Homo sapiens - Gene Expression Nebulas


Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns. Enge M, Arda HE, Mignardi M, Beausang J, Bottino R, Kim SK, Quake SR. Cell. 2017-09-28; 171 (2) PMID: 28965763 DOI: 10.1016/j.cell.2017.09.004
CD40L-Dependent Pathway Is Active at Various Stages of Rheumatoid Arthritis Disease Progression. 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. J Immunol. 2017-04-28; 198 (11) PMID: 28455435 DOI: 10.4049/jimmunol.1601988
The Long Non-coding RNA NRIR Drives IFN-Response in Monocytes: Implication for Systemic Sclerosis. Mariotti B, Servaas NH, Rossato M, Tamassia N, Cassatella MA, Cossu M, Beretta L, van der Kroef M, Radstake TRDJ, Bazzoni F. Front Immunol. 2019-01-31; 10 PMID: 30804934 DOI: 10.3389/fimmu.2019.00100
Transcriptional Programs Define Intratumoral Heterogeneity of Ewing Sarcoma at Single-Cell Resolution. 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. Cell Rep. 2020-02-01; 30 (6) PMID: 32049009 DOI: 10.1016/j.celrep.2020.01.049
Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline. 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. Nat Commun. 2018-10-01; 9 (1) PMID: 30275468 DOI: 10.1038/s41467-018-06353-4
Prosurvival kinase PIM2 is a therapeutic target for eradication of chronic myeloid leukemia stem cells. Ma L, Pak ML, Ou J, Yu J, St Louis P, Shan Y, Hutchinson L, Li S, Brehm MA, Zhu LJ, Green MR. Proc Natl Acad Sci U S A. 2019-05-08; 116 (21) PMID: 31068472 DOI: 10.1073/pnas.1903550116
Functional inflammatory profiles distinguish myelin-reactive T cells from patients with multiple sclerosis. Cao Y, Goods BA, Raddassi K, Nepom GT, Kwok WW, Love JC, Hafler DA. Sci Transl Med. 2015-05-01; 7 (287) PMID: 25972006 DOI: 10.1126/scitranslmed.aaa8038
Human Naive Pluripotent Stem Cells Model X Chromosome Dampening and X Inactivation. Sahakyan A, Kim R, Chronis C, Sabri S, Bonora G, Theunissen TW, Kuoy E, Langerman J, Clark AT, Jaenisch R, Plath K. Cell Stem Cell. 2016-12-15; 20 (1) PMID: 27989770 DOI: 10.1016/j.stem.2016.10.006
Bronchial extracellular matrix from COPD patients induces altered gene expression in repopulated primary human bronchial epithelial cells. Hedström U, Hallgren O, Öberg L, DeMicco A, Vaarala O, Westergren-Thorsson G, Zhou X. Sci Rep. 2018-02-22; 8 (1) PMID: 29472603 DOI: 10.1038/s41598-018-21727-w
Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration. Menon M, Mohammadi S, Davila-Velderrain J, Goods BA, Cadwell TD, Xing Y, Stemmer-Rachamimov A, Shalek AK, Love JC, Kellis M, Hafler BP. Nat Commun. 2019-10-25; 10 (1) PMID: 31653841 DOI: 10.1038/s41467-019-12780-8
Predicting bacterial infection outcomes using single cell RNA-sequencing analysis of human immune cells. Bossel Ben-Moshe N, Hen-Avivi S, Levitin N, Yehezkel D, Oosting M, Joosten LAB, Netea MG, Avraham R. Nat Commun. 2019-07-22; 10 (1) PMID: 31332193 DOI: 10.1038/s41467-019-11257-y
Modeling Steatohepatitis in Humans with Pluripotent Stem Cell-Derived Organoids. 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. Cell Metab. 2019-05-30; 30 (2) PMID: 31155493 DOI: 10.1016/j.cmet.2019.05.007
Population and single‑cell transcriptome analyses reveal diverse transcriptional changes associated with radioresistance in esophageal squamous cell carcinoma. Wu H, Yu J, Kong D, Xu Y, Zhang Z, Shui J, Li Z, Luo H, Wang K. Int J Oncol. 2019-10-14; 55 (6) PMID: 31638164 DOI: 10.3892/ijo.2019.4897
Diversity of peripheral blood human NK cells identified by single-cell RNA sequencing. 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. Blood Adv. 2020-04-01; 4 (7) PMID: 32271902 DOI: 10.1182/bloodadvances.2019000699
Deletion of the Polycomb-Group Protein EZH2 Leads to Compromised Self-Renewal and Differentiation Defects in Human Embryonic Stem Cells. Collinson A, Collier AJ, Morgan NP, Sienerth AR, Chandra T, Andrews S, Rugg-Gunn PJ. Cell Rep. 2016-12-01; 17 (10) PMID: 27926872 DOI: 10.1016/j.celrep.2016.11.032
Copy number loss of the interferon gene cluster in melanomas is linked to reduced T cell infiltrate and poor patient prognosis. Linsley PS, Speake C, Whalen E, Chaussabel D. PLoS One. 2014-10-14; 9 (10) PMID: 25314013 DOI: 10.1371/journal.pone.0109760
Transcriptome analysis of psoriasis in a large case-control sample: RNA-seq provides insights into disease mechanisms. 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. J Invest Dermatol. 2014-01-17; 134 (7) PMID: 24441097 DOI: 10.1038/jid.2014.28
Single-cell transcriptomics of the human placenta: inferring the cell communication network of the maternal-fetal interface. Pavličev M, Wagner GP, Chavan AR, Owens K, Maziarz J, Dunn-Fletcher C, Kallapur SG, Muglia L, Jones H. Genome Res. 2017-02-07; 27 (3) PMID: 28174237 DOI: 10.1101/gr.207597.116
Batch effects and the effective design of single-cell gene expression studies. Tung PY, Blischak JD, Hsiao CJ, Knowles DA, Burnett JE, Pritchard JK, Gilad Y. Sci Rep. 2017-01-03; 7 PMID: 28045081 DOI: 10.1038/srep39921
Charting cellular identity during human in vitro β-cell differentiation. Veres A, Faust AL, Bushnell HL, Engquist EN, Kenty JH, Harb G, Poh YC, Sintov E, Gürtler M, Pagliuca FW, Peterson QP, Melton DA. Nature. 2019-05-08; 569 (7756) PMID: 31068696 DOI: 10.1038/s41586-019-1168-5
Chromatin Accessibility Landscape in Human Early Embryos and Its Association with Evolution. 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. Cell. 2018-03-08; 173 (1) PMID: 29526463 DOI: 10.1016/j.cell.2018.02.028
Cerebral organoids at the air-liquid interface generate diverse nerve tracts with functional output. 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. Nat Neurosci. 2019-03-18; 22 (4) PMID: 30886407 DOI: 10.1038/s41593-019-0350-2
Single-cell RNA sequencing reveals metallothionein heterogeneity during hESC differentiation to definitive endoderm. Lu J, Baccei A, Lummertz da Rocha E, Guillermier C, McManus S, Finney LA, Zhang C, Steinhauser ML, Li H, Lerou PH. Stem Cell Res. 2018-01-31; 28 PMID: 29427839 DOI: 10.1016/j.scr.2018.01.015
Alterations in the Transcriptional Programs of Myeloma Cells and the Microenvironment during Extramedullary Progression Affect Proliferation and Immune Evasion. Ryu D, Kim SJ, Hong Y, Jo A, Kim N, Kim HJ, Lee HO, Kim K, Park WY. Clin Cancer Res. 2019-09-26; 26 (4) PMID: 31558476 DOI: 10.1158/1078-0432.ccr-19-0694
Hemopoietic-specific Sf3b1-K700E knock-in mice display the splicing defect seen in human MDS but develop anemia without ring sideroblasts. 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. Leukemia. 2016-09-08; 31 (3) PMID: 27604819 DOI: 10.1038/leu.2016.251
Dissecting the Single-Cell Transcriptome Network Underlying Gastric Premalignant Lesions and Early Gastric Cancer. Zhang P, Yang M, Zhang Y, Xiao S, Lai X, Tan A, Du S, Li S. Cell Rep. 2019-05-01; 27 (6) PMID: 31067475 DOI: 10.1016/j.celrep.2019.04.052
Plasma extracellular vesicle long RNA profiling identifies a diagnostic signature for the detection of pancreatic ductal adenocarcinoma. 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. Gut. 2019-09-27; 69 (3) PMID: 31562239 DOI: 10.1136/gutjnl-2019-318860
Cancer-Associated SF3B1 Hotspot Mutations Induce Cryptic 3' Splice Site Selection through Use of a Different Branch Point. 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. Cell Rep. 2015-10-22; 13 (5) PMID: 26565915 DOI: 10.1016/j.celrep.2015.09.053
Single-cell RNA sequencing reveals the heterogeneity of liver-resident immune cells in human. 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. Cell Discov. 2020-04-28; 6 PMID: 32351704 DOI: 10.1038/s41421-020-0157-z
Pseudotime Dynamics in Melanoma Single-Cell Transcriptomes Reveals Different Mechanisms of Tumor Progression. Loeffler-Wirth H, Binder H, Willscher E, Gerber T, Kunz M. Biology (Basel). 2018-04-03; 7 (2) PMID: 29614062 DOI: 10.3390/biology7020023
Pharmacodynamic biomarkers and differential effects of TNF- and GM-CSF-targeting biologics in rheumatoid arthritis. Guo X, Wang S, Godwood A, Close D, Ryan PC, Roskos LK, White WI. Int J Rheum Dis. 2018-10-24; 22 (4) PMID: 30358109 DOI: 10.1111/1756-185x.13395
Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. 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. Science. 2014-06-12; 344 (6190) PMID: 24925914 DOI: 10.1126/science.1254257
RNA-seq and flow-cytometry of conventional, scalp, and palmoplantar psoriasis reveal shared and distinct molecular pathways. 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. Sci Rep. 2018-07-27; 8 (1) PMID: 30054515 DOI: 10.1038/s41598-018-29472-w
Genomic analysis of DNA repair genes and androgen signaling in prostate cancer. Jividen K, Kedzierska KZ, Yang CS, Szlachta K, Ratan A, Paschal BM. BMC Cancer. 2018-10-10; 18 (1) PMID: 30305041 DOI: 10.1186/s12885-018-4848-x
Cell fixation and preservation for droplet-based single-cell transcriptomics. Alles J, Karaiskos N, Praktiknjo SD, Grosswendt S, Wahle P, Ruffault PL, Ayoub S, Schreyer L, Boltengagen A, Birchmeier C, Zinzen R, Kocks C, Rajewsky N. BMC Biol. 2017-05-19; 15 (1) PMID: 28526029 DOI: 10.1186/s12915-017-0383-5
Single-cell analyses reveal increased intratumoral heterogeneity after the onset of therapy resistance in small-cell lung cancer. 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. Nat Cancer. 2020-02-17; 1 PMID: 33521652 DOI: 10.1038/s43018-019-0020-z
Controlled modelling of human epiblast and amnion development using stem cells. Zheng Y, Xue X, Shao Y, Wang S, Esfahani SN, Li Z, Muncie JM, Lakins JN, Weaver VM, Gumucio DL, Fu J. Nature. 2019-09-11; 573 (7774) PMID: 31511693 DOI: 10.1038/s41586-019-1535-2
The K666N mutation in SF3B1 is associated with increased progression of MDS and distinct RNA splicing. Dalton WB, Helmenstine E, Pieterse L, Li B, Gocke CD, Donaldson J, Xiao Z, Gondek LP, Ghiaur G, Gojo I, Smith BD, Levis MJ, DeZern AE. Blood Adv. 2020-04-01; 4 (7) PMID: 32211880 DOI: 10.1182/bloodadvances.2019001127
Molecular characterization of foveal versus peripheral human retina by single-cell RNA sequencing. Voigt AP, Whitmore SS, Flamme-Wiese MJ, Riker MJ, Wiley LA, Tucker BA, Stone EM, Mullins RF, Scheetz TE. Exp Eye Res. 2019-05-08; 184 PMID: 31075224 DOI: 10.1016/j.exer.2019.05.001
Direct pericyte-to-neuron reprogramming via unfolding of a neural stem cell-like program. 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. Nat Neurosci. 2018-06-18; 21 (7) PMID: 29915193 DOI: 10.1038/s41593-018-0168-3
Genome wide abnormal DNA methylome of human blastocyst in assisted reproductive technology. 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. J Genet Genomics. 2017-09-06; 44 (10) PMID: 29037989 DOI: 10.1016/j.jgg.2017.09.001
Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients. 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. Emerg Microbes Infect. 2020-12-01; 9 (1) PMID: 32228226 DOI: 10.1080/22221751.2020.1747363
Ultraconserved Enhancers Are Required for Normal Development. 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. Cell. 2018-01-18; 172 (3) PMID: 29358049 DOI: 10.1016/j.cell.2017.12.017
Single-Cell RNA-seq Reveals a Subpopulation of Prostate Cancer Cells with Enhanced Cell-Cycle-Related Transcription and Attenuated Androgen Response. 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. Cancer Res. 2017-12-12; 78 (4) PMID: 29233929 DOI: 10.1158/0008-5472.can-17-1924
Single-cell transcriptomics reveals gene expression dynamics of human fetal kidney development. 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. PLoS Biol. 2019-02-21; 17 (2) PMID: 30789893 DOI: 10.1371/journal.pbio.3000152
Single-Cell Analysis of Human Retina Identifies Evolutionarily Conserved and Species-Specific Mechanisms Controlling Development. 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. Dev Cell. 2020-05-07; 53 (4) PMID: 32386599 DOI: 10.1016/j.devcel.2020.04.009
Single-cell RNA sequencing unveils the shared and the distinct cytotoxic hallmarks of human TCRVδ1 and TCRVδ2 γδ T lymphocytes. 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. Proc Natl Acad Sci U S A. 2019-05-22; 116 (24) PMID: 31118283 DOI: 10.1073/pnas.1818488116
Systems approach to the pharmacological actions of HDAC inhibitors reveals EP300 activities and convergent mechanisms of regulation in diabetes. Rafehi H, Kaspi A, Ziemann M, Okabe J, Karagiannis TC, El-Osta A, El-Osta A. Epigenetics. 2017-01-01; 12 (11) PMID: 28886276 DOI: 10.1080/15592294.2017.1371892
Triple DMARD treatment in early rheumatoid arthritis modulates synovial T cell activation and plasmablast/plasma cell differentiation pathways. Walsh AM, Wechalekar MD, Guo Y, Yin X, Weedon H, Proudman SM, Smith MD, Nagpal S. PLoS One. 2017-09-01; 12 (9) PMID: 28863153 DOI: 10.1371/journal.pone.0183928
Risk variants disrupting enhancers of TH1 and TREG cells in type 1 diabetes. Gao P, Uzun Y, He B, Salamati SE, Coffey JKM, Tsalikian E, Tan K. Proc Natl Acad Sci U S A. 2019-03-25; 116 (15) PMID: 30910956 DOI: 10.1073/pnas.1815336116
Zika virus shedding in the stool and infection through the anorectal mucosa in mice. 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. Emerg Microbes Infect. 2018-10-17; 7 (1) PMID: 30333476 DOI: 10.1038/s41426-018-0170-6
Single-cell transcriptional profiles in human skeletal muscle. 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. Sci Rep. 2020-01-14; 10 (1) PMID: 31937892 DOI: 10.1038/s41598-019-57110-6
Defining the three cell lineages of the human blastocyst by single-cell RNA-seq. Blakeley P, Fogarty NM, del Valle I, Wamaitha SE, Hu TX, Elder K, Snell P, Christie L, Robson P, Niakan KK. Development. 2015-08-20; 142 (18) PMID: 26293300 DOI: 10.1242/dev.123547
Stromal Microenvironment Shapes the Intratumoral Architecture of Pancreatic Cancer. 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. Cell. 2019-05-30; 178 (1) PMID: 31155233 DOI: 10.1016/j.cell.2019.05.012
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, Lennon NJ, Livak KJ, Mikkelsen TS, Rinn JL. Nat Biotechnol. 2014-03-23; 32 (4) PMID: 24658644 DOI: 10.1038/nbt.2859
A single-cell atlas of entorhinal cortex from individuals with Alzheimer's disease reveals cell-type-specific gene expression regulation. 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. Nat Neurosci. 2019-12-01; 22 (12) PMID: 31768052 DOI: 10.1038/s41593-019-0539-4
Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease. Szabo PA, Levitin HM, Miron M, Snyder ME, Senda T, Yuan J, Cheng YL, Bush EC, Dogra P, Thapa P, Farber DL, Sims PA. Nat Commun. 2019-10-17; 10 (1) PMID: 31624246 DOI: 10.1038/s41467-019-12464-3
Single cell sequencing reveals heterogeneity within ovarian cancer epithelium and cancer associated stromal cells. 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. Gynecol Oncol. 2017-01-19; 144 (3) PMID: 28111004 DOI: 10.1016/j.ygyno.2017.01.015
Adaptive from Innate: Human IFN-γ⁺CD4⁺ T Cells Can Arise Directly from CXCL8-Producing Recent Thymic Emigrants in Babies and Adults. Das A, Rouault-Pierre K, Kamdar S, Gomez-Tourino I, Wood K, Donaldson I, Mein CA, Bonnet D, Hayday AC, Gibbons DL. J Immunol. 2017-07-28; 199 (5) PMID: 28754679 DOI: 10.4049/jimmunol.1700551
Identification of RUNX1 as a Mediator of Aberrant Retinal Angiogenesis. 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. Diabetes. 2017-04-11; 66 (7) PMID: 28400392 DOI: 10.2337/db16-1035
RNA-seq Analysis Reveals Unique Transcriptome Signatures in Systemic Lupus Erythematosus Patients with Distinct Autoantibody Specificities. Rai R, Chauhan SK, Singh VV, Rai M, Rai G. PLoS One. 2016-11-11; 11 (11) PMID: 27835693 DOI: 10.1371/journal.pone.0166312
A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure. 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. Cell Syst. 2016-09-22; 3 (4) PMID: 27667365 DOI: 10.1016/j.cels.2016.08.011
Heterogeneity of human bone marrow and blood natural killer cells defined by single-cell transcriptome. 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. Nat Commun. 2019-09-02; 10 (1) PMID: 31477722 DOI: 10.1038/s41467-019-11947-7
Single-cell RNA sequencing reveals the impact of chromosomal instability on glioblastoma cancer stem cells. Zhao Y, Carter R, Natarajan S, Varn FS, Compton DA, Gawad C, Cheng C, Godek KM. BMC Med Genomics. 2019-05-31; 12 (1) PMID: 31151460 DOI: 10.1186/s12920-019-0532-5
Joint-specific DNA methylation and transcriptome signatures in rheumatoid arthritis identify distinct pathogenic processes. Ai R, Hammaker D, Boyle DL, Morgan R, Walsh AM, Fan S, Firestein GS, Wang W. Nat Commun. 2016-06-10; 7 PMID: 27282753 DOI: 10.1038/ncomms11849
Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, Tirosh I, Bialas AR, Kamitaki N, Martersteck EM, Trombetta JJ, Weitz DA, Sanes JR, Shalek AK, Regev A, McCarroll SA. Cell. 2015-05-01; 161 (5) PMID: 26000488 DOI: 10.1016/j.cell.2015.05.002
Association Between Response to Etrolizumab and Expression of Integrin αE and Granzyme A in Colon Biopsies of Patients With Ulcerative Colitis. 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. Gastroenterology. 2015-10-30; 150 (2) PMID: 26522261 DOI: 10.1053/j.gastro.2015.10.041
Immune Landscape of Viral- and Carcinogen-Driven Head and Neck Cancer. Cillo AR, Kürten CHL, Tabib T, Qi Z, Onkar S, Wang T, Liu A, Duvvuri U, Kim S, Soose RJ, Oesterreich S, Chen W, Lafyatis R, Bruno TC, Ferris RL, Vignali DAA. Immunity. 2020-01-07; 52 (1) PMID: 31924475 DOI: 10.1016/j.immuni.2019.11.014
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FEBS Lett. 2019-10-17; 594 (3)

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Single-cell multiomics sequencing and analyses of human colorectal cancer.

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.

Science. 2018-11-01; 362 (6418)

PMID: 30498128 DOI: 10.1126/science.aao3791

Single cell transcriptome profiling of the human alcohol-dependent brain.

Brenner E, Tiwari GR, Kapoor M, Liu Y, Brock A, Mayfield RD.

Hum Mol Genet. 2020-05-01; 29 (7)

PMID: 32142123 DOI: 10.1093/hmg/ddaa038

Wnt1 silences chemokine genes in dendritic cells and induces adaptive immune resistance in lung adenocarcinoma.

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.

Nat Commun. 2019-03-29; 10 (1)

PMID: 30926812 DOI: 10.1038/s41467-019-09370-z

Aryl Hydrocarbon Receptor Controls Monocyte Differentiation into Dendritic Cells versus Macrophages.

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.

Immunity. 2017-09-01; 47 (3)

PMID: 28930664 DOI: 10.1016/j.immuni.2017.08.016

Human oocyte developmental potential is predicted by mechanical properties within hours after fertilization.

Yanez LZ, Han J, Behr BB, Pera RAR, Camarillo DB.

Nat Commun. 2016-02-24; 7

PMID: 26904963 DOI: 10.1038/ncomms10809

COX-2 mediates tumor-stromal prolactin signaling to initiate tumorigenesis.

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.

Proc Natl Acad Sci U S A. 2019-02-28; 116 (12)

PMID: 30819896 DOI: 10.1073/pnas.1819303116

A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa.

Zhang H, Lee CAA, Li Z, Garbe JR, Eide CR, Petegrosso R, Kuang R, Tolar J.

PLoS Comput Biol. 2018-04-09; 14 (4)

PMID: 29630593 DOI: 10.1371/journal.pcbi.1006053

Tracing the temporal-spatial transcriptome landscapes of the human fetal digestive tract using single-cell RNA-sequencing.

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.

Nat Cell Biol. 2018-05-25; 20 (6)

PMID: 29802404 DOI: 10.1038/s41556-018-0105-4

Single-cell transcriptomics of East-Asian pancreatic islets cells.

Dorajoo R, Ali Y, Tay VSY, Kang J, Samydurai S, Liu J, Boehm BO.

Sci Rep. 2017-07-10; 7 (1)

PMID: 28694456 DOI: 10.1038/s41598-017-05266-4

Single-cell analysis reveals congruence between kidney organoids and human fetal kidney.

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Genome Med. 2019-01-23; 11 (1)

PMID: 30674341 DOI: 10.1186/s13073-019-0615-0

A pilot systematic genomic comparison of recurrence risks of hepatitis B virus-associated hepatocellular carcinoma with low- and high-degree liver fibrosis.

Yoo S, Wang W, Wang Q, Fiel MI, Lee E, Hiotis SP, Zhu J.

BMC Med. 2017-12-07; 15 (1)

PMID: 29212479 DOI: 10.1186/s12916-017-0973-7

BRN2 suppresses apoptosis, reprograms DNA damage repair, and is associated with a high somatic mutation burden in melanoma.

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.

Genes Dev. 2019-02-25; 33 (5-6)

PMID: 30804224 DOI: 10.1101/gad.314633.118

Network analysis of psoriasis reveals biological pathways and roles for coding and long non-coding RNAs.

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BMC Genomics. 2016-10-28; 17 (1)

PMID: 27793094 DOI: 10.1186/s12864-016-3188-y

Cellular senescence mediates fibrotic pulmonary disease.

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.

Nat Commun. 2017-02-23; 8

PMID: 28230051 DOI: 10.1038/ncomms14532

Single-Cell Transcriptomics of Human Oocytes: Environment-Driven Metabolic Competition and Compensatory Mechanisms During Oocyte Maturation.

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.

Antioxid Redox Signal. 2018-04-13; 30 (4)

PMID: 29486586 DOI: 10.1089/ars.2017.7151

Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis.

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.

Sci Immunol. 2018-01-01; 3 (19)

PMID: 29352091 DOI: 10.1126/sciimmunol.aan8664

The single-cell transcriptomic landscape of early human diabetic nephropathy.

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Proc Natl Acad Sci U S A. 2019-09-10; 116 (39)

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Whole blood human transcriptome and virome analysis of ME/CFS patients experiencing post-exertional malaise following cardiopulmonary exercise testing.

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.

PLoS One. 2019-03-21; 14 (3)

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Defective structural RNA processing in relapsing-remitting multiple sclerosis.

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Genome Biol. 2015-03-25; 16

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Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma.

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Genome Biol. 2016-04-29; 17

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Resident T Cells in Resolved Psoriasis Steer Tissue Responses that Stratify Clinical Outcome.

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.

J Invest Dermatol. 2018-03-03; 138 (8)

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Integrated Multi-omic Analysis of Esthesioneuroblastomas Identifies Two Subgroups Linked to Cell Ontogeny.

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Cell Rep. 2018-10-01; 25 (3)

PMID: 30332658 DOI: 10.1016/j.celrep.2018.09.047

Single-Cell Analysis of Human Mononuclear Phagocytes Reveals Subset-Defining Markers and Identifies Circulating Inflammatory Dendritic Cells.

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Immunity. 2019-08-29; 51 (3)

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Organoid single cell profiling identifies a transcriptional signature of glomerular disease.

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JCI Insight. 2019-01-10; 4 (1)

PMID: 30626756 DOI: 10.1172/jci.insight.122697

Integrating the Epigenome to Identify Drivers of Hepatocellular Carcinoma.

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Hepatology. 2019-01-05; 69 (2)

PMID: 30136421 DOI: 10.1002/hep.30211

MET-Oncogenic and JAK2-Inactivating Alterations Are Independent Factors That Affect Regulation of PD-L1 Expression in Lung Cancer.

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.

Clin Cancer Res. 2018-06-13; 24 (18)

PMID: 29898990 DOI: 10.1158/1078-0432.ccr-18-0267

A survey of human brain transcriptome diversity at the single cell level.

Darmanis S, Sloan SA, Zhang Y, Enge M, Caneda C, Shuer LM, Hayden Gephart MG, Barres BA, Quake SR.

Proc Natl Acad Sci U S A. 2015-05-18; 112 (23)

PMID: 26060301 DOI: 10.1073/pnas.1507125112

A gene network regulated by the transcription factor VGLL3 as a promoter of sex-biased autoimmune diseases.

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.

Nat Immunol. 2016-12-19; 18 (2)

PMID: 27992404 DOI: 10.1038/ni.3643

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