Gene Expression Nebulas

Publications

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.
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