Gene Expression Nebulas


Project ID Pubmed ID Title Journal Year Author Corresponding Author Institution of Corresponding Author
25706956 Phenotypic responses of differentiated asthmatic human airway epithelial cultures to rhinovirus. PloS one 2015 Bai J, Smock SL, Jackson GR, MacIsaac KD, Huang Y, Mankus C, Oldach J, Roberts B, Ma YL, Klappenbach JA, Crackower MA, Alves SE, Hayden PJ.
26186191 FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders. Cell 2015 Mariani J, Coppola G, Zhang P, Abyzov A, Provini L, Tomasini L, Amenduni M, Szekely A, Palejev D, Wilson M, Gerstein M, Grigorenko EL, Chawarska K, Pelphrey KA, Howe JR, Vaccarino FM.
26565915 Cancer-Associated SF3B1 Hotspot Mutations Induce Cryptic 3' Splice Site Selection through Use of a Different Branch Point. Cell reports 2015 Darman RB, Seiler M, Agrawal AA, Lim KH, Peng S, Aird D, Bailey SL, Bhavsar EB, Chan B, Colla S, Corson L, Feala J, Fekkes P, Ichikawa K, Keaney GF, Lee L, Kumar P, Kunii K, MacKenzie C, Matijevic M, Mizui Y, Myint K, Park ES, Puyang X, Selvaraj A, Thomas MP, Tsai J, Wang JY, Warmuth M, Yang H, Zhu P, Garcia-Manero G, Furman RR, Yu L, Smith PG, Buonamici S.
27604819 Hemopoietic-specific Sf3b1-K700E knock-in mice display the splicing defect seen in human MDS but develop anemia without ring sideroblasts. Leukemia 2017 Mupo A, Seiler M, Sathiaseelan V, Pance A, Yang Y, Agrawal AA, Iorio F, Bautista R, Pacharne S, Tzelepis K, Manes N, Wright P, Papaemmanuil E, Kent DG, Campbell PC, Buonamici S, Bolli N, Vassiliou GS.
28886276 Systems approach to the pharmacological actions of HDAC inhibitors reveals EP300 activities and convergent mechanisms of regulation in diabetes. Epigenetics 2017 Rafehi H, Kaspi A, Ziemann M, Okabe J, Karagiannis TC, El-Osta A, El-Osta A.
28145428 Collagen synthesis disruption and downregulation of core elements of TGF-β, Hippo, and Wnt pathways in keratoconus corneas. European journal of human genetics : EJHG 2017 Kabza M, Karolak JA, Rydzanicz M, Szcześniak MW, Nowak DM, Ginter-Matuszewska B, Polakowski P, Ploski R, Szaflik JP, Gajecka M.
28230051 Cellular senescence mediates fibrotic pulmonary disease. Nature communications 2017 Schafer MJ, White TA, Iijima K, Haak AJ, Ligresti G, Atkinson EJ, Oberg AL, Birch J, Salmonowicz H, Zhu Y, Mazula DL, Brooks RW, Fuhrmann-Stroissnigg H, Pirtskhalava T, Prakash YS, Tchkonia T, Robbins PD, Aubry MC, Passos JF, Kirkland JL, Tschumperlin DJ, Kita H, LeBrasseur NK.
30694689 Airway Smooth Muscle-Specific Transcriptomic Signatures of Glucocorticoid Exposure. American journal of respiratory cell and molecular biology 2019 Kan M, Koziol-White C, Shumyatcher M, Johnson M, Jester W, Panettieri RA, Himes BE.
29212479 A pilot systematic genomic comparison of recurrence risks of hepatitis B virus-associated hepatocellular carcinoma with low- and high-degree liver fibrosis. BMC medicine 2017 Yoo S, Wang W, Wang Q, Fiel MI, Lee E, Hiotis SP, Zhu J.
29472603 Bronchial extracellular matrix from COPD patients induces altered gene expression in repopulated primary human bronchial epithelial cells. Scientific reports 2018 Hedström U, Hallgren O, Öberg L, DeMicco A, Vaarala O, Westergren-Thorsson G, Zhou X.
29898990 MET-Oncogenic and JAK2-Inactivating Alterations Are Independent Factors That Affect Regulation of PD-L1 Expression in Lung Cancer. Clinical cancer research : an official journal of the American Association for Cancer Research 2018 Saigi M, Alburquerque-Bejar JJ, Mc Leer-Florin A, Pereira C, Pros E, Romero OA, Baixeras N, Esteve-Codina A, Nadal E, Brambilla E, Sanchez-Cespedes M.
29895574 Primary T Cells from Cutaneous T-cell Lymphoma Skin Explants Display an Exhausted Immune Checkpoint Profile. Cancer immunology research 2018 Querfeld C, Leung S, Myskowski PL, Curran SA, Goldman DA, Heller G, Wu X, Kil SH, Sharma S, Finn KJ, Horwitz S, Moskowitz A, Mehrara B, Rosen ST, Halpern AC, Young JW.
31434901 Tuberculous meningitis in children is characterized by compartmentalized immune responses and neural excitotoxicity. Nature communications 2019 Rohlwink UK, Figaji A, Wilkinson KA, Horswell S, Sesay AK, Deffur A, Enslin N, Solomons R, Van Toorn R, Eley B, Levin M, Wilkinson RJ, Lai RPJ.
30804934 The Long Non-coding RNA NRIR Drives IFN-Response in Monocytes: Implication for Systemic Sclerosis. Frontiers in immunology 2019 Mariotti B, Servaas NH, Rossato M, Tamassia N, Cassatella MA, Cossu M, Beretta L, van der Kroef M, Radstake TRDJ, Bazzoni F.
24393808 RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder. Molecular psychiatry 2014 Akula N, Barb J, Jiang X, Wendland JR, Choi KH, Sen SK, Hou L, Chen DT, Laje G, Johnson K, Lipska BK, Kleinman JE, Corrada-Bravo H, Detera-Wadleigh S, Munson PJ, McMahon FJ.
26873097 Longitudinal Transcriptome Analysis Reveals a Sustained Differential Gene Expression Signature in Patients Treated for Acute Lyme Disease. mBio 2016 Bouquet J, Soloski MJ, Swei A, Cheadle C, Federman S, Billaud JN, Rebman AW, Kabre B, Halpert R, Boorgula M, Aucott JN, Chiu CY.
27658890 A Randomized Phase IIb Trial of myo-Inositol in Smokers with Bronchial Dysplasia. Cancer prevention research (Philadelphia, Pa.) 2016 Lam S, Mandrekar SJ, Gesthalter Y, Allen Ziegler KL, Seisler DK, Midthun DE, Mao JT, Aubry MC, McWilliams A, Sin DD, Shaipanich T, Liu G, Johnson E, Bild A, Lenburg ME, Ionescu DN, Mayo J, Yi JE, Tazelaar H, Harmsen WS, Smith J, Spira AE, Beane J, Limburg PJ, Szabo E, Cancer Prevention Network.
30325352 A radiogenomic dataset of non-small cell lung cancer. Scientific data 2018 Bakr S, Gevaert O, Echegaray S, Ayers K, Zhou M, Shafiq M, Zheng H, Benson JA, Zhang W, Leung ANC, Kadoch M, Hoang CD, Shrager J, Quon A, Rubin DL, Plevritis SK, Napel S.
30332658 Integrated Multi-omic Analysis of Esthesioneuroblastomas Identifies Two Subgroups Linked to Cell Ontogeny. Cell reports 2018 Classe M, Yao H, Mouawad R, Creighton CJ, Burgess A, Allanic F, Wassef M, Leroy X, Verillaud B, Mortuaire G, Bielle F, Le Tourneau C, Kurtz JE, Khayat D, Su X, Malouf GG.
30358109 Pharmacodynamic biomarkers and differential effects of TNF- and GM-CSF-targeting biologics in rheumatoid arthritis. International journal of rheumatic diseases 2019 Guo X, Wang S, Godwood A, Close D, Ryan PC, Roskos LK, White WI.
30897114 Whole blood human transcriptome and virome analysis of ME/CFS patients experiencing post-exertional malaise following cardiopulmonary exercise testing. PloS one 2019 Bouquet J, Li T, Gardy JL, Kang X, Stevens S, Stevens J, VanNess M, Snell C, Potts J, Miller RR, Morshed M, McCabe M, Parker S, Uyaguari M, Tang P, Steiner T, Chan WS, De Souza AM, Mattman A, Patrick DM, Chiu CY.
31562239 Plasma extracellular vesicle long RNA profiling identifies a diagnostic signature for the detection of pancreatic ductal adenocarcinoma. Gut 2020 Yu S, Li Y, Liao Z, Wang Z, Wang Z, Li Y, Qian L, Zhao J, Zong H, Kang B, Zou WB, Chen K, He X, Meng Z, Chen Z, Huang S, Wang P.
32416070 Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19. Cell 2020 Blanco-Melo D, Nilsson-Payant BE, Liu WC, Uhl S, Hoagland D, Møller R, Jordan TX, Oishi K, Panis M, Sachs D, Wang TT, Schwartz RE, Lim JK, Albrecht RA, tenOever BR.
24441097 Transcriptome analysis of psoriasis in a large case-control sample: RNA-seq provides insights into disease mechanisms. The Journal of investigative dermatology 2014 Li B, Tsoi LC, Swindell WR, Gudjonsson JE, Tejasvi T, Johnston A, Ding J, Stuart PE, Xing X, Kochkodan JJ, Voorhees JJ, Kang HM, Nair RP, Abecasis GR, Elder JT.
25723451 Analysis of long non-coding RNAs highlights tissue-specific expression patterns and epigenetic profiles in normal and psoriatic skin. Genome biology 2015 Tsoi LC, Iyer MK, Stuart PE, Swindell WR, Gudjonsson JE, Tejasvi T, Sarkar MK, Li B, Ding J, Voorhees JJ, Kang HM, Nair RP, Chinnaiyan AM, Abecasis GR, Elder JT.
27992404 A gene network regulated by the transcription factor VGLL3 as a promoter of sex-biased autoimmune diseases. Nature immunology 2017 Liang Y, Tsoi LC, Xing X, Beamer MA, Swindell WR, Sarkar MK, Berthier CC, Stuart PE, Harms PW, Nair RP, Elder JT, Voorhees JJ, Kahlenberg JM, Gudjonsson JE.
25314013 Copy number loss of the interferon gene cluster in melanomas is linked to reduced T cell infiltrate and poor patient prognosis. PloS one 2014 Linsley PS, Speake C, Whalen E, Chaussabel D.
25885816 Defective structural RNA processing in relapsing-remitting multiple sclerosis. Genome biology 2015 Spurlock CF, Tossberg JT, Guo Y, Sriram S, Crooke PS, Aune TM.
25972006 Functional inflammatory profiles distinguish myelin-reactive T cells from patients with multiple sclerosis. Science translational medicine 2015 Cao Y, Goods BA, Raddassi K, Nepom GT, Kwok WW, Love JC, Hafler DA.
26522261 Association Between Response to Etrolizumab and Expression of Integrin αE and Granzyme A in Colon Biopsies of Patients With Ulcerative Colitis. Gastroenterology 2016 Tew GW, Hackney JA, Gibbons D, Lamb CA, Luca D, Egen JG, Diehl L, Eastham Anderson J, Vermeire S, Mansfield JC, Feagan BG, Panes J, Baumgart DC, Schreiber S, Dotan I, Sandborn WJ, Kirby JA, Irving PM, De Hertogh G, Van Assche GA, Rutgeerts P, O'Byrne S, Hayday A, Keir ME.
27015450 Landscape of Long Noncoding RNAs in Psoriatic and Healthy Skin. The Journal of investigative dermatology 2016 Gupta R, Ahn R, Lai K, Mullins E, Debbaneh M, Dimon M, Arron S, Liao W.
27793094 Network analysis of psoriasis reveals biological pathways and roles for coding and long non-coding RNAs. BMC genomics 2016 Ahn R, Gupta R, Lai K, Chopra N, Arron ST, Liao W.
27282753 Joint-specific DNA methylation and transcriptome signatures in rheumatoid arthritis identify distinct pathogenic processes. Nature communications 2016 Ai R, Hammaker D, Boyle DL, Morgan R, Walsh AM, Fan S, Firestein GS, Wang W.
27835693 RNA-seq Analysis Reveals Unique Transcriptome Signatures in Systemic Lupus Erythematosus Patients with Distinct Autoantibody Specificities. PloS one 2016 Rai R, Chauhan SK, Singh VV, Rai M, Rai G.
28221248 Early Transcriptomic Changes in the Ileal Pouch Provide Insight into the Molecular Pathogenesis of Pouchitis and Ulcerative Colitis. Inflammatory bowel diseases 2017 Huang Y, Dalal S, Antonopoulos D, Hubert N, Raffals LH, Dolan K, Weber C, Messer JS, Jabri B, Bendelac A, Eren AM, Rubin DT, Sogin M, Chang EB.
28455435 CD40L-Dependent Pathway Is Active at Various Stages of Rheumatoid Arthritis Disease Progression. Journal of immunology (Baltimore, Md. : 1950) 2017 Guo Y, Walsh AM, Fearon U, Smith MD, Wechalekar MD, Yin X, Cole S, Orr C, McGarry T, Canavan M, Kelly S, Lin TA, Liu X, Proudman SM, Veale DJ, Pitzalis C, Nagpal S.
28863153 Triple DMARD treatment in early rheumatoid arthritis modulates synovial T cell activation and plasmablast/plasma cell differentiation pathways. PloS one 2017 Walsh AM, Wechalekar MD, Guo Y, Yin X, Weedon H, Proudman SM, Smith MD, Nagpal S.
28148290 Discovery of new candidate genes for rheumatoid arthritis through integration of genetic association data with expression pathway analysis. Arthritis research & therapy 2017 Shchetynsky K, Diaz-Gallo LM, Folkersen L, Hensvold AH, Catrina AI, Berg L, Klareskog L, Padyukov L.
28400392 Identification of RUNX1 as a Mediator of Aberrant Retinal Angiogenesis. Diabetes 2017 Lam JD, Oh DJ, Wong LL, Amarnani D, Park-Windhol C, Sanchez AV, Cardona-Velez J, McGuone D, Stemmer-Rachamimov AO, Eliott D, Bielenberg DR, van Zyl T, Shen L, Gai X, D'Amore PA, Kim LA, Arboleda-Velasquez JF.
29510191 Resident T Cells in Resolved Psoriasis Steer Tissue Responses that Stratify Clinical Outcome. The Journal of investigative dermatology 2018 Gallais Sérézal I, Classon C, Cheuk S, Barrientos-Somarribas M, Wadman E, Martini E, Chang D, Xu Landén N, Ehrström M, Nylén S, Eidsmo L.
29348297 Changes in macrophage transcriptome associate with systemic sclerosis and mediate GSDMA contribution to disease risk. Annals of the rheumatic diseases 2018 Moreno-Moral A, Bagnati M, Koturan S, Ko JH, Fonseca C, Harmston N, Game L, Martin J, Ong V, Abraham DJ, Denton CP, Behmoaras J, Petretto E.
29717110 IL-21 drives expansion and plasma cell differentiation of autoreactive CD11chiT-bet+ B cells in SLE. Nature communications 2018 Wang S, Wang J, Kumar V, Karnell JL, Naiman B, Gross PS, Rahman S, Zerrouki K, Hanna R, Morehouse C, Holoweckyj N, Liu H, Autoimmunity Molecular Medicine Team, Manna Z, Goldbach-Mansky R, Hasni S, Siegel R, Sanjuan M, Streicher K, Cancro MP, Kolbeck R, Ettinger R.
29950172 Disease-specific regulation of gene expression in a comparative analysis of juvenile idiopathic arthritis and inflammatory bowel disease. Genome medicine 2018 Mo A, Marigorta UM, Arafat D, Chan LHK, Ponder L, Jang SR, Prince J, Kugathasan S, Prahalad S, Gibson G.
30054515 RNA-seq and flow-cytometry of conventional, scalp, and palmoplantar psoriasis reveal shared and distinct molecular pathways. Scientific reports 2018 Ahn R, Yan D, Chang HW, Lee K, Bhattarai S, Huang ZM, Nakamura M, Singh R, Afifi L, Taravati K, Munoz-Sandoval P, Pauli M, Rosenblum MD, Liao W.
30641038 Atopic Dermatitis Is an IL-13-Dominant Disease with Greater Molecular Heterogeneity Compared to Psoriasis. The Journal of investigative dermatology 2019 Tsoi LC, Rodriguez E, Degenhardt F, Baurecht H, Wehkamp U, Volks N, Szymczak S, Swindell WR, Sarkar MK, Raja K, Shao S, Patrick M, Gao Y, Uppala R, Perez White BE, Getsios S, Harms PW, Maverakis E, Elder JT, Franke A, Gudjonsson JE, Weidinger S.
31535015 Deconvolution of transcriptional networks identifies TCF4 as a master regulator in schizophrenia. Science advances 2019 Doostparast Torshizi A, Armoskus C, Zhang H, Forrest MP, Zhang S, Souaiaia T, Evgrafov OV, Knowles JA, Duan J, Wang K.
30910956 Risk variants disrupting enhancers of TH1 and TREG cells in type 1 diabetes. Proceedings of the National Academy of Sciences of the United States of America 2019 Gao P, Uzun Y, He B, Salamati SE, Coffey JKM, Tsalikian E, Tan K.
30589872 A distinct epigenetic profile distinguishes stenotic from non-inflamed fibroblasts in the ileal mucosa of Crohn's disease patients. PloS one 2018 Li Yim AYF, de Bruyn JR, Duijvis NW, Sharp C, Ferrero E, de Jonge WJ, Wildenberg ME, Mannens MMAM, Buskens CJ, D'Haens GR, Henneman P, Te Velde AA.
30305041 Genomic analysis of DNA repair genes and androgen signaling in prostate cancer. BMC cancer 2018 Jividen K, Kedzierska KZ, Yang CS, Szlachta K, Ratan A, Paschal BM.
25381879 Targeting miR-155 restores abnormal microglia and attenuates disease in SOD1 mice. Annals of neurology 2015 Butovsky O, Jedrychowski MP, Cialic R, Krasemann S, Murugaiyan G, Fanek Z, Greco DJ, Wu PM, Doykan CE, Kiner O, Lawson RJ, Frosch MP, Pochet N, Fatimy RE, Krichevsky AM, Gygi SP, Lassmann H, Berry J, Cudkowicz ME, Weiner HL.
29973527 Pain-Associated Transcriptome Changes in Synovium of Knee Osteoarthritis Patients. Genes 2018 Bratus-Neuenschwander A, Castro-Giner F, Frank-Bertoncelj M, Aluri S, Fucentese SF, Schlapbach R, Sprott H.
29681516 Super-Obese Patient-Derived iPSC Hypothalamic Neurons Exhibit Obesogenic Signatures and Hormone Responses. Cell stem cell 2018 Rajamani U, Gross AR, Hjelm BE, Sequeira A, Vawter MP, Tang J, Gangalapudi V, Wang Y, Andres AM, Gottlieb RA, Sareen D.
28893800 VHL Deficiency Drives Enhancer Activation of Oncogenes in Clear Cell Renal Cell Carcinoma. Cancer discovery 2017 Yao X, Tan J, Lim KJ, Koh J, Ooi WF, Li Z, Huang D, Xing M, Chan YS, Qu JZ, Tay ST, Wijaya G, Lam YN, Hong JH, Lee-Lim AP, Guan P, Ng MSW, He CZ, Lin JS, Nandi T, Qamra A, Xu C, Myint SS, Davies JOJ, Goh JY, Loh G, Tan BC, Rozen SG, Yu Q, Tan IBH, Cheng CWS, Li S, Chang KTE, Tan PH, Silver DL, Lezhava A, Steger G, Hughes JR, Teh BT, Tan P.
28967919 Chromosome 1q21.3 amplification is a trackable biomarker and actionable target for breast cancer recurrence. Nature medicine 2017 Goh JY, Feng M, Wang W, Oguz G, Yatim SMJM, Lee PL, Bao Y, Lim TH, Wang P, Tam WL, Kodahl AR, Lyng MB, Sarma S, Lin SY, Lezhava A, Yap YS, Lim AST, Hoon DSB, Ditzel HJ, Lee SC, Tan EY, Yu Q.
30136421 Integrating the Epigenome to Identify Drivers of Hepatocellular Carcinoma. Hepatology (Baltimore, Md.) 2019 Hlady RA, Sathyanarayan A, Thompson JJ, Zhou D, Wu Q, Pham K, Lee JH, Liu C, Robertson KD.
30602780 RORγt inhibition selectively targets IL-17 producing iNKT and γδ-T cells enriched in Spondyloarthritis patients. Nature communications 2019 Venken K, Jacques P, Mortier C, Labadia ME, Decruy T, Coudenys J, Hoyt K, Wayne AL, Hughes R, Turner M, Van Gassen S, Martens L, Smith D, Harcken C, Wahle J, Wang CT, Verheugen E, Schryvers N, Varkas G, Cypers H, Wittoek R, Piette Y, Gyselbrecht L, Van Calenbergh S, Van den Bosch F, Saeys Y, Nabozny G, Elewaut D.
32228226 Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients. Emerging microbes & infections 2020 Xiong Y, Liu Y, Cao L, Wang D, Guo M, Jiang A, Guo D, Hu W, Yang J, Tang Z, Wu H, Lin Y, Zhang M, Zhang Q, Shi M, Liu Y, Zhou Y, Lan K, Chen Y.
29037989 Genome wide abnormal DNA methylome of human blastocyst in assisted reproductive technology. Journal of genetics and genomics = Yi chuan xue bao 2017 Li G, Yu Y, Fan Y, Li C, Xu X, Duan J, Li R, Kang X, Ma X, Chen X, Ke Y, Yan J, Lian Y, Liu P, Zhao Y, Zhao H, Chen Y, Sun X, Liu J, Qiao J, Liu J.
29526463 Chromatin Accessibility Landscape in Human Early Embryos and Its Association with Evolution. Cell 2018 Gao L, Wu K, Liu Z, Yao X, Yuan S, Tao W, Yi L, Yu G, Hou Z, Fan D, Tian Y, Liu J, Chen ZJ, Liu J.
30333476 Zika virus shedding in the stool and infection through the anorectal mucosa in mice. Emerging microbes & infections 2018 Li C, Deng YQ, Zu S, Quanquin N, Shang J, Tian M, Ji X, Zhang NN, Dong HL, Xu YP, Zhao LZ, Zhang FC, Li XF, Wu A, Cheng G, Qin CF.
31527024 Azithromycin Protects against Zika virus Infection by Upregulating virus-induced Type I and III Interferon Responses. Antimicrobial agents and chemotherapy 2019 Li C, Zu S, Deng YQ, Li D, Parvatiyar K, Quanquin N, Shang J, Sun N, Su J, Liu Z, Wang M, Aliyari SR, Li XF, Wu A, Ma F, Shi Y, Nielsevn-Saines K, Jung JU, Qin FX, Qin CF, Cheng G.
31178893 A Systems Analysis of the Relationships Between Anemia and Ischemic Stroke Rehabilitation Based on RNA-Seq Data. Frontiers in genetics 2019 Wang Y, Huang X, Liu J, Zhao X, Yu H, Cai Y.
30804224 BRN2 suppresses apoptosis, reprograms DNA damage repair, and is associated with a high somatic mutation burden in melanoma. Genes & development 2019 Herbert K, Binet R, Lambert JP, Louphrasitthiphol P, Kalkavan H, Sesma-Sanz L, Robles-Espinoza CD, Sarkar S, Suer E, Andrews S, Chauhan J, Roberts ND, Middleton MR, Gingras AC, Masson JY, Larue L, Falletta P, Goding CR.
23934149 Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nature structural & molecular biology 2013 Yan L, Yang M, Guo H, Yang L, Wu J, Li R, Liu P, Lian Y, Zheng X, Yan J, Huang J, Li M, Wu X, Wen L, Lao K, Li R, Qiao J, Tang F.
24658644 The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nature biotechnology 2014 Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, Lennon NJ, Livak KJ, Mikkelsen TS, Rinn JL.
26904963 Human oocyte developmental potential is predicted by mechanical properties within hours after fertilization. Nature communications 2016 Yanez LZ, Han J, Behr BB, Pera RAR, Camarillo DB.
26293300 Defining the three cell lineages of the human blastocyst by single-cell RNA-seq. Development (Cambridge, England) 2015 Blakeley P, Fogarty NM, del Valle I, Wamaitha SE, Hu TX, Elder K, Snell P, Christie L, Robson P, Niakan KK.
26060301 A survey of human brain transcriptome diversity at the single cell level. Proceedings of the National Academy of Sciences of the United States of America 2015 Darmanis S, Sloan SA, Zhang Y, Enge M, Caneda C, Shuer LM, Hayden Gephart MG, Barres BA, Quake SR.
26084335 Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells. Genome biology 2015 Kim KT, Lee HW, Lee HO, Kim SC, Seo YJ, Chung W, Eum HH, Nam DH, Kim J, Joo KM, Park WY.
26740550 Assessing similarity to primary tissue and cortical layer identity in induced pluripotent stem cell-derived cortical neurons through single-cell transcriptomics. Human molecular genetics 2016 Handel AE, Chintawar S, Lalic T, Whiteley E, Vowles J, Giustacchini A, Argoud K, Sopp P, Nakanishi M, Bowden R, Cowley S, Newey S, Akerman C, Ponting CP, Cader MZ.
26524239 Fixed single-cell transcriptomic characterization of human radial glial diversity. Nature methods 2016 Thomsen ER, Mich JK, Yao Z, Hodge RD, Doyle AM, Jang S, Shehata SI, Nelson AM, Shapovalova NV, Levi BP, Ramanathan S.
27139883 Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma. Genome biology 2016 Kim KT, Lee HW, Lee HO, Song HJ, Jeong da E, Shin S, Kim H, Shin Y, Nam DH, Jeong BC, Kirsch DG, Joo KM, Park WY.
27263970 A Primate lncRNA Mediates Notch Signaling during Neuronal Development by Sequestering miRNA. Neuron 2016 Rani N, Nowakowski TJ, Zhou H, Godshalk SE, Lisi V, Kriegstein AR, Kosik KS.
28474673 Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer. Nature communications 2017 Chung W, Eum HH, Lee HO, Lee KM, Lee HB, Kim KT, Ryu HS, Kim S, Lee JE, Park YH, Kan Z, Han W, Park WY.
28045081 Batch effects and the effective design of single-cell gene expression studies. Scientific reports 2017 Tung PY, Blischak JD, Hsiao CJ, Knowles DA, Burnett JE, Pritchard JK, Gilad Y.
28346451 SC3: consensus clustering of single-cell RNA-seq data. Nature methods 2017 Kiselev VY, Kirschner K, Schaub MT, Andrews T, Yiu A, Chandra T, Natarajan KN, Reik W, Barahona M, Green AR, Hemberg M.
29614062 Pseudotime Dynamics in Melanoma Single-Cell Transcriptomes Reveals Different Mechanisms of Tumor Progression. Biology 2018 Loeffler-Wirth H, Binder H, Willscher E, Gerber T, Kunz M.
27568284 Zika Virus Disrupts Phospho-TBK1 Localization and Mitosis in Human Neuroepithelial Stem Cells and Radial Glia. Cell reports 2016 Onorati M, Li Z, Liu F, Sousa AMM, Nakagawa N, Li M, Dell'Anno MT, Gulden FO, Pochareddy S, Tebbenkamp ATN, Han W, Pletikos M, Gao T, Zhu Y, Bichsel C, Varela L, Szigeti-Buck K, Lisgo S, Zhang Y, Testen A, Gao XB, Mlakar J, Popovic M, Flamand M, Strittmatter SM, Kaczmarek LK, Anton ES, Horvath TL, Lindenbach BD, Sestan N.
27926872 Deletion of the Polycomb-Group Protein EZH2 Leads to Compromised Self-Renewal and Differentiation Defects in Human Embryonic Stem Cells. Cell reports 2016 Collinson A, Collier AJ, Morgan NP, Sienerth AR, Chandra T, Andrews S, Rugg-Gunn PJ.
28965763 Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns. Cell 2017 Enge M, Arda HE, Mignardi M, Beausang J, Bottino R, Kim SK, Quake SR.
31534222 Electrical and synaptic integration of glioma into neural circuits. Nature 2019 Venkatesh HS, Morishita W, Geraghty AC, Silverbush D, Gillespie SM, Arzt M, Tam LT, Espenel C, Ponnuswami A, Ni L, Woo PJ, Taylor KR, Agarwal A, Regev A, Brang D, Vogel H, Hervey-Jumper S, Bergles DE, Suvà ML, Malenka RC, Monje M.
28930664 Aryl Hydrocarbon Receptor Controls Monocyte Differentiation into Dendritic Cells versus Macrophages. Immunity 2017 Goudot C, Coillard A, Villani AC, Gueguen P, Cros A, Sarkizova S, Tang-Huau TL, Bohec M, Baulande S, Hacohen N, Amigorena S, Segura E.
29352091 Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis. Science immunology 2018 Patil VS, Madrigal A, Schmiedel BJ, Clarke J, O'Rourke P, de Silva AD, Harris E, Peters B, Seumois G, Weiskopf D, Sette A, Vijayanand P.
30089904 Genetic and transcriptional evolution alters cancer cell line drug response. Nature 2018 Ben-David U, Siranosian B, Ha G, Tang H, Oren Y, Hinohara K, Strathdee CA, Dempster J, Lyons NJ, Burns R, Nag A, Kugener G, Cimini B, Tsvetkov P, Maruvka YE, O'Rourke R, Garrity A, Tubelli AA, Bandopadhayay P, Tsherniak A, Vazquez F, Wong B, Birger C, Ghandi M, Thorner AR, Bittker JA, Meyerson M, Getz G, Beroukhim R, Golub TR.
30789893 Single-cell transcriptomics reveals gene expression dynamics of human fetal kidney development. PLoS biology 2019 Hochane M, van den Berg PR, Fan X, Bérenger-Currias N, Adegeest E, Bialecka M, Nieveen M, Menschaart M, Chuva de Sousa Lopes SM, Semrau S.
30575716 Molecular and functional heterogeneity of IL-10-producing CD4+ T cells. Nature communications 2018 Brockmann L, Soukou S, Steglich B, Czarnewski P, Zhao L, Wende S, Bedke T, Ergen C, Manthey C, Agalioti T, Geffken M, Seiz O, Parigi SM, Sorini C, Geginat J, Fujio K, Jacobs T, Roesch T, Izbicki JR, Lohse AW, Flavell RA, Krebs C, Gustafsson JA, Antonson P, Roncarolo MG, Villablanca EJ, Gagliani N, Huber S.
30726734 The Neonatal and Adult Human Testis Defined at the Single-Cell Level. Cell reports 2019 Sohni A, Tan K, Song HW, Burow D, de Rooij DG, Laurent L, Hsieh TC, Rabah R, Hammoud SS, Vicini E, Wilkinson MF.
31118283 Single-cell RNA sequencing unveils the shared and the distinct cytotoxic hallmarks of human TCRVδ1 and TCRVδ2 γδ T lymphocytes. Proceedings of the National Academy of Sciences of the United States of America 2019 Pizzolato G, Kaminski H, Tosolini M, Franchini DM, Pont F, Martins F, Valle C, Labourdette D, Cadot S, Quillet-Mary A, Poupot M, Laurent C, Ysebaert L, Meraviglia S, Dieli F, Merville P, Milpied P, Déchanet-Merville J, Fournié JJ.
31558476 Alterations in the Transcriptional Programs of Myeloma Cells and the Microenvironment during Extramedullary Progression Affect Proliferation and Immune Evasion. Clinical cancer research : an official journal of the American Association for Cancer Research 2020 Ryu D, Kim SJ, Hong Y, Jo A, Kim N, Kim HJ, Lee HO, Kim K, Park WY.
28737769 Local lung hypoxia determines epithelial fate decisions during alveolar regeneration. Nature cell biology 2017 Xi Y, Kim T, Brumwell AN, Driver IH, Wei Y, Tan V, Jackson JR, Xu J, Lee DK, Gotts JE, Matthay MA, Shannon JM, Chapman HA, Vaughan AE.
29630593 A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa. PLoS computational biology 2018 Zhang H, Lee CAA, Li Z, Garbe JR, Eide CR, Petegrosso R, Kuang R, Tolar J.
29427839 Single-cell RNA sequencing reveals metallothionein heterogeneity during hESC differentiation to definitive endoderm. Stem cell research 2018 Lu J, Baccei A, Lummertz da Rocha E, Guillermier C, McManus S, Finney LA, Zhang C, Steinhauser ML, Li H, Lerou PH.
29486586 Single-Cell Transcriptomics of Human Oocytes: Environment-Driven Metabolic Competition and Compensatory Mechanisms During Oocyte Maturation. Antioxidants & redox signaling 2019 Zhao H, Li T, Zhao Y, Tan T, Liu C, Liu Y, Chang L, Huang N, Li C, Fan Y, Yu Y, Li R, Qiao J.
30681766 CRX Expression in Pluripotent Stem Cell-Derived Photoreceptors Marks a Transplantable Subpopulation of Early Cones. Stem cells (Dayton, Ohio) 2019 Collin J, Zerti D, Queen R, Santos-Ferreira T, Bauer R, Coxhead J, Hussain R, Steel D, Mellough C, Ader M, Sernagor E, Armstrong L, Lako M.
30463007 The Molecular Signature of Megakaryocyte-Erythroid Progenitors Reveals a Role for the Cell Cycle in Fate Specification. Cell reports 2018 Lu YC, Sanada C, Xavier-Ferrucio J, Wang L, Zhang PX, Grimes HL, Venkatasubramanian M, Chetal K, Aronow B, Salomonis N, Krause DS.
30926812 Wnt1 silences chemokine genes in dendritic cells and induces adaptive immune resistance in lung adenocarcinoma. Nature communications 2019 Kerdidani D, Chouvardas P, Arjo AR, Giopanou I, Ntaliarda G, Guo YA, Tsikitis M, Kazamias G, Potaris K, Stathopoulos GT, Zakynthinos S, Kalomenidis I, Soumelis V, Kollias G, Tsoumakidou M.
28111004 Single cell sequencing reveals heterogeneity within ovarian cancer epithelium and cancer associated stromal cells. Gynecologic oncology 2017 Winterhoff BJ, Maile M, Mitra AK, Sebe A, Bazzaro M, Geller MA, Abrahante JE, Klein M, Hellweg R, Mullany SA, Beckman K, Daniel J, Starr TK.
24925914 Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science (New York, N.Y.) 2014 Patel AP, Tirosh I, Trombetta JJ, Shalek AK, Gillespie SM, Wakimoto H, Cahill DP, Nahed BV, Curry WT, Martuza RL, Louis DN, Rozenblatt-Rosen O, Suvà ML, Regev A, Bernstein BE.
31068472 Prosurvival kinase PIM2 is a therapeutic target for eradication of chronic myeloid leukemia stem cells. Proceedings of the National Academy of Sciences of the United States of America 2019 Ma L, Pak ML, Ou J, Yu J, St Louis P, Shan Y, Hutchinson L, Li S, Brehm MA, Zhu LJ, Green MR.
29233929 Single-Cell RNA-seq Reveals a Subpopulation of Prostate Cancer Cells with Enhanced Cell-Cycle-Related Transcription and Attenuated Androgen Response. Cancer research 2018 Horning AM, Wang Y, Lin CK, Louie AD, Jadhav RR, Hung CN, Wang CM, Lin CL, Kirma NB, Liss MA, Kumar AP, Sun L, Liu Z, Chao WT, Wang Q, Jin VX, Chen CL, Huang TH.
30819896 COX-2 mediates tumor-stromal prolactin signaling to initiate tumorigenesis. Proceedings of the National Academy of Sciences of the United States of America 2019 Zheng Y, Comaills V, Burr R, Boulay G, Miyamoto DT, Wittner BS, Emmons E, Sil S, Koulopoulos MW, Broderick KT, Tai E, Rengarajan S, Kulkarni AS, Shioda T, Wu CL, Ramaswamy S, Ting DT, Toner M, Rivera MN, Maheswaran S, Haber DA.
30451854 Invasive Salmonella exploits divergent immune evasion strategies in infected and bystander dendritic cell subsets. Nature communications 2018 Aulicino A, Rue-Albrecht KC, Preciado-Llanes L, Napolitani G, Ashley N, Cribbs A, Koth J, Lagerholm BC, Ambrose T, Gordon MA, Sims D, Simmons A, Simmons A.
29694901 Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated HIV-Infected Cells. Cell reports 2018 Golumbeanu M, Cristinelli S, Rato S, Munoz M, Cavassini M, Beerenwinkel N, Ciuffi A.
31428694 Single-cell landscape in mammary epithelium reveals bipotent-like cells associated with breast cancer risk and outcome. Communications biology 2019 Chen W, Morabito SJ, Kessenbrock K, Enver T, Meyer KB, Teschendorff AE.
29802404 Tracing the temporal-spatial transcriptome landscapes of the human fetal digestive tract using single-cell RNA-sequencing. Nature cell biology 2018 Gao S, Yan L, Wang R, Li J, Yong J, Zhou X, Wei Y, Wu X, Wang X, Fan X, Yan J, Zhi X, Gao Y, Guo H, Jin X, Wang W, Mao Y, Wang F, Wen L, Fu W, Ge H, Qiao J, Tang F.
30275468 Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline. Nature communications 2018 Hennrich ML, Romanov N, Horn P, Jaeger S, Eckstein V, Steeples V, Ye F, Ding X, Poisa-Beiro L, Lai MC, Lang B, Boultwood J, Luft T, Zaugg JB, Pellagatti A, Bork P, Aloy P, Gavin AC, Ho AD.
30607001 Molecular signatures of multiple myeloma progression through single cell RNA-Seq. Blood cancer journal 2019 Jang JS, Li Y, Mitra AK, Bi L, Abyzov A, van Wijnen AJ, Baughn LB, Van Ness B, Rajkumar V, Kumar S, Jen J.
31155233 Stromal Microenvironment Shapes the Intratumoral Architecture of Pancreatic Cancer. Cell 2019 Ligorio M, Sil S, Malagon-Lopez J, Nieman LT, Misale S, Di Pilato M, Ebright RY, Karabacak MN, Kulkarni AS, Liu A, Vincent Jordan N, Franses JW, Philipp J, Kreuzer J, Desai N, Arora KS, Rajurkar M, Horwitz E, Neyaz A, Tai E, Magnus NKC, Vo KD, Yashaswini CN, Marangoni F, Boukhali M, Fatherree JP, Damon LJ, Xega K, Desai R, Choz M, Bersani F, Langenbucher A, Thapar V, Morris R, Wellner UF, Schilling O, Lawrence MS, Liss AS, Rivera MN, Deshpande V, Benes CH, Maheswaran S, Haber DA, Fernandez-Del-Castillo C, Ferrone CR, Haas W, Aryee MJ, Ting DT.
31151460 Single-cell RNA sequencing reveals the impact of chromosomal instability on glioblastoma cancer stem cells. BMC medical genomics 2019 Zhao Y, Carter R, Natarajan S, Varn FS, Compton DA, Gawad C, Cheng C, Godek KM.
29915193 Direct pericyte-to-neuron reprogramming via unfolding of a neural stem cell-like program. Nature neuroscience 2018 Karow M, Camp JG, Falk S, Gerber T, Pataskar A, Gac-Santel M, Kageyama J, Brazovskaja A, Garding A, Fan W, Riedemann T, Casamassa A, Smiyakin A, Schichor C, Götz M, Tiwari VK, Treutlein B, Berninger B.
29539641 A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex. Nature 2018 Zhong S, Zhang S, Fan X, Wu Q, Yan L, Dong J, Zhang H, Li L, Sun L, Pan N, Xu X, Tang F, Zhang J, Qiao J, Wang X.
29622030 Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing. Genome biology 2018 Han X, Chen H, Huang D, Chen H, Fei L, Cheng C, Huang H, Yuan GC, Guo G.
28754679 Adaptive from Innate: Human IFN-γ+CD4+ T Cells Can Arise Directly from CXCL8-Producing Recent Thymic Emigrants in Babies and Adults. Journal of immunology (Baltimore, Md. : 1950) 2017 Das A, Rouault-Pierre K, Kamdar S, Gomez-Tourino I, Wood K, Donaldson I, Mein CA, Bonnet D, Hayday AC, Gibbons DL.
29025019 Differing molecular response of young and advanced maternal age human oocytes to IVM. Human reproduction (Oxford, England) 2017 Reyes JM, Silva E, Chitwood JL, Schoolcraft WB, Krisher RL, Ross PJ.
28878125 Human hepatic organoids for the analysis of human genetic diseases. JCI insight 2017 Guan Y, Xu D, Garfin PM, Ehmer U, Hurwitz M, Enns G, Michie S, Wu M, Zheng M, Nishimura T, Sage J, Peltz G.
29657097 Single-Cell Transcriptomic Profiling of Pluripotent Stem Cell-Derived SCGB3A2+ Airway Epithelium. Stem cell reports 2018 McCauley KB, Alysandratos KD, Jacob A, Hawkins F, Caballero IS, Vedaie M, Yang W, Slovik KJ, Morley M, Carraro G, Kook S, Guttentag SH, Stripp BR, Morrisey EE, Kotton DN.
28694456 Single-cell transcriptomics of East-Asian pancreatic islets cells. Scientific reports 2017 Dorajoo R, Ali Y, Tay VSY, Kang J, Samydurai S, Liu J, Boehm BO.
28566371 Single-Cell RNA Sequencing Reveals Expanded Clones of Islet Antigen-Reactive CD4+ T Cells in Peripheral Blood of Subjects with Type 1 Diabetes. Journal of immunology (Baltimore, Md. : 1950) 2017 Cerosaletti K, Barahmand-Pour-Whitman F, Yang J, DeBerg HA, Dufort MJ, Murray SA, Israelsson E, Speake C, Gersuk VH, Eddy JA, Reijonen H, Greenbaum CJ, Kwok WW, Wambre E, Prlic M, Gottardo R, Nepom GT, Linsley PS.
31638164 Population and single‑cell transcriptome analyses reveal diverse transcriptional changes associated with radioresistance in esophageal squamous cell carcinoma. International journal of oncology 2019 Wu H, Yu J, Kong D, Xu Y, Zhang Z, Shui J, Li Z, Luo H, Wang K.
28445465 Assembly of functionally integrated human forebrain spheroids. Nature 2017 Birey F, Andersen J, Makinson CD, Islam S, Wei W, Huber N, Fan HC, Metzler KRC, Panagiotakos G, Thom N, O'Rourke NA, Steinmetz LM, Bernstein JA, Hallmayer J, Huguenard JR, Paşca SP.
31350390 Single cell analysis of human foetal liver captures the transcriptional profile of hepatobiliary hybrid progenitors. Nature communications 2019 Segal JM, Kent D, Wesche DJ, Ng SS, Serra M, Oulès B, Kar G, Emerton G, Blackford SJI, Darmanis S, Miquel R, Luong TV, Yamamoto R, Bonham A, Jassem W, Heaton N, Vigilante A, King A, Sancho R, Teichmann S, Quake SR, Nakauchi H, Rashid ST.
31543471 Single-Cell RNA Sequencing of hESC-Derived 3D Retinal Organoids Reveals Novel Genes Regulating RPC Commitment in Early Human Retinogenesis. Stem cell reports 2019 Mao X, An Q, Xi H, Yang XJ, Zhang X, Yuan S, Wang J, Hu Y, Liu Q, Fan G.
31474513 Single-Cell Analysis of Human Mononuclear Phagocytes Reveals Subset-Defining Markers and Identifies Circulating Inflammatory Dendritic Cells. Immunity 2019 Dutertre CA, Becht E, Irac SE, Khalilnezhad A, Narang V, Khalilnezhad S, Ng PY, van den Hoogen LL, Leong JY, Lee B, Chevrier M, Zhang XM, Yong PJA, Koh G, Lum J, Howland SW, Mok E, Chen J, Larbi A, Tan HKK, Lim TKH, Karagianni P, Tzioufas AG, Malleret B, Brody J, Albani S, van Roon J, Radstake T, Newell EW, Ginhoux F.
29391249 Spatial and Single-Cell Transcriptional Profiling Identifies Functionally Distinct Human Dermal Fibroblast Subpopulations. The Journal of investigative dermatology 2018 Philippeos C, Telerman SB, Oulès B, Pisco AO, Shaw TJ, Elgueta R, Lombardi G, Driskell RR, Soldin M, Lynch MD, Watt FM.
30759401 Single-Cell Transcriptome Analysis Maps the Developmental Track of the Human Heart. Cell reports 2019 Cui Y, Zheng Y, Liu X, Yan L, Fan X, Yong J, Hu Y, Dong J, Li Q, Wu X, Gao S, Li J, Wen L, Qiao J, Tang F.
31561267 Single-cell RNA sequencing reveals chemokine self-feeding of myeloma cells promotes extramedullary metastasis. FEBS letters 2020 Geng S, Wang J, Zhang X, Zhang JJ, Wu F, Pang Y, Zhong Y, Wang J, Wang W, Lyu X, Huang Y, Jing H.
31566584 Early adaptive immune activation detected in monozygotic twins with prodromal multiple sclerosis. The Journal of clinical investigation 2019 Beltrán E, Gerdes LA, Hansen J, Flierl-Hecht A, Krebs S, Blum H, Ertl-Wagner B, Barkhof F, Kümpfel T, Hohlfeld R, Dornmair K.
28673540 Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation. Molecular cell 2017 Song Y, Botvinnik OB, Lovci MT, Kakaradov B, Liu P, Xu JL, Yeo GW.
28457750 Single-Cell RNA-Seq Analysis Maps Development of Human Germline Cells and Gonadal Niche Interactions. Cell stem cell 2017 Li L, Dong J, Yan L, Yong J, Liu X, Hu Y, Fan X, Wu X, Guo H, Wang X, Zhu X, Li R, Yan J, Wei Y, Zhao Y, Wang W, Ren Y, Yuan P, Yan Z, Hu B, Guo F, Wen L, Tang F, Qiao J.
28061811 The nature and nurture of cell heterogeneity: accounting for macrophage gene-environment interactions with single-cell RNA-Seq. BMC genomics 2017 Wills QF, Mellado-Gomez E, Nolan R, Warner D, Sharma E, Broxholme J, Wright B, Lockstone H, James W, Lynch M, Gonzales M, West J, Leyrat A, Padilla-Parra S, Filippi S, Holmes C, Moore MD, Bowden R.
27989770 Human Naive Pluripotent Stem Cells Model X Chromosome Dampening and X Inactivation. Cell stem cell 2017 Sahakyan A, Kim R, Chronis C, Sabri S, Bonora G, Theunissen TW, Kuoy E, Langerman J, Clark AT, Jaenisch R, Plath K.
28174237 Single-cell transcriptomics of the human placenta: inferring the cell communication network of the maternal-fetal interface. Genome research 2017 Pavličev M, Wagner GP, Chavan AR, Owens K, Maziarz J, Dunn-Fletcher C, Kallapur SG, Muglia L, Jones H.
30042384 Single-cell RNA-seq reveals the diversity of trophoblast subtypes and patterns of differentiation in the human placenta. Cell research 2018 Liu Y, Fan X, Wang R, Lu X, Dang YL, Wang H, Lin HY, Zhu C, Ge H, Cross JC, Wang H.
29867213 Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysis. Cell research 2018 Fan X, Dong J, Zhong S, Wei Y, Wu Q, Yan L, Yong J, Sun L, Wang X, Zhao Y, Wang W, Yan J, Wang X, Qiao J, Tang F.
30174296 Single-Cell RNA Sequencing Analysis Reveals Sequential Cell Fate Transition during Human Spermatogenesis. Cell stem cell 2018 Wang M, Liu X, Chang G, Chen Y, An G, Yan L, Gao S, Xu Y, Cui Y, Dong J, Chen Y, Fan X, Hu Y, Song K, Zhu X, Gao Y, Yao Z, Bian S, Hou Y, Lu J, Wang R, Fan Y, Lian Y, Tang W, Wang Y, Liu J, Zhao L, Wang L, Liu Z, Yuan R, Shi Y, Hu B, Ren X, Tang F, Zhao XY, Qiao J.
31269016 Dissecting the transcriptome landscape of the human fetal neural retina and retinal pigment epithelium by single-cell RNA-seq analysis. PLoS biology 2019 Hu Y, Wang X, Hu B, Mao Y, Chen Y, Yan L, Yong J, Dong J, Wei Y, Wang W, Wen L, Qiao J, Tang F.
30257215 Dissecting the Global Dynamic Molecular Profiles of Human Fetal Kidney Development by Single-Cell RNA Sequencing. Cell reports 2018 Wang P, Chen Y, Yong J, Cui Y, Wang R, Wen L, Qiao J, Tang F.
30548510 Deconstructing Retinal Organoids: Single Cell RNA-Seq Reveals the Cellular Components of Human Pluripotent Stem Cell-Derived Retina. Stem cells (Dayton, Ohio) 2019 Collin J, Queen R, Zerti D, Dorgau B, Hussain R, Coxhead J, Cockell S, Lako M.
32049009 Transcriptional Programs Define Intratumoral Heterogeneity of Ewing Sarcoma at Single-Cell Resolution. Cell reports 2020 Aynaud MM, Mirabeau O, Gruel N, Grossetête S, Boeva V, Durand S, Surdez D, Saulnier O, Zaïdi S, Gribkova S, Fouché A, Kairov U, Raynal V, Tirode F, Grünewald TGP, Bohec M, Baulande S, Janoueix-Lerosey I, Vert JP, Barillot E, Delattre O, Zinovyev A.
30498128 Single-cell multiomics sequencing and analyses of human colorectal cancer. Science (New York, N.Y.) 2018 Bian S, Hou Y, Zhou X, Li X, Yong J, Wang Y, Wang W, Yan J, Hu B, Guo H, Wang J, Gao S, Mao Y, Dong J, Zhu P, Xiu D, Yan L, Wen L, Qiao J, Tang F, Fu W.
28416141 Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells. Molecular cell 2017 Xie S, Duan J, Li B, Zhou P, Hon GC.
29358049 Ultraconserved Enhancers Are Required for Normal Development. Cell 2018 Dickel DE, Ypsilanti AR, Pla R, Zhu Y, Barozzi I, Mannion BJ, Khin YS, Fukuda-Yuzawa Y, Plajzer-Frick I, Pickle CS, Lee EA, Harrington AN, Pham QT, Garvin TH, Kato M, Osterwalder M, Akiyama JA, Afzal V, Rubenstein JLR, Pennacchio LA, Visel A.
29796188 The effects of restricted glycolysis on stem-cell like characteristics of breast cancer cells. Oncotarget 2018 Banerjee A, Arvinrad P, Darley M, Laversin SA, Parker R, Rose-Zerilli MJJ, Townsend PA, Cutress RI, Beers SA, Houghton FD, Birts CN, Blaydes JP.
29779890 High-Throughput Screening Enhances Kidney Organoid Differentiation from Human Pluripotent Stem Cells and Enables Automated Multidimensional Phenotyping. Cell stem cell 2018 Czerniecki SM, Cruz NM, Harder JL, Menon R, Annis J, Otto EA, Gulieva RE, Islas LV, Kim YK, Tran LM, Martins TJ, Pippin JW, Fu H, Kretzler M, Shankland SJ, Himmelfarb J, Moon RT, Paragas N, Freedman BS.
30626756 Organoid single cell profiling identifies a transcriptional signature of glomerular disease. JCI insight 2019 Harder JL, Menon R, Otto EA, Zhou J, Eddy S, Wys NL, O'Connor C, Luo J, Nair V, Cebrian C, Spence JR, Bitzer M, Troyanskaya OG, Hodgin JB, Wiggins RC, Freedman BS, Kretzler M, European Renal cDNA Bank (ERCB), Nephrotic Syndrome Study Network (NEPTUNE).
31090537 HSV-1 single-cell analysis reveals the activation of anti-viral and developmental programs in distinct sub-populations. eLife 2019 Drayman N, Patel P, Vistain L, Tay S.
27667365 A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure. Cell systems 2016 Baron M, Veres A, Wolock SL, Faust AL, Gaujoux R, Vetere A, Ryu JH, Wagner BK, Shen-Orr SS, Klein AM, Melton DA, Yanai I.
28514439 Haematopoietic stem and progenitor cells from human pluripotent stem cells. Nature 2017 Sugimura R, Jha DK, Han A, Soria-Valles C, da Rocha EL, Lu YF, Goettel JA, Serrao E, Rowe RG, Malleshaiah M, Wong I, Sousa P, Zhu TN, Ditadi A, Keller G, Engelman AN, Snapper SB, Doulatov S, Daley GQ.
29980650 Single-Cell Transcriptomics of a Human Kidney Allograft Biopsy Specimen Defines a Diverse Inflammatory Response. Journal of the American Society of Nephrology : JASN 2018 Wu H, Malone AF, Donnelly EL, Kirita Y, Uchimura K, Ramakrishnan SM, Gaut JP, Humphreys BD.
31068696 Charting cellular identity during human in vitro β-cell differentiation. Nature 2019 Veres A, Faust AL, Bushnell HL, Engquist EN, Kenty JH, Harb G, Poh YC, Sintov E, Gürtler M, Pagliuca FW, Peterson QP, Melton DA.
29149607 Classifying Drosophila Olfactory Projection Neuron Subtypes by Single-Cell RNA Sequencing. Cell 2017 Li H, Horns F, Wu B, Xie Q, Li J, Li T, Luginbuhl DJ, Quake SR, Luo L.
30002204 Integrated Analysis of Quantitative Proteome and Transcriptional Profiles Reveals the Dynamic Function of Maternally Expressed Proteins After Parthenogenetic Activation of Buffalo Oocyte. Molecular & cellular proteomics : MCP 2018 Chen F, Fu Q, Pu L, Zhang P, Huang Y, Hou Z, Xu Z, Chen D, Huang F, Deng T, Liang X, Lu Y, Zhang M.
33380778 Single-cell transcriptomic profiling provides insights into retinal endothelial barrier properties. Molecular vision 2020 Watson MI, Barabas P, McGahon M, McMahon M, Fuchs MA, Curtis TM, Simpson DA.
32059767 Single-Cell Transcriptomes Reveal Diverse Regulatory Strategies for Olfactory Receptor Expression and Axon Targeting. Current biology : CB 2020 Li H, Li T, Horns F, Li J, Xie Q, Xu C, Wu B, Kebschull JM, McLaughlin CN, Kolluru SS, Jones RC, Vacek D, Xie A, Luginbuhl DJ, Quake SR, Luo L.
33427646 Temporal evolution of single-cell transcriptomes of Drosophila olfactory projection neurons. eLife 2021 Xie Q, Brbic M, Horns F, Kolluru SS, Jones RC, Li J, Reddy AR, Xie A, Kohani S, Li Z, McLaughlin CN, Li T, Xu C, Vacek D, Luginbuhl DJ, Leskovec J, Quake SR, Luo L, Li H.
30718350 Single-Cell RNA Sequencing Resolves Molecular Relationships Among Individual Plant Cells. Plant physiology 2019 Ryu KH, Huang L, Kang HM, Schiefelbein J.
28585562 Sperm cells are passive cargo of the pollen tube in plant fertilization. Nature plants 2017 Zhang J, Huang Q, Zhong S, Bleckmann A, Huang J, Guo X, Lin Q, Gu H, Dong J, Dresselhaus T, Qu LJ.
32035984 Single-cell transcriptome analysis of human skin identifies novel fibroblast subpopulation and enrichment of immune subsets in atopic dermatitis. The Journal of allergy and clinical immunology 2020 He H, Suryawanshi H, Morozov P, Gay-Mimbrera J, Del Duca E, Kim HJ, Kameyama N, Estrada Y, Der E, Krueger JG, Ruano J, Tuschl T, Guttman-Yassky E.
32042191 Regenerative lineages and immune-mediated pruning in lung cancer metastasis. Nature medicine 2020 Laughney AM, Hu J, Campbell NR, Bakhoum SF, Setty M, Lavallée VP, Xie Y, Masilionis I, Carr AJ, Kottapalli S, Allaj V, Mattar M, Rekhtman N, Xavier JB, Mazutis L, Poirier JT, Rudin CM, Pe'er D, Massagué J.
31624246 Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease. Nature communications 2019 Szabo PA, Levitin HM, Miron M, Snyder ME, Senda T, Yuan J, Cheng YL, Bush EC, Dogra P, Thapa P, Farber DL, Sims PA.
31768052 A single-cell atlas of entorhinal cortex from individuals with Alzheimer's disease reveals cell-type-specific gene expression regulation. Nature neuroscience 2019 Grubman A, Chew G, Ouyang JF, Sun G, Choo XY, McLean C, Simmons RK, Buckberry S, Vargas-Landin DB, Poppe D, Pflueger J, Lister R, Rackham OJL, Petretto E, Polo JM.
31653841 Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration. Nature communications 2019 Menon M, Mohammadi S, Davila-Velderrain J, Goods BA, Cadwell TD, Xing Y, Stemmer-Rachamimov A, Shalek AK, Love JC, Kellis M, Hafler BP.
31506348 The single-cell transcriptomic landscape of early human diabetic nephropathy. Proceedings of the National Academy of Sciences of the United States of America 2019 Wilson PC, Wu H, Kirita Y, Uchimura K, Ledru N, Rennke HG, Welling PA, Waikar SS, Humphreys BD.
31402260 Single-Cell Survey of Human Lymphatics Unveils Marked Endothelial Cell Heterogeneity and Mechanisms of Homing for Neutrophils. Immunity 2019 Takeda A, Hollmén M, Dermadi D, Pan J, Brulois KF, Kaukonen R, Lönnberg T, Boström P, Koskivuo I, Irjala H, Miyasaka M, Salmi M, Butcher EC, Jalkanen S.
32327715 Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming. Communications biology 2020 Solé-Boldo L, Raddatz G, Schütz S, Mallm JP, Rippe K, Lonsdorf AS, Rodríguez-Paredes M, Lyko F.
31937892 Single-cell transcriptional profiles in human skeletal muscle. Scientific reports 2020 Rubenstein AB, Smith GR, Raue U, Begue G, Minchev K, Ruf-Zamojski F, Nair VD, Nair VD, Wang X, Zhou L, Zaslavsky E, Trappe TA, Trappe S, Sealfon SC.
32238801 Endothelialization of arterial vascular grafts by circulating monocytes. Nature communications 2020 Smith RJ, Nasiri B, Kann J, Yergeau D, Bard JE, Swartz DD, Andreadis ST.
30886407 Cerebral organoids at the air-liquid interface generate diverse nerve tracts with functional output. Nature neuroscience 2019 Giandomenico SL, Mierau SB, Gibbons GM, Wenger LMD, Masullo L, Sit T, Sutcliffe M, Boulanger J, Tripodi M, Derivery E, Paulsen O, Lakatos A, Lancaster MA.
32109367 Aberrant Development Corrected in Adult-Onset Huntington's Disease iPSC-Derived Neuronal Cultures via WNT Signaling Modulation. Stem cell reports 2020 Smith-Geater C, Hernandez SJ, Lim RG, Adam M, Wu J, Stocksdale JT, Wassie BT, Gold MP, Wang KQ, Miramontes R, Kopan L, Orellana I, Joy S, Kemp PJ, Allen ND, Fraenkel E, Thompson LM.
32054662 Comparative single-cell RNA sequencing (scRNA-seq) reveals liver metastasis-specific targets in a patient with small intestinal neuroendocrine cancer. Cold Spring Harbor molecular case studies 2020 Rao M, Oh K, Moffitt R, Thompson P, Li J, Liu J, Sasson A, Georgakis G, Kim J, Choi M, Powers S.
31511693 Controlled modelling of human epiblast and amnion development using stem cells. Nature 2019 Zheng Y, Xue X, Shao Y, Wang S, Esfahani SN, Li Z, Muncie JM, Lakins JN, Weaver VM, Gumucio DL, Fu J.
31317052 Single-cell RNA-Seq analysis identifies a putative epithelial stem cell population in human primary prostate cells in monolayer and organoid culture conditions. American journal of clinical and experimental urology 2019 McCray T, Moline D, Baumann B, Vander Griend DJ, Nonn L.
31332193 Predicting bacterial infection outcomes using single cell RNA-sequencing analysis of human immune cells. Nature communications 2019 Bossel Ben-Moshe N, Hen-Avivi S, Levitin N, Yehezkel D, Oosting M, Joosten LAB, Netea MG, Avraham R.
31155493 Modeling Steatohepatitis in Humans with Pluripotent Stem Cell-Derived Organoids. Cell metabolism 2019 Ouchi R, Togo S, Kimura M, Shinozawa T, Koido M, Koike H, Thompson W, Karns RA, Mayhew CN, McGrath PS, McCauley HA, Zhang RR, Lewis K, Hakozaki S, Ferguson A, Saiki N, Yoneyama Y, Takeuchi I, Mabuchi Y, Akazawa C, Yoshikawa HY, Wells JM, Takebe T.
31477722 Heterogeneity of human bone marrow and blood natural killer cells defined by single-cell transcriptome. Nature communications 2019 Yang C, Siebert JR, Burns R, Gerbec ZJ, Bonacci B, Rymaszewski A, Rau M, Riese MJ, Rao S, Carlson KS, Routes JM, Verbsky JW, Thakar MS, Malarkannan S.
32142123 Single cell transcriptome profiling of the human alcohol-dependent brain. Human molecular genetics 2020 Brenner E, Tiwari GR, Kapoor M, Liu Y, Brock A, Mayfield RD.
31928944 The Dynamic Transcriptional Cell Atlas of Testis Development during Human Puberty. Cell stem cell 2020 Guo J, Nie X, Giebler M, Mlcochova H, Wang Y, Grow EJ, DonorConnect, Kim R, Tharmalingam M, Matilionyte G, Lindskog C, Carrell DT, Mitchell RT, Goriely A, Hotaling JM, Cairns BR.
33521652 Single-cell analyses reveal increased intratumoral heterogeneity after the onset of therapy resistance in small-cell lung cancer. Nature cancer 2020 Stewart CA, Gay CM, Xi Y, Sivajothi S, Sivakamasundari V, Fujimoto J, Bolisetty M, Hartsfield PM, Balasubramaniyan V, Chalishazar MD, Moran C, Kalhor N, Stewart J, Tran H, Swisher SG, Roth JA, Zhang J, de Groot J, Glisson B, Oliver TG, Heymach JV, Wistuba I, Robson P, Wang J, Byers LA.
32271902 Diversity of peripheral blood human NK cells identified by single-cell RNA sequencing. Blood advances 2020 Smith SL, Kennedy PR, Stacey KB, Worboys JD, Yarwood A, Seo S, Solloa EH, Mistretta B, Chatterjee SS, Gunaratne P, Allette K, Wang YC, Smith ML, Sebra R, Mace EM, Horowitz A, Thomson W, Martin P, Eyre S, Davis DM.
30664737 Memory CD4+ T cells are generated in the human fetal intestine. Nature immunology 2019 Li N, van Unen V, Abdelaal T, Guo N, Kasatskaya SA, Ladell K, McLaren JE, Egorov ES, Izraelson M, Chuva de Sousa Lopes SM, Höllt T, Britanova OV, Eggermont J, de Miranda NFCC, Chudakov DM, Price DA, Lelieveldt BPF, Koning F.
30674341 Single-cell analysis reveals congruence between kidney organoids and human fetal kidney. Genome medicine 2019 Combes AN, Zappia L, Er PX, Oshlack A, Little MH.
32386599 Single-Cell Analysis of Human Retina Identifies Evolutionarily Conserved and Species-Specific Mechanisms Controlling Development. Developmental cell 2020 Lu Y, Shiau F, Yi W, Lu S, Wu Q, Pearson JD, Kallman A, Zhong S, Hoang T, Zuo Z, Zhao F, Zhang M, Tsai N, Zhuo Y, He S, Zhang J, Stein-O'Brien GL, Sherman TD, Duan X, Fertig EJ, Goff LA, Zack DJ, Handa JT, Xue T, Bremner R, Blackshaw S, Wang X, Clark BS.
31907413 Multipotent RAG1+ progenitors emerge directly from haemogenic endothelium in human pluripotent stem cell-derived haematopoietic organoids. Nature cell biology 2020 Motazedian A, Bruveris FF, Kumar SV, Schiesser JV, Chen T, Ng ES, Chidgey AP, Wells CA, Elefanty AG, Stanley EG.
31861624 Single-Cell Expression Variability Implies Cell Function. Cells 2019 Osorio D, Yu X, Zhong Y, Li G, Yu P, Serpedin E, Huang JZ, Cai JJ.
31075224 Molecular characterization of foveal versus peripheral human retina by single-cell RNA sequencing. Experimental eye research 2019 Voigt AP, Whitmore SS, Flamme-Wiese MJ, Riker MJ, Wiley LA, Tucker BA, Stone EM, Mullins RF, Scheetz TE.
32351704 Single-cell RNA sequencing reveals the heterogeneity of liver-resident immune cells in human. Cell discovery 2020 Zhao J, Zhang S, Liu Y, He X, Qu M, Xu G, Wang H, Huang M, Pan J, Liu Z, Li Z, Liu L, Zhang Z.
31067475 Dissecting the Single-Cell Transcriptome Network Underlying Gastric Premalignant Lesions and Early Gastric Cancer. Cell reports 2019 Zhang P, Yang M, Zhang Y, Xiao S, Lai X, Tan A, Du S, Li S.
30356220 Gene expression variability across cells and species shapes innate immunity. Nature 2018 Hagai T, Chen X, Miragaia RJ, Rostom R, Gomes T, Kunowska N, Henriksson J, Park JE, Proserpio V, Donati G, Bossini-Castillo L, Vieira Braga FA, Naamati G, Fletcher J, Stephenson E, Vegh P, Trynka G, Kondova I, Dennis M, Haniffa M, Nourmohammad A, Lässig M, Teichmann SA.
30154223 Single-cell RNA-sequencing reveals the existence of naive and primed pluripotency in pre-implantation rhesus monkey embryos. Genome research 2018 Liu D, Wang X, He D, Sun C, He X, Yan L, Li Y, Han JJ, Zheng P.
32058160 Elevated circulating Th2 but not group 2 innate lymphoid cell responses characterize canine atopic dermatitis. Veterinary immunology and immunopathology 2020 Früh SP, Saikia M, Eule J, Mazulis CA, Miller JE, Cowulich JM, Oyesola OO, Webb LM, Peng SA, Cubitt RL, Danko CG, Miller WH, Tait Wojno ED.
33197070 Characterization of sheep spermatogenesis through single-cell RNA sequencing. FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2021 Yang H, Ma J, Wan Z, Wang Q, Wang Z, Zhao J, Wang F, Zhang Y.
32268081 Insights into Gonadal Sex Differentiation Provided by Single-Cell Transcriptomics in the Chicken Embryo. Cell reports 2020 Estermann MA, Williams S, Hirst CE, Roly ZY, Serralbo O, Adhikari D, Powell D, Major AT, Smith CA.
29678445 Spatial patterns of gene expression are unveiled in the chick primitive streak by ordering single-cell transcriptomes. Developmental biology 2018 Vermillion KL, Bacher R, Tannenbaum AP, Swanson S, Jiang P, Chu LF, Stewart R, Thomson JA, Vereide DT.
31117954 A single-cell transcriptomic atlas of the developing chicken limb. BMC genomics 2019 Feregrino C, Sacher F, Parnas O, Tschopp P.
32680935 Prdm8 regulates pMN progenitor specification for motor neuron and oligodendrocyte fates by modulating the Shh signaling response. Development (Cambridge, England) 2020 Scott K, O'Rourke R, Gillen A, Appel B.
32900993 Single-cell transcriptome maps of myeloid blood cell lineages in Drosophila. Nature communications 2020 Cho B, Yoon SH, Lee D, Koranteng F, Tattikota SG, Cha N, Shin M, Do H, Hu Y, Oh SY, Lee D, Vipin Menon A, Moon SJ, Perrimon N, Nam JW, Shim J.
29700227 The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution. Science (New York, N.Y.) 2018 Briggs JA, Weinreb C, Wagner DE, Megason S, Peshkin L, Kirschner MW, Klein AM.
31488706 A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution. Science (New York, N.Y.) 2019 Packer JS, Zhu Q, Huynh C, Sivaramakrishnan P, Preston E, Dueck H, Stefanik D, Tan K, Trapnell C, Kim J, Waterston RH, Murray JI.
32973030 A single-cell RNA-seq atlas of Schistosoma mansoni identifies a key regulator of blood feeding. Science (New York, N.Y.) 2020 Wendt G, Zhao L, Chen R, Liu C, O'Donoghue AJ, Caffrey CR, Reese ML, Collins JJ.
30096287 Exploring parasite heterogeneity using single-cell RNA-seq reveals a gene signature among sexual stage Plasmodium falciparum parasites. Experimental cell research 2018 Ngara M, Palmkvist M, Sagasser S, Hjelmqvist D, Björklund ÅK, Wahlgren M, Ankarklev J, Sandberg R.
32420869 A new protocol for single-cell RNA-seq reveals stochastic gene expression during lag phase in budding yeast. eLife 2020 Jariani A, Vermeersch L, Cerulus B, Perez-Samper G, Voordeckers K, Van Brussel T, Thienpont B, Lambrechts D, Verstrepen KJ.
32255425 Cell and molecular transitions during efficient dedifferentiation. eLife 2020 Nichols JM, Antolović V, Reich JD, Brameyer S, Paschke P, Chubb JR.
31417977 Network-based feature selection reveals substructures of gene modules responding to salt stress in rice. Plant direct 2019 Du Q, Campbell M, Yu H, Liu K, Walia H, Zhang Q, Zhang C.
32513103 Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa). BMC genomics 2020 Campbell MT, Du Q, Liu K, Sharma S, Zhang C, Walia H.
27859855 Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation. The Plant journal : for cell and molecular biology 2017 Narsai R, Secco D, Schultz MD, Ecker JR, Lister R, Whelan J.
31959799 Rice pyramided line IRBB67 (Xa4/Xa7) homeostasis under combined stress of high temperature and bacterial blight. Scientific reports 2020 Dossa GS, Quibod I, Atienza-Grande G, Oliva R, Maiss E, Vera Cruz C, Wydra K.
30253806 Dynamics and functional interplay of histone lysine butyrylation, crotonylation, and acetylation in rice under starvation and submergence. Genome biology 2018 Lu Y, Xu Q, Liu Y, Yu Y, Cheng ZY, Zhao Y, Zhou DX.
29265542 Stress-responsive regulation of long non-coding RNA polyadenylation in Oryza sativa. The Plant journal : for cell and molecular biology 2018 Yuan J, Li J, Yang Y, Tan C, Zhu Y, Hu L, Qi Y, Lu ZJ.
29314052 OsPRR37 confers an expanded regulation of the diurnal rhythms of the transcriptome and photoperiodic flowering pathways in rice. Plant, cell & environment 2018 Liu C, Qu X, Zhou Y, Song G, Abiri N, Xiao Y, Liang F, Jiang D, Hu Z, Yang D.
28821707 Molecular bases for differential aging programs between flag and second leaves during grain-filling in rice. Scientific reports 2017 Lee S, Jeong H, Lee S, Lee J, Kim SJ, Park JW, Woo HR, Lim PO, An G, Nam HG, Hwang D.
29094353 Rice SUB1A constrains remodelling of the transcriptome and metabolome during submergence to facilitate post-submergence recovery. Plant, cell & environment 2018 Locke AM, Barding GA, Sathnur S, Larive CK, Bailey-Serres J.
28653111 Seed weight differences between wild and domesticated soybeans are associated with specific changes in gene expression. Plant cell reports 2017 Yu C, Qu Z, Zhang Y, Zhang X, Lan T, Adelson DL, Wang D, Zhu Y.
24755115 Identification and characterization of transcript polymorphisms in soybean lines varying in oil composition and content. BMC genomics 2014 Goettel W, Xia E, Upchurch R, Wang ML, Chen P, An YQ.
26678836 Genome-wide transcriptome analyses of developing seeds from low and normal phytic acid soybean lines. BMC genomics 2015 Redekar NR, Biyashev RM, Jensen RV, Helm RF, Grabau EA, Maroof MA.
25070765 Transcription factors and glyoxylate cycle genes prominent in the transition of soybean cotyledons to the first functional leaves of the seedling. Functional & integrative genomics 2014 Shamimuzzaman M, Vodkin L.
23555009 Using RNA-Seq to profile soybean seed development from fertilization to maturity. PloS one 2013 Jones SI, Vodkin LO.
25635113 Direct detection of transcription factors in cotyledons during seedling development using sensitive silicon-substrate photonic crystal protein arrays. Plant physiology 2015 Jones SI, Tan Y, Shamimuzzaman M, George S, Cunningham BT, Vodkin L.
31456133 Pod-shattering characteristics differences between two groups of soybeans are associated with specific changes in gene expression. Functional & integrative genomics 2020 Kang X, Cai J, Chen Y, Yan Y, Yang S, He R, Wang D, Zhu Y.
31757957 Glycerol-3-phosphate mediates rhizobia-induced systemic signaling in soybean. Nature communications 2019 Shine MB, Gao QM, Chowda-Reddy RV, Singh AK, Kachroo P, Kachroo A.
26689712 Transcriptome profiling of soybean (Glycine max) roots challenged with pathogenic and non-pathogenic isolates of Fusarium oxysporum. BMC genomics 2015 Lanubile A, Muppirala UK, Severin AJ, Marocco A, Munkvold GP.
31341170 Transcriptome profiling of interaction effects of soybean cyst nematodes and soybean aphids on soybean. Scientific data 2019 Neupane S, Mathew FM, Varenhorst AJ, Nepal MP.
26350764 Identification of Soybean Proteins and Genes Differentially Regulated in Near Isogenic Lines Differing in Resistance to Aphid Infestation. Journal of proteome research 2015 Brechenmacher L, Nguyen TH, Zhang N, Jun TH, Xu D, Mian MA, Stacey G.
31182145 Transcriptome profiling of induced susceptibility effects on soybean-soybean aphid (Hemiptera: Aphididae) interaction. BMC research notes 2019 Neupane S, Varenhorst AJ, Nepal MP.
30041471 Early Transcriptomic Response to Phosphate Deprivation in Soybean Leaves as Revealed by RNA-Sequencing. International journal of molecular sciences 2018 Zeng H, Zhang X, Zhang X, Pi E, Xiao L, Zhu Y.
30261621 Genome Wide Transcriptome Analysis Reveals Complex Regulatory Mechanisms Underlying Phosphate Homeostasis in Soybean Nodules. International journal of molecular sciences 2018 Xue Y, Zhuang Q, Zhu S, Xiao B, Liang C, Liao H, Tian J.
31964983 Transcriptional trajectories of anther development provide candidates for engineering male fertility in sorghum. Scientific reports 2020 Dhaka N, Krishnan K, Kandpal M, Vashisht I, Pal M, Sharma MK, Sharma R.
30875440 Sorghum tiller bud growth is repressed by contact with the overlying leaf. Plant, cell & environment 2019 Liu R, Finlayson SA.
31806758 Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses. Proceedings of the National Academy of Sciences of the United States of America 2019 Varoquaux N, Cole B, Gao C, Pierroz G, Baker CR, Patel D, Madera M, Jeffers T, Hollingsworth J, Sievert J, Yoshinaga Y, Owiti JA, Singan VR, DeGraaf S, Xu L, Blow MJ, Harrison MJ, Visel A, Jansson C, Niyogi KK, Hutmacher R, Coleman-Derr D, O'Malley RC, Taylor JW, Dahlberg J, Vogel JP, Lemaux PG, Purdom E.
24597475 Identification of differentially expressed genes between sorghum genotypes with contrasting nitrogen stress tolerance by genome-wide transcriptional profiling. BMC genomics 2014 Gelli M, Duo Y, Konda AR, Zhang C, Holding D, Dweikat I.
30778362 The Impact of the Wheat Rht-B1b Semi-Dwarfing Allele on Photosynthesis and Seed Development Under Field Conditions. Frontiers in plant science 2019 Jobson EM, Johnston RE, Oiestad AJ, Martin JM, Giroux MJ.
31628162 The Transcriptional Landscape of Polyploid Wheats and Their Diploid Ancestors during Embryogenesis and Grain Development. The Plant cell 2019 Xiang D, Quilichini TD, Liu Z, Gao P, Pan Y, Li Q, Nilsen KT, Venglat P, Esteban E, Pasha A, Wang Y, Wen R, Zhang Z, Hao Z, Wang E, Wei Y, Cuthbert R, Kochian LV, Sharpe A, Provart N, Weijers D, Gillmor CS, Pozniak C, Datla R.
30804501 A linear nonribosomal octapeptide from Fusarium graminearum facilitates cell-to-cell invasion of wheat. Nature communications 2019 Jia LJ, Tang HY, Wang WQ, Yuan TL, Wei WQ, Pang B, Gong XM, Wang SF, Li YJ, Zhang D, Liu W, Tang WH.
24249833 Spatio-temporal transcript profiling of rice roots and shoots in response to phosphate starvation and recovery. The Plant cell 2013 Secco D, Jabnoune M, Walker H, Shou H, Wu P, Poirier Y, Whelan J.
25517485 Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice. Genome biology 2014 Zhang YC, Liao JY, Li ZY, Yu Y, Zhang JP, Li QF, Qu LH, Shu WS, Chen YQ.
24816929 Genome-wide transcriptome analysis reveals that cadmium stress signaling controls the expression of genes in drought stress signal pathways in rice. PloS one 2014 Oono Y, Yazawa T, Kawahara Y, Kanamori H, Kobayashi F, Sasaki H, Mori S, Wu J, Handa H, Itoh T, Matsumoto T.
24577842 Genome-wide disruption of gene expression in allopolyploids but not hybrids of rice subspecies. Molecular biology and evolution 2014 Xu C, Bai Y, Lin X, Zhao N, Hu L, Gong Z, Wendel JF, Liu B.
25002488 Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality. Proceedings of the National Academy of Sciences of the United States of America 2014 Hu L, Li N, Xu C, Zhong S, Lin X, Yang J, Zhou T, Yuliang A, Wu Y, Chen YR, Cao X, Zemach A, Rustgi S, von Wettstein D, Liu B.
24635777 Rice germline-specific Argonaute MEL1 protein binds to phasiRNAs generated from more than 700 lincRNAs. The Plant journal : for cell and molecular biology 2014 Komiya R, Ohyanagi H, Niihama M, Watanabe T, Nakano M, Kurata N, Nonomura K.
22042334 Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes. Genome biology and evolution 2011 Sakai H, Mizuno H, Kawahara Y, Wakimoto H, Ikawa H, Kawahigashi H, Kanamori H, Matsumoto T, Itoh T, Gaut BS.
23857470 Diversity in the complexity of phosphate starvation transcriptomes among rice cultivars based on RNA-Seq profiles. Plant molecular biology 2013 Oono Y, Kawahara Y, Yazawa T, Kanamori H, Kuramata M, Yamagata H, Hosokawa S, Minami H, Ishikawa S, Wu J, Antonio B, Handa H, Itoh T, Matsumoto T.
22537016 Comparative transcriptome analysis of transporters, phytohormone and lipid metabolism pathways in response to arsenic stress in rice (Oryza sativa). The New phytologist 2012 Yu LJ, Luo YF, Liao B, Xie LJ, Chen L, Xiao S, Li JT, Hu SN, Shu WS.
26243209 Loss of function mutations in the rice chromomethylase OsCMT3a cause a burst of transposition. The Plant journal : for cell and molecular biology 2015 Cheng C, Tarutani Y, Miyao A, Ito T, Yamazaki M, Sakai H, Fukai E, Hirochika H.
26257749 TAL effectors and activation of predicted host targets distinguish Asian from African strains of the rice pathogen Xanthomonas oryzae pv. oryzicola while strict conservation suggests universal importance of five TAL effectors. Frontiers in plant science 2015 Wilkins KE, Booher NJ, Wang L, Bogdanove AJ.
26821568 A transcription activator-like effector from Xanthomonas oryzae pv. oryzicola elicits dose-dependent resistance in rice. Molecular plant pathology 2017 Hummel AW, Wilkins KE, Wang L, Cernadas RA, Bogdanove AJ.
26196146 Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements. eLife 2015 Secco D, Wang C, Shou H, Schultz MD, Chiarenza S, Nussaume L, Ecker JR, Whelan J, Lister R.
32553274 Pan-Genome of Wild and Cultivated Soybeans. Cell 2020 Liu Y, Du H, Li P, Shen Y, Peng H, Liu S, Zhou GA, Zhang H, Liu Z, Shi M, Huang X, Li Y, Zhang M, Wang Z, Zhu B, Han B, Liang C, Tian Z.
32398875 Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19. Nature medicine 2020 Liao M, Liu Y, Yuan J, Wen Y, Xu G, Zhao J, Cheng L, Li J, Wang X, Wang F, Liu L, Amit I, Zhang S, Zhang Z.