Journal Article
. 2017 Jun; 14(7):687-690.
doi: 10.1038/nmeth.4324.

Differential analysis of RNA-seq incorporating quantification uncertainty

Harold Pimentel 1 Nicolas L Bray 2 Suzette Puente 3 Páll Melsted 4 Lior Pachter 5 
Affiliations
  • PMID: 28581496
  •     509 citations

Abstract

We describe sleuth (http://pachterlab.github.io/sleuth), a method for the differential analysis of gene expression data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance. sleuth is implemented in an interactive shiny app that utilizes kallisto quantifications and bootstraps for fast and accurate analysis of data from RNA-seq experiments.

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Interpretation of differential gene expression results of RNA-seq data: review and integration.
Adam McDermaid, Brandon Monier, +2 authors, Qin Ma.
Brief Bioinform, 2018 Aug 14; 20(6). PMID: 30099484    Free PMC article.
Review.
Chronic stress reduces spermatogenic cell proliferation in rat testis.
Pengxiang Tian, Pin Lv, +3 authors, Bo Wen.
Int J Clin Exp Pathol, 2020 Jan 15; 12(5). PMID: 31934015    Free PMC article.
Complex patterns of cell growth in the placenta in normal pregnancy and as adaptations to maternal diet restriction.
Malcolm Eaton, Alastair H Davies, +9 authors, James C Cross.
PLoS One, 2020 Jan 10; 15(1). PMID: 31917811    Free PMC article.
HOTAIRM1 lncRNA is downregulated in clear cell renal cell carcinoma and inhibits the hypoxia pathway.
Michael J Hamilton, Matthew Young, +5 authors, Ernest Martinez.
Cancer Lett, 2019 Dec 22; 472. PMID: 31862408    Free PMC article.
Translation of the intrinsically disordered protein α-synuclein is inhibited by a small molecule targeting its structured mRNA.
Peiyuan Zhang, Hye-Jin Park, +11 authors, Matthew D Disney.
Proc Natl Acad Sci U S A, 2020 Jan 05; 117(3). PMID: 31900363    Free PMC article.
Expansion, in vivo-ex vivo cycling, and genetic manipulation of primary human hepatocytes.
Eleftherios Michailidis, Koen Vercauteren, +23 authors, Ype P de Jong.
Proc Natl Acad Sci U S A, 2020 Jan 10; 117(3). PMID: 31915293    Free PMC article.
Alternative splicing coupled with transcript degradation modulates OAS1g antiviral activity.
Luke Frankiw, Mati Mann, +2 authors, David Baltimore.
RNA, 2019 Nov 20; 26(2). PMID: 31740586    Free PMC article.
Interactions between the gut microbiome and host gene regulation in cystic fibrosis.
Gargi Dayama, Sambhawa Priya, +2 authors, Ran Blekhman.
Genome Med, 2020 Jan 30; 12(1). PMID: 31992345    Free PMC article.
CATION-CHLORIDE CO-TRANSPORTER 1 (CCC1) Mediates Plant Resistance against Pseudomonas syringae.
Baoda Han, Yunhe Jiang, +7 authors, Heribert Hirt.
Plant Physiol, 2019 Dec 07; 182(2). PMID: 31806735    Free PMC article.
Acetate supplementation restores chromatin accessibility and promotes tumor cell differentiation under hypoxia.
Yang Li, Joshua J Gruber, +11 authors, Jiangbin Ye.
Cell Death Dis, 2020 Feb 08; 11(2). PMID: 32029721    Free PMC article.
Spaceflight and simulated microgravity conditions increase virulence of Serratia marcescens in the Drosophila melanogaster infection model.
Rachel Gilbert, Medaya Torres, +4 authors, Sharmila Bhattacharya.
NPJ Microgravity, 2020 Feb 13; 6. PMID: 32047838    Free PMC article.
Control of human hemoglobin switching by LIN28B-mediated regulation of BCL11A translation.
Anindita Basak, Mathias Munschauer, +18 authors, Vijay G Sankaran.
Nat Genet, 2020 Jan 22; 52(2). PMID: 31959994    Free PMC article.
Functional and transcriptomic characterization of cisplatin-resistant AGS and MKN-28 gastric cancer cell lines.
Barbara Mora-Lagos, Irene Cartas-Espinel, +8 authors, Priscilla Brebi.
PLoS One, 2020 Jan 29; 15(1). PMID: 31990955    Free PMC article.
Analysis of zebrafish periderm enhancers facilitates identification of a regulatory variant near human KRT8/18.
Huan Liu, Kaylia Duncan, +10 authors, Robert A Cornell.
Elife, 2020 Feb 08; 9. PMID: 32031521    Free PMC article.
Systematic Immunotherapy Target Discovery Using Genome-Scale In Vivo CRISPR Screens in CD8 T Cells.
Matthew B Dong, Guangchuan Wang, +17 authors, Sidi Chen.
Cell, 2019 Aug 24; 178(5). PMID: 31442407    Free PMC article.
Exome sequencing of bulked segregants identified a novel TaMKK3-A allele linked to the wheat ERA8 ABA-hypersensitive germination phenotype.
Shantel A Martinez, Oluwayesi Shorinola, +4 authors, Camille M Steber.
Theor Appl Genet, 2020 Jan 30; 133(3). PMID: 31993676    Free PMC article.
Novel Data Transformations for RNA-seq Differential Expression Analysis.
Zeyu Zhang, Danyang Yu, +3 authors, Weiliang Qiu.
Sci Rep, 2019 Mar 20; 9(1). PMID: 30886278    Free PMC article.
Precise small-molecule cleavage of an r(CUG) repeat expansion in a myotonic dystrophy mouse model.
Alicia J Angelbello, Suzanne G Rzuczek, +6 authors, Matthew D Disney.
Proc Natl Acad Sci U S A, 2019 Mar 31; 116(16). PMID: 30926669    Free PMC article.
Highly Cited.
Electrotaxis of Glioblastoma and Medulloblastoma Spheroidal Aggregates.
Johnathan G Lyon, Sheridan L Carroll, Nassir Mokarram, Ravi V Bellamkonda.
Sci Rep, 2019 Mar 31; 9(1). PMID: 30926929    Free PMC article.
RNA Sequencing Provides Novel Insights into the Transcriptome of Aldosterone Producing Adenomas.
Samuel Backman, Tobias Åkerström, +4 authors, Peyman Björklund.
Sci Rep, 2019 Apr 20; 9(1). PMID: 31000732    Free PMC article.
Cell type specific transcriptional reprogramming of maize leaves during Ustilago maydis induced tumor formation.
Mitzi Villajuana-Bonequi, Alexandra Matei, +3 authors, Gunther Doehlemann.
Sci Rep, 2019 Jul 17; 9(1). PMID: 31308451    Free PMC article.
Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq.
Claire R Williams, Alyssa Baccarella, Jay Z Parrish, Charles C Kim.
BMC Bioinformatics, 2017 Jan 18; 18(1). PMID: 28095772    Free PMC article.
GIRK2 splice variants and neuronal G protein-gated K+ channels: implications for channel function and behavior.
Ezequiel Marron Fernandez de Velasco, Lei Zhang, +8 authors, Kevin Wickman.
Sci Rep, 2017 May 11; 7(1). PMID: 28487514    Free PMC article.
TGF-β1 Evokes Human Airway Smooth Muscle Cell Shortening and Hyperresponsiveness via Smad3.
Christie A Ojiaku, Gaoyuan Cao, +5 authors, Reynold A Panettieri.
Am J Respir Cell Mol Biol, 2017 Oct 07; 58(5). PMID: 28984468    Free PMC article.
GPCRomics: An Approach to Discover GPCR Drug Targets.
Paul A Insel, Krishna Sriram, +4 authors, Amy M Chinn.
Trends Pharmacol Sci, 2019 May 13; 40(6). PMID: 31078319    Free PMC article.
Review.
Bootstrapping and Empirical Bayes Methods Improve Rhythm Detection in Sparsely Sampled Data.
Alan L Hutchison, Ravi Allada, Aaron R Dinner.
J Biol Rhythms, 2018 Aug 14; 33(4). PMID: 30101659    Free PMC article.
Targeted m6A Reader Proteins To Study Epitranscriptomic Regulation of Single RNAs.
Simone Rauch, Chuan He, Bryan C Dickinson.
J Am Chem Soc, 2018 Sep 06; 140(38). PMID: 30183280    Free PMC article.
SequencEnG: an interactive knowledge base of sequencing techniques.
Yi Zhang, Mohith Manjunath, +2 authors, Jun S Song.
Bioinformatics, 2018 Sep 12; 35(8). PMID: 30202870    Free PMC article.
Desiccation Tolerance Evolved through Gene Duplication and Network Rewiring in Lindernia.
Robert VanBuren, Ching Man Wai, +4 authors, Dorothea Bartels.
Plant Cell, 2018 Oct 27; 30(12). PMID: 30361236    Free PMC article.
SETDB1 Links the Meiotic DNA Damage Response to Sex Chromosome Silencing in Mice.
Takayuki Hirota, Paul Blakeley, +8 authors, James M A Turner.
Dev Cell, 2018 Nov 06; 47(5). PMID: 30393076    Free PMC article.
Escherichia coli Lrp Regulates One-Third of the Genome via Direct, Cooperative, and Indirect Routes.
Grace M Kroner, Michael B Wolfe, Peter L Freddolino.
J Bacteriol, 2018 Nov 14; 201(3). PMID: 30420454    Free PMC article.
Retrograde BMP signaling activates neuronal gene expression through widespread deployment of a conserved BMP-responsive cis-regulatory activation element.
Robin Vuilleumier, Tianshun Lian, +4 authors, Douglas W Allan.
Nucleic Acids Res, 2018 Nov 27; 47(2). PMID: 30476189    Free PMC article.
Cell-type specific polysome profiling from mammalian tissues.
Joseph Seimetz, Waqar Arif, +2 authors, Auinash Kalsotra.
Methods, 2018 Dec 01; 155. PMID: 30500367    Free PMC article.
Tissue-Specific cis-Regulatory Divergence Implicates eloF in Inhibiting Interspecies Mating in Drosophila.
Peter A Combs, Joshua J Krupp, +4 authors, Hunter B Fraser.
Curr Biol, 2018 Dec 07; 28(24). PMID: 30503619    Free PMC article.
Global analysis of RNA metabolism using bio-orthogonal labeling coupled with next-generation RNA sequencing.
Michael B Wolfe, Aaron C Goldstrohm, Peter L Freddolino.
Methods, 2018 Dec 12; 155. PMID: 30529548    Free PMC article.
Review.
Gene expression is implicated in the ability of pikas to occupy Himalayan elevational gradient.
Katherine A Solari, Uma Ramakrishnan, Elizabeth A Hadly.
PLoS One, 2018 Dec 13; 13(12). PMID: 30540800    Free PMC article.
CD71+VISTA+ erythroid cells promote the development and function of regulatory T cells through TGF-β.
Shima Shahbaz, Najmeh Bozorgmehr, +4 authors, Shokrollah Elahi.
PLoS Biol, 2018 Dec 15; 16(12). PMID: 30550561    Free PMC article.
iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data.
Steven Xijin Ge, Eun Wo Son, Runan Yao.
BMC Bioinformatics, 2018 Dec 21; 19(1). PMID: 30567491    Free PMC article.
Highly Cited.
A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens.
Molly Gasperini, Andrew J Hill, +10 authors, Jay Shendure.
Cell, 2019 Jan 08; 176(1-2). PMID: 30612741    Free PMC article.
Highly Cited.
Immune genes are hotspots of shared positive selection across birds and mammals.
Allison J Shultz, Timothy B Sackton.
Elife, 2019 Jan 09; 8. PMID: 30620335    Free PMC article.
Highly Cited.
Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation.
Johan Henriksson, Xi Chen, +8 authors, Sarah A Teichmann.
Cell, 2019 Jan 15; 176(4). PMID: 30639098    Free PMC article.
HSP90 inhibitor geldanamycin reverts IL-13- and IL-17-induced airway goblet cell metaplasia.
Alejandro A Pezzulo, Rosarie A Tudas, +5 authors, Joseph Zabner.
J Clin Invest, 2019 Jan 15; 129(2). PMID: 30640172    Free PMC article.
A Platform for Generation of Chamber-Specific Cardiac Tissues and Disease Modeling.
Yimu Zhao, Naimeh Rafatian, +19 authors, Milica Radisic.
Cell, 2019 Jan 29; 176(4). PMID: 30686581    Free PMC article.
Highly Cited.
tRNA Genes Affect Chromosome Structure and Function via Local Effects.
Omar Hamdani, Namrita Dhillon, +14 authors, Rohinton T Kamakaka.
Mol Cell Biol, 2019 Feb 06; 39(8). PMID: 30718362    Free PMC article.
TGFβ/BMP immune signaling affects abundance and function of C. elegans gut commensals.
Maureen Berg, David Monnin, +3 authors, Michael Shapira.
Nat Commun, 2019 Feb 07; 10(1). PMID: 30723205    Free PMC article.
Identification and characterization of a direct activator of a gene transfer agent.
Paul C M Fogg.
Nat Commun, 2019 Feb 07; 10(1). PMID: 30723210    Free PMC article.
Overriding FUS autoregulation in mice triggers gain-of-toxic dysfunctions in RNA metabolism and autophagy-lysosome axis.
Shuo-Chien Ling, Somasish Ghosh Dastidar, +25 authors, Don W Cleveland.
Elife, 2019 Feb 13; 8. PMID: 30747709    Free PMC article.
Highly Cited.
Optogenetic and transcriptomic interrogation of enhanced muscle function in the paralyzed mouse whisker pad.
Thomas J Vajtay, Akhil Bandi, +4 authors, David J Margolis.
J Neurophysiol, 2019 Feb 21; 121(4). PMID: 30785807    Free PMC article.
Convergent Identification and Interrogation of Tumor-Intrinsic Factors that Modulate Cancer Immunity In Vivo.
Adan Codina, Paul A Renauer, +16 authors, Sidi Chen.
Cell Syst, 2019 Feb 25; 8(2). PMID: 30797773    Free PMC article.
Assembly and functionality of the ribosome with tethered subunits.
Nikolay A Aleksashin, Margus Leppik, +5 authors, Alexander S Mankin.
Nat Commun, 2019 Feb 26; 10(1). PMID: 30804338    Free PMC article.
Integrative analysis of Paneth cell proteomic and transcriptomic data from intestinal organoids reveals functional processes dependent on autophagy.
Emily J Jones, Zoe J Matthews, +17 authors, Tamas Korcsmaros.
Dis Model Mech, 2019 Mar 01; 12(3). PMID: 30814064    Free PMC article.
Integration of Transcriptomic Data Identifies Global and Cell-Specific Asthma-Related Gene Expression Signatures.
Mengyuan Kan, Maya Shumyatcher, +2 authors, Blanca E Himes.
AMIA Annu Symp Proc, 2019 Mar 01; 2018. PMID: 30815178    Free PMC article.
Common workflow language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data.
Pasi K Korhonen, Ross S Hall, Neil D Young, Robin B Gasser.
Gigascience, 2019 Mar 02; 8(4). PMID: 30821816    Free PMC article.
Energetic Trade-Offs and Hypometabolic States Promote Disease Tolerance.
Kirthana Ganeshan, Joni Nikkanen, +7 authors, Ajay Chawla.
Cell, 2019 Mar 12; 177(2). PMID: 30853215    Free PMC article.
Highly Cited.
Developmental Dieldrin Exposure Alters DNA Methylation at Genes Related to Dopaminergic Neuron Development and Parkinson's Disease in Mouse Midbrain.
Joseph Kochmanski, Sarah E VanOeveren, Joseph R Patterson, Alison I Bernstein.
Toxicol Sci, 2019 Mar 13; 169(2). PMID: 30859219    Free PMC article.
Insights into the Biology of Hearing and Deafness Revealed by Single-Cell RNA Sequencing.
Paul T Ranum, Alexander T Goodwin, +5 authors, Richard J H Smith.
Cell Rep, 2019 Mar 14; 26(11). PMID: 30865901    Free PMC article.
Highly Cited.
RNA Sequencing Reveals Specific TranscriptomicSignatures Distinguishing Effects of the [SWI⁺] Prion and SWI1 Deletion in Yeast Saccharomyces cerevisiae.
Yury V Malovichko, Kirill S Antonets, +3 authors, Anton A Nizhnikov.
Genes (Basel), 2019 Mar 16; 10(3). PMID: 30871095    Free PMC article.
Specificity of the Metallothionein-1 Response by Cadmium-Exposed Normal Human Urothelial Cells.
Rhiannon V McNeill, Andrew S Mason, +2 authors, Jennifer Southgate.
Int J Mol Sci, 2019 Mar 20; 20(6). PMID: 30884885    Free PMC article.
Epigenetic Changes Induced by Bacteroides fragilis Toxin.
Jawara Allen, Stephanie Hao, Cynthia L Sears, Winston Timp.
Infect Immun, 2019 Mar 20; 87(6). PMID: 30885929    Free PMC article.
A novel transcriptome-derived SNPs array for tench (Tinca tinca L.).
Girish Kumar, Jorge Langa, +4 authors, Andone Estonba.
PLoS One, 2019 Mar 20; 14(3). PMID: 30889192    Free PMC article.
Relative Abundance of Transcripts ( RATs): Identifying differential isoform abundance from RNA-seq.
Kimon Froussios, Kira Mourão, +2 authors, Nicholas Schurch.
F1000Res, 2019 Mar 25; 8. PMID: 30906538    Free PMC article.
Combined Transcriptome and Proteome Analysis of Immortalized Human Keratinocytes Expressing Human Papillomavirus 16 (HPV16) Oncogenes Reveals Novel Key Factors and Networks in HPV-Induced Carcinogenesis.
Ruwen Yang, Jana Klimentová, +7 authors, Martina Niebler.
mSphere, 2019 Mar 29; 4(2). PMID: 30918060    Free PMC article.
A Multiscale Map of the Stem Cell State in Pancreatic Adenocarcinoma.
Nikki K Lytle, L Paige Ferguson, +30 authors, Tannishtha Reya.
Cell, 2019 Apr 09; 177(3). PMID: 30955884    Free PMC article.
Variation in pigmentation gene expression is associated with distinct aposematic color morphs in the poison frog Dendrobates auratus.
Adam M M Stuckert, Emily Moore, +4 authors, Kyle Summers.
BMC Evol Biol, 2019 Apr 19; 19(1). PMID: 30995908    Free PMC article.
Correction of gene model annotations improves isoform abundance estimates: the example of ketohexokinase ( Khk).
Christophe D Chabbert, Tanja Eberhart, +2 authors, Werner J Kovacs.
F1000Res, 2019 Apr 23; 7. PMID: 31001414    Free PMC article.
Little Evidence of Antagonistic Selection in the Evolutionary Strata of Fungal Mating-Type Chromosomes (Microbotryum lychnidis-dioicae).
Anna Liza Bazzicalupo, Fantin Carpentier, Sarah Perin Otto, Tatiana Giraud.
G3 (Bethesda), 2019 Apr 25; 9(6). PMID: 31015196    Free PMC article.
High Dietary Sugar Reshapes Sweet Taste to Promote Feeding Behavior in Drosophila melanogaster.
Christina E May, Anoumid Vaziri, +8 authors, Monica Dus.
Cell Rep, 2019 May 09; 27(6). PMID: 31067455    Free PMC article.
SREBP1 drives Keratin-80-dependent cytoskeletal changes and invasive behavior in endocrine-resistant ERα breast cancer.
Ylenia Perone, Aaron J Farrugia, +16 authors, Luca Magnani.
Nat Commun, 2019 May 11; 10(1). PMID: 31073170    Free PMC article.
Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation.
Shengbo He, Martin Vickers, Jingyi Zhang, Xiaoqi Feng.
Elife, 2019 May 29; 8. PMID: 31135340    Free PMC article.
Using equivalence class counts for fast and accurate testing of differential transcript usage.
Marek Cmero, Nadia M Davidson, Alicia Oshlack.
F1000Res, 2019 Jun 04; 8. PMID: 31143443    Free PMC article.
Culturing C2C12 myotubes on micromolded gelatin hydrogels accelerates myotube maturation.
Lance T Denes, Lance A Riley, +4 authors, Eric T Wang.
Skelet Muscle, 2019 Jun 09; 9(1). PMID: 31174599    Free PMC article.
ZEB1 insufficiency causes corneal endothelial cell state transition and altered cellular processing.
Ricardo F Frausto, Doug D Chung, +14 authors, Anthony J Aldave.
PLoS One, 2019 Jun 14; 14(6). PMID: 31194824    Free PMC article.
Host-dependent nitrogen recycling as a mechanism of symbiont control in Aiptasia.
Guoxin Cui, Yi Jin Liew, +5 authors, Manuel Aranda.
PLoS Genet, 2019 Jun 25; 15(6). PMID: 31233506    Free PMC article.
SPX4 Acts on PHR1-Dependent and -Independent Regulation of Shoot Phosphorus Status in Arabidopsis.
Marina Borges Osorio, Sophia Ng, +5 authors, Ricarda Jost.
Plant Physiol, 2019 Jul 03; 181(1). PMID: 31262954    Free PMC article.
Transgeneratonal inheritance of ethanol preference is caused by maternal NPF repression.
Julianna Bozler, Balint Z Kacsoh, Giovanni Bosco.
Elife, 2019 Jul 10; 8. PMID: 31287057    Free PMC article.
PrediTALE: A novel model learned from quantitative data allows for new perspectives on TALE targeting.
Annett Erkes, Stefanie Mücke, +2 authors, Jan Grau.
PLoS Comput Biol, 2019 Jul 12; 15(7). PMID: 31295249    Free PMC article.
Choroid plexus-derived miR-204 regulates the number of quiescent neural stem cells in the adult brain.
Tjasa Lepko, Melanie Pusch, +17 authors, Jovica Ninkovic.
EMBO J, 2019 Jul 16; 38(17). PMID: 31304985    Free PMC article.
Mutant CEBPA directly drives the expression of the targetable tumor-promoting factor CD73 in AML.
Janus S Jakobsen, Linea G Laursen, +15 authors, Bo T Porse.
Sci Adv, 2019 Jul 17; 5(7). PMID: 31309149    Free PMC article.
Conditional expression explains molecular evolution of social genes in a microbe.
Janaina Lima de Oliveira, Atahualpa Castillo Morales, +8 authors, Jason B Wolf.
Nat Commun, 2019 Jul 25; 10(1). PMID: 31337766    Free PMC article.
A new family of cell surface located purine transporters in Microsporidia and related fungal endoparasites.
Peter Major, Kacper M Sendra, +5 authors, Robert P Hirt.
Elife, 2019 Jul 30; 8. PMID: 31355745    Free PMC article.
Dissection of acute stimulus-inducible nucleosome remodeling in mammalian cells.
Federico Comoglio, Marta Simonatto, +4 authors, Gioacchino Natoli.
Genes Dev, 2019 Aug 03; 33(17-18). PMID: 31371436    Free PMC article.
Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding.
Andrew D Johnston, Claudia A Simões-Pires, +2 authors, John M Greally.
Nat Commun, 2019 Aug 04; 10(1). PMID: 31375681    Free PMC article.
Systematic identification of cancer cell vulnerabilities to natural killer cell-mediated immune surveillance.
Matthew F Pech, Linda E Fong, +7 authors, Jeffrey Settleman.
Elife, 2019 Aug 28; 8. PMID: 31452512    Free PMC article.
Retrotransposon insertions can initiate colorectal cancer and are associated with poor survival.
Tatiana Cajuso, Päivi Sulo, +20 authors, Lauri A Aaltonen.
Nat Commun, 2019 Sep 08; 10(1). PMID: 31492840    Free PMC article.
Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing.
Mingui Zhao, Tianzuo Wang, +3 authors, Wen-Hao Zhang.
BMC Plant Biol, 2020 Mar 07; 20(1). PMID: 32138663    Free PMC article.
Programmable RNA-Guided RNA Effector Proteins Built from Human Parts.
Simone Rauch, Emily He, +3 authors, Bryan C Dickinson.
Cell, 2019 Jun 25; 178(1). PMID: 31230714    Free PMC article.
Circulating miR-338 Cluster activities on osteoblast differentiation: Potential Diagnostic and Therapeutic Targets for Postmenopausal Osteoporosis.
Chujiao Lin, Shuaitong Yu, +9 authors, Zhi Chen.
Theranostics, 2019 Jul 10; 9(13). PMID: 31281513    Free PMC article.
Hippocampal DNA Methylation in a Mouse Model of Fetal Alcohol Spectrum Disorder That Includes Maternal Separation Stress Only Partially Explains Changes in Gene Expression.
Bonnie L J Alberry, Shiva M Singh.
Front Genet, 2020 Mar 17; 11. PMID: 32174962    Free PMC article.
Evolutionary Dynamics of the POTE Gene Family in Human and Nonhuman Primates.
Flavia Angela Maria Maggiolini, Ludovica Mercuri, +9 authors, Mario Ventura.
Genes (Basel), 2020 Feb 23; 11(2). PMID: 32085667    Free PMC article.
Network Modeling of Liver Metabolism to Predict Plasma Metabolite Changes During Short-Term Fasting in the Laboratory Rat.
Kalyan C Vinnakota, Venkat R Pannala, +9 authors, Anders Wallqvist.
Front Physiol, 2019 Mar 19; 10. PMID: 30881311    Free PMC article.
Mechanistic identification of biofluid metabolite changes as markers of acetaminophen-induced liver toxicity in rats.
Venkat R Pannala, Kalyan C Vinnakota, +8 authors, Anders Wallqvist.
Toxicol Appl Pharmacol, 2019 Apr 12; 372. PMID: 30974156    Free PMC article.
Eya2 promotes cell cycle progression by regulating DNA damage response during vertebrate limb regeneration.
Konstantinos Sousounis, Donald M Bryant, +7 authors, Jessica L Whited.
Elife, 2020 Mar 07; 9. PMID: 32142407    Free PMC article.
Comprehensive metagenomic analysis of blastic plasmacytoid dendritic cell neoplasm.
Jason Nomburg, Susan Bullman, +8 authors, Andrew A Lane.
Blood Adv, 2020 Mar 18; 4(6). PMID: 32182365    Free PMC article.
IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis.
Brandon Monier, Adam McDermaid, +4 authors, Qin Ma.
PLoS Comput Biol, 2019 Feb 15; 15(2). PMID: 30763315    Free PMC article.
Comparative Molecular Life History of Spontaneous Canine and Human Gliomas.
Samirkumar B Amin, Kevin J Anderson, +28 authors, Roel G W Verhaak.
Cancer Cell, 2020 Feb 13; 37(2). PMID: 32049048    Free PMC article.
The Notch signaling pathway promotes basophil responses during helminth-induced type 2 inflammation.
Lauren M Webb, Oyebola O Oyesola, +10 authors, Elia D Tait Wojno.
J Exp Med, 2019 Apr 13; 216(6). PMID: 30975892    Free PMC article.
Loss of SRSF3 in Cardiomyocytes Leads to Decapping of Contraction-Related mRNAs and Severe Systolic Dysfunction.
Paula Ortiz-Sánchez, María Villalba-Orero, +11 authors, Enrique Lara-Pezzi.
Circ Res, 2019 May 31; 125(2). PMID: 31145021    Free PMC article.
Transcriptomic Insights into Mechanisms of Early Seed Maturation in the Garden Pea (Pisum sativum L.).
Yury V Malovichko, Oksana Y Shtark, +2 authors, Kirill S Antonets.
Cells, 2020 Mar 27; 9(3). PMID: 32210065    Free PMC article.
Induction of desiccation tolerance in desiccation sensitive Citrus limon seeds.
Alexandre Marques, Harm Nijveen, +2 authors, Henk Hilhorst.
J Integr Plant Biol, 2019 Jan 31; 61(5). PMID: 30697936    Free PMC article.
Being red, blue and green: the genetic basis of coloration differences in the strawberry poison frog (Oophaga pumilio).
Ariel Rodríguez, Nicholas I Mundy, Roberto Ibáñez, Heike Pröhl.
BMC Genomics, 2020 Apr 16; 21(1). PMID: 32293261    Free PMC article.
Chronic maternal interleukin-17 and autism-related cortical gene expression, neurobiology, and behavior.
Serena Banu Gumusoglu, Benjamin Wen Qing Hing, +3 authors, Hanna Elizabeth Stevens.
Neuropsychopharmacology, 2020 Feb 20; 45(6). PMID: 32074626    Free PMC article.
Short paired-end reads trump long single-end reads for expression analysis.
Adam H Freedman, John M Gaspar, Timothy B Sackton.
BMC Bioinformatics, 2020 Apr 21; 21(1). PMID: 32306895    Free PMC article.
Computational Oncology in the Multi-Omics Era: State of the Art.
Guillermo de Anda-Jáuregui, Enrique Hernández-Lemus.
Front Oncol, 2020 Apr 23; 10. PMID: 32318338    Free PMC article.
Review.
Lgr5+ telocytes are a signaling source at the intestinal villus tip.
Keren Bahar Halpern, Hassan Massalha, +14 authors, Shalev Itzkovitz.
Nat Commun, 2020 Apr 24; 11(1). PMID: 32321913    Free PMC article.
Tankyrase inhibition sensitizes melanoma to PD-1 immune checkpoint blockade in syngeneic mouse models.
Jo Waaler, Line Mygland, +16 authors, Stefan Krauss.
Commun Biol, 2020 Apr 26; 3(1). PMID: 32332858    Free PMC article.
Spatially regulated editing of genetic information within a neuron.
Isabel C Vallecillo-Viejo, Noa Liscovitch-Brauer, +6 authors, Joshua J C Rosenthal.
Nucleic Acids Res, 2020 Mar 24; 48(8). PMID: 32201888    Free PMC article.
Phenotypic and functional characterization of corneal endothelial cells during in vitro expansion.
Ricardo F Frausto, Vinay S Swamy, +12 authors, Anthony J Aldave.
Sci Rep, 2020 May 06; 10(1). PMID: 32366916    Free PMC article.
The rRNA m6A methyltransferase METTL5 is involved in pluripotency and developmental programs.
Valentina V Ignatova, Paul Stolz, +28 authors, Robert Schneider.
Genes Dev, 2020 Mar 29; 34(9-10). PMID: 32217665    Free PMC article.
Dissecting the phenotypic and functional heterogeneity of mouse inflammatory osteoclasts by the expression of Cx3cr1.
Maria-Bernadette Madel, Lidia Ibáñez, +9 authors, Claudine Blin-Wakkach.
Elife, 2020 May 14; 9. PMID: 32400390    Free PMC article.
Human vtRNA1-1 Levels Modulate Signaling Pathways and Regulate Apoptosis in Human Cancer Cells.
Lisamaria Bracher, Iolanda Ferro, +3 authors, Norbert Polacek.
Biomolecules, 2020 Apr 23; 10(4). PMID: 32316166    Free PMC article.
Transcriptome analysis and functional identification of adipose-derived mesenchymal stem cells in secondary lymphedema.
Qinqin Xiang, Fen Xu, +9 authors, Zhou Zhou.
Gland Surg, 2020 May 19; 9(2). PMID: 32420291    Free PMC article.
Transcriptional and biochemical analyses of gibberellin expression and content in germinated barley grain.
Natalie S Betts, Christoph Dockter, +8 authors, Geoffrey B Fincher.
J Exp Bot, 2019 Dec 11; 71(6). PMID: 31819970    Free PMC article.
Hippocampal transcriptome analysis following maternal separation implicates altered RNA processing in a mouse model of fetal alcohol spectrum disorder.
Bonnie L J Alberry, Christina A Castellani, Shiva M Singh.
J Neurodev Disord, 2020 May 18; 12(1). PMID: 32416732    Free PMC article.
Advances in Transcriptomics: Investigating Cardiovascular Disease at Unprecedented Resolution.
Robert C Wirka, Milos Pjanic, Thomas Quertermous.
Circ Res, 2018 Apr 28; 122(9). PMID: 29700068    Free PMC article.
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Intragenic repeat expansion in the cell wall protein gene HPF1 controls yeast chronological aging.
Benjamin P Barré, Johan Hallin, +8 authors, Gianni Liti.
Genome Res, 2020 Apr 12; 30(5). PMID: 32277013    Free PMC article.
Acellular bioscaffolds redirect cardiac fibroblasts and promote functional tissue repair in rodents and humans with myocardial injury.
Daniyil A Svystonyuk, Holly E M Mewhort, +14 authors, Paul W M Fedak.
Sci Rep, 2020 Jun 13; 10(1). PMID: 32528051    Free PMC article.
RABL6A Is an Essential Driver of MPNSTs that Negatively Regulates the RB1 Pathway and Sensitizes Tumor Cells to CDK4/6 Inhibitors.
Jordan L Kohlmeyer, Courtney A Kaemmer, +15 authors, Dawn E Quelle.
Clin Cancer Res, 2020 Feb 23; 26(12). PMID: 32086342    Free PMC article.
Human interleukin-4-treated regulatory macrophages promote epithelial wound healing and reduce colitis in a mouse model.
Timothy S Jayme, Gabriella Leung, +8 authors, Derek M McKay.
Sci Adv, 2020 Jun 18; 6(23). PMID: 32548267    Free PMC article.
Pharmacological target-focused transcriptomic analysis of native vs cultured human and mouse dorsal root ganglia.
Andi Wangzhou, Lisa A McIlvried, +8 authors, Theodore J Price.
Pain, 2020 Mar 21; 161(7). PMID: 32197039    Free PMC article.
Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment.
Zachary D Blount, Rohan Maddamsetti, +9 authors, Richard E Lenski.
Elife, 2020 May 30; 9. PMID: 32469311    Free PMC article.
Evaluation of M2-like macrophage enrichment after diffuse traumatic brain injury through transient interleukin-4 expression from engineered mesenchymal stromal cells.
Syed Faaiz Enam, Sajidur Rahman Kader, +8 authors, Ravi Venkat Bellamkonda.
J Neuroinflammation, 2020 Jun 22; 17(1). PMID: 32563258    Free PMC article.
Concordance between Thioacetamide-Induced Liver Injury in Rat and Human In Vitro Gene Expression Data.
Patric Schyman, Richard L Printz, +3 authors, Anders Wallqvist.
Int J Mol Sci, 2020 Jun 10; 21(11). PMID: 32512829    Free PMC article.
RNA sequencing analysis of the human retina and associated ocular tissues.
Scott T Schumacker, Krista R Coppage, Ray A Enke.
Sci Data, 2020 Jun 26; 7(1). PMID: 32581312    Free PMC article.
Heating quinoa shoots results in yield loss by inhibiting fruit production and delaying maturity.
Jose C Tovar, Carlos Quillatupa, +6 authors, Malia A Gehan.
Plant J, 2020 Jan 24; 102(5). PMID: 31971639    Free PMC article.
Macrophages and Associated Ligands in the Aged Injured Nerve: A Defective Dynamic That Contributes to Reduced Axonal Regrowth.
Jo Anne Stratton, Shane Eaton, +5 authors, Jeff Biernaskie.
Front Aging Neurosci, 2020 Jul 01; 12. PMID: 32595489    Free PMC article.
mitch: multi-contrast pathway enrichment for multi-omics and single-cell profiling data.
Antony Kaspi, Mark Ziemann.
BMC Genomics, 2020 Jul 01; 21(1). PMID: 32600408    Free PMC article.
Limited influence of the microbiome on the transcriptional profile of female Aedes aegypti mosquitoes.
Josephine Hyde, Maria A Correa, +2 authors, Doug E Brackney.
Sci Rep, 2020 Jul 04; 10(1). PMID: 32616765    Free PMC article.
Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data.
Hirak Sarkar, Avi Srivastava, +2 authors, Rob Patro.
Bioinformatics, 2020 Jul 14; 36(Suppl_1). PMID: 32657377    Free PMC article.
CRISPR screens in cancer spheroids identify 3D growth-specific vulnerabilities.
Kyuho Han, Sarah E Pierce, +22 authors, Michael C Bassik.
Nature, 2020 Apr 03; 580(7801). PMID: 32238925    Free PMC article.
Sex Chromosomes and Sex Phenotype Contribute to Biased DNA Methylation in Mouse Liver.
Qinwei Kim-Wee Zhuang, Jose Hector Galvez, +5 authors, Anna K Naumova.
Cells, 2020 Jun 13; 9(6). PMID: 32527045    Free PMC article.
Comparative transcriptome analyses reveal two distinct transcriptional modules associated with pollen shedding time in pine.
Jing-Jing Ma, Shuang-Wei Liu, +3 authors, Shi-Hui Niu.
BMC Genomics, 2020 Jul 24; 21(1). PMID: 32698817    Free PMC article.
Genome-Wide Identification of RNA Silencing-Related Genes and Their Expressional Analysis in Response to Heat Stress in Barley (Hordeum vulgare L.).
Éva Hamar, Henrik Mihály Szaker, +7 authors, Zoltán Havelda.
Biomolecules, 2020 Jun 24; 10(6). PMID: 32570964    Free PMC article.
Evidence of capacitation in the parasitoid wasp, Nasonia vitripennis, and its potential role in sex allocation.
Alun R C Jones, Eamonn B Mallon.
Ecol Evol, 2020 Aug 08; 10(14). PMID: 32760522    Free PMC article.
Lipo-chitooligosaccharides as regulatory signals of fungal growth and development.
Tomás Allen Rush, Virginie Puech-Pagès, +27 authors, Jean-Michel Ané.
Nat Commun, 2020 Aug 06; 11(1). PMID: 32753587    Free PMC article.
Abnormal Cone and Rod Photoreceptor Morphogenesis in gdf6a Mutant Zebrafish.
Nathan J Nadolski, Spencer D Balay, +2 authors, Jennifer C Hocking.
Invest Ophthalmol Vis Sci, 2020 Apr 16; 61(4). PMID: 32293666    Free PMC article.
Caenorhabditis elegans AF4/FMR2 Family Homolog affl-2 Regulates Heat-Shock-Induced Gene Expression.
Sophie J Walton, Han Wang, +2 authors, Paul W Sternberg.
Genetics, 2020 Jun 11; 215(4). PMID: 32518061    Free PMC article.
Transcriptomic analysis at organ and time scale reveals gene regulatory networks controlling the sulfate starvation response of Solanum lycopersicum.
Javier Canales, Felipe Uribe, +3 authors, Elena A Vidal.
BMC Plant Biol, 2020 Aug 25; 20(1). PMID: 32831040    Free PMC article.
Transcriptomic Changes Resulting From STK32B Overexpression Identify Pathways Potentially Relevant to Essential Tremor.
Calwing Liao, Faezeh Sarayloo, +10 authors, Guy A Rouleau.
Front Genet, 2020 Aug 28; 11. PMID: 32849812    Free PMC article.
Transcription of intragenic CpG islands influences spatiotemporal host gene pre-mRNA processing.
Samuele M Amante, Bertille Montibus, +8 authors, Rebecca J Oakey.
Nucleic Acids Res, 2020 Jul 06; 48(15). PMID: 32621610    Free PMC article.
Alignment and mapping methodology influence transcript abundance estimation.
Avi Srivastava, Laraib Malik, +6 authors, Rob Patro.
Genome Biol, 2020 Sep 08; 21(1). PMID: 32894187    Free PMC article.
Azithromycin ameliorates sulfur dioxide-induced airway epithelial damage and inflammatory responses.
Jon Petur Joelsson, Jennifer A Kricker, +7 authors, Saevar Ingthorsson.
Respir Res, 2020 Sep 12; 21(1). PMID: 32912304    Free PMC article.
Large Differences in Gene Expression Responses to Drought and Heat Stress between Elite Barley Cultivar Scarlett and a Spanish Landrace.
Carlos P Cantalapiedra, María J García-Pereira, +3 authors, Bruno Contreras-Moreira.
Front Plant Sci, 2017 May 17; 8. PMID: 28507554    Free PMC article.
The Photorespiratory BOU Gene Mutation Alters Sulfur Assimilation and Its Crosstalk With Carbon and Nitrogen Metabolism in Arabidopsis thaliana.
Sladjana Samuilov, Dominik Brilhaus, +8 authors, Heinz Rennenberg.
Front Plant Sci, 2018 Dec 19; 9. PMID: 30559749    Free PMC article.
Knock-Down of the Phosphoserine Phosphatase Gene Effects Rather N- Than S-Metabolism in Arabidopsis thaliana.
Sladjana Samuilov, Nadine Rademacher, +6 authors, Heinz Rennenberg.
Front Plant Sci, 2019 Jan 09; 9. PMID: 30619403    Free PMC article.
Transcriptional Reprogramming of Rice Cells by Xanthomonas oryzae TALEs.
Stefanie Mücke, Maik Reschke, +7 authors, Jens Boch.
Front Plant Sci, 2019 Mar 13; 10. PMID: 30858855    Free PMC article.
Designing and Engineering Methylorubrum extorquens AM1 for Itaconic Acid Production.
Chee Kent Lim, Juan C Villada, +3 authors, Patrick K H Lee.
Front Microbiol, 2019 May 31; 10. PMID: 31143170    Free PMC article.
Transcriptomic Analysis of Two Thioalkalivibrio Species Under Arsenite Stress Revealed a Potential Candidate Gene for an Alternative Arsenite Oxidation Pathway.
Anne-Catherine Ahn, Lucia Cavalca, +3 authors, Gerard Muyzer.
Front Microbiol, 2019 Jul 25; 10. PMID: 31333619    Free PMC article.
Modeling and analysis of RNA-seq data: a review from a statistical perspective.
Wei Vivian Li, Jingyi Jessica Li.
Quant Biol, 2019 Aug 29; 6(3). PMID: 31456901    Free PMC article.
Neuroprotective activity of ursodeoxycholic acid in CHMP2BIntron5 models of frontotemporal dementia.
Ryan J H West, Chris Ugbode, Laura Fort-Aznar, Sean T Sweeney.
Neurobiol Dis, 2020 Aug 18; 144. PMID: 32801000    Free PMC article.
Pattern regulation in a regenerating jellyfish.
Chiara Sinigaglia, Sophie Peron, +5 authors, Lucas Leclère.
Elife, 2020 Sep 08; 9. PMID: 32894220    Free PMC article.
SARS-CoV-2 transcriptome analysis and molecular cataloguing of immunodominant epitopes for multi-epitope based vaccine design.
Sandeep Kumar Kushwaha, Veerbhan Kesarwani, +2 authors, Shailesh Sharma.
Genomics, 2020 Sep 14; 112(6). PMID: 32920121    Free PMC article.
Ambrisentan, an endothelin receptor type A-selective antagonist, inhibits cancer cell migration, invasion, and metastasis.
Lucy Kappes, Ruba L Amer, +23 authors, Otavio Cabral-Marques.
Sci Rep, 2020 Sep 29; 10(1). PMID: 32985601    Free PMC article.
Regulation of stem/progenitor cell maintenance by BMP5 in prostate homeostasis and cancer initiation.
Mathieu Tremblay, Sophie Viala, +3 authors, Maxime Bouchard.
Elife, 2020 Sep 08; 9. PMID: 32894216    Free PMC article.
Mitochondrial DNA copy number can influence mortality and cardiovascular disease via methylation of nuclear DNA CpGs.
Christina A Castellani, Ryan J Longchamps, +21 authors, Dan E Arking.
Genome Med, 2020 Sep 30; 12(1). PMID: 32988399    Free PMC article.
Excessive Neutrophils and Neutrophil Extracellular Traps in COVID-19.
Jun Wang, Qian Li, +7 authors, Yuanwang Qiu.
Front Immunol, 2020 Oct 06; 11. PMID: 33013872    Free PMC article.
Transcriptional Analyses Identify Genes That Modulate Bovine Macrophage Response to Toxoplasma Infection and Immune Stimulation.
Anton Gossner, Musa A Hassan.
Front Cell Infect Microbiol, 2020 Oct 06; 10. PMID: 33014886    Free PMC article.
Genome-wide effects of the antimicrobial peptide apidaecin on translation termination in bacteria.
Kyle Mangano, Tanja Florin, +6 authors, Nora Vázquez-Laslop.
Elife, 2020 Oct 09; 9. PMID: 33031031    Free PMC article.
Duplication of Symbiotic Lysin Motif Receptors Predates the Evolution of Nitrogen-Fixing Nodule Symbiosis.
Luuk Rutten, Kana Miyata, +9 authors, Rene Geurts.
Plant Physiol, 2020 Jul 17; 184(2). PMID: 32669419    Free PMC article.
The Wheat GENIE3 Network Provides Biologically-Relevant Information in Polyploid Wheat.
Sophie A Harrington, Anna E Backhaus, +2 authors, Cristobal Uauy.
G3 (Bethesda), 2020 Aug 05; 10(10). PMID: 32747342    Free PMC article.
Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression.
Jonathan A Beagan, Elissa D Pastuzyn, +6 authors, Jennifer E Phillips-Cremins.
Nat Neurosci, 2020 May 27; 23(6). PMID: 32451484    Free PMC article.
The Molecular Effects of a High Fat Diet on Endometrial Tumour Biology.
Michael Wilkinson, Piriyah Sinclair, +11 authors, Donal J Brennan.
Life (Basel), 2020 Sep 16; 10(9). PMID: 32927694    Free PMC article.
Expression of the Neuronal tRNA n-Tr20 Regulates Synaptic Transmission and Seizure Susceptibility.
Mridu Kapur, Archan Ganguly, +4 authors, Susan L Ackerman.
Neuron, 2020 Aug 28; 108(1). PMID: 32853550    Free PMC article.
Early pathogenesis of cystic fibrosis gallbladder disease in a porcine model.
Keyan Zarei, Mallory R Stroik, +8 authors, David A Stoltz.
Lab Invest, 2020 Jul 29; 100(11). PMID: 32719544    Free PMC article.
Transcription factor expression defines subclasses of developing projection neurons highly similar to single-cell RNA-seq subtypes.
Whitney E Heavner, Shaoyi Ji, +6 authors, Susan K McConnell.
Proc Natl Acad Sci U S A, 2020 Sep 20; 117(40). PMID: 32948690    Free PMC article.
Differential Modulation of Mouse Heart Gene Expression by Infection With Two Trypanosoma cruzi Strains: A Transcriptome Analysis.
Tiago Bruno Rezende de Castro, Maria Cecilia Campos Canesso, +9 authors, Gloria Regina Franco.
Front Genet, 2020 Oct 23; 11. PMID: 33088283    Free PMC article.
Transcriptomic Analysis Revealed an Emerging Role of Alternative Splicing in Embryonal Tumor with Multilayered Rosettes.
Dina Hesham, Shahenda El-Naggar.
Genes (Basel), 2020 Sep 26; 11(9). PMID: 32971786    Free PMC article.
Conserved and Opposite Transcriptome Patterns during Germination in Hordeum vulgare and Arabidopsis thaliana.
Yanqiao Zhu, Oliver Berkowitz, +5 authors, James Whelan.
Int J Mol Sci, 2020 Oct 11; 21(19). PMID: 33036486    Free PMC article.
Developmentally controlled changes during Arabidopsis leaf development indicate causes for loss of stress tolerance with age.
Aakansha Kanojia, Saurabh Gupta, +4 authors, Paul P Dijkwel.
J Exp Bot, 2020 Jul 29; 71(20). PMID: 32720687    Free PMC article.
Thapsigargin at Non-Cytotoxic Levels Induces a Potent Host Antiviral Response that Blocks Influenza A Virus Replication.
Leah V Goulding, Jiayun Yang, +7 authors, Kin-Chow Chang.
Viruses, 2020 Oct 01; 12(10). PMID: 32992478    Free PMC article.
A Novel Gene Underlies Bleomycin-Response Variation in Caenorhabditis elegans.
Shannon C Brady, Stefan Zdraljevic, +5 authors, Erik C Andersen.
Genetics, 2019 Jun 07; 212(4). PMID: 31171655    Free PMC article.
Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways.
Lynn Yi, Harold Pimentel, Lior Pachter.
PLoS One, 2017 Apr 28; 12(4). PMID: 28448519    Free PMC article.
seekCRIT: Detecting and characterizing differentially expressed circular RNAs using high-throughput sequencing data.
Mohamed Chaabane, Kalina Andreeva, +3 authors, Nigel G F Cooper.
PLoS Comput Biol, 2020 Oct 21; 16(10). PMID: 33079938    Free PMC article.
Viral Perturbation of Alternative Splicing of a Host Transcript Benefits Infection.
Kaitong Du, Tong Jiang, +6 authors, Tao Zhou.
Plant Physiol, 2020 Sep 23; 184(3). PMID: 32958561    Free PMC article.
Correcting for experiment-specific variability in expression compendia can remove underlying signals.
Alexandra J Lee, YoSon Park, +2 authors, Casey S Greene.
Gigascience, 2020 Nov 04; 9(11). PMID: 33140829    Free PMC article.
Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection.
Chun Jimmie Ye, Jenny Chen, +19 authors, Nir Hacohen.
Genome Res, 2018 Nov 18; 28(12). PMID: 30446528    Free PMC article.
Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm.
Stephen R Doyle, Alan Tracey, +25 authors, James A Cotton.
Commun Biol, 2020 Nov 11; 3(1). PMID: 33168940    Free PMC article.
Toxicant-Induced Metabolic Alterations in Lipid and Amino Acid Pathways Are Predictive of Acute Liver Toxicity in Rats.
Venkat R Pannala, Shanea K Estes, +8 authors, Anders Wallqvist.
Int J Mol Sci, 2020 Nov 08; 21(21). PMID: 33158035    Free PMC article.
GTPBP1 resolves paused ribosomes to maintain neuronal homeostasis.
Markus Terrey, Scott I Adamson, +4 authors, Susan L Ackerman.
Elife, 2020 Nov 14; 9. PMID: 33186095    Free PMC article.
CD103+CD8+ TRM Cells Accumulate in Tumors of Anti-PD-1-Responder Lung Cancer Patients and Are Tumor-Reactive Lymphocytes Enriched with Tc17.
Stéphanie Corgnac, Ines Malenica, +19 authors, Fathia Mami-Chouaib.
Cell Rep Med, 2020 Nov 19; 1(7). PMID: 33205076    Free PMC article.
T Cell Receptor Is Required for Differentiation, but Not Maintenance, of Intestinal CD4+ Intraepithelial Lymphocytes.
Angelina M Bilate, Mariya London, +6 authors, Daniel Mucida.
Immunity, 2020 Oct 07; 53(5). PMID: 33022229    Free PMC article.
Repression of interrupted and intact rDNA by the SUMO pathway in Drosophila melanogaster.
Yicheng Luo, Elena Fefelova, +2 authors, Alexei A Aravin.
Elife, 2020 Nov 10; 9. PMID: 33164748    Free PMC article.
The Genetic Architecture of Carbon Tetrachloride-Induced Liver Fibrosis in Mice.
Iina Tuominen, Brie K Fuqua, +20 authors, Simon W Beaven.
Cell Mol Gastroenterol Hepatol, 2020 Sep 01; 11(1). PMID: 32866618    Free PMC article.
Transcriptional rewiring over evolutionary timescales changes quantitative and qualitative properties of gene expression.
Chiraj K Dalal, Ignacio A Zuleta, +3 authors, Alexander D Johnson.
Elife, 2016 Oct 18; 5. PMID: 27614020    Free PMC article.
Condition-specific RNA editing in the coral symbiont Symbiodinium microadriaticum.
Yi Jin Liew, Yong Li, +2 authors, Manuel Aranda.
PLoS Genet, 2017 Mar 01; 13(2). PMID: 28245292    Free PMC article.
Fate-restricted retinal progenitor cells adopt a molecular profile and spatial position distinct from multipotent progenitor cells.
Diego F Buenaventura, Miruna G Ghinia-Tegla, Mark M Emerson.
Dev Biol, 2018 Aug 27; 443(1). PMID: 30145104    Free PMC article.
Role of SUMOylation in differential ERα transcriptional repression by tamoxifen and fulvestrant in breast cancer cells.
Tatiana Traboulsi, Mohamed El Ezzy, +2 authors, Sylvie Mader.
Oncogene, 2018 Sep 08; 38(7). PMID: 30190545    Free PMC article.
Rapid identification of a candidate nicosulfuron sensitivity gene (Nss) in maize (Zea mays L.) via combining bulked segregant analysis and RNA-seq.
Xiaomin Liu, Bo Bi, +7 authors, J Scott McElroy.
Theor Appl Genet, 2019 Jan 18; 132(5). PMID: 30652203
Functional and transcriptomic characterization of carboplatin-resistant A2780 ovarian cancer cell line.
Tamara Viscarra, Kurt Buchegger, +8 authors, Priscilla Brebi.
Biol Res, 2019 Mar 22; 52(1). PMID: 30894224    Free PMC article.
Gene expression profiles at different stages for formation of pearl sac and pearl in the pearl oyster Pinctada fucata.
Mariom, Saori Take, +6 authors, Shigeharu Kinoshita.
BMC Genomics, 2019 Mar 27; 20(1). PMID: 30909870    Free PMC article.
Use of near-isogenic lines to precisely map and validate a major QTL for grain weight on chromosome 4AL in bread wheat (Triticum aestivum L.).
Panfeng Guan, Na Di, +13 authors, Huiru Peng.
Theor Appl Genet, 2019 May 24; 132(8). PMID: 31119311
Transcriptome sequencing of Festulolium accessions under salt stress.
A Teshome, S L Byrne, +4 authors, S Barth.
BMC Res Notes, 2019 Jun 04; 12(1). PMID: 31151479    Free PMC article.
Differential analysis of combinatorial protein complexes with CompleXChange.
Thorsten Will, Volkhard Helms.
BMC Bioinformatics, 2019 Jun 05; 20(1). PMID: 31159772    Free PMC article.
Azithromycin induces epidermal differentiation and multivesicular bodies in airway epithelia.
Ari Jon Arason, Jon Petur Joelsson, +14 authors, Jennifer A Kricker.
Respir Res, 2019 Jun 27; 20(1). PMID: 31234850    Free PMC article.
Mapping non-host resistance to the stem rust pathogen in an interspecific barberry hybrid.
Radhika Bartaula, Arthur T O Melo, +2 authors, Iago Hale.
BMC Plant Biol, 2019 Jul 18; 19(1). PMID: 31311507    Free PMC article.
Uncovering the mouse olfactory long non-coding transcriptome with a novel machine-learning model.
Antonio P Camargo, Thiago S Nakahara, +7 authors, Fabio Papes.
DNA Res, 2019 Jul 20; 26(4). PMID: 31321403    Free PMC article.
bayNorm: Bayesian gene expression recovery, imputation and normalization for single-cell RNA-sequencing data.
Wenhao Tang, François Bertaux, +4 authors, Vahid Shahrezaei.
Bioinformatics, 2019 Oct 05; 36(4). PMID: 31584606    Free PMC article.
CRISPR-GEMM Pooled Mutagenic Screening Identifies KMT2D as a Major Modulator of Immune Checkpoint Blockade.
Guangchuan Wang, Ryan D Chow, +16 authors, Sidi Chen.
Cancer Discov, 2020 Sep 06; 10(12). PMID: 32887696    Free PMC article.
Small molecule recognition of disease-relevant RNA structures.
Samantha M Meyer, Christopher C Williams, +5 authors, Matthew D Disney.
Chem Soc Rev, 2020 Sep 26; 49(19). PMID: 32975549    Free PMC article.
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The Transcription Factor EIL1 Participates in the Regulation of Sulfur-Deficiency Response.
Christof Dietzen, Anna Koprivova, +4 authors, Stanislav Kopriva.
Plant Physiol, 2020 Oct 17; 184(4). PMID: 33060195    Free PMC article.
A stem cell reporter based platform to identify and target drug resistant stem cells in myeloid leukemia.
Kyle Spinler, Jeevisha Bajaj, +16 authors, Tannishtha Reya.
Nat Commun, 2020 Nov 28; 11(1). PMID: 33243988    Free PMC article.
SAMMY-seq reveals early alteration of heterochromatin and deregulation of bivalent genes in Hutchinson-Gilford Progeria Syndrome.
Endre Sebestyén, Fabrizia Marullo, +9 authors, Chiara Lanzuolo.
Nat Commun, 2020 Dec 10; 11(1). PMID: 33293552    Free PMC article.
Development of a human primary gut-on-a-chip to model inflammatory processes.
Claudia Beaurivage, Auste Kanapeckaite, +3 authors, Richard A J Janssen.
Sci Rep, 2020 Dec 10; 10(1). PMID: 33293676    Free PMC article.
Hypoxic response regulators RHY-1 and EGL-9/PHD promote longevity through a VHL-1-independent transcriptional response.
Joseph C P Kruempel, Hillary A Miller, +5 authors, Scott F Leiser.
Geroscience, 2020 May 14; 42(6). PMID: 32399915    Free PMC article.
Coexpression Clusters and Allele-Specific Expression in Metabolism-Based Herbicide Resistance.
Darci A Giacomini, Eric L Patterson, +3 authors, Patrick J Tranel.
Genome Biol Evol, 2020 Sep 12; 12(12). PMID: 32915951    Free PMC article.
Regulation of Collective Metastasis by Nanolumenal Signaling.
Emma D Wrenn, Ami Yamamoto, +8 authors, Kevin J Cheung.
Cell, 2020 Oct 03; 183(2). PMID: 33007268    Free PMC article.
Impact of constitutional TET2 haploinsufficiency on molecular and clinical phenotype in humans.
Eevi Kaasinen, Outi Kuismin, +32 authors, Lauri A Aaltonen.
Nat Commun, 2019 Mar 21; 10(1). PMID: 30890702    Free PMC article.
Long non-coding and coding RNA profiling using strand-specific RNA-seq in human hypertrophic cardiomyopathy.
Xuanyu Liu, Yi Ma, +9 authors, Zhou Zhou.
Sci Data, 2019 Jun 15; 6(1). PMID: 31197155    Free PMC article.
Concurrent Mutations in STK11 and KEAP1 Promote Ferroptosis Protection and SCD1 Dependence in Lung Cancer.
Corrin A Wohlhieter, Allison L Richards, +16 authors, Charles M Rudin.
Cell Rep, 2020 Dec 03; 33(9). PMID: 33264619    Free PMC article.
Neoantigen prediction in human breast cancer using RNA sequencing data.
Sachie Hashimoto, Emiko Noguchi, +4 authors, Hisato Hara.
Cancer Sci, 2020 Nov 07; 112(1). PMID: 33155341    Free PMC article.
Molecular Bases of Fruit Quality in Prunus Species: An Integrated Genomic, Transcriptomic, and Metabolic Review with a Breeding Perspective.
Beatriz E García-Gómez, Juan A Salazar, +4 authors, Pedro Martínez-Gómez.
Int J Mol Sci, 2021 Jan 06; 22(1). PMID: 33396946    Free PMC article.
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Chromatin loop anchors contain core structural components of the gene expression machinery in maize.
Stéphane Deschamps, John A Crow, +5 authors, Gregory D May.
BMC Genomics, 2021 Jan 08; 22(1). PMID: 33407087    Free PMC article.
Dysfunction in nonsense-mediated decay, protein homeostasis, mitochondrial function, and brain connectivity in ALS-FUS mice with cognitive deficits.
Wan Yun Ho, Ira Agrawal, +12 authors, Shuo-Chien Ling.
Acta Neuropathol Commun, 2021 Jan 08; 9(1). PMID: 33407930    Free PMC article.
The p53-induced RNA-binding protein ZMAT3 is a splicing regulator that inhibits the splicing of oncogenic CD44 variants in colorectal carcinoma.
Bruna R Muys, Dimitrios G Anastasakis, +9 authors, Markus Hafner.
Genes Dev, 2020 Dec 19; 35(1-2). PMID: 33334821    Free PMC article.
RNA-Seq identifies genes whose proteins are upregulated during syncytia development in murine C2C12 myoblasts and human BeWo trophoblasts.
Christopher Azar, Mark C Valentine, +4 authors, Alan L Schwartz.
Physiol Rep, 2021 Jan 07; 9(1). PMID: 33403800    Free PMC article.
Bacterial chemolithoautotrophy via manganese oxidation.
Hang Yu, Jared R Leadbetter.
Nature, 2020 Jul 17; 583(7816). PMID: 32669693    Free PMC article.
Quantitative trait loci and transcriptome signatures associated with avian heritable resistance to Campylobacter.
Androniki Psifidi, Andreas Kranis, +14 authors, Mark P Stevens.
Sci Rep, 2021 Jan 14; 11(1). PMID: 33436657    Free PMC article.
Longitudinal saliva omics responses to immune perturbation: a case study.
George I Mias, Vikas Vikram Singh, +6 authors, Jin He.
Sci Rep, 2021 Jan 14; 11(1). PMID: 33436912    Free PMC article.
Characteristics of monolayer formation in vitro by the chytrid Batrachochytrium dendrobatidis.
Shalika Silva, Lisa Matz, Moamen M Elmassry, Michael J San Francisco.
Biofilm, 2019 Oct 31; 1. PMID: 33447796    Free PMC article.
Identification and genetic diversity analysis of a male-sterile gene (MS1) in Japanese cedar (Cryptomeria japonica D. Don).
Yoichi Hasegawa, Saneyoshi Ueno, +11 authors, Yoshinari Moriguchi.
Sci Rep, 2021 Jan 17; 11(1). PMID: 33452328    Free PMC article.
Genome-wide landscape of RNA-binding protein target site dysregulation reveals a major impact on psychiatric disorder risk.
Christopher Y Park, Jian Zhou, +4 authors, Olga G Troyanskaya.
Nat Genet, 2021 Jan 20; 53(2). PMID: 33462483    Free PMC article.
Chemosensory Neurons Modulate the Response to Oomycete Recognition in Caenorhabditis elegans.
Michael K Fasseas, Manish Grover, +4 authors, Michalis Barkoulas.
Cell Rep, 2021 Jan 14; 34(2). PMID: 33440164    Free PMC article.
A mixed community of skin microbiome representatives influences cutaneous processes more than individual members.
Kristin H Loomis, Susan K Wu, +4 authors, David K Karig.
Microbiome, 2021 Jan 24; 9(1). PMID: 33482907    Free PMC article.
Arabidopsis bZIP18 and bZIP52 Accumulate in Nuclei Following Heat Stress where They Regulate the Expression of a Similar Set of Genes.
Anna J Wiese, Lenka Steinbachová, +8 authors, David Honys.
Int J Mol Sci, 2021 Jan 13; 22(2). PMID: 33430325    Free PMC article.
Nonstructural Protein 1 of SARS-CoV-2 Is a Potent Pathogenicity Factor Redirecting Host Protein Synthesis Machinery toward Viral RNA.
Shuai Yuan, Lei Peng, +8 authors, Yong Xiong.
Mol Cell, 2020 Nov 15; 80(6). PMID: 33188728    Free PMC article.
Altered offspring neurodevelopment in an arginine vasopressin preeclampsia model.
Serena Banu Gumusoglu, Akanksha Sri Satya Chilukuri, +7 authors, Hanna Elizabeth Stevens.
Transl Psychiatry, 2021 Jan 30; 11(1). PMID: 33510137    Free PMC article.
H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions.
Yichao Cai, Ying Zhang, +10 authors, Melissa Jane Fullwood.
Nat Commun, 2021 Jan 31; 12(1). PMID: 33514712    Free PMC article.
CLAVATA Signaling Ensures Reproductive Development in Plants across Thermal Environments.
Daniel S Jones, Amala John, Kylie R VanDerMolen, Zachary L Nimchuk.
Curr Biol, 2020 Nov 07; 31(1). PMID: 33157018    Free PMC article.
Whole-Genome Transcriptome Analyses of Native Symbionts Reveal Host Coral Genomic Novelties for Establishing Coral-Algae Symbioses.
Yuki Yoshioka, Hiroshi Yamashita, +6 authors, Chuya Shinzato.
Genome Biol Evol, 2020 Nov 14; 13(1). PMID: 33185681    Free PMC article.
MITF reprograms the extracellular matrix and focal adhesion in melanoma.
Ramile Dilshat, Valerie Fock, +18 authors, Eirikur Steingrimsson.
Elife, 2021 Jan 14; 10. PMID: 33438577    Free PMC article.
Loss of Cnot6l Impairs Inosine RNA Modifications in Mouse Oocytes.
Pavla Brachova, Nehemiah S Alvarez, Lane K Christenson.
Int J Mol Sci, 2021 Feb 04; 22(3). PMID: 33530472    Free PMC article.
DNA damage triggers reprogramming of differentiated cells into stem cells in Physcomitrella.
Nan Gu, Yosuke Tamada, +7 authors, Mitsuyasu Hasebe.
Nat Plants, 2020 Aug 19; 6(9). PMID: 32807952
Bayesian correlation is a robust gene similarity measure for single-cell RNA-seq data.
Daniel Sanchez-Taltavull, Theodore J Perkins, +5 authors, Guido Beldi.
NAR Genom Bioinform, 2021 Feb 13; 2(1). PMID: 33575552    Free PMC article.
Tissue-autonomous immune response regulates stress signaling during hypertrophy.
Robert Krautz, Dilan Khalili, Ulrich Theopold.
Elife, 2020 Dec 31; 9. PMID: 33377870    Free PMC article.
Modified Significance Analysis of Microarrays in Heterogeneous Diseases.
I-Shiang Tzeng.
J Pers Med, 2021 Jan 28; 11(2). PMID: 33498359    Free PMC article.
TOXPANEL: A Gene-Set Analysis Tool to Assess Liver and Kidney Injuries.
Patric Schyman, Zhen Xu, Valmik Desai, Anders Wallqvist.
Front Pharmacol, 2021 Feb 27; 12. PMID: 33633572    Free PMC article.
Transcriptome profiling of Lymnaea stagnalis (Gastropoda) for ecoimmunological research.
Otto Seppälä, Jean-Claude Walser, +3 authors, Coen M Adema.
BMC Genomics, 2021 Mar 03; 22(1). PMID: 33648459    Free PMC article.
A coffee berry borer (Hypothenemus hampei) genome assembly reveals a reduced chemosensory receptor gene repertoire and male-specific genome sequences.
Lucio Navarro-Escalante, Erick M Hernandez-Hernandez, +9 authors, Pablo Benavides.
Sci Rep, 2021 Mar 03; 11(1). PMID: 33649370    Free PMC article.
Stepwise chromatin and transcriptional acquisition of an intraepithelial lymphocyte program.
Mariya London, Angelina M Bilate, +2 authors, Daniel Mucida.
Nat Immunol, 2021 Mar 10; 22(4). PMID: 33686285    Free PMC article.
Proteolysis-targeting chimera against BCL-XL destroys tumor-infiltrating regulatory T cells.
Ryan Kolb, Umasankar De, +16 authors, Weizhou Zhang.
Nat Commun, 2021 Feb 26; 12(1). PMID: 33627663    Free PMC article.
Construction of a reference transcriptome for the analysis of male sterility in sugi (Cryptomeria japonica D. Don) focusing on MALE STERILITY 1 (MS1).
Fu-Jin Wei, Saneyoshi Ueno, +7 authors, Yoshinari Moriguchi.
PLoS One, 2021 Feb 26; 16(2). PMID: 33630910    Free PMC article.
Chromosome-Scale Genome Assemblies of Aphids Reveal Extensively Rearranged Autosomes and Long-Term Conservation of the X Chromosome.
Thomas C Mathers, Roland H M Wouters, +3 authors, Saskia A Hogenhout.
Mol Biol Evol, 2020 Sep 24; 38(3). PMID: 32966576    Free PMC article.
A broadly neutralizing monoclonal antibody induces broad protection against heterogeneous PRRSV strains in piglets.
Zhigang Zhang, Tianshu Zhai, +9 authors, Chunyan Wu.
Vet Res, 2021 Mar 18; 52(1). PMID: 33726857    Free PMC article.
DeepIsoFun: a deep domain adaptation approach to predict isoform functions.
Dipan Shaw, Hao Chen, Tao Jiang.
Bioinformatics, 2018 Dec 12; 35(15). PMID: 30535380    Free PMC article.
Cysteinyl-specialized proresolving mediators link resolution of infectious inflammation and tissue regeneration via TRAF3 activation.
Nan Chiang, Xavier de la Rosa, +3 authors, Charles N Serhan.
Proc Natl Acad Sci U S A, 2021 Mar 03; 118(10). PMID: 33649212    Free PMC article.
Targeting immunosuppressive macrophages overcomes PARP inhibitor resistance in BRCA1-associated triple-negative breast cancer.
Anita K Mehta, Emily M Cheney, +25 authors, Jennifer L Guerriero.
Nat Cancer, 2021 Mar 20; 2(1). PMID: 33738458    Free PMC article.
Introducing the ArsR-Regulated Arsenic Stimulon.
Rachel Rawle, Tara C Saley, +4 authors, Timothy R McDermott.
Front Microbiol, 2021 Mar 23; 12. PMID: 33746923    Free PMC article.
Combined change of behavioral traits for domestication and gene-networks in mice selectively bred for active tameness.
Yuki Matsumoto, Hiromichi Nagayama, +3 authors, Tsuyoshi Koide.
Genes Brain Behav, 2020 Dec 15; 20(3). PMID: 33314580    Free PMC article.
Genome-Scale Model-Based Identification of Metabolite Indicators for Early Detection of Kidney Toxicity.
Venkat R Pannala, Kalyan C Vinnakota, +9 authors, Anders Wallqvist.
Toxicol Sci, 2019 Nov 14; 173(2). PMID: 31722432    Free PMC article.
Enhanced Glycolysis Is Required for Antileishmanial Functions of Neutrophils Upon Infection With Leishmania donovani.
Mareike Ohms, Carolina Ferreira, +4 authors, Tamás Laskay.
Front Immunol, 2021 Apr 06; 12. PMID: 33815385    Free PMC article.
Thiazoline-related innate fear stimuli orchestrate hypothermia and anti-hypoxia via sensory TRPA1 activation.
Tomohiko Matsuo, Tomoko Isosaka, +17 authors, Ko Kobayakawa.
Nat Commun, 2021 Apr 08; 12(1). PMID: 33824316    Free PMC article.
Allelic Expression Imbalance Analysis Identified YAP1 Amplification in p53- Dependent Osteosarcoma.
Guanglin Niu, Agnieszka Bak, +5 authors, Krzysztof Flisikowski.
Cancers (Basel), 2021 Apr 04; 13(6). PMID: 33803512    Free PMC article.
Altered RNA Splicing by Mutant p53 Activates Oncogenic RAS Signaling in Pancreatic Cancer.
Luisa F Escobar-Hoyos, Alex Penson, +41 authors, Steven D Leach.
Cancer Cell, 2020 Jun 20; 38(2). PMID: 32559497    Free PMC article.
Statistical Modeling of High Dimensional Counts.
Michael I Love.
Methods Mol Biol, 2021 Apr 10; 2284. PMID: 33835440
A bird-like genome from a frog: Mechanisms of genome size reduction in the ornate burrowing frog, Platyplectrum ornatum.
Sangeet Lamichhaney, Renee Catullo, +3 authors, Tariq Ezaz.
Proc Natl Acad Sci U S A, 2021 Apr 11; 118(11). PMID: 33836564    Free PMC article.
Transcriptome analysis revealed the regulation of gibberellin and the establishment of photosynthetic system promote rapid seed germination and early growth of seedling in pearl millet.
Bingchao Wu, Min Sun, +11 authors, Linkai Huang.
Biotechnol Biofuels, 2021 Apr 13; 14(1). PMID: 33840392    Free PMC article.
Characterizing the genetic basis of copper toxicity in Drosophila reveals a complex pattern of allelic, regulatory, and behavioral variation.
Elizabeth R Everman, Kristen M Cloud-Richardson, Stuart J Macdonald.
Genetics, 2021 Mar 09; 217(1). PMID: 33683361    Free PMC article.
Prey sensing and response in a nematode-trapping fungus is governed by the MAPK pheromone response pathway.
Sheng-An Chen, Hung-Che Lin, Frank C Schroeder, Yen-Ping Hsueh.
Genetics, 2021 Mar 17; 217(2). PMID: 33724405    Free PMC article.
Scrt1, a transcriptional regulator of β-cell proliferation identified by differential chromatin accessibility during islet maturation.
Jonathan Sobel, Claudiane Guay, +6 authors, Romano Regazzi.
Sci Rep, 2021 Apr 24; 11(1). PMID: 33888791    Free PMC article.
Dream: powerful differential expression analysis for repeated measures designs.
Gabriel E Hoffman, Panos Roussos.
Bioinformatics, 2020 Jul 31; 37(2). PMID: 32730587    Free PMC article.
Best practices on the differential expression analysis of multi-species RNA-seq.
Matthew Chung, Vincent M Bruno, +6 authors, Julie C Dunning Hotopp.
Genome Biol, 2021 May 01; 22(1). PMID: 33926528    Free PMC article.
Review.
Defects in translation-dependent quality control pathways lead to convergent molecular and neurodevelopmental pathology.
Markus Terrey, Scott I Adamson, Jeffrey H Chuang, Susan L Ackerman.
Elife, 2021 Apr 27; 10. PMID: 33899734    Free PMC article.
Genomic Imprinting at the Porcine PLAGL1 Locus and the Orthologous Locus in the Human.
Jinsoo Ahn, In-Sul Hwang, +2 authors, Kichoon Lee.
Genes (Basel), 2021 May 01; 12(4). PMID: 33918057    Free PMC article.
Role of epigenetics in unicellular to multicellular transition in Dictyostelium.
Simon Yuan Wang, Elizabeth Ann Pollina, +8 authors, Eric Lieberman Greer.
Genome Biol, 2021 May 06; 22(1). PMID: 33947439    Free PMC article.
Single-nucleotide-level mapping of DNA regulatory elements that control fetal hemoglobin expression.
Li Cheng, Yichao Li, +12 authors, Yong Cheng.
Nat Genet, 2021 May 08; 53(6). PMID: 33958780    Free PMC article.
Molecular and Physiological Adaptations to Low Temperature in Thioalkalivibrio Strains Isolated from Soda Lakes with Different Temperature Regimes.
Anne-Catherine Ahn, Evelien Jongepier, +6 authors, Gerard Muyzer.
mSystems, 2021 Apr 29; 6(2). PMID: 33906913    Free PMC article.
Transcriptional heterogeneity of stemness phenotypes in the ovarian epithelium.
Lauren E Carter, David P Cook, +7 authors, Barbara C Vanderhyden.
Commun Biol, 2021 May 07; 4(1). PMID: 33953351    Free PMC article.
Pan-genomic characterization of high-risk pediatric papillary thyroid carcinoma.
Adam Stenman, Samuel Backman, +4 authors, C Christofer Juhlin.
Endocr Relat Cancer, 2021 Apr 08; 28(5). PMID: 33827048    Free PMC article.
Beta cell adaptation to pregnancy requires prolactin action on both beta and non-beta cells.
Vipul Shrivastava, Megan Lee, +4 authors, Carol Huang.
Sci Rep, 2021 May 16; 11(1). PMID: 33990661    Free PMC article.
Transcriptome Analysis of Seed Weight Plasticity in Brassica napus.
Javier Canales, José Verdejo, +3 authors, Daniel F Calderini.
Int J Mol Sci, 2021 May 01; 22(9). PMID: 33923211    Free PMC article.
Overarching control of autophagy and DNA damage response by CHD6 revealed by modeling a rare human pathology.
Yulia Kargapolova, Rizwan Rehimi, +27 authors, Argyris Papantonis.
Nat Commun, 2021 May 23; 12(1). PMID: 34021162    Free PMC article.
Tuning promoter boundaries improves regulatory motif discovery in nonmodel plants: the peach example.
Najla Ksouri, Jaime A Castro-Mondragón, +3 authors, Yolanda Gogorcena.
Plant Physiol, 2021 Mar 22; 185(3). PMID: 33744946    Free PMC article.
Non-cell autonomous mechanism of Parkinson's disease pathology caused by G2019S LRRK2 mutation in Ashkenazi Jewish patient: Single cell analysis.
Jeffrey Kim, Marcel M Daadi.
Brain Res, 2019 Jul 23; 1722. PMID: 31330122    Free PMC article.
Review.
SON inhibits megakaryocytic differentiation via repressing RUNX1 and the megakaryocytic gene expression program in acute megakaryoblastic leukemia.
Lana Vukadin, Jung-Hyun Kim, +10 authors, Eun-Young Erin Ahn.
Cancer Gene Ther, 2020 Nov 29; 28(9). PMID: 33247227    Free PMC article.
Comparative evaluation of full-length isoform quantification from RNA-Seq.
Dimitra Sarantopoulou, Thomas G Brooks, +3 authors, Gregory R Grant.
BMC Bioinformatics, 2021 May 27; 22(1). PMID: 34034652    Free PMC article.
Review.
Polee: RNA-Seq analysis using approximate likelihood.
Daniel C Jones, Walter L Ruzzo.
NAR Genom Bioinform, 2021 Jun 01; 3(2). PMID: 34056596    Free PMC article.
Long non-coding RNA exploration for mesenchymal stem cell characterisation.
Sébastien Riquier, Marc Mathieu, +6 authors, Thérèse Commes.
BMC Genomics, 2021 Jun 06; 22(1). PMID: 34088266    Free PMC article.
Transcriptome-wide association study uncovers the role of essential genes in anthracycline-induced cardiotoxicity.
Erika N Scott, Galen E B Wright, +8 authors, Colin J D Ross.
NPJ Genom Med, 2021 May 23; 6(1). PMID: 34021165    Free PMC article.
Organ-, sex- and age-dependent patterns of endogenous L1 mRNA expression at a single locus resolution.
Emily C Stow, Tiffany Kaul, +11 authors, Victoria P Belancio.
Nucleic Acids Res, 2021 May 24; 49(10). PMID: 34023901    Free PMC article.
Molecular Competition in G1 Controls When Cells Simultaneously Commit to Terminally Differentiate and Exit the Cell Cycle.
Michael L Zhao, Atefeh Rabiee, +3 authors, Mary N Teruel.
Cell Rep, 2020 Jun 20; 31(11). PMID: 32553172    Free PMC article.
Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis.
Zhi-Qiang Chen, Yanjun Zan, +10 authors, Harry X Wu.
Genome Biol, 2021 Jun 15; 22(1). PMID: 34120648    Free PMC article.
Comprehensive Comparison of RNA-Seq Data of SARS-CoV-2, SARS-CoV and MERS-CoV Infections: Alternative Entry Routes and Innate Immune Responses.
Yingying Cao, Xintian Xu, +4 authors, Daniel Hoffmann.
Front Immunol, 2021 Jun 15; 12. PMID: 34122413    Free PMC article.
Gene dosage compensation of rRNA transcript levels in Arabidopsis thaliana lines with reduced ribosomal gene copy number.
Francesca B Lopez, Antoine Fort, +10 authors, Charles Spillane.
Plant Cell, 2021 Apr 02; 33(4). PMID: 33793816    Free PMC article.
Robustness of differential gene expression analysis of RNA-seq.
A Stupnikov, C E McInerney, +6 authors, D G McArt.
Comput Struct Biotechnol J, 2021 Jul 01; 19. PMID: 34188784    Free PMC article.
Critical COVID-19 is associated with distinct leukocyte phenotypes and transcriptome patterns.
E E Christensen, M J Jørgensen, +13 authors, A M Dyrhol-Riise.
J Intern Med, 2021 Jun 04; 290(3). PMID: 34080738    Free PMC article.
Role of the transcriptional regulator SP140 in resistance to bacterial infections via repression of type I interferons.
Daisy X Ji, Kristen C Witt, +13 authors, Russell E Vance.
Elife, 2021 Jun 22; 10. PMID: 34151776    Free PMC article.
Characterization of microglial transcriptomes in the brain and spinal cord of mice in early and late experimental autoimmune encephalomyelitis using a RiboTag strategy.
Shaona Acharjee, Paul M K Gordon, +4 authors, Quentin J Pittman.
Sci Rep, 2021 Jul 14; 11(1). PMID: 34253764    Free PMC article.
Genetics of white color and iridophoroma in "Lemon Frost" leopard geckos.
Longhua Guo, Joshua Bloom, +8 authors, Leonid Kruglyak.
PLoS Genet, 2021 Jun 25; 17(6). PMID: 34166378    Free PMC article.
Compression of quantification uncertainty for scRNA-seq counts.
Scott Van Buren, Hirak Sarkar, +3 authors, Michael I Love.
Bioinformatics, 2021 Jan 21;. PMID: 33471073    Free PMC article.
Sulfate differentially stimulates but is not respired by diverse anaerobic methanotrophic archaea.
Hang Yu, Connor T Skennerton, +4 authors, Victoria J Orphan.
ISME J, 2021 Jul 22; 16(1). PMID: 34285362    Free PMC article.
Synteny-Based Genome Assembly for 16 Species of Heliconius Butterflies, and an Assessment of Structural Variation across the Genus.
Fernando A Seixas, Nathaniel B Edelman, James Mallet.
Genome Biol Evol, 2021 Apr 02; 13(7). PMID: 33792688    Free PMC article.
Transcriptomic Analysis of Skin Color in Anole Lizards.
Pietro Longo Hollanda de Mello, Paul M Hime, Richard E Glor.
Genome Biol Evol, 2021 May 15; 13(7). PMID: 33988681    Free PMC article.
Embryonic development in the acoel Hofstenia miamia.
Julian O Kimura, Lorenzo Ricci, Mansi Srivastava.
Development, 2021 Jul 02; 148(13). PMID: 34196362    Free PMC article.
NRG4-ErbB4 signaling represses proinflammatory macrophage activity.
Michael A Schumacher, Isabella C Dennis, +6 authors, Mark R Frey.
Am J Physiol Gastrointest Liver Physiol, 2021 Apr 08; 320(6). PMID: 33826403    Free PMC article.
Dynamic landscape of protein occupancy across the Escherichia coli chromosome.
Peter L Freddolino, Haley M Amemiya, Thomas J Goss, Saeed Tavazoie.
PLoS Biol, 2021 Jun 26; 19(6). PMID: 34170902    Free PMC article.
Transcriptomics differentiate two novel bioactive strains of Paenibacillus sp. isolated from the perennial ryegrass seed microbiome.
Tongda Li, Ross Mann, +2 authors, Timothy Sawbridge.
Sci Rep, 2021 Aug 01; 11(1). PMID: 34330961    Free PMC article.
Integrated transcriptomic analysis of human tuberculosis granulomas and a biomimetic model identifies therapeutic targets.
Michaela T Reichmann, Liku B Tezera, +12 authors, Paul Elkington.
J Clin Invest, 2021 Jun 16; 131(15). PMID: 34128839    Free PMC article.
Doxycycline host-directed therapy in human pulmonary tuberculosis.
Qing Hao Miow, Andres F Vallejo, +20 authors, Catherine Wm Ong.
J Clin Invest, 2021 Jun 16; 131(15). PMID: 34128838    Free PMC article.
New Insights From Transcriptomic Data Reveal Differential Effects of CO2 Acidification Stress on Photosynthesis of an Endosymbiotic Dinoflagellate in hospite.
Marcela Herrera, Yi Jin Liew, +5 authors, Manuel Aranda.
Front Microbiol, 2021 Aug 06; 12. PMID: 34349734    Free PMC article.
The Most Common VHL Point Mutation R167Q in Hereditary VHL Disease Interferes with Cell Plasticity Regulation.
Stéphanie Buart, Stéphane Terry, +7 authors, Salem Chouaib.
Cancers (Basel), 2021 Aug 08; 13(15). PMID: 34359798    Free PMC article.
Regeneration in starved planarians depends on TRiC/CCT subunits modulating the unfolded protein response.
Óscar Gutiérrez-Gutiérrez, Daniel A Felix, +6 authors, Cristina González-Estévez.
EMBO Rep, 2021 Jul 01; 22(8). PMID: 34190393    Free PMC article.
Epigenetic rewiring of skeletal muscle enhancers after exercise training supports a role in whole-body function and human health.
Kristine Williams, Germán D Carrasquilla, +8 authors, Romain Barrès.
Mol Metab, 2021 Jul 13; 53. PMID: 34252634    Free PMC article.
Hydroxycarbamide effects on DNA methylation and gene expression in myeloproliferative neoplasms.
Stephania Contreras Castillo, Bertille Montibus, +7 authors, Rebecca J Oakey.
Genome Res, 2021 Jul 11; 31(8). PMID: 34244229    Free PMC article.
Comparative Transcriptomic Analysis of Staphylococcus aureus Associated with Periprosthetic Joint Infection under in Vivo and in Vitro Conditions.
Thao Le Masters, Stephen Johnson, +5 authors, Robin Patel.
J Mol Diagn, 2021 Jun 08; 23(8). PMID: 34098085    Free PMC article.
Transcriptome analysis reveals sexual disparities in gene expression in rat brain microvessels.
Partha K Chandra, Sinisa Cikic, +5 authors, David W Busija.
J Cereb Blood Flow Metab, 2021 Mar 16; 41(9). PMID: 33715494    Free PMC article.
ARMT: An automatic RNA-seq data mining tool based on comprehensive and integrative analysis in cancer research.
Guanda Huang, Haibo Zhang, +4 authors, Hongli Du.
Comput Struct Biotechnol J, 2021 Sep 03; 19. PMID: 34471489    Free PMC article.
The Cell Surface Receptors Ror1/2 Control Cardiac Myofibroblast Differentiation.
Nicholas W Chavkin, Soichi Sano, +13 authors, Kenneth Walsh.
J Am Heart Assoc, 2021 Jun 23; 10(13). PMID: 34155901    Free PMC article.
Production of functional oocytes requires maternally expressed PIWI genes and piRNAs in golden hamsters.
Hidetoshi Hasuwa, Yuka W Iwasaki, +4 authors, Haruhiko Siomi.
Nat Cell Biol, 2021 Sep 08; 23(9). PMID: 34489571
Mammalian retrovirus-like protein PEG10 packages its own mRNA and can be pseudotyped for mRNA delivery.
Michael Segel, Blake Lash, +7 authors, Feng Zhang.
Science, 2021 Aug 21; 373(6557). PMID: 34413232    Free PMC article.
The Transcriptional Landscape and Hub Genes Associated with Physiological Responses to Drought Stress in Pinus tabuliformis.
Tariq Pervaiz, Shuang-Wei Liu, +3 authors, Harry X Wu.
Int J Mol Sci, 2021 Sep 11; 22(17). PMID: 34502511    Free PMC article.
TET2 as a tumor suppressor and therapeutic target in T-cell acute lymphoblastic leukemia.
Maike Bensberg, Olof Rundquist, +6 authors, Colm E Nestor.
Proc Natl Acad Sci U S A, 2021 Aug 21; 118(34). PMID: 34413196    Free PMC article.
A prion accelerates proliferation at the expense of lifespan.
David M Garcia, Edgar A Campbell, +5 authors, Daniel F Jarosz.
Elife, 2021 Sep 22; 10. PMID: 34545808    Free PMC article.
A Trifecta of New Insights into Ovine Footrot for Infection Drivers, Immune Response, and Host-Pathogen Interactions.
Adam M Blanchard, Ceri E Staley, +8 authors, Sabine Tötemeyer.
Infect Immun, 2021 Jul 07; 89(10). PMID: 34227837    Free PMC article.
Cell-type-specific meQTLs extend melanoma GWAS annotation beyond eQTLs and inform melanocyte gene-regulatory mechanisms.
Tongwu Zhang, Jiyeon Choi, +14 authors, Kevin M Brown.
Am J Hum Genet, 2021 Jul 23; 108(9). PMID: 34293285    Free PMC article.
Altered regulation of DPF3, a member of the SWI/SNF complexes, underlies the 14q24 renal cancer susceptibility locus.
Leandro M Colli, Lea Jessop, +14 authors, Stephen J Chanock.
Am J Hum Genet, 2021 Aug 15; 108(9). PMID: 34390653    Free PMC article.
Transcriptome Analyses of Barley Roots Inoculated with Novel Paenibacillus sp. and Erwinia gerundensis Strains Reveal Beneficial Early-Stage Plant-Bacteria Interactions.
Tongda Li, Ross Mann, +2 authors, Timothy Sawbridge.
Plants (Basel), 2021 Sep 29; 10(9). PMID: 34579335    Free PMC article.
Cancer DEIso: An integrative analysis platform for investigating differentially expressed gene-level and isoform-level human cancer markers.
Tzu-Hsien Yang, Yu-Hsuan Chiang, +6 authors, Wei-Sheng Wu.
Comput Struct Biotechnol J, 2021 Oct 01; 19. PMID: 34589189    Free PMC article.
CD177 modulates the function and homeostasis of tumor-infiltrating regulatory T cells.
Myung-Chul Kim, Nicholas Borcherding, +32 authors, Weizhou Zhang.
Nat Commun, 2021 Oct 03; 12(1). PMID: 34599187    Free PMC article.
Endonuclease V Regulates Atherosclerosis Through C-C Motif Chemokine Ligand 2-Mediated Monocyte Infiltration.
Xiang Yi Kong, Camilla Huse, +21 authors, Tuva Børresdatter Dahl.
J Am Heart Assoc, 2021 Jul 15; 10(14). PMID: 34259011    Free PMC article.
Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes.
Grégoire Vernaz, Milan Malinsky, +7 authors, Eric A Miska.
Nat Commun, 2021 Oct 09; 12(1). PMID: 34620871    Free PMC article.
Impact of human gene annotations on RNA-seq differential expression analysis.
Yu Hamaguchi, Chao Zeng, Michiaki Hamada.
BMC Genomics, 2021 Oct 10; 22(1). PMID: 34625021    Free PMC article.
DIOXYGENASE FOR AUXIN OXIDATION 1 catalyzes the oxidation of IAA amino acid conjugates.
Karel Müller, Petre Ivanov Dobrev, +12 authors, Jan Petrášek.
Plant Physiol, 2021 Oct 08; 187(1). PMID: 34618129    Free PMC article.
MADS-box transcription factors MADS11 and DAL1 interact to mediate the vegetative-to-reproductive transition in pine.
Jing-Jing Ma, Xi Chen, +10 authors, Shi-Hui Niu.
Plant Physiol, 2021 Oct 08; 187(1). PMID: 34618133    Free PMC article.
Comparative transcriptomic analysis of races 1, 2, 5 and 6 of Fusarium oxysporum f.sp. pisi in a susceptible pea host identifies differential pathogenicity profiles.
Saidi R Achari, Jacqueline Edwards, +3 authors, Brett A Summerell.
BMC Genomics, 2021 Oct 11; 22(1). PMID: 34627148    Free PMC article.
Genomics and metabolomics of early-stage thioacetamide-induced liver injury: An interspecies study between guinea pig and rat.
Patric Schyman, Richard L Printz, +6 authors, Anders Wallqvist.
Toxicol Appl Pharmacol, 2021 Sep 08; 430. PMID: 34492290    Free PMC article.
Dye-Mediated Photo-Oxidation Biomaterial Fixation: Analysis of Bioinductivity and Mechanical Properties of Bovine Pericardium for Use in Cardiac Surgery.
Simranjit S Pattar, Vishnu Vasanthan, +5 authors, Paul W M Fedak.
Int J Mol Sci, 2021 Oct 14; 22(19). PMID: 34639108    Free PMC article.
miR-124 promotes apoptosis and inhibits the proliferation of vessel endothelial cells through P38/MAPK and PI3K/AKT pathways, making it a potential mechanism of vessel endothelial injury in acute myocardial infarction.
Weimin Ma, Xin Zhang, Yang Liu.
Exp Ther Med, 2021 Oct 16; 22(6). PMID: 34650631    Free PMC article.
Comprehensive molecular characterization of lung tumors implicates AKT and MYC signaling in adenocarcinoma to squamous cell transdifferentiation.
Alvaro Quintanal-Villalonga, Hirokazu Taniguchi, +27 authors, Charles M Rudin.
J Hematol Oncol, 2021 Oct 18; 14(1). PMID: 34656143    Free PMC article.
High expression of SARS-CoV2 viral entry-related proteins in human limbal stem cells.
Yuzuru Sasamoto, Catherine A A Lee, +4 authors, Natasha Y Frank.
Ocul Surf, 2021 Oct 16; 23. PMID: 34653711    Free PMC article.
Kpna6 deficiency causes infertility in male mice by disrupting spermatogenesis.
Na Liu, Fatimunnisa Qadri, +6 authors, Franziska Rother.
Development, 2021 Sep 03; 148(19). PMID: 34473250    Free PMC article.
The Clp1 R140H mutation alters tRNA metabolism and mRNA 3' processing in mouse models of pontocerebellar hypoplasia.
Caitlin E Monaghan, Scott I Adamson, +2 authors, Susan L Ackerman.
Proc Natl Acad Sci U S A, 2021 Sep 23; 118(39). PMID: 34548404    Free PMC article.
RNA-seq profile of African American men with a clinically localized prostate cancer.
Naoya Nagaya, Jeffrey Rosenfeld, Geun Taek Lee, Isaac Yi Kim.
Prostate Int, 2021 Oct 26; 9(3). PMID: 34692584    Free PMC article.
Symbiosis maintenance in the facultative coral, Oculina arbuscula, relies on nitrogen cycling, cell cycle modulation, and immunity.
H E Rivera, S W Davies.
Sci Rep, 2021 Oct 29; 11(1). PMID: 34707162    Free PMC article.
Metabolic switching in pluripotent stem cells reorganizes energy metabolism and subcellular organelles.
Carla O'Reilly, Ji-Hoon Cho, +8 authors, Min-Joon Han.
Exp Cell Res, 2019 Mar 30; 379(1). PMID: 30922922    Free PMC article.
Combining Multiple RNA-Seq Data Analysis Algorithms Using Machine Learning Improves Differential Isoform Expression Analysis.
Alexandros C Dimopoulos, Konstantinos Koukoutegos, Fotis E Psomopoulos, Panagiotis Moulos.
Methods Protoc, 2021 Oct 27; 4(4). PMID: 34698224    Free PMC article.
Infection of C. elegans by Haptoglossa Species Reveals Shared Features in the Host Response to Oomycete Detection.
Manish Grover, Michael K Fasseas, +5 authors, Michalis Barkoulas.
Front Cell Infect Microbiol, 2021 Nov 02; 11. PMID: 34722333    Free PMC article.
Identification of Rac guanine nucleotide exchange factors promoting Lgl1 phosphorylation in glioblastoma.
Sylvie J Lavictoire, Danny Jomaa, +3 authors, Ian A J Lorimer.
J Biol Chem, 2021 Oct 09; 297(5). PMID: 34624316    Free PMC article.
Metacyclogenesis defects and gene expression hallmarks of histone deacetylase 4-deficient Trypanosoma cruzi cells.
Gisele Fernanda Assine Picchi-Constante, Eloise Pavão Guerra-Slompo, +8 authors, Nilson Ivo Tonin Zanchin.
Sci Rep, 2021 Nov 06; 11(1). PMID: 34737385    Free PMC article.
Genome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency.
Jeffrey R Haswell, Kaia Mattioli, +7 authors, Frank J Slack.
PLoS One, 2021 Nov 04; 16(11). PMID: 34731163    Free PMC article.
Stem cell-derived neurons reflect features of protein networks, neuropathology, and cognitive outcome of their aged human donors.
Valentina N Lagomarsino, Richard V Pearse, +32 authors, Tracy L Young-Pearse.
Neuron, 2021 Sep 03; 109(21). PMID: 34473944    Free PMC article.
Benchmarking association analyses of continuous exposures with RNA-seq in observational studies.
Tamar Sofer, Nuzulul Kurniansyah, +10 authors, Kent D Taylor.
Brief Bioinform, 2021 May 21; 22(6). PMID: 34015820    Free PMC article.
RBFOX splicing factors contribute to a broad but selective recapitulation of peripheral tissue splicing patterns in the thymus.
Kathrin Jansen, Noriko Shikama-Dorn, +5 authors, Stephen N Sansom.
Genome Res, 2021 Oct 16; 31(11). PMID: 34649931    Free PMC article.
3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists.
Wenbin Guo, Nikoleta A Tzioutziou, +5 authors, Runxuan Zhang.
RNA Biol, 2020 Dec 22; 18(11). PMID: 33345702    Free PMC article.
Gene Expression Signature Associated with Clinical Outcome in ALK-Positive Anaplastic Large Cell Lymphoma.
Camille Daugrois, Chloé Bessiere, +8 authors, Laurence Lamant.
Cancers (Basel), 2021 Nov 14; 13(21). PMID: 34771686    Free PMC article.
Adaptations in Hippo-Yap signaling and myofibroblast fate underlie scar-free ear appendage wound healing in spiny mice.
Chris M Brewer, Branden R Nelson, +9 authors, Mark W Majesky.
Dev Cell, 2021 Oct 06; 56(19). PMID: 34610329    Free PMC article.
Transcriptomic dataset for Sardina pilchardus: Assembly, annotation, and expression of nine tissues.
Jorge Langa, Martin Huret, +2 authors, Andone Estonba.
Data Brief, 2021 Dec 02; 39. PMID: 34849383    Free PMC article.
Cell division- and DNA replication-free reprogramming of somatic nuclei for embryonic transcription.
Junko Tomikawa, Christopher A Penfold, +5 authors, Kei Miyamoto.
iScience, 2021 Dec 02; 24(11). PMID: 34849463    Free PMC article.
Flimma: a federated and privacy-aware tool for differential gene expression analysis.
Olga Zolotareva, Reza Nasirigerdeh, +12 authors, Jan Baumbach.
Genome Biol, 2021 Dec 16; 22(1). PMID: 34906207    Free PMC article.
The MathIOmica Toolbox: General Analysis Utilities for Dynamic Omics Datasets.
George I Mias, Minzhang Zheng.
Curr Protoc Bioinformatics, 2019 Dec 19; 69(1). PMID: 31851777    Free PMC article.
Ion Channel and Ubiquitin Differential Expression during Erythromycin-Induced Anhidrosis in Foals.
Laura Patterson Rosa, Martha F Mallicote, Robert J MacKay, Samantha A Brooks.
Animals (Basel), 2021 Dec 25; 11(12). PMID: 34944156    Free PMC article.
Comparative Genomics, Evolution, and Drought-Induced Expression of Dehydrin Genes in Model Brachypodium Grasses.
Maria Angeles Decena, Sergio Gálvez-Rojas, +5 authors, Pilar Catalán.
Plants (Basel), 2021 Dec 29; 10(12). PMID: 34961135    Free PMC article.
β-catenin links cell seeding density to global gene expression during mouse embryonic stem cell differentiation.
Lucy LeBlanc, Mijeong Kim, +3 authors, Jonghwan Kim.
iScience, 2022 Jan 04; 25(1). PMID: 34977504    Free PMC article.
Genome evolution drives transcriptomic and phenotypic adaptation in Pseudomonas aeruginosa during 20 years of infection.
Samuel J T Wardell, Jeff Gauthier, +4 authors, Iain L Lamont.
Microb Genom, 2021 Nov 27; 7(11). PMID: 34826267    Free PMC article.
Transcriptomic and Physiological Response of Durum Wheat Grain to Short-Term Heat Stress during Early Grain Filling.
Anita Arenas-M, Francisca M Castillo, +2 authors, Daniel F Calderini.
Plants (Basel), 2022 Jan 12; 11(1). PMID: 35009063    Free PMC article.
CyVerse for Reproducible Research: RNA-Seq Analysis.
Jason Williams.
Methods Mol Biol, 2022 Jan 18; 2443. PMID: 35037200
Loss of major nutrient sensing and signaling pathways suppresses starvation lethality in electron transport chain mutants.
Alisha G Lewis, Robert Caldwell, +7 authors, Patrick A Gibney.
Mol Biol Cell, 2021 Oct 21; 32(22). PMID: 34668730    Free PMC article.
METTL3 Regulates Liver Homeostasis, Hepatocyte Ploidy, and Circadian Rhythm-Controlled Gene Expression in Mice.
Juan M Barajas, Cho-Hao Lin, +10 authors, Kalpana Ghoshal.
Am J Pathol, 2021 Oct 03; 192(1). PMID: 34599880    Free PMC article.
NetSeekR: a network analysis pipeline for RNA-Seq time series data.
Himangi Srivastava, Drew Ferrell, George V Popescu.
BMC Bioinformatics, 2022 Jan 30; 23(1). PMID: 35090393    Free PMC article.
Modern Approaches for Transcriptome Analyses in Plants.
Diego Mauricio Riaño-Pachón, Hector Fabio Espitia-Navarro, John Jaime Riascos, Gabriel Rodrigues Alves Margarido.
Adv Exp Med Biol, 2022 Feb 04; 1346. PMID: 35113394
Rlf-Mycl Gene Fusion Drives Tumorigenesis and Metastasis in a Mouse Model of Small Cell Lung Cancer.
Metamia Ciampricotti, Triantafyllia Karakousi, +22 authors, Charles M Rudin.
Cancer Discov, 2021 Aug 05; 11(12). PMID: 34344693    Free PMC article.
Inhibition of XPO1 Sensitizes Small Cell Lung Cancer to First- and Second-Line Chemotherapy.
Alvaro Quintanal-Villalonga, Hirokazu Taniguchi, +23 authors, Charles M Rudin.
Cancer Res, 2021 Nov 25; 82(3). PMID: 34815254    Free PMC article.
Crohn's disease therapeutic dietary intervention (CD-TDI): study protocol for a randomised controlled trial.
Maitreyi Raman, Christopher Ma, +12 authors, Subrata Ghosh.
BMJ Open Gastroenterol, 2022 Jan 21; 9(1). PMID: 35046093    Free PMC article.
Cross-species transcriptomic analyses reveals common and opposite responses in Arabidopsis, rice and barley following oxidative stress and hormone treatment.
Andreas Hartmann, Oliver Berkowitz, James Whelan, Reena Narsai.
BMC Plant Biol, 2022 Feb 06; 22(1). PMID: 35120438    Free PMC article.
Transcriptomic Landscape of Herbivore Oviposition in Arabidopsis: A Systematic Review.
Dairon Ojeda-Martinez, Isabel Diaz, M Estrella Santamaria.
Front Plant Sci, 2022 Feb 08; 12. PMID: 35126411    Free PMC article.
Systematic Review.
Single-cell RNA sequencing identifies an Il1rn+/Trem1+ macrophage subpopulation as a cellular target for mitigating the progression of thoracic aortic aneurysm and dissection.
Xuanyu Liu, Wen Chen, +5 authors, Zhou Zhou.
Cell Discov, 2022 Feb 09; 8(1). PMID: 35132073    Free PMC article.
Superoxide Initiates the Hyphal Differentiation to Microsclerotia Formation of Macrophomina phaseolina.
Hsien-Hao Liu, Cheng-Chun Huang, +2 authors, Hao-Xun Chang.
Microbiol Spectr, 2022 Jan 27; 10(1). PMID: 35080446    Free PMC article.
Arabidopsis TBP-ASSOCIATED FACTOR 12 ortholog NOBIRO6 controls root elongation with unfolded protein response cofactor activity.
June-Sik Kim, Yuki Sakamoto, +5 authors, Kazuo Shinozaki.
Proc Natl Acad Sci U S A, 2022 Feb 05; 119(6). PMID: 35115407    Free PMC article.
Transcriptomes across fertilization and seed development in the water lily Nymphaea thermarum (Nymphaeales): evidence for epigenetic patterning during reproduction.
Rebecca A Povilus, William E Friedman.
Plant Reprod, 2022 Feb 21;. PMID: 35184212
Gut microbial trimethylamine is elevated in alcohol-associated hepatitis and contributes to ethanol-induced liver injury in mice.
Robert N Helsley, Tatsunori Miyata, +33 authors, Jonathan Mark Brown.
Elife, 2022 Jan 28; 11. PMID: 35084335    Free PMC article.
Induction of APOBEC3-mediated genomic damage in urothelium implicates BK polyomavirus (BKPyV) as a hit-and-run driver for bladder cancer.
Simon C Baker, Andrew S Mason, +8 authors, Jennifer Southgate.
Oncogene, 2022 Feb 24; 41(15). PMID: 35194151    Free PMC article.
APP and DYRK1A regulate axonal and synaptic vesicle protein networks and mediate Alzheimer's pathology in trisomy 21 neurons.
Chun-I Wu, Elizabeth A Vinton, +10 authors, Tracy L Young-Pearse.
Mol Psychiatry, 2022 Feb 24; 27(4). PMID: 35194165
A structure-specific small molecule inhibits a miRNA-200 family member precursor and reverses a type 2 diabetes phenotype.
Hafeez S Haniff, Xiaohui Liu, +7 authors, Matthew D Disney.
Cell Chem Biol, 2021 Jul 29; 29(2). PMID: 34320373    Free PMC article.
Increased Fibrosis in a Mouse Model of Anti-Laminin 332 Mucous Membrane Pemphigoid Remains Unaltered by Inhibition of Aldehyde Dehydrogenase.
Sabrina Patzelt, Manuela Pigors, +8 authors, Enno Schmidt.
Front Immunol, 2022 Feb 25; 12. PMID: 35197965    Free PMC article.
Translating in vitro CFTR rescue into small molecule correctors for cystic fibrosis using the Library of Integrated Network-based Cellular Signatures drug discovery platform.
Matthew D Strub, Shyam Ramachandran, +6 authors, Paul B McCray.
CPT Pharmacometrics Syst Pharmacol, 2021 Dec 09; 11(2). PMID: 34877817    Free PMC article.
Follistatin promotes LIN28B-mediated supporting cell reprogramming and hair cell regeneration in the murine cochlea.
Xiao-Jun Li, Charles Morgan, Loyal A Goff, Angelika Doetzlhofer.
Sci Adv, 2022 Feb 12; 8(6). PMID: 35148175    Free PMC article.
Klf4 Promotes Dentinogenesis and Odontoblastic Differentiation via Modulation of TGF-β Signaling Pathway and Interaction With Histone Acetylation.
Huangheng Tao, Heng Lin, +5 authors, Zhi Chen.
J Bone Miner Res, 2019 May 22; 34(8). PMID: 31112333    Free PMC article.
Long-term Follow-up and Patterns of Response, Progression, and Hyperprogression in Patients after PD-1 Blockade in Advanced Sarcoma.
Nicholas D Klemen, Sinchun Hwang, +16 authors, Sandra P D'Angelo.
Clin Cancer Res, 2021 Dec 31; 28(5). PMID: 34965948    Free PMC article.
Deriving Ranges of Optimal Estimated Transcript Expression due to Nonidentifiability.
Hongyu Zheng, Cong Ma, Carl Kingsford.
J Comput Biol, 2022 Jan 19; 29(2). PMID: 35041494    Free PMC article.
Adaptive immunity induces mutualism between commensal eukaryotes.
Kyla S Ost, Teresa R O'Meara, +18 authors, June L Round.
Nature, 2021 Jul 16; 596(7870). PMID: 34262174    Free PMC article.
Modulation of miR-181 influences dopaminergic neuronal degeneration in a mouse model of Parkinson's disease.
Colleen S Stein, Jared M McLendon, Nathan H Witmer, Ryan L Boudreau.
Mol Ther Nucleic Acids, 2022 Mar 15; 28. PMID: 35280925    Free PMC article.
Pathogen infection and cholesterol deficiency activate the C. elegans p38 immune pathway through a TIR-1/SARM1 phase transition.
Nicholas D Peterson, Janneke D Icso, +3 authors, Read Pukkila-Worley.
Elife, 2022 Feb 01; 11. PMID: 35098926    Free PMC article.
VIVA1: a more invasive subclone of MDA-MB-134VI invasive lobular carcinoma cells with increased metastatic potential in xenograft models.
Victoria Allen, Josée Coulombe, +7 authors, Christina L Addison.
Br J Cancer, 2022 Mar 24;. PMID: 35318435
Odorant-receptor-mediated regulation of chemosensory gene expression in the malaria mosquito Anopheles gambiae.
Sarah E Maguire, Ali Afify, Loyal A Goff, Christopher J Potter.
Cell Rep, 2022 Mar 10; 38(10). PMID: 35263579    Free PMC article.
GXP: Analyze and Plot Plant Omics Data in Web Browsers.
Constantin Eiteneuer, David Velasco, +10 authors, Asis Hallab.
Plants (Basel), 2022 Mar 27; 11(6). PMID: 35336631    Free PMC article.
A comparison of transcriptome analysis methods with reference genome.
Xu Liu, Jialu Zhao, +4 authors, Haihong Ye.
BMC Genomics, 2022 Mar 27; 23(1). PMID: 35337265    Free PMC article.
Dynamic evolution of small signalling peptide compensation in plant stem cell control.
Choon-Tak Kwon, Lingli Tang, +6 authors, Zachary B Lippman.
Nat Plants, 2022 Mar 30; 8(4). PMID: 35347264
GWAS on multiple traits identifies mitochondrial ACONITASE3 as important for acclimation to submergence stress.
Xiangxiang Meng, Lu Li, +9 authors, Oliver Berkowitz.
Plant Physiol, 2022 Jan 20; 188(4). PMID: 35043967    Free PMC article.
Impact of gene annotation choice on the quantification of RNA-seq data.
David Chisanga, Yang Liao, Wei Shi.
BMC Bioinformatics, 2022 Apr 01; 23(1). PMID: 35354358    Free PMC article.
A genome-scale gain-of-function CRISPR screen in CD8 T cells identifies proline metabolism as a means to enhance CAR-T therapy.
Lupeng Ye, Jonathan J Park, +17 authors, Sidi Chen.
Cell Metab, 2022 Mar 12; 34(4). PMID: 35276062    Free PMC article.
Integration of Aspergillus niger transcriptomic profile with metabolic model identifies potential targets to optimise citric acid production from lignocellulosic hydrolysate.
Daniel J Upton, Mehak Kaushal, +5 authors, A Jamie Wood.
Biotechnol Biofuels Bioprod, 2022 Apr 15; 15(1). PMID: 35418297    Free PMC article.
Clinical, genomic, and transcriptomic correlates of response to immune checkpoint blockade-based therapy in a cohort of patients with angiosarcoma treated at a single center.
Evan Rosenbaum, Cristina R Antonescu, +19 authors, Sandra D'Angelo.
J Immunother Cancer, 2022 Apr 03; 10(4). PMID: 35365586    Free PMC article.
MYC overexpression leads to increased chromatin interactions at super-enhancers and MYC binding sites.
Yi Xiang See, Kaijing Chen, Melissa J Fullwood.
Genome Res, 2022 Feb 05; 32(4). PMID: 35115371    Free PMC article.
The Fungal Endophyte Penicillium olsonii ML37 Reduces Fusarium Head Blight by Local Induced Resistance in Wheat Spikes.
Edward C Rojas, Birgit Jensen, +3 authors, David B Collinge.
J Fungi (Basel), 2022 Apr 22; 8(4). PMID: 35448576    Free PMC article.
AP-2α and AP-2β cooperatively function in the craniofacial surface ectoderm to regulate chromatin and gene expression dynamics during facial development.
Eric Van Otterloo, Isaac Milanda, +4 authors, Trevor Williams.
Elife, 2022 Mar 26; 11. PMID: 35333176    Free PMC article.
Nuclear transfer system for the direct induction of embryonic transcripts from intra- and cross-species nuclei using mouse 4-cell embryos.
Junko Tomikawa, Christopher A Penfold, Rena Hatakeyama, Kei Miyamoto.
STAR Protoc, 2022 Apr 26; 3(2). PMID: 35463476    Free PMC article.
Endoluminal Biopsy for Molecular Profiling of Human Brain Vascular Malformations.
Ethan Winkler, David Wu, +12 authors, Daniel Cooke.
Neurology, 2022 Feb 12; 98(16). PMID: 35145012    Free PMC article.
Systems genetics in the rat HXB/BXH family identifies Tti2 as a pleiotropic quantitative trait gene for adult hippocampal neurogenesis and serum glucose.
Anna N Senko, Rupert W Overall, +10 authors, Gerd Kempermann.
PLoS Genet, 2022 Apr 05; 18(4). PMID: 35377872    Free PMC article.
Chronic psychological stress alters gene expression in rat colon epithelial cells promoting chromatin remodeling, barrier dysfunction and inflammation.
John W Wiley, Gerald A Higgins, Shuangsong Hong.
PeerJ, 2022 May 06; 10. PMID: 35509963    Free PMC article.
Nutritional control regulates symbiont proliferation and life history in coral-dinoflagellate symbiosis.
Guoxin Cui, Yi Jin Liew, +7 authors, Manuel Aranda.
BMC Biol, 2022 May 14; 20(1). PMID: 35549698    Free PMC article.
ZFP36L2 suppresses mTORc1 through a P53-dependent pathway to prevent peripartum cardiomyopathy in mice.
Hidemichi Kouzu, Yuki Tatekoshi, +9 authors, Hossein Ardehali.
J Clin Invest, 2022 Mar 23; 132(10). PMID: 35316214    Free PMC article.
Genomics and Pathways Involved in Maize Resistance to Fusarium Ear Rot and Kernel Contamination With Fumonisins.
Ana Cao, María de la Fuente, +3 authors, Ana Butrón.
Front Plant Sci, 2022 May 20; 13. PMID: 35586219    Free PMC article.
Pilot study of bempegaldesleukin in combination with nivolumab in patients with metastatic sarcoma.
Sandra P D'Angelo, Allison L Richards, +27 authors, William D Tap.
Nat Commun, 2022 Jun 18; 13(1). PMID: 35710741
The impact of species-wide gene expression variation on Caenorhabditis elegans complex traits.
Gaotian Zhang, Nicole M Roberto, +2 authors, Erik C Andersen.
Nat Commun, 2022 Jun 18; 13(1). PMID: 35710766