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

¹ Department of Computer Science, University of California, Berkeley, Berkeley, California, USA.
² Innovative Genomics Institute and Department of Molecular &Cell Biology, University of California, Berkeley, Berkeley, California, USA.
³ Department of Statistics, University of California, Berkeley, Berkeley, California, USA.
⁴ Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, Reykjavík, Iceland.
⁵ Division of Biology and Biological Engineering, Caltech, Pasadena, California, USA.

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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RNA Sequencing Provides Novel Insights into the Transcriptome of Aldosterone Producing Adenomas. Samuel Backman, Tobias Åkerström, +4 authors, Peyman Björklund. less Sci Rep, 2019 Apr 20; 9(1). PMID: 31000732 Free PMC article.
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A novel transcriptome-derived SNPs array for tench (Tinca tinca L.). Girish Kumar, Jorge Langa, +4 authors, Andone Estonba. less PLoS One, 2019 Mar 20; 14(3). PMID: 30889192 Free PMC article.
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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. less mSphere, 2019 Mar 29; 4(2). PMID: 30918060 Free PMC article.
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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. less Front Physiol, 2019 Mar 19; 10. PMID: 30881311 Free PMC article.
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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. less 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. less Circ Res, 2019 May 31; 125(2). PMID: 31145021 Free PMC article.
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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. less 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. less 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. less Vet Res, 2021 Mar 18; 52(1). PMID: 33726857 Free PMC article.
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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. less Nat Cancer, 2021 Mar 20; 2(1). PMID: 33738458 Free PMC article.
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Enhanced Glycolysis Is Required for Antileishmanial Functions of Neutrophils Upon Infection With Leishmania donovani. Mareike Ohms, Carolina Ferreira, +4 authors, Tamás Laskay. less 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. less 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. less Cancers (Basel), 2021 Apr 04; 13(6). PMID: 33803512 Free PMC article.
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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. less 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. less 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. less Sci Rep, 2021 Apr 24; 11(1). PMID: 33888791 Free PMC article.
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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, Mi-Ryung Park, Seongsoo Hwang, Kichoon Lee. less 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. less 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. less 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. less mSystems, 2021 Apr 29; 6(2). PMID: 33906913 Free PMC article.
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Pan-genomic characterization of high-risk pediatric papillary thyroid carcinoma. Adam Stenman, Samuel Backman, +4 authors, C Christofer Juhlin. less 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. less 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. less 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. less 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. less 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.
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Comparative evaluation of full-length isoform quantification from RNA-Seq. Dimitra Sarantopoulou, Thomas G Brooks, +3 authors, Gregory R Grant. less BMC Bioinformatics, 2021 May 27; 22(1). PMID: 34034652 Free PMC article. Review.
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Long non-coding RNA exploration for mesenchymal stem cell characterisation. Sébastien Riquier, Marc Mathieu, +6 authors, Thérèse Commes. less 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. less 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. less 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. less 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. less 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. less 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. less Plant Cell, 2021 Apr 02; 33(4). PMID: 33793816 Free PMC article.
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Critical COVID-19 is associated with distinct leukocyte phenotypes and transcriptome patterns. E E Christensen, M J Jørgensen, +13 authors, A M Dyrhol-Riise. less 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. less 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. less 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. less 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. less 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. less 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. less 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, Jatinder Kaur, German Spangenberg, Timothy Sawbridge. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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, Jatinder Kaur, German Spangenberg, Timothy Sawbridge. less 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. less 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. less 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. less 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. less Nat Commun, 2021 Oct 09; 12(1). PMID: 34620871 Free PMC article.
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DIOXYGENASE FOR AUXIN OXIDATION 1 catalyzes the oxidation of IAA amino acid conjugates. Karel Müller, Petre Ivanov Dobrev, +12 authors, Jan Petrášek. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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, Mridu Kapur, Jeffrey H Chuang, Susan L Ackerman. less 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.
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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. less 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. less 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. less 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. less 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. less 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. less 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. less Genome Res, 2021 Oct 16; 31(11). PMID: 34649931 Free PMC article.
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Gene Expression Signature Associated with Clinical Outcome in ALK-Positive Anaplastic Large Cell Lymphoma. Camille Daugrois, Chloé Bessiere, +8 authors, Laurence Lamant. less 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. less 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, Iratxe Montes, Darrell Conklin, Andone Estonba. less 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. less iScience, 2021 Dec 02; 24(11). PMID: 34849463 Free PMC article.
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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. less 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. less 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. less 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, Diego Godoy, Javier Canales, Daniel F Calderini. less 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. less 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. less 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. less 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. less 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. less 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. less 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, Ying-Hong Lin, Min-Nan Tseng, Hao-Xun Chang. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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. less 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, Daehan Lee, Steffen R Hahnel, Erik C Andersen. less Nat Commun, 2022 Jun 18; 13(1). PMID: 35710766

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