53(1). PMID: 29250983    Free PMC article.
Review.
Reconstructing differentiation networks and their regulation from time series single-cell expression data.
Jun Ding, Bruce J Aronow, +3 authors, Ziv Bar-Joseph.
Genome Res, 2018 Jan 11;. PMID: 29317474    Free PMC article.
Fusobacterium's link to colorectal neoplasia sequenced: A systematic review and future insights.
Hisham Hussan, Steven K Clinton, Kristen Roberts, Michael T Bailey.
World J Gastroenterol, 2018 Jan 24; 23(48). PMID: 29358871    Free PMC article.
Systematic Review.
Single cell analysis of Crohn's disease patient-derived small intestinal organoids reveals disease activity-dependent modification of stem cell properties.
Kohei Suzuki, Tatsuro Murano, +19 authors, Ryuichi Okamoto.
J Gastroenterol, 2018 Jan 29; 53(9). PMID: 29374777    Free PMC article.
Design and Application of Sensors for Chemical Cytometry.
Brianna M Vickerman, Matthew M Anttila, +2 authors, David S Lawrence.
ACS Chem Biol, 2018 Jan 30; 13(7). PMID: 29376326    Free PMC article.
Review.
Targeting minimal residual disease: a path to cure?
Marlise R Luskin, Mark A Murakami, Scott R Manalis, David M Weinstock.
Nat Rev Cancer, 2018 Jan 30; 18(4). PMID: 29376520    Free PMC article.
Review.
Specific Labeling of Stem Cell Activity in Human Colorectal Organoids Using an ASCL2-Responsive Minigene.
Koen C Oost, Lisa van Voorthuijsen, +11 authors, Hugo J G Snippert.
Cell Rep, 2018 Feb 10; 22(6). PMID: 29425513    Free PMC article.
Single cell on-chip whole genome amplification via micropillar arrays for reduced amplification bias.
Harvey C Tian, Jaime J Benitez, Harold G Craighead.
PLoS One, 2018 Feb 13; 13(2). PMID: 29432426    Free PMC article.
Convergence of Wnt, growth factor, and heterotrimeric G protein signals on the guanine nucleotide exchange factor Daple.
Nicolas Aznar, Jason Ear, +9 authors, Pradipta Ghosh.
Sci Signal, 2018 Mar 01; 11(519). PMID: 29487190    Free PMC article.
Ensemble methods for stochastic networks with special reference to the biological clock of Neurospora crassa.
C Caranica, A Al-Omari, +5 authors, H-B Schüttler.
PLoS One, 2018 May 17; 13(5). PMID: 29768444    Free PMC article.
MicroRNA expression profiles identify biomarkers for predicting the response to chemoradiotherapy in rectal cancer.
Binbin Du, Xiaoying Wang, +6 authors, Weisheng Zhang.
Mol Med Rep, 2018 Jun 30; 18(2). PMID: 29956755    Free PMC article.
Geometry of Gene Expression Space of Wilms' Tumors From Human Patients.
Ariel Trink, Itamar Kanter, +3 authors, Tomer Kalisky.
Neoplasia, 2018 Jul 22; 20(8). PMID: 30029183    Free PMC article.
Engineering cell heterogeneity into organs-on-a-chip.
David R Mertz, Tasdiq Ahmed, Shuichi Takayama.
Lab Chip, 2018 Jul 25; 18(16). PMID: 30040104    Free PMC article.
Review.
Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation.
Lakshmipuram Seshadri Swapna, Alyssa M Molinaro, +2 authors, John Parkinson.
Genome Biol, 2018 Aug 26; 19(1). PMID: 30143032    Free PMC article.
A single-cell translocation and secretion assay (TransSeA).
Wei Cai, Yu-Jui Chiu, +3 authors, Yu-Hwa Lo.
Lab Chip, 2018 Sep 05; 18(20). PMID: 30179236    Free PMC article.
Novel digital signatures of tissue phenotypes for predicting distant metastasis in colorectal cancer.
Korsuk Sirinukunwattana, David Snead, +5 authors, Nasir Rajpoot.
Sci Rep, 2018 Sep 14; 8(1). PMID: 30209315    Free PMC article.
Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data.
Qian Zhu, Sheel Shah, +2 authors, Guo-Cheng Yuan.
Nat Biotechnol, 2018 Oct 30;. PMID: 30371680    Free PMC article.
The Development of an Effective Bacterial Single-Cell Lysis Method Suitable for Whole Genome Amplification in Microfluidic Platforms.
Yuguang Liu, Dirk Schulze-Makuch, +4 authors, Marina Walther-Antonio.
Micromachines (Basel), 2018 Nov 15; 9(8). PMID: 30424300    Free PMC article.
Understanding tumor ecosystems by single-cell sequencing: promises and limitations.
Xianwen Ren, Boxi Kang, Zemin Zhang.
Genome Biol, 2018 Dec 05; 19(1). PMID: 30509292    Free PMC article.
Review.
Single Cell Gene Expression to Understand the Dynamic Architecture of the Heart.
Andrea Massaia, Patricia Chaves, +4 authors, Michela Noseda.
Front Cardiovasc Med, 2018 Dec 14; 5. PMID: 30525044    Free PMC article.
Review.
Molecular classification of colorectal cancer using the gene expression profile of tumor samples.
Mamoon Rashid, Ramesh K Vishwakarma, +2 authors, Mohammad A Aziz.
Exp Biol Med (Maywood), 2019 May 17; 244(12). PMID: 31091989    Free PMC article.
miR-221 Targets QKI to Enhance the Tumorigenic Capacity of Human Colorectal Cancer Stem Cells.
Junko Mukohyama, Taichi Isobe, +13 authors, Yohei Shimono.
Cancer Res, 2019 Aug 17; 79(20). PMID: 31416845    Free PMC article.
Metastasis of Cancer Stem Cells Developed in the Microenvironment of Hepatocellular Carcinoma.
Said M Afify, Ghmkin Hassan, +11 authors, Masaharu Seno.
Bioengineering (Basel), 2019 Aug 28; 6(3). PMID: 31450740    Free PMC article.
Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation.
Nezha S Benabdallah, Iain Williamson, +6 authors, Wendy A Bickmore.
Mol Cell, 2019 Sep 09; 76(3). PMID: 31494034    Free PMC article.
Highly Cited.
Cell Heterogeneity and Phenotypic Plasticity in Metastasis Formation: The Case of Colon Cancer.
Miriam Teeuwssen, Riccardo Fodde.
Cancers (Basel), 2019 Sep 22; 11(9). PMID: 31540068    Free PMC article.
Review.
Serum-Free Culture System for Spontaneous Human Mesenchymal Stem Cell Spheroid Formation.
Guoyi Dong, Shengpeng Wang, +10 authors, Ying Gu.
Stem Cells Int, 2019 Nov 19; 2019. PMID: 31737076    Free PMC article.
Improving single-cell transcriptome sequencing efficiency with a microfluidic phase-switch device.
Baoyue Zhang, Hong Xu, +5 authors, Yan Chen.
Analyst, 2019 Nov 07; 144(24). PMID: 31688860    Free PMC article.
Non-Genetic Intra-Tumor Heterogeneity Is a Major Predictor of Phenotypic Heterogeneity and Ongoing Evolutionary Dynamics in Lung Tumors.
Anchal Sharma, Elise Merritt, +7 authors, Subhajyoti De.
Cell Rep, 2019 Nov 21; 29(8). PMID: 31747591    Free PMC article.
The application of single-cell sequencing technology in the diagnosis and treatment of hepatocellular carcinoma.
Kai Kang, Xuezhu Wang, +4 authors, Haifeng Xu.
Ann Transl Med, 2020 Feb 12; 7(23). PMID: 32042806    Free PMC article.
Review.
Tracking intratumoral heterogeneity in glioblastoma via regularized classification of single-cell RNA-Seq data.
Marta B Lopes, Susana Vinga.
BMC Bioinformatics, 2020 Feb 20; 21(1). PMID: 32070274    Free PMC article.
Stem cells in cancer initiation and progression.
Jeevisha Bajaj, Emily Diaz, Tannishtha Reya.
J Cell Biol, 2019 Dec 25; 219(1). PMID: 31874116    Free PMC article.
Review.
Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine.
Yalong Wang, Wanlu Song, +6 authors, Ye-Guang Chen.
J Exp Med, 2019 Nov 23; 217(2). PMID: 31753849    Free PMC article.
Parsimonious Gene Correlation Network Analysis (PGCNA): a tool to define modular gene co-expression for refined molecular stratification in cancer.
Matthew A Care, David R Westhead, Reuben M Tooze.
NPJ Syst Biol Appl, 2019 Apr 18; 5. PMID: 30993001    Free PMC article.
Loss of PKM2 in Lgr5+ intestinal stem cells promotes colitis-associated colorectal cancer.
Yeji Kim, Yong-Soo Lee, +9 authors, Mi-Na Kweon.
Sci Rep, 2019 Apr 19; 9(1). PMID: 30996297    Free PMC article.
Pheno-seq - linking visual features and gene expression in 3D cell culture systems.
Stephan M Tirier, Jeongbin Park, +17 authors, Christian Conrad.
Sci Rep, 2019 Aug 28; 9(1). PMID: 31451731    Free PMC article.
CCR5 Governs DNA Damage Repair and Breast Cancer Stem Cell Expansion.
Xuanmao Jiao, Marco A Velasco-Velázquez, +20 authors, Richard G Pestell.
Cancer Res, 2018 Jan 24; 78(7). PMID: 29358169    Free PMC article.
Comparison of EpCAMhighCD44+ cancer stem cells with EpCAMhighCD44- tumor cells in colon cancer by single-cell sequencing.
Mingshan Liu, Jiabo Di, +4 authors, Xiangqian Su.
Cancer Biol Ther, 2018 Mar 28; 19(10). PMID: 29580161    Free PMC article.
Spatial Analysis of Single Fiber Cells of the Developing Ocular Lens Reveals Regulated Heterogeneity of Gene Expression.
Rajendra K Gangalum, Dongjae Kim, +4 authors, Suraj P Bhat.
iScience, 2018 Dec 06; 10. PMID: 30508719    Free PMC article.
Molecular signatures of multiple myeloma progression through single cell RNA-Seq.
Jin Sung Jang, Ying Li, +8 authors, Jin Jen.
Blood Cancer J, 2019 Jan 05; 9(1). PMID: 30607001    Free PMC article.
Loss of BCL9/9l suppresses Wnt driven tumourigenesis in models that recapitulate human cancer.
David M Gay, Rachel A Ridgway, +10 authors, Owen J Sansom.
Nat Commun, 2019 Feb 15; 10(1). PMID: 30760720    Free PMC article.
FXR Regulates Intestinal Cancer Stem Cell Proliferation.
Ting Fu, Sally Coulter, +17 authors, Ronald M Evans.
Cell, 2019 Feb 23; 176(5). PMID: 30794774    Free PMC article.
Highly Cited.
Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics.
Leif S Ludwig, Caleb A Lareau, +17 authors, Vijay G Sankaran.
Cell, 2019 Mar 05; 176(6). PMID: 30827679    Free PMC article.
Highly Cited.
Fusobacterium nucleatum promotes colorectal cancer by inducing Wnt/β-catenin modulator Annexin A1.
Mara Roxana Rubinstein, Jung Eun Baik, +6 authors, Yiping W Han.
EMBO Rep, 2019 Mar 06; 20(4). PMID: 30833345    Free PMC article.
Low tumour PPM1H indicates poor prognosis in colorectal cancer via activation of cancer-associated fibroblasts.
Xiaowen Xu, Li Zhu, +6 authors, Fuao Cao.
Br J Cancer, 2019 Apr 17; 120(10). PMID: 30988394    Free PMC article.
A predictive computational model reveals that GIV/girdin serves as a tunable valve for EGFR-stimulated cyclic AMP signals.
Michael Getz, Lee Swanson, +2 authors, Padmini Rangamani.
Mol Biol Cell, 2019 Apr 25; 30(13). PMID: 31017840    Free PMC article.
Novel reference genes in colorectal cancer identify a distinct subset of high stage tumors and their associated histologically normal colonic tissues.
Lai Xu, Helen Luo, +9 authors, Amy S Rosenberg.
BMC Med Genet, 2019 Aug 15; 20(1). PMID: 31409279    Free PMC article.
The Gα-interacting vesicle-associated protein interacts with and promotes cell surface localization of GRP78 during endoplasmic reticulum stress.
Clariss Limso, Jordan Matthew Ngo, +5 authors, Deepali Bhandari.
FEBS Lett, 2019 Nov 19; 594(6). PMID: 31736058    Free PMC article.
Non-invasive evaluation of the equine gastrointestinal mucosal transcriptome.
Michelle C Coleman, Canaan Whitfield-Cargile, +7 authors, Robert S Chapkin.
PLoS One, 2020 Mar 17; 15(3). PMID: 32176710    Free PMC article.
Cancer cell-intrinsic function of CD177 in attenuating β-catenin signaling.
Paige N Kluz, Ryan Kolb, +18 authors, Weizhou Zhang.
Oncogene, 2020 Feb 12; 39(14). PMID: 32042113    Free PMC article.
Functional Phenotypic Diversity of Regulatory T Cells Remaining in Inflamed Skin.
Ryoyo Ikebuchi, Maika Fujimoto, +4 authors, Michio Tomura.
Front Immunol, 2019 Jun 04; 10. PMID: 31156643    Free PMC article.
Cell Atlas technologies and insights into tissue architecture.
Anna Wilbrey-Clark, Kenny Roberts, Sarah A Teichmann.
Biochem J, 2020 Apr 28; 477(8). PMID: 32339226    Free PMC article.
Review.
GIV/Girdin and Exo70 Collaboratively Regulate the Mammalian Polarized Exocytic Machinery.
Cristina Rohena, Navin Rajapakse, +3 authors, Pradipta Ghosh.
iScience, 2020 Jun 27; 23(7). PMID: 32590327    Free PMC article.
An Improved Anticancer Drug-Response Prediction Based on an Ensemble Method Integrating Matrix Completion and Ridge Regression.
Chuanying Liu, Dong Wei, +6 authors, Jialiang Yang.
Mol Ther Nucleic Acids, 2020 Aug 08; 21. PMID: 32759058    Free PMC article.
Intratumoral heterogeneity of hepatocellular carcinoma: From single-cell to population-based studies.
Qi Zhang, Yu Lou, Xue-Li Bai, Ting-Bo Liang.
World J Gastroenterol, 2020 Aug 11; 26(26). PMID: 32774053    Free PMC article.
Review.
Single-cell RNA sequencing in breast cancer: Understanding tumor heterogeneity and paving roads to individualized therapy.
Shuning Ding, Xiaosong Chen, Kunwei Shen.
Cancer Commun (Lond), 2020 Jul 13; 40(8). PMID: 32654419    Free PMC article.
Review.
Biological and Medical Importance of Cellular Heterogeneity Deciphered by Single-Cell RNA Sequencing.
Rishikesh Kumar Gupta, Jacek Kuznicki.
Cells, 2020 Jul 28; 9(8). PMID: 32707839    Free PMC article.
Review.
Advances in Therapeutic Targeting of Cancer Stem Cells within the Tumor Microenvironment: An Updated Review.
Kevin Dzobo, Dimakatso Alice Senthebane, +3 authors, Collet Dandara.
Cells, 2020 Aug 23; 9(8). PMID: 32823711    Free PMC article.
Review.
Single-Cell Ssequencing in Cancer: Recent Applications to Immunogenomics and Multi-omics Tools.
Michael C Sierant, Jungmin Choi.
Genomics Inform, 2019 Jan 03; 16(4). PMID: 30602078    Free PMC article.
Characterization of cancer genomic heterogeneity by next-generation sequencing advances precision medicine in cancer treatment.
Jialing Zhang, Stephan Stanislaw Späth, +2 authors, Xinghua Pan.
Precis Clin Med, 2019 Jan 29; 1(1). PMID: 30687561    Free PMC article.
Highly Cited. Review.
Single Cell Omics of Breast Cancer: An Update on Characterization and Diagnosis.
Shailendra Dwivedi, Purvi Purohit, +5 authors, Praveen Sharma.
Indian J Clin Biochem, 2019 Feb 08; 34(1). PMID: 30728668    Free PMC article.
Review.
F-Box/WD Repeat Domain-Containing 7 Induces Chemotherapy Resistance in Colorectal Cancer Stem Cells.
Shusaku Honma, Shigeo Hisamori, +4 authors, Yoshiharu Sakai.
Cancers (Basel), 2019 May 10; 11(5). PMID: 31067777    Free PMC article.
Multilayered skyscraper microchips fabricated by hybrid "all-in-one" femtosecond laser processing.
Chaowei Wang, Liang Yang, +8 authors, Koji Sugioka.
Microsyst Nanoeng, 2019 May 10; 5. PMID: 31069108    Free PMC article.
Interrogation of Phenotypic Plasticity between Epithelial and Mesenchymal States in Breast Cancer.
Sugandha Bhatia, James Monkman, +4 authors, Erik W Thompson.
J Clin Med, 2019 Jun 27; 8(6). PMID: 31234417    Free PMC article.
Identification of gene expression logical invariants in Arabidopsis.
Sonalisa Pandey, Debashis Sahoo.
Plant Direct, 2019 Jun 28; 3(3). PMID: 31245766    Free PMC article.
Divide and conquer: A perspective on biochips for single-cell and rare-molecule analysis by next-generation sequencing.
A C Lee, Y Lee, D Lee, S Kwon.
APL Bioeng, 2019 Aug 23; 3(2). PMID: 31431936    Free PMC article.
Understanding EGFR heterogeneity in lung cancer.
Antonio Passaro, Umberto Malapelle, +13 authors, Christian Rolfo.
ESMO Open, 2020 Oct 18; 5(5). PMID: 33067323    Free PMC article.
Review.
Transcriptomic analysis of CIC and ATXN1L reveal a functional relationship exploited by cancer.
Derek Wong, Kohl Lounsbury, +6 authors, Stephen Yip.
Oncogene, 2018 Aug 11; 38(2). PMID: 30093628
Dedifferentiation process driven by TGF-beta signaling enhances stem cell properties in human colorectal cancer.
Michitaka Nakano, Yoshikane Kikushige, +12 authors, Koichi Akashi.
Oncogene, 2018 Sep 06; 38(6). PMID: 30181548
Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris.
Tabula Muris Consortium, Overall coordination, +7 authors, Principal investigators.
Nature, 2018 Oct 05; 562(7727). PMID: 30283141    Free PMC article.
Highly Cited.
Quantitative imaging of lipid droplets in single cells.
Anushka Gupta, Gabriel F Dorlhiac, Aaron M Streets.
Analyst, 2018 Oct 26; 144(3). PMID: 30357117    Free PMC article.
Review.
Tumour heterogeneity and metastasis at single-cell resolution.
Devon A Lawson, Kai Kessenbrock, +2 authors, Zena Werb.
Nat Cell Biol, 2018 Nov 30; 20(12). PMID: 30482943    Free PMC article.
Highly Cited. Review.
Gene expression profiles in genome instability-based classes of colorectal cancer.
Vincenza Barresi, Giacomo Cinnirella, +4 authors, Daniele F Condorelli.
BMC Cancer, 2018 Dec 20; 18(1). PMID: 30563495    Free PMC article.
Intratumoral heterogeneity of EGFR-activating mutations in advanced NSCLC patients at the single-cell level.
Longhua Guo, Zhihong Chen, +9 authors, Qing Zhou.
BMC Cancer, 2019 Apr 25; 19(1). PMID: 31014278    Free PMC article.
Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs.
Shuai He, Lin-He Wang, +12 authors, Zhiyong Guo.
Genome Biol, 2020 Dec 09; 21(1). PMID: 33287869    Free PMC article.
Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas.
Reuben Moncada, Dalia Barkley, +6 authors, Itai Yanai.
Nat Biotechnol, 2020 Jan 15; 38(3). PMID: 31932730
GIV•Kindlin Interaction Is Required for Kindlin-Mediated Integrin Recognition and Activation.
Cristina Rohena, Nicholas Kalogriopoulos, +5 authors, Pradipta Ghosh.
iScience, 2020 Jun 15; 23(6). PMID: 32535026    Free PMC article.
The Application of Single-Cell RNA Sequencing in Studies of Autoimmune Diseases: a Comprehensive Review.
Mingming Zhao, Jiao Jiang, +3 authors, Qianjin Lu.
Clin Rev Allergy Immunol, 2020 Nov 26; 60(1). PMID: 33236283
Review.
Multiregion single-cell sequencing reveals the transcriptional landscape of the immune microenvironment of colorectal cancer.
Wei Wang, Yu Zhong, +26 authors, Xueqing Yao.
Clin Transl Med, 2021 Jan 20; 11(1). PMID: 33463049    Free PMC article.
Colonoids From Patients With Pediatric Inflammatory Bowel Disease Exhibit Decreased Growth Associated With Inflammation Severity and Durable Upregulation of Antigen Presentation Genes.
Judith R Kelsen, Noor Dawany, +23 authors, Kathryn E Hamilton.
Inflamm Bowel Dis, 2020 Jun 20; 27(2). PMID: 32556182    Free PMC article.
Control of replication stress and mitosis in colorectal cancer stem cells through the interplay of PARP1, MRE11 and RAD51.
Gwenola Manic, Martina Musella, +23 authors, Ilio Vitale.
Cell Death Differ, 2021 Feb 04; 28(7). PMID: 33531658    Free PMC article.
Boolean implication analysis unveils candidate universal relationships in microbiome data.
Daniella Vo, Shayal Charisma Singh, Sara Safa, Debashis Sahoo.
BMC Bioinformatics, 2021 Feb 07; 22(1). PMID: 33546590    Free PMC article.
Spatiotemporal analysis of human intestinal development at single-cell resolution.
David Fawkner-Corbett, Agne Antanaviciute, +11 authors, Alison Simmons.
Cell, 2021 Jan 07; 184(3). PMID: 33406409    Free PMC article.
Understanding cell-cell communication and signaling in the colorectal cancer microenvironment.
Shaikha AlMusawi, Mehreen Ahmed, Abdolrahman S Nateri.
Clin Transl Med, 2021 Feb 27; 11(2). PMID: 33635003    Free PMC article.
Review.
Enabling Technologies for Personalized and Precision Medicine.
Dean Ho, Stephen R Quake, +13 authors, Ali Zarrinpar.
Trends Biotechnol, 2020 Jan 26; 38(5). PMID: 31980301    Free PMC article.
Review.
Mixed Distribution Models Based on Single-Cell RNA Sequencing Data.
Min Wu, Junhua Xu, Tao Ding, Jie Gao.
Interdiscip Sci, 2021 Mar 24; 13(3). PMID: 33754241
Group phenotypic composition in cancer.
Jean-Pascal Capp, James DeGregori, +10 authors, Frédéric Thomas.
Elife, 2021 Mar 31; 10. PMID: 33784238    Free PMC article.
Review.
Functional States in Tumor-Initiating Cell Differentiation in Human Colorectal Cancer.
Martina K Zowada, Stephan M Tirier, +19 authors, Claudia R Ball.
Cancers (Basel), 2021 Apr 04; 13(5). PMID: 33806447    Free PMC article.
Decoding Cancer Biology One Cell at a Time.
L Nicolas Gonzalez Castro, Itay Tirosh, Mario L Suvà.
Cancer Discov, 2021 Apr 04; 11(4). PMID: 33811126    Free PMC article.
Review.
Tumor proportion in colon cancer: results from a semiautomatic image analysis approach.
Benedikt Martin, Bettina Monika Banner, +4 authors, Bruno Märkl.
Virchows Arch, 2020 Feb 23; 477(2). PMID: 32076815    Free PMC article.
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Nat Genet, 2020 May 27; 52(6). PMID: 32451460
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Adv Sci (Weinh), 2021 Apr 27; 8(8). PMID: 33898197    Free PMC article.
Comparative Analysis of Patient-Matched PDOs Revealed a Reduction in OLFM4-Associated Clusters in Metastatic Lesions in Colorectal Cancer.
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Stem Cell Reports, 2021 Mar 13; 16(4). PMID: 33711267    Free PMC article.
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Colon Crypts of Subjects With Familial Adenomatous Polyposis Show an Increased Number of LGR5+ Ectopic Stem Cells.
Lucas T Jennelle, Christopher H Dampier, +2 authors, Graham Casey.
Clin Transl Gastroenterol, 2021 May 18; 12(5). PMID: 33999013    Free PMC article.
Plasma Membrane Localized GCaMP-MS4A12 by Orai1 Co-Expression Shows Thapsigargin- and Ca2+-Dependent Fluorescence Increases.
Jung Woo Han, Woon Heo, +8 authors, Joo Young Kim.
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Sci Rep, 2021 May 28; 11(1). PMID: 34040065    Free PMC article.
A comprehensive survey of regulatory network inference methods using single cell RNA sequencing data.
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Single-Cell Sequencing and Organoids: A Powerful Combination for Modelling Organ Development and Diseases.
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Rev Physiol Biochem Pharmacol, 2021 Feb 24; 179. PMID: 33619630
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An integrated enrichment system to facilitate isolation and molecular characterization of single cancer cells from whole blood.
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Integrating Spatial Transcriptomics and Single-Cell RNA-seq Reveals the Gene Expression Profling of the Human Embryonic Liver.
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Front Cell Dev Biol, 2021 Jun 08; 9. PMID: 34095116    Free PMC article.
Genetic and biological hallmarks of colorectal cancer.
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AI-guided discovery of the invariant host response to viral pandemics.
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EBioMedicine, 2021 Jun 16; 68. PMID: 34127431    Free PMC article.
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μCB-seq: microfluidic cell barcoding and sequencing for high-resolution imaging and sequencing of single cells.
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Anal Chem, 2021 Jun 18; 93(25). PMID: 34137250    Free PMC article.
Artificial intelligence guided discovery of a barrier-protective therapy in inflammatory bowel disease.
Debashis Sahoo, Lee Swanson, +11 authors, Pradipta Ghosh.
Nat Commun, 2021 Jul 14; 12(1). PMID: 34253728    Free PMC article.
LIN28B induces a differentiation program through CDX2 in colon cancer.
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JCI Insight, 2021 Mar 24; 6(9). PMID: 33755595    Free PMC article.
A Transcriptomic Approach Reveals Selective Ribosomal Remodelling in the Tumour Versus the Stromal Compartment of Metastatic Colorectal Cancer.
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Bacterial Single Cell Whole Transcriptome Amplification in Microfluidic Platform Shows Putative Gene Expression Heterogeneity.
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Functional genomics approaches to improve pre-clinical drug screening and biomarker discovery.
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Elife, 2021 Sep 01; 10. PMID: 34463615    Free PMC article.
Methods and platforms for analysis of nucleic acids from single-cell based on microfluidics.
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Nat Commun, 2021 Oct 03; 12(1). PMID: 34599187    Free PMC article.
Cancer cell states and emergent properties of the dynamic tumor system.
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SPT6 loss permits the transdifferentiation of keratinocytes into an intestinal fate that resembles Barrett's metaplasia.
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Nucleic Acids Res, 2021 Jul 08; 49(18). PMID: 34233007    Free PMC article.
Single-Cell Analysis of Antigen-Specific CD8+ T-Cell Transcripts Reveals Profiles Specific to mRNA or Adjuvanted Protein Vaccines.
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Front Immunol, 2021 Nov 16; 12. PMID: 34777370    Free PMC article.
Isolation of Circulating Tumor Cells from Peripheral Blood Samples of Cancer Patients Using Microfluidic Technology.
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J Gastroenterol, 2022 Mar 05; 57(6). PMID: 35244768
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Commun Biol, 2022 Mar 16; 5(1). PMID: 35288651    Free PMC article.
StemSC: a cross-dataset human stemness index for single-cell samples.
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Single-cell and spatial analysis reveal interaction of FAP+ fibroblasts and SPP1+ macrophages in colorectal cancer.
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Semantic clustering analysis of E3-ubiquitin ligases in gastrointestinal tract defines genes ontology clusters with tissue expression patterns.
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Functional patient-derived organoid screenings identify MCLA-158 as a therapeutic EGFR × LGR5 bispecific antibody with efficacy in epithelial tumors.
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