Download | Dataset ID | BioProject ID | Project ID | Dataset Name | Species | Strategy | Sample Number | Tissue | Cell Type | Cell Line | Healthy Condition | Development Stage | Case Detail | Control Detail | Cell Number | Biological Condition | Quality and Quantity | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Baseline | Genetic | Phenotypic | Environmental | Spatial | Temporal | RNA Type | Median Mapping Quality | Median Coverage | Max Sequencing Length | Max Replicate# |
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
|
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
|
Chromatin state dynamics confers specific therapeutic strategies in enhancer subtypes of colorectal cancer.
Orouji E, Raman AT, Singh AK, Sorokin A, Arslan E, Ghosh AK, Schulz J, Terranova C, Jiang S, Tang M, Maitituoheti M, Callahan SC, Barrodia P, Tomczak K, Jiang Y, Jiang Z, Davis JS, Ghosh S, Lee HM, Reyes-Uribe L, Chang K, Liu Y, Chen H, Azhdarinia A, Morris J, Vilar E, Carmon KS, Kopetz SE, Rai K.
Gut. 2021-05-31; 71 (5)
PMID: 34059508 DOI: 10.1136/gutjnl-2020-322835
|
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)
PMID: 30897114 DOI: 10.1371/journal.pone.0212193
|
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
|
SC3: consensus clustering of single-cell RNA-seq data.
Kiselev VY, Kirschner K, Schaub MT, Andrews T, Yiu A, Chandra T, Natarajan KN, Reik W, Barahona M, Green AR, Hemberg M.
Nat Methods. 2017-03-27; 14 (5)
PMID: 28346451 DOI: 10.1038/nmeth.4236
|
Cutaneous and systemic hyperinflammation drives maculopapular drug exanthema in severely ill COVID-19 patients.
Mitamura Y, Schulz D, Oro S, Li N, Kolm I, Lang C, Ziadlou R, Tan G, Bodenmiller B, Steiger P, Marzano A, de Prost N, Caudin O, Levesque M, Stoffel C, Schmid-Grendelmeier P, Maverakis E, Akdis CA, Brüggen MC.
Allergy. 2021-06-22;
PMID: 34157151 DOI: 10.1111/all.14983
|
Integrating the Epigenome to Identify Drivers of Hepatocellular Carcinoma.
Hlady RA, Sathyanarayan A, Thompson JJ, Zhou D, Wu Q, Pham K, Lee JH, Liu C, Robertson KD.
Hepatology. 2019-01-05; 69 (2)
PMID: 30136421 DOI: 10.1002/hep.30211
|
Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma.
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.
Genome Biol. 2016-04-29; 17
PMID: 27139883 DOI: 10.1186/s13059-016-0945-9
|
A Systems Analysis of the Relationships Between Anemia and Ischemic Stroke Rehabilitation Based on RNA-Seq Data.
Wang Y, Huang X, Liu J, Zhao X, Yu H, Cai Y.
Front Genet. 2019-05-24; 10
PMID: 31178893 DOI: 10.3389/fgene.2019.00456
|
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
|
An EZH2-NF-κB regulatory axis drives expression of pro-oncogenic gene signatures in triple negative breast cancer.
Dardis GJ, Wang J, Simon JM, Wang GG, Baldwin AS.
iScience. 2023-06-14; 26 (7)
PMID: 37416481 DOI: 10.1016/j.isci.2023.107115
|
A specific low-density neutrophil population correlates with hypercoagulation and disease severity in hospitalized COVID-19 patients.
Morrissey SM, Geller AE, Hu X, Tieri D, Ding C, Klaes CK, Cooke EA, Woeste MR, Martin ZC, Chen O, Bush SE, Zhang HG, Cavallazzi R, Clifford SP, Chen J, Ghare S, Barve SS, Cai L, Kong M, Rouchka EC, McLeish KR, Uriarte SM, Watson CT, Huang J, Yan J.
JCI Insight. 2021-05-10; 6 (9)
PMID: 33986193 DOI: 10.1172/jci.insight.148435
|
Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation.
Song Y, Botvinnik OB, Lovci MT, Kakaradov B, Liu P, Xu JL, Yeo GW.
Mol Cell. 2017-06-29; 67 (1)
PMID: 28673540 DOI: 10.1016/j.molcel.2017.06.003
|
Single-cell RNA-Seq analysis identifies a putative epithelial stem cell population in human primary prostate cells in monolayer and organoid culture conditions.
McCray T, Moline D, Baumann B, Vander Griend DJ, Nonn L.
Am J Clin Exp Urol. 2019-06-15; 7 (3)
PMID: 31317052 DOI:
|
Single-cell RNA sequencing reveals chemokine self-feeding of myeloma cells promotes extramedullary metastasis.
Geng S, Wang J, Zhang X, Zhang JJ, Wu F, Pang Y, Zhong Y, Wang J, Wang W, Lyu X, Huang Y, Jing H.
FEBS Lett. 2019-10-17; 594 (3)
PMID: 31561267 DOI: 10.1002/1873-3468.13623
|
Human hepatic organoids for the analysis of human genetic diseases.
Guan Y, Xu D, Garfin PM, Ehmer U, Hurwitz M, Enns G, Michie S, Wu M, Zheng M, Nishimura T, Sage J, Peltz G.
JCI Insight. 2017-09-07; 2 (17)
PMID: 28878125 DOI: 10.1172/jci.insight.94954
|
Comparative single-cell RNA sequencing (scRNA-seq) reveals liver metastasis-specific targets in a patient with small intestinal neuroendocrine cancer.
Rao M, Oh K, Moffitt R, Thompson P, Li J, Liu J, Sasson A, Georgakis G, Kim J, Choi M, Powers S.
Cold Spring Harb Mol Case Stud. 2020-04-01; 6 (2)
PMID: 32054662 DOI: 10.1101/mcs.a004978
|
Convalescent COVID-19 Patients Without Comorbidities Display Similar Immunophenotypes Over Time Despite Divergent Disease Severities.
Chu CF, Sabath F, Fibi-Smetana S, Sun S, Öllinger R, Noeßner E, Chao YY, Rinke L, Winheim E, Rad R, Krug AB, Taher L, Zielinski CE.
Front Immunol. 2021-08-19; 12
PMID: 34867933 DOI: 10.3389/fimmu.2021.601080
|
Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes.
Rahman M, MacNeil SM, Jenkins DF, Shrestha G, Wyatt SR, McQuerry JA, Piccolo SR, Heiser LM, Gray JW, Johnson WE, Bild AH.
Genome Med. 2017-04-26; 9 (1)
PMID: 28446242 DOI: 10.1186/s13073-017-0429-x
|
The Neonatal and Adult Human Testis Defined at the Single-Cell Level.
Sohni A, Tan K, Song HW, Burow D, de Rooij DG, Laurent L, Hsieh TC, Rabah R, Hammoud SS, Vicini E, Wilkinson MF.
Cell Rep. 2019-02-01; 26 (6)
PMID: 30726734 DOI: 10.1016/j.celrep.2019.01.045
|
Gene expression variability across cells and species shapes innate immunity.
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.
Nature. 2018-10-24; 563 (7730)
PMID: 30356220 DOI: 10.1038/s41586-018-0657-2
|
Invasive Salmonella exploits divergent immune evasion strategies in infected and bystander dendritic cell subsets.
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.
Nat Commun. 2018-11-19; 9 (1)
PMID: 30451854 DOI: 10.1038/s41467-018-07329-0
|
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
|
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
|
RNA-Seq of Tumor-Educated Platelets Enables Blood-Based Pan-Cancer, Multiclass, and Molecular Pathway Cancer Diagnostics.
Best MG, Sol N, Kooi I, Tannous J, Westerman BA, Rustenburg F, Schellen P, Verschueren H, Post E, Koster J, Ylstra B, Ameziane N, Dorsman J, Smit EF, Verheul HM, Noske DP, Reijneveld JC, Nilsson RJA, Tannous BA, Wesseling P, Wesseling P, Wurdinger T.
Cancer Cell. 2015-10-29; 28 (5)
PMID: 26525104 DOI: 10.1016/j.ccell.2015.09.018
|
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
|
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
|
Comprehensive analysis of metastatic gastric cancer tumour cells using single-cell RNA-seq.
Wang B, Zhang Y, Qing T, Xing K, Li J, Zhen T, Zhu S, Zhan X.
Sci Rep. 2021-01-13; 11 (1)
PMID: 33441952 DOI: 10.1038/s41598-020-80881-2
|
Aberrant Development Corrected in Adult-Onset Huntington's Disease iPSC-Derived Neuronal Cultures via WNT Signaling Modulation.
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.
Stem Cell Reports. 2020-02-27; 14 (3)
PMID: 32109367 DOI: 10.1016/j.stemcr.2020.01.015
|
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
|
Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19.
Bernardes JP, Mishra N, Tran F, Bahmer T, Best L, Blase JI, Bordoni D, Franzenburg J, Geisen U, Josephs-Spaulding J, Köhler P, Künstner A, Rosati E, Aschenbrenner AC, Bacher P, Baran N, Boysen T, Brandt B, Bruse N, Dörr J, Dräger A, Elke G, Ellinghaus D, Fischer J, Forster M, Franke A, Franzenburg S, Frey N, Friedrichs A, Fuß J, Glück A, Hamm J, Hinrichsen F, Hoeppner MP, Imm S, Junker R, Kaiser S, Kan YH, Knoll R, Lange C, Laue G, Lier C, Lindner M, Marinos G, Markewitz R, Nattermann J, Noth R, Pickkers P, Rabe KF, Renz A, Röcken C, Rupp J, Schaffarzyk A, Scheffold A, Schulte-Schrepping J, Schunk D, Skowasch D, Ulas T, Wandinger KP, Wittig M, Zimmermann J, Busch H, Hoyer BF, Kaleta C, Heyckendorf J, Kox M, Rybniker J, Schreiber S, Schultze JL, Rosenstiel P, HCA Lung Biological Network, Deutsche COVID-19 Omics Initiative (DeCOI).
Immunity. 2020-11-26; 53 (6)
PMID: 33296687 DOI: 10.1016/j.immuni.2020.11.017
|
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
|
Atopic Dermatitis Is an IL-13-Dominant Disease with Greater Molecular Heterogeneity Compared to Psoriasis.
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.
J Invest Dermatol. 2019-01-11; 139 (7)
PMID: 30641038 DOI: 10.1016/j.jid.2018.12.018
|
Single-cell transcriptome analysis of human skin identifies novel fibroblast subpopulation and enrichment of immune subsets in atopic dermatitis.
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.
J Allergy Clin Immunol. 2020-02-07; 145 (6)
PMID: 32035984 DOI: 10.1016/j.jaci.2020.01.042
|
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
|
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
|
Immune signatures underlying post-acute COVID-19 lung sequelae.
Cheon IS, Li C, Son YM, Goplen NP, Wu Y, Cassmann T, Wang Z, Wei X, Tang J, Li Y, Marlow H, Hughes S, Hammel L, Cox TM, Goddery E, Ayasoufi K, Weiskopf D, Boonyaratanakornkit J, Dong H, Li H, Chakraborty R, Johnson AJ, Edell E, Taylor JJ, Kaplan MH, Sette A, Bartholmai BJ, Kern R, Vassallo R, Sun J.
Sci Immunol. 2021-11-12; 6 (65)
PMID: 34591653 DOI: 10.1126/sciimmunol.abk1741
|
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
|
Virus-induced senescence is a driver and therapeutic target in COVID-19.
Lee S, Yu Y, Trimpert J, Benthani F, Mairhofer M, Richter-Pechanska P, Wyler E, Belenki D, Kaltenbrunner S, Pammer M, Kausche L, Firsching TC, Dietert K, Schotsaert M, Martínez-Romero C, Singh G, Kunz S, Niemeyer D, Ghanem R, Salzer HJF, Paar C, Mülleder M, Uccellini M, Michaelis EG, Khan A, Lau A, Schönlein M, Habringer A, Tomasits J, Adler JM, Kimeswenger S, Gruber AD, Hoetzenecker W, Steinkellner H, Purfürst B, Motz R, Di Pierro F, Lamprecht B, Osterrieder N, Landthaler M, Drosten C, García-Sastre A, Langer R, Ralser M, Eils R, Reimann M, Fan DNY, Schmitt CA.
Nature. 2021-09-13;
PMID: 34517409 DOI: 10.1038/s41586-021-03995-1
|
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
|
CD177, a specific marker of neutrophil activation, is associated with coronavirus disease 2019 severity and death.
Lévy Y, Wiedemann A, Hejblum BP, Durand M, Lefebvre C, Surénaud M, Lacabaratz C, Perreau M, Foucat E, Déchenaud M, Tisserand P, Blengio F, Hivert B, Gauthier M, Cervantes-Gonzalez M, Bachelet D, Laouénan C, Bouadma L, Timsit JF, Yazdanpanah Y, Pantaleo G, Hocini H, Thiébaut R, French COVID cohort study group.
iScience. 2021-06-10; 24 (7)
PMID: 34127958 DOI: 10.1016/j.isci.2021.102711
|
Training in Aging as a Diversity Factor: Education, Knowledge, and Attitudes Amongst Psychology Doctoral Students.
Graham KL, Moye J.
Psychol Learn Teach. 2022-10-19; 22 (1)
PMID: 36787228 DOI: 10.1177/14757257221130483
|
Postmortem high-dimensional immune profiling of severe COVID-19 patients reveals distinct patterns of immunosuppression and immunoactivation.
Wu H, He P, Ren Y, Xiao S, Wang W, Liu Z, Li H, Wang Z, Zhang D, Cai J, Zhou X, Jiang D, Fei X, Zhao L, Zhang H, Liu Z, Chen R, Li W, Wang C, Zhang S, Qin J, Nashan B, Sun C.
Nat Commun. 2022-01-12; 13 (1)
PMID: 35022412 DOI: 10.1038/s41467-021-27723-5
|
TIM3+ TRBV11-2 T cells and IFNγ signature in patrolling monocytes and CD16+ NK cells delineate MIS-C.
Hoste L, Roels L, Naesens L, Bosteels V, Vanhee S, Dupont S, Bosteels C, Browaeys R, Vandamme N, Verstaen K, Roels J, Van Damme KFA, Maes B, De Leeuw E, Declercq J, Aegerter H, Seys L, Smole U, De Prijck S, Vanheerswynghels M, Claes K, Debacker V, Van Isterdael G, Backers L, Claes KBM, Bastard P, Jouanguy E, Zhang SY, Mets G, Dehoorne J, Vandekerckhove K, Schelstraete P, Willems J, MIS-C Clinicians, Stordeur P, Janssens S, Beyaert R, Saeys Y, Casanova JL, Lambrecht BN, Haerynck F, Tavernier SJ.
J Exp Med. 2021-12-16; 219 (2)
PMID: 34914824 DOI: 10.1084/jem.20211381
|
4-1BB Delineates Distinct Activation Status of Exhausted Tumor-Infiltrating CD8+ T Cells in Hepatocellular Carcinoma.
Kim HD, Park S, Jeong S, Lee YJ, Lee H, Kim CG, Kim KH, Hong SM, Lee JY, Kim S, Kim HK, Min BS, Chang JH, Ju YS, Shin EC, Song GW, Hwang S, Park SH.
Hepatology. 2019-10-18; 71 (3)
PMID: 31353502 DOI: 10.1002/hep.30881
|
Low-Avidity CD4+ T Cell Responses to SARS-CoV-2 in Unexposed Individuals and Humans with Severe COVID-19.
Bacher P, Rosati E, Esser D, Martini GR, Saggau C, Schiminsky E, Dargvainiene J, Schröder I, Wieters I, Khodamoradi Y, Eberhardt F, Vehreschild MJGT, Neb H, Sonntagbauer M, Conrad C, Tran F, Rosenstiel P, Markewitz R, Wandinger KP, Augustin M, Rybniker J, Kochanek M, Leypoldt F, Cornely OA, Koehler P, Franke A, Scheffold A.
Immunity. 2020-11-26; 53 (6)
PMID: 33296686 DOI: 10.1016/j.immuni.2020.11.016
|
Haematopoietic stem and progenitor cells from human pluripotent stem cells.
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.
Nature. 2017-05-17; 545 (7655)
PMID: 28514439 DOI: 10.1038/nature22370
|
Discovery of new candidate genes for rheumatoid arthritis through integration of genetic association data with expression pathway analysis.
Shchetynsky K, Diaz-Gallo LM, Folkersen L, Hensvold AH, Catrina AI, Berg L, Klareskog L, Padyukov L.
Arthritis Res Ther. 2017-02-02; 19 (1)
PMID: 28148290 DOI: 10.1186/s13075-017-1220-5
|
Androgen Signaling Regulates SARS-CoV-2 Receptor Levels and Is Associated with Severe COVID-19 Symptoms in Men.
Samuel RM, Majd H, Richter MN, Ghazizadeh Z, Zekavat SM, Navickas A, Ramirez JT, Asgharian H, Simoneau CR, Bonser LR, Koh KD, Garcia-Knight M, Tassetto M, Sunshine S, Farahvashi S, Kalantari A, Liu W, Andino R, Zhao H, Natarajan P, Erle DJ, Ott M, Goodarzi H, Fattahi F.
Cell Stem Cell. 2020-11-17; 27 (6)
PMID: 33232663 DOI: 10.1016/j.stem.2020.11.009
|
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
|
Robust innate responses to SARS-CoV-2 in children resolve faster than in adults without compromising adaptive immunity.
Vono M, Huttner A, Lemeille S, Martinez-Murillo P, Meyer B, Baggio S, Sharma S, Thiriard A, Marchant A, Godeke GJ, Reusken C, Alvarez C, Perez-Rodriguez F, Eckerle I, Kaiser L, Loevy N, Eberhardt CS, Blanchard-Rohner G, Siegrist CA, Didierlaurent AM.
Cell Rep. 2021-09-15; 37 (1)
PMID: 34587479 DOI: 10.1016/j.celrep.2021.109773
|
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
|
CRX Expression in Pluripotent Stem Cell-Derived Photoreceptors Marks a Transplantable Subpopulation of Early Cones.
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.
Stem Cells. 2019-01-30; 37 (5)
PMID: 30681766 DOI: 10.1002/stem.2974
|
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
|
Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19.
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.
Nat Med. 2020-05-12; 26 (6)
PMID: 32398875 DOI: 10.1038/s41591-020-0901-9
|
Analysis of Bulk RNA Sequencing Data Reveals Novel Transcription Factors Associated With Immune Infiltration Among Multiple Cancers.
Liu L, Zhao Q, Cheng C, Yi J, Sun H, Wang Q, Quan W, Xue Y, Sun L, Cong X, Zhang Y.
Front Immunol. 2021-08-20; 12
PMID: 34489925 DOI: 10.3389/fimmu.2021.644350
|
Identification of conserved SARS-CoV-2 spike epitopes that expand public cTfh clonotypes in mild COVID-19 patients.
Lu X, Hosono Y, Nagae M, Ishizuka S, Ishikawa E, Motooka D, Ozaki Y, Sax N, Maeda Y, Kato Y, Morita T, Shinnakasu R, Inoue T, Onodera T, Matsumura T, Shinkai M, Sato T, Nakamura S, Mori S, Kanda T, Nakayama EE, Shioda T, Kurosaki T, Takeda K, Kumanogoh A, Arase H, Nakagami H, Yamashita K, Takahashi Y, Yamasaki S.
J Exp Med. 2021-10-14; 218 (12)
PMID: 34647971 DOI: 10.1084/jem.20211327
|
Single-cell RNA-seq reveals the diversity of trophoblast subtypes and patterns of differentiation in the human placenta.
Liu Y, Fan X, Wang R, Lu X, Dang YL, Wang H, Lin HY, Zhu C, Ge H, Cross JC, Wang H.
Cell Res. 2018-07-24; 28 (8)
PMID: 30042384 DOI: 10.1038/s41422-018-0066-y
|
Deconvolution of transcriptional networks identifies TCF4 as a master regulator in schizophrenia.
Doostparast Torshizi A, Armoskus C, Zhang H, Forrest MP, Zhang S, Souaiaia T, Evgrafov OV, Knowles JA, Duan J, Wang K.
Sci Adv. 2019-09-11; 5 (9)
PMID: 31535015 DOI: 10.1126/sciadv.aau4139
|
VHL Deficiency Drives Enhancer Activation of Oncogenes in Clear Cell Renal Cell Carcinoma.
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.
Cancer Discov. 2017-09-11; 7 (11)
PMID: 28893800 DOI: 10.1158/2159-8290.cd-17-0375
|
Single-Cell Transcriptomics of a Human Kidney Allograft Biopsy Specimen Defines a Diverse Inflammatory Response.
Wu H, Malone AF, Donnelly EL, Kirita Y, Uchimura K, Ramakrishnan SM, Gaut JP, Humphreys BD.
J Am Soc Nephrol. 2018-07-06; 29 (8)
PMID: 29980650 DOI: 10.1681/asn.2018020125
|
Persistent viral activity, cytokine storm, and lung fibrosis in a case of severe COVID-19.
Xu G, Liu Y, Liao M, Gou J, Wang X, Yuan J, Liu W, Zhou G, Zhang S, Liu L, Zhang Z.
Clin Transl Med. 2020-11-01; 10 (7)
PMID: 33252859 DOI: 10.1002/ctm2.224
|
Exploring Markers of Exhausted CD8 T Cells to Predict Response to Immune Checkpoint Inhibitor Therapy for Hepatocellular Carcinoma.
Hsu CL, Ou DL, Bai LY, Chen CW, Lin L, Huang SF, Cheng AL, Jeng YM, Hsu C.
Liver Cancer. 2021-05-12; 10 (4)
PMID: 34414122 DOI: 10.1159/000515305
|
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
|
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
|
ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways.
Shen Y, Rahman M, Piccolo SR, Gusenleitner D, El-Chaar NN, Cheng L, Monti S, Bild AH, Johnson WE.
Bioinformatics. 2015-01-22; 31 (11)
PMID: 25617415 DOI: 10.1093/bioinformatics/btv031
|
Nopp140-chaperoned 2'-O-methylation of small nuclear RNAs in Cajal bodies ensures splicing fidelity.
Bizarro J, Deryusheva S, Wacheul L, Gupta V, Ernst FGM, Lafontaine DLJ, Gall JG, Meier UT.
Genes Dev. 2021-07-22; 35 (15-16)
PMID: 34301768 DOI: 10.1101/gad.348660.121
|
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
|
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
|
Collagen synthesis disruption and downregulation of core elements of TGF-β, Hippo, and Wnt pathways in keratoconus corneas.
Kabza M, Karolak JA, Rydzanicz M, Szcześniak MW, Nowak DM, Ginter-Matuszewska B, Polakowski P, Ploski R, Szaflik JP, Gajecka M.
Eur J Hum Genet. 2017-02-01; 25 (5)
PMID: 28145428 DOI: 10.1038/ejhg.2017.4
|
Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19.
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.
Cell. 2020-05-15; 181 (5)
PMID: 32416070 DOI: 10.1016/j.cell.2020.04.026
|
Chromosome 1q21.3 amplification is a trackable biomarker and actionable target for breast cancer recurrence.
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.
Nat Med. 2017-09-25; 23 (11)
PMID: 28967919 DOI: 10.1038/nm.4405
|
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
|
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
|
Molecular and functional heterogeneity of IL-10-producing CD4+ T cells.
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.
Nat Commun. 2018-12-21; 9 (1)
PMID: 30575716 DOI: 10.1038/s41467-018-07581-4
|
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
|
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
|
Natural mucosal barriers and COVID-19 in children.
Pierce CA, Sy S, Galen B, Goldstein DY, Orner E, Keller MJ, Herold KC, Herold BC.
JCI Insight. 2021-05-10; 6 (9)
PMID: 33822777 DOI: 10.1172/jci.insight.148694
|
Changes in macrophage transcriptome associate with systemic sclerosis and mediate GSDMA contribution to disease risk.
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.
Ann Rheum Dis. 2018-01-17; 77 (4)
PMID: 29348297 DOI: 10.1136/annrheumdis-2017-212454
|
Large-scale genomic study reveals robust activation of the immune system following advanced Inner Engineering meditation retreat.
Chandran V, Bermúdez ML, Koka M, Chandran B, Pawale D, Vishnubhotla R, Alankar S, Maturi R, Subramaniam B, Sadhasivam S.
Proc Natl Acad Sci U S A. 2021-12-01; 118 (51)
PMID: 34907015 DOI: 10.1073/pnas.2110455118
|
Pain-Associated Transcriptome Changes in Synovium of Knee Osteoarthritis Patients.
Bratus-Neuenschwander A, Castro-Giner F, Frank-Bertoncelj M, Aluri S, Fucentese SF, Schlapbach R, Sprott H.
Genes (Basel). 2018-07-04; 9 (7)
PMID: 29973527 DOI: 10.3390/genes9070338
|
Single-Cell RNA-Seq Analysis Maps Development of Human Germline Cells and Gonadal Niche Interactions.
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.
Cell Stem Cell. 2017-04-27; 20 (6)
PMID: 28457750 DOI: 10.1016/j.stem.2017.03.007
|
Single-cell analysis reveals congruence between kidney organoids and human fetal kidney.
Combes AN, Zappia L, Er PX, Oshlack A, Little MH.
Genome Med. 2019-01-23; 11 (1)
PMID: 30674341 DOI: 10.1186/s13073-019-0615-0
|
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
|
Clofazimine is a broad-spectrum coronavirus inhibitor that antagonizes SARS-CoV-2 replication in primary human cell culture and hamsters.
Yuan S, Yin X, Meng X, Chan J, Ye ZW, Riva L, Pache L, Chan CC, Lai PM, Chan C, Poon V, Matsunaga N, Pu Y, Yuen CK, Cao J, Liang R, Tang K, Sheng L, Du Y, Xu W, Sze KH, Zhang J, Chu H, Kok KH, To K, Jin DY, Sun R, Chanda S, Yuen KY.
Res Sq. 2020-10-07;
PMID: 33052331 DOI: 10.21203/rs.3.rs-86169/v1
|
Adult Stem Cell-derived Complete Lung Organoid Models Emulate Lung Disease in COVID-19.
Tindle C, Fuller M, Fonseca A, Taheri S, Ibeawuchi SR, Beutler N, Katkar G, Claire A, Castillo V, Hernandez M, Russo H, Duran J, Crotty Alexander LE, Tipps A, Lin G, Thistlethwaite PA, Chattopadhyay R, Rogers TF, Sahoo D, Ghosh P, Das S.
bioRxiv. 2021-05-05;
PMID: 33106807 DOI: 10.1101/2020.10.17.344002
|
Super-Obese Patient-Derived iPSC Hypothalamic Neurons Exhibit Obesogenic Signatures and Hormone Responses.
Rajamani U, Gross AR, Hjelm BE, Sequeira A, Vawter MP, Tang J, Gangalapudi V, Wang Y, Andres AM, Gottlieb RA, Sareen D.
Cell Stem Cell. 2018-04-19; 22 (5)
PMID: 29681516 DOI: 10.1016/j.stem.2018.03.009
|
Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming.
Solé-Boldo L, Raddatz G, Schütz S, Mallm JP, Rippe K, Lonsdorf AS, Rodríguez-Paredes M, Lyko F.
Commun Biol. 2020-04-23; 3 (1)
PMID: 32327715 DOI: 10.1038/s42003-020-0922-4
|
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
|
Fixed single-cell transcriptomic characterization of human radial glial diversity.
Thomsen ER, Mich JK, Yao Z, Hodge RD, Doyle AM, Jang S, Shehata SI, Nelson AM, Shapovalova NV, Levi BP, Ramanathan S.
Nat Methods. 2015-11-16; 13 (1)
PMID: 26524239 DOI: 10.1038/nmeth.3629
|
Platelets contribute to disease severity in COVID-19.
Barrett TJ, Bilaloglu S, Cornwell M, Burgess HM, Virginio VW, Drenkova K, Ibrahim H, Yuriditsky E, Aphinyanaphongs Y, Lifshitz M, Xia Liang F, Alejo J, Smith G, Pittaluga S, Rapkiewicz AV, Wang J, Iancu-Rubin C, Mohr I, Ruggles K, Stapleford KA, Hochman J, Berger JS.
J Thromb Haemost. 2021-09-29; 19 (12)
PMID: 34538015 DOI: 10.1111/jth.15534
|
Modeling cross-talk of RNA modification enzymes reveals tumor microenvironment-associated clinical significance and immunotherapy prediction in hepatobiliary malignancy.
Qi F, Li J, Qi Z, Zhou B, Yang B, Zhang J, Qin W.
MedComm (2020). 2023-04-18; 4 (3)
PMID: 37090117 DOI: 10.1002/mco2.256
|
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
|
Activation of Interferon-Stimulated Transcriptomes and ACE2 Isoforms in Human Airway Epithelium Is Curbed by Janus Kinase Inhibitors.
Lee HK, Jung O, Hennighausen L.
Res Sq. 2020-12-11;
PMID: 33330857 DOI: 10.21203/rs.3.rs-119695/v1
|
Single-Cell RNA Sequencing of Tocilizumab-Treated Peripheral Blood Mononuclear Cells as an in vitro Model of Inflammation.
Zarinsefat A, Hartoularos G, Rychkov D, Rashmi P, Chandran S, Vincenti F, Yee CJ, Sarwal MM.
Front Genet. 2020-01-01; 11
PMID: 33469465 DOI: 10.3389/fgene.2020.610682
|
Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer.
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.
Nat Commun. 2017-05-05; 8
PMID: 28474673 DOI: 10.1038/ncomms15081
|
Multipotent RAG1+ progenitors emerge directly from haemogenic endothelium in human pluripotent stem cell-derived haematopoietic organoids.
Motazedian A, Bruveris FF, Kumar SV, Schiesser JV, Chen T, Ng ES, Chidgey AP, Wells CA, Elefanty AG, Stanley EG.
Nat Cell Biol. 2020-01-06; 22 (1)
PMID: 31907413 DOI: 10.1038/s41556-019-0445-8
|
High-Throughput Screening Enhances Kidney Organoid Differentiation from Human Pluripotent Stem Cells and Enables Automated Multidimensional Phenotyping.
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.
Cell Stem Cell. 2018-05-17; 22 (6)
PMID: 29779890 DOI: 10.1016/j.stem.2018.04.022
|
Assembly of functionally integrated human forebrain spheroids.
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.
Nature. 2017-04-26; 545 (7652)
PMID: 28445465 DOI: 10.1038/nature22330
|
IGF2BP1 is the first positive marker for anaplastic thyroid carcinoma diagnosis.
Haase J, Misiak D, Bauer M, Pazaitis N, Braun J, Pötschke R, Mensch A, Bell JL, Dralle H, Siebolts U, Wickenhauser C, Lorenz K, Hüttelmaier S.
Mod Pathol. 2020-07-27; 34 (1)
PMID: 32719445 DOI: 10.1038/s41379-020-0630-0
|
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
|
Transcriptomic Profiles Reveal Downregulation of Low-Density Lipoprotein Particle Receptor Pathway Activity in Patients Surviving Severe COVID-19.
Vlasov I, Panteleeva A, Usenko T, Nikolaev M, Izumchenko A, Gavrilova E, Shlyk I, Miroshnikova V, Shadrina M, Polushin Y, Pchelina S, Slonimsky P.
Cells. 2021-12-10; 10 (12)
PMID: 34944005 DOI: 10.3390/cells10123495
|
Targeting polyploid giant cancer cells potentiates a therapeutic response and overcomes resistance to PARP inhibitors in ovarian cancer.
Zhang X, Yao J, Li X, Niu N, Liu Y, Hajek RA, Peng G, Westin S, Sood AK, Liu J.
Sci Adv. 2023-07-21; 9 (29)
PMID: 37478190 DOI: 10.1126/sciadv.adf7195
|
Outcome of SARS-CoV-2 infection is linked to MAIT cell activation and cytotoxicity.
Flament H, Rouland M, Beaudoin L, Toubal A, Bertrand L, Lebourgeois S, Rousseau C, Soulard P, Gouda Z, Cagninacci L, Monteiro AC, Hurtado-Nedelec M, Luce S, Bailly K, Andrieu M, Saintpierre B, Letourneur F, Jouan Y, Si-Tahar M, Baranek T, Paget C, Boitard C, Vallet-Pichard A, Gautier JF, Ajzenberg N, Terrier B, Pène F, Ghosn J, Lescure X, Yazdanpanah Y, Visseaux B, Descamps D, Timsit JF, Monteiro RC, Lehuen A.
Nat Immunol. 2021-02-02; 22 (3)
PMID: 33531712 DOI: 10.1038/s41590-021-00870-z
|
The single-cell transcriptomic landscape of early human diabetic nephropathy.
Wilson PC, Wu H, Kirita Y, Uchimura K, Ledru N, Rennke HG, Welling PA, Waikar SS, Humphreys BD.
Proc Natl Acad Sci U S A. 2019-09-10; 116 (39)
PMID: 31506348 DOI: 10.1073/pnas.1908706116
|
Severe COVID-19 Is Characterized by an Impaired Type I Interferon Response and Elevated Levels of Arginase Producing Granulocytic Myeloid Derived Suppressor Cells.
Dean MJ, Ochoa JB, Sanchez-Pino MD, Zabaleta J, Garai J, Del Valle L, Wyczechowska D, Baiamonte LB, Philbrook P, Majumder R, Vander Heide RS, Dunkenberger L, Thylur RP, Nossaman B, Roberts WM, Chapple AG, Wu J, Hicks C, Collins J, Luke B, Johnson R, Koul HK, Rees CA, Morris CR, Garcia-Diaz J, Ochoa AC.
Front Immunol. 2021-07-14; 12
PMID: 34341659 DOI: 10.3389/fimmu.2021.695972
|
A virus-derived microRNA targets immune response genes during SARS-CoV-2 infection.
Singh M, Chazal M, Quarato P, Bourdon L, Malabat C, Vallet T, Vignuzzi M, van der Werf S, Behillil S, Donati F, Sauvonnet N, Nigro G, Bourgine M, Jouvenet N, Cecere G.
EMBO Rep. 2021-12-16; 23 (2)
PMID: 34914162 DOI: 10.15252/embr.202154341
|
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
|
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
|
Zika Virus Disrupts Phospho-TBK1 Localization and Mitosis in Human Neuroepithelial Stem Cells and Radial Glia.
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.
Cell Rep. 2016-08-24; 16 (10)
PMID: 27568284 DOI: 10.1016/j.celrep.2016.08.038
|
Single-Cell Analysis of Human Mononuclear Phagocytes Reveals Subset-Defining Markers and Identifies Circulating Inflammatory Dendritic Cells.
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.
Immunity. 2019-08-29; 51 (3)
PMID: 31474513 DOI: 10.1016/j.immuni.2019.08.008
|
Long-term perturbation of the peripheral immune system months after SARS-CoV-2 infection.
Ryan FJ, Hope CM, Masavuli MG, Lynn MA, Mekonnen ZA, Yeow AEL, Garcia-Valtanen P, Al-Delfi Z, Gummow J, Ferguson C, O'Connor S, Reddi BAJ, Hissaria P, Shaw D, Kok-Lim C, Gleadle JM, Beard MR, Barry SC, Grubor-Bauk B, Lynn DJ.
BMC Med. 2022-01-14; 20 (1)
PMID: 35027067 DOI: 10.1186/s12916-021-02228-6
|
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
|
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
|
Potential diagnostic and prognostic marker dimethylglycine dehydrogenase (DMGDH) suppresses hepatocellular carcinoma metastasis in vitro and in vivo.
Liu G, Hou G, Li L, Li Y, Zhou W, Liu L.
Oncotarget. 2016-05-01; 7 (22)
PMID: 27119355 DOI: 10.18632/oncotarget.8927
|
Recurrently deregulated lncRNAs in hepatocellular carcinoma.
Yang Y, Chen L, Gu J, Zhang H, Yuan J, Lian Q, Lv G, Wang S, Wu Y, Yang YT, Wang D, Liu Y, Tang J, Luo G, Li Y, Hu L, Sun X, Wang D, Guo M, Xi Q, Xi J, Wang H, Zhang MQ, Lu ZJ.
Nat Commun. 2017-02-13; 8
PMID: 28194035 DOI: 10.1038/ncomms14421
|
Recurrent read-through fusion transcripts in breast cancer.
Varley KE, Gertz J, Roberts BS, Davis NS, Bowling KM, Kirby MK, Nesmith AS, Oliver PG, Grizzle WE, Forero A, Buchsbaum DJ, LoBuglio AF, Myers RM.
Breast Cancer Res Treat. 2014-06-15; 146 (2)
PMID: 24929677 DOI: 10.1007/s10549-014-3019-2
|
RORγt inhibition selectively targets IL-17 producing iNKT and γδ-T cells enriched in Spondyloarthritis patients.
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.
Nat Commun. 2019-01-02; 10 (1)
PMID: 30602780 DOI: 10.1038/s41467-018-07911-6
|
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
|
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
|
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
|
A Primate lncRNA Mediates Notch Signaling during Neuronal Development by Sequestering miRNA.
Rani N, Nowakowski TJ, Zhou H, Godshalk SE, Lisi V, Kriegstein AR, Kosik KS.
Neuron. 2016-06-02; 90 (6)
PMID: 27263970 DOI: 10.1016/j.neuron.2016.05.005
|
Interferon-regulated genetic programs and JAK/STAT pathway activate the intronic promoter of the short ACE2 isoform in renal proximal tubules.
Jankowski J, Lee HK, Wilflingseder J, Hennighausen L.
bioRxiv. 2021-01-19;
PMID: 33501441 DOI: 10.1101/2021.01.15.426908
|
Hsa_Circ_0098181 Suppresses Hepatocellular Carcinoma by Sponging miR-18a-3p and Targeting PPARA.
Luo YY, Tao KG, Lu YT, Li BB, Wu KM, Ding CH, Yan FZ, Liu Y, Lin Y, Zhang X, Zeng X.
Front Pharmacol. 2022-02-21; 13
PMID: 35264957 DOI: 10.3389/fphar.2022.819735
|
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
|
Highly Efficient SARS-CoV-2 Infection of Human Cardiomyocytes: Spike Protein-Mediated Cell Fusion and Its Inhibition.
Navaratnarajah CK, Pease DR, Halfmann PJ, Taye B, Barkhymer A, Howell KG, Charlesworth JE, Christensen TA, Kawaoka Y, Cattaneo R, Schneider JW, Wanek Family Program for HLHS-Stem Cell Pipeline.
J Virol. 2021-10-06; 95 (24)
PMID: 34613786 DOI: 10.1128/jvi.01368-21
|
Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated HIV-Infected Cells.
Golumbeanu M, Cristinelli S, Rato S, Munoz M, Cavassini M, Beerenwinkel N, Ciuffi A.
Cell Rep. 2018-04-01; 23 (4)
PMID: 29694901 DOI: 10.1016/j.celrep.2018.03.102
|
Disease-specific regulation of gene expression in a comparative analysis of juvenile idiopathic arthritis and inflammatory bowel disease.
Mo A, Marigorta UM, Arafat D, Chan LHK, Ponder L, Jang SR, Prince J, Kugathasan S, Prahalad S, Gibson G.
Genome Med. 2018-06-27; 10 (1)
PMID: 29950172 DOI: 10.1186/s13073-018-0558-x
|
SARS-CoV-2 Receptors and Entry Genes Are Expressed in the Human Olfactory Neuroepithelium and Brain.
Fodoulian L, Tuberosa J, Rossier D, Boillat M, Kan C, Pauli V, Egervari K, Lobrinus JA, Landis BN, Carleton A, Rodriguez I.
iScience. 2020-11-25; 23 (12)
PMID: 33251489 DOI: 10.1016/j.isci.2020.101839
|
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
|
The Dynamic Transcriptional Cell Atlas of Testis Development during Human Puberty.
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.
Cell Stem Cell. 2020-01-09; 26 (2)
PMID: 31928944 DOI: 10.1016/j.stem.2019.12.005
|
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
|
A Randomized Phase IIb Trial of myo-Inositol in Smokers with Bronchial Dysplasia.
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.
Cancer Prev Res (Phila). 2016-09-22; 9 (12)
PMID: 27658890 DOI: 10.1158/1940-6207.capr-15-0254
|
Identification of driver genes for critical forms of COVID-19 in a deeply phenotyped young patient cohort.
Carapito R, Li R, Helms J, Carapito C, Gujja S, Rolli V, Guimaraes R, Malagon-Lopez J, Spinnhirny P, Lederle A, Mohseninia R, Hirschler A, Muller L, Bastard P, Gervais A, Zhang Q, Danion F, Ruch Y, Schenck M, Collange O, Chamaraux-Tran TN, Molitor A, Pichot A, Bernard A, Tahar O, Bibi-Triki S, Wu H, Paul N, Mayeur S, Larnicol A, Laumond G, Frappier J, Schmidt S, Hanauer A, Macquin C, Stemmelen T, Simons M, Mariette X, Hermine O, Fafi-Kremer S, Goichot B, Drenou B, Kuteifan K, Pottecher J, Mertes PM, Kailasan S, Aman MJ, Pin E, Nilsson P, Thomas A, Viari A, Sanlaville D, Schneider F, Sibilia J, Tharaux PL, Casanova JL, Hansmann Y, Lidar D, Radosavljevic M, Gulcher JR, Meziani F, Moog C, Chittenden TW, Bahram S.
Sci Transl Med. 2021-10-26;
PMID: 34698500 DOI: 10.1126/scitranslmed.abj7521
|
Regenerative lineages and immune-mediated pruning in lung cancer metastasis.
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.
Nat Med. 2020-02-10; 26 (2)
PMID: 32042191 DOI: 10.1038/s41591-019-0750-6
|
Comprehensive transcriptome profiling of Taiwanese colorectal cancer implicates an ethnic basis for pathogenesis.
Wu SM, Tsai WS, Chiang SF, Lai YH, Ma CP, Wang JH, Lin J, Lu PS, Yang CY, Tan BC, Liu H.
Sci Rep. 2020-03-11; 10 (1)
PMID: 32161294 DOI: 10.1038/s41598-020-61273-y
|
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
|
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
|
Persistent COVID-19 Symptoms Minimally Impact the Development of SARS-CoV-2-Specific T Cell Immunity.
Fang H, Wegman AD, Ripich K, Friberg H, Currier JR, Thomas SJ, Endy TP, Waickman AT.
Viruses. 2021-05-15; 13 (5)
PMID: 34063463 DOI: 10.3390/v13050916
|
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
|
Detection of SARS-CoV-2 genome and whole transcriptome sequencing in frontal cortex of COVID-19 patients.
Gagliardi S, Poloni ET, Pandini C, Garofalo M, Dragoni F, Medici V, Davin A, Visonà SD, Moretti M, Sproviero D, Pansarasa O, Guaita A, Ceroni M, Tronconi L, Cereda C.
Brain Behav Immun. 2021-05-19; 97
PMID: 34022369 DOI: 10.1016/j.bbi.2021.05.012
|
A high-resolution temporal atlas of the SARS-CoV-2 translatome and transcriptome.
Kim D, Kim S, Park J, Chang HR, Chang J, Ahn J, Park H, Park J, Son N, Kang G, Kim J, Kim K, Park MS, Kim YK, Baek D.
Nat Commun. 2021-08-25; 12 (1)
PMID: 34433827 DOI: 10.1038/s41467-021-25361-5
|
Circular RNA circYPEL2: A Novel Biomarker in Cervical Cancer.
Zhang X, Yang S, Chen W, Dong X, Zhang R, Ye H, Mei X, Liu H, Fang Y, He C.
Genes (Basel). 2021-12-23; 13 (1)
PMID: 35052380 DOI: 10.3390/genes13010038
|
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
|
Primary T Cells from Cutaneous T-cell Lymphoma Skin Explants Display an Exhausted Immune Checkpoint Profile.
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.
Cancer Immunol Res. 2018-06-12; 6 (8)
PMID: 29895574 DOI: 10.1158/2326-6066.cir-17-0270
|
Global absence and targeting of protective immune states in severe COVID-19.
Combes AJ, Courau T, Kuhn NF, Hu KH, Ray A, Chen WS, Chew NW, Cleary SJ, Kushnoor D, Reeder GC, Shen A, Tsui J, Hiam-Galvez KJ, Muñoz-Sandoval P, Zhu WS, Lee DS, Sun Y, You R, Magnen M, Rodriguez L, Im KW, Serwas NK, Leligdowicz A, Zamecnik CR, Loudermilk RP, Wilson MR, Ye CJ, Fragiadakis GK, Looney MR, Chan V, Ward A, Carrillo S, UCSF COMET Consortium, Matthay M, Erle DJ, Woodruff PG, Langelier C, Kangelaris K, Hendrickson CM, Calfee C, Rao AA, Krummel MF.
Nature. 2021-01-25; 591 (7848)
PMID: 33494096 DOI: 10.1038/s41586-021-03234-7
|
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
|
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
|
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
|
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
|
Single-Cell RNA Sequencing of Urinary Cells Reveals Distinct Cellular Diversity in COVID-19-Associated AKI.
Cheung MD, Erman EN, Liu S, Erdmann NB, Ghajar-Rahimi G, Moore KH, Edberg JC, George JF, Agarwal A.
Kidney360. 2021-11-05; 3 (1)
PMID: 35368565 DOI: 10.34067/kid.0005522021
|
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
|
Blood platelet RNA profiles do not enable for nivolumab response prediction at baseline in patients with non-small cell lung cancer.
Muller M, Best MG, van der Noort V, Hiltermann TJN, Niemeijer AN, Post E, Sol N, In 't Veld SGJG, Nogarede T, Visser L, Schouten RD, van den Broek D, Hummelink K, Monkhorst K, de Langen AJ, Schuuring E, Smit EF, Groen HJM, Wurdinger T, van den Heuvel MM.
Tumour Biol. 2023-05-26;
PMID: 37270827 DOI: 10.3233/tub-220037
|
Multi-omic profiling of peritoneal metastases in gastric cancer identifies molecular subtypes and therapeutic vulnerabilities.
Tanaka Y, Chiwaki F, Kojima S, Kawazu M, Komatsu M, Ueno T, Inoue S, Sekine S, Matsusaki K, Matsushita H, Boku N, Kanai Y, Yatabe Y, Sasaki H, Mano H.
Nat Cancer. 2021-08-16; 2 (9)
PMID: 35121863 DOI: 10.1038/s43018-021-00240-6
|
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
|
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
|
Early adaptive immune activation detected in monozygotic twins with prodromal multiple sclerosis.
Beltrán E, Gerdes LA, Hansen J, Flierl-Hecht A, Krebs S, Blum H, Ertl-Wagner B, Barkhof F, Kümpfel T, Hohlfeld R, Dornmair K.
J Clin Invest. 2019-11-01; 129 (11)
PMID: 31566584 DOI: 10.1172/jci128475
|
Early Transcriptomic Changes in the Ileal Pouch Provide Insight into the Molecular Pathogenesis of Pouchitis and Ulcerative Colitis.
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.
Inflamm Bowel Dis. 2017-03-01; 23 (3)
PMID: 28221248 DOI: 10.1097/mib.0000000000001027
|
Molecular Profiling of Coronavirus Disease 2019 (COVID-19) Autopsies Uncovers Novel Disease Mechanisms.
Pujadas E, Beaumont M, Shah H, Schrode N, Francoeur N, Shroff S, Bryce C, Grimes Z, Gregory J, Donnelly R, Fowkes ME, Beaumont KG, Sebra R, Cordon-Cardo C.
Am J Pathol. 2021-09-08; 191 (12)
PMID: 34506752 DOI: 10.1016/j.ajpath.2021.08.009
|
Organoid single cell profiling identifies a transcriptional signature of glomerular disease.
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).
JCI Insight. 2019-01-10; 4 (1)
PMID: 30626756 DOI: 10.1172/jci.insight.122697
|
HSV-1 single-cell analysis reveals the activation of anti-viral and developmental programs in distinct sub-populations.
Drayman N, Patel P, Vistain L, Tay S.
Elife. 2019-05-15; 8
PMID: 31090537 DOI: 10.7554/elife.46339
|
Endothelialization of arterial vascular grafts by circulating monocytes.
Smith RJ, Nasiri B, Kann J, Yergeau D, Bard JE, Swartz DD, Andreadis ST.
Nat Commun. 2020-04-01; 11 (1)
PMID: 32238801 DOI: 10.1038/s41467-020-15361-2
|
Temporal and spatial heterogeneity of host response to SARS-CoV-2 pulmonary infection.
Desai N, Neyaz A, Szabolcs A, Shih AR, Chen JH, Thapar V, Nieman LT, Solovyov A, Mehta A, Lieb DJ, Kulkarni AS, Jaicks C, Xu KH, Raabe MJ, Pinto CJ, Juric D, Chebib I, Colvin RB, Kim AY, Monroe R, Warren SE, Danaher P, Reeves JW, Gong J, Rueckert EH, Greenbaum BD, Hacohen N, Lagana SM, Rivera MN, Sholl LM, Stone JR, Ting DT, Deshpande V.
Nat Commun. 2020-12-09; 11 (1)
PMID: 33298930 DOI: 10.1038/s41467-020-20139-7
|
Host transcriptional response to SARS-CoV-2 infection in COVID-19 patients.
Singh NK, Srivastava S, Zaveri L, Bingi TC, Mesipogu R, Kumar V S, Gaur N, Hajirnis N, Machha P, Shambhavi S, Khan S, Soujanya M, Nagabandi T, Mishra RK, Tallapaka KB, Sowpati DT.
Clin Transl Med. 2021-09-01; 11 (9)
PMID: 34586723 DOI: 10.1002/ctm2.534
|
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
|
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
|
B cell-specific XIST complex enforces X-inactivation and restrains atypical B cells.
Yu B, Qi Y, Li R, Shi Q, Satpathy AT, Chang HY.
Cell. 2021-03-17; 184 (7)
PMID: 33735607 DOI: 10.1016/j.cell.2021.02.015
|
An organoid-derived bronchioalveolar model for SARS-CoV-2 infection of human alveolar type II-like cells.
Lamers MM, van der Vaart J, Knoops K, Riesebosch S, Breugem TI, Mykytyn AZ, Beumer J, Schipper D, Bezstarosti K, Koopman CD, Groen N, Ravelli RBG, Duimel HQ, Demmers JAA, Verjans GMGM, Koopmans MPG, Muraro MJ, Peters PJ, Clevers H, Haagmans BL.
EMBO J. 2021-01-11; 40 (5)
PMID: 33283287 DOI: 10.15252/embj.2020105912
|
Maturation signatures of conventional dendritic cell subtypes in COVID-19 suggest direct viral sensing.
Marongiu L, Protti G, Facchini FA, Valache M, Mingozzi F, Ranzani V, Putignano AR, Salviati L, Bevilacqua V, Curti S, Crosti M, Sarnicola ML, D'Angiò M, Bettini LR, Biondi A, Nespoli L, Tamini N, Clementi N, Mancini N, Abrignani S, Spreafico R, Granucci F.
Eur J Immunol. 2021-10-01; 52 (1)
PMID: 34333764 DOI: 10.1002/eji.202149298
|
A distinct epigenetic profile distinguishes stenotic from non-inflamed fibroblasts in the ileal mucosa of Crohn's disease patients.
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.
PLoS One. 2018-12-27; 13 (12)
PMID: 30589872 DOI: 10.1371/journal.pone.0209656
|
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
|
Molecular signatures of multiple myeloma progression through single cell RNA-Seq.
Jang JS, Li Y, Mitra AK, Bi L, Abyzov A, van Wijnen AJ, Baughn LB, Van Ness B, Rajkumar V, Kumar S, Jen J.
Blood Cancer J. 2019-01-03; 9 (1)
PMID: 30607001 DOI: 10.1038/s41408-018-0160-x
|
Differing molecular response of young and advanced maternal age human oocytes to IVM.
Reyes JM, Silva E, Chitwood JL, Schoolcraft WB, Krisher RL, Ross PJ.
Hum Reprod. 2017-11-01; 32 (11)
PMID: 29025019 DOI: 10.1093/humrep/dex284
|
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)
PMID: 29510191 DOI: 10.1016/j.jid.2018.02.030
|
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
|
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
|
Transcriptomic characteristics and impaired immune function of patients who retest positive for SARS-CoV-2 RNA.
Wang D, Wang D, Huang M, Zheng X, Shen Y, Fu B, Zhao H, Chen X, Peng P, Zhu Q, Zhou Y, Zhang J, Tian Z, Guan W, Wang G, Wei H.
J Mol Cell Biol. 2021-12-01; 13 (10)
PMID: 34687295 DOI: 10.1093/jmcb/mjab067
|
Longitudinal Transcriptome Analysis Reveals a Sustained Differential Gene Expression Signature in Patients Treated for Acute Lyme Disease.
Bouquet J, Soloski MJ, Swei A, Cheadle C, Federman S, Billaud JN, Rebman AW, Kabre B, Halpert R, Boorgula M, Aucott JN, Chiu CY.
mBio. 2016-02-12; 7 (1)
PMID: 26873097 DOI: 10.1128/mbio.00100-16
|
Assessing similarity to primary tissue and cortical layer identity in induced pluripotent stem cell-derived cortical neurons through single-cell transcriptomics.
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.
Hum Mol Genet. 2016-01-05; 25 (5)
PMID: 26740550 DOI: 10.1093/hmg/ddv637
|
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
|
The effects of restricted glycolysis on stem-cell like characteristics of breast cancer cells.
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.
Oncotarget. 2018-05-01; 9 (33)
PMID: 29796188 DOI: 10.18632/oncotarget.25299
|
Spatial and Single-Cell Transcriptional Profiling Identifies Functionally Distinct Human Dermal Fibroblast Subpopulations.
Philippeos C, Telerman SB, Oulès B, Pisco AO, Shaw TJ, Elgueta R, Lombardi G, Driskell RR, Soldin M, Lynch MD, Watt FM.
J Invest Dermatol. 2018-01-31; 138 (4)
PMID: 29391249 DOI: 10.1016/j.jid.2018.01.016
|
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
|
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
|
Platelets amplify endotheliopathy in COVID-19.
Barrett TJ, Cornwell M, Myndzar K, Rolling CC, Xia Y, Drenkova K, Biebuyck A, Fields AT, Tawil M, Luttrell-Williams E, Yuriditsky E, Smith G, Cotzia P, Neal MD, Kornblith LZ, Pittaluga S, Rapkiewicz AV, Burgess HM, Mohr I, Stapleford KA, Voora D, Ruggles K, Hochman J, Berger JS.
Sci Adv. 2021-09-08; 7 (37)
PMID: 34516880 DOI: 10.1126/sciadv.abh2434
|
An Immuno-Cardiac Model for Macrophage-Mediated Inflammation in COVID-19 Hearts.
Yang L, Han Y, Jaffré F, Nilsson-Payant BE, Bram Y, Wang P, Zhu J, Zhang T, Redmond D, Houghton S, Uhl S, Borczuk A, Huang Y, Richardson C, Chandar V, Acklin JA, Lim JK, Chen Z, Xiang J, Ho DD, tenOever BR, Schwartz RE, Evans T, Chen S.
Circ Res. 2021-04-15; 129 (1)
PMID: 33853355 DOI: 10.1161/circresaha.121.319060
|
The nature and nurture of cell heterogeneity: accounting for macrophage gene-environment interactions with single-cell RNA-Seq.
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.
BMC Genomics. 2017-01-07; 18 (1)
PMID: 28061811 DOI: 10.1186/s12864-016-3445-0
|
Clinico-histopathologic and single nuclei RNA sequencing insights into cardiac injury and microthrombi in critical COVID-19.
Brener MI, Hulke ML, Fukuma N, Golob S, Zilinyi RS, Zhou Z, Tzimas C, Russo I, McGroder C, Pfeiffer RD, Chong A, Zhang G, Burkhoff D, Leon MB, Maurer MS, Moses JW, Uhlemann AC, Hibshoosh H, Uriel N, Szabolcs MJ, Redfors B, Marboe CC, Baldwin MR, Tucker NR, Tsai EJ.
JCI Insight. 2021-12-14;
PMID: 34905515 DOI: 10.1172/jci.insight.154633
|
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
|
Integrated single-cell analysis unveils diverging immune features of COVID-19, influenza, and other community-acquired pneumonia.
Schuurman AR, Reijnders TDY, Saris A, Ramirez Moral I, Schinkel M, de Brabander J, van Linge C, Vermeulen L, Scicluna BP, Wiersinga WJ, Vieira Braga FA, van der Poll T.
Elife. 2021-08-23; 10
PMID: 34424199 DOI: 10.7554/elife.69661
|
Identification of key genes associated with papillary thyroid microcarcinoma characteristics by integrating transcriptome sequencing and weighted gene co-expression network analysis.
Yang F, Lian M, Ma H, Feng L, Shen X, Chen J, Fang J.
Gene. 2021-11-29; 811
PMID: 34856364 DOI: 10.1016/j.gene.2021.146086
|
IL-21 drives expansion and plasma cell differentiation of autoreactive CD11chiT-bet+ B cells in SLE.
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.
Nat Commun. 2018-05-01; 9 (1)
PMID: 29717110 DOI: 10.1038/s41467-018-03750-7
|
MiR-1253 exerts tumor-suppressive effects in medulloblastoma via inhibition of CDK6 and CD276 (B7-H3).
Kanchan RK, Perumal N, Atri P, Chirravuri Venkata R, Thapa I, Klinkebiel DL, Donson AM, Perry D, Punsoni M, Talmon GA, Coulter DW, Boue' DR, Snuderl M, Nasser MW, Batra SK, Vibhakar R, Mahapatra S.
Brain Pathol. 2020-03-30; 30 (4)
PMID: 32145124 DOI: 10.1111/bpa.12829
|
Tuberculous meningitis in children is characterized by compartmentalized immune responses and neural excitotoxicity.
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.
Nat Commun. 2019-08-21; 10 (1)
PMID: 31434901 DOI: 10.1038/s41467-019-11783-9
|
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
|
Multi-Omic Data Integration Allows Baseline Immune Signatures to Predict Hepatitis B Vaccine Response in a Small Cohort.
Shannon CP, Blimkie TM, Ben-Othman R, Gladish N, Amenyogbe N, Drissler S, Edgar RD, Chan Q, Krajden M, Foster LJ, Kobor MS, Mohn WW, Brinkman RR, Le Cao KA, Scheuermann RH, Tebbutt SJ, Hancock REW, Koff WC, Kollmann TR, Sadarangani M, Lee AH.
Front Immunol. 2020-11-30; 11
PMID: 33329547 DOI: 10.3389/fimmu.2020.578801
|
Integrated Multi-omic Analysis of Esthesioneuroblastomas Identifies Two Subgroups Linked to Cell Ontogeny.
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.
Cell Rep. 2018-10-01; 25 (3)
PMID: 30332658 DOI: 10.1016/j.celrep.2018.09.047
|
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
|
Defective structural RNA processing in relapsing-remitting multiple sclerosis.
Spurlock CF, Tossberg JT, Guo Y, Sriram S, Crooke PS, Aune TM.
Genome Biol. 2015-03-25; 16
PMID: 25885816 DOI: 10.1186/s13059-015-0629-x
|
Deciphering the state of immune silence in fatal COVID-19 patients.
Bost P, De Sanctis F, Canè S, Ugel S, Donadello K, Castellucci M, Eyal D, Fiore A, Anselmi C, Barouni RM, Trovato R, Caligola S, Lamolinara A, Iezzi M, Facciotti F, Mazzariol A, Gibellini D, De Nardo P, Tacconelli E, Gottin L, Polati E, Schwikowski B, Amit I, Bronte V.
Nat Commun. 2021-03-05; 12 (1)
PMID: 33674591 DOI: 10.1038/s41467-021-21702-6
|
Memory CD4+ T cells are generated in the human fetal intestine.
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.
Nat Immunol. 2019-01-21; 20 (3)
PMID: 30664737 DOI: 10.1038/s41590-018-0294-9
|
FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders.
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.
Cell. 2015-07-01; 162 (2)
PMID: 26186191 DOI: 10.1016/j.cell.2015.06.034
|
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
|
Associations of creatinine/cystatin C ratio and postoperative pulmonary complications in elderly patients undergoing off-pump coronary artery bypass surgery: a retrospective study.
Kim HJ, Kim HB, Kim HY, Shim JK, Lee C, Kwak YL.
Sci Rep. 2021-08-19; 11 (1)
PMID: 34413410 DOI: 10.1038/s41598-021-96442-0
|
Local lung hypoxia determines epithelial fate decisions during alveolar regeneration.
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.
Nat Cell Biol. 2017-07-24; 19 (8)
PMID: 28737769 DOI: 10.1038/ncb3580
|
Phenotypic responses of differentiated asthmatic human airway epithelial cultures to rhinovirus.
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.
PLoS One. 2015-02-23; 10 (2)
PMID: 25706956 DOI: 10.1371/journal.pone.0118286
|
Early immune responses have long-term associations with clinical, virologic, and immunologic outcomes in patients with COVID-19.
Hu Z, van der Ploeg K, Chakraborty S, Arunachalam P, Mori D, Jacobson K, Bonilla H, Parsonnet J, Andrews J, Hedlin H, de la Parte L, Dantzler K, Ty M, Tan G, Blish C, Takahashi S, Rodriguez-Barraquer I, Greenhouse B, Butte A, Singh U, Pulendran B, Wang T, Jagannathan P.
Res Sq. 2022-02-02;
PMID: 35132407 DOI: 10.21203/rs.3.rs-847082/v1
|
Single-Cell Expression Variability Implies Cell Function.
Osorio D, Yu X, Zhong Y, Li G, Yu P, Serpedin E, Huang JZ, Cai JJ.
Cells. 2019-12-19; 9 (1)
PMID: 31861624 DOI: 10.3390/cells9010014
|
Modeling SARS-CoV-2 infection and its individual differences with ACE2-expressing human iPS cells.
Sano E, Deguchi S, Sakamoto A, Mimura N, Hirabayashi A, Muramoto Y, Noda T, Yamamoto T, Takayama K.
iScience. 2021-04-16; 24 (5)
PMID: 33880436 DOI: 10.1016/j.isci.2021.102428
|
Single-Cell Survey of Human Lymphatics Unveils Marked Endothelial Cell Heterogeneity and Mechanisms of Homing for Neutrophils.
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.
Immunity. 2019-08-08; 51 (3)
PMID: 31402260 DOI: 10.1016/j.immuni.2019.06.027
|
Identification of Candidate COVID-19 Therapeutics using hPSC-derived Lung Organoids.
Han Y, Yang L, Duan X, Duan F, Nilsson-Payant BE, Yaron TM, Wang P, Tang X, Zhang T, Zhao Z, Bram Y, Redmond D, Houghton S, Nguyen D, Xu D, Wang X, Uhl S, Huang Y, Johnson JL, Xiang J, Wang H, Pan FC, Cantley LC, tenOever BR, Ho DD, Evans T, Schwartz RE, Chen HJ, Chen S.
bioRxiv. 2020-05-05;
PMID: 32511403 DOI: 10.1101/2020.05.05.079095
|
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
|
Molecular Analysis of the Kidney From a Patient With COVID-19-Associated Collapsing Glomerulopathy.
Meliambro K, Li X, Salem F, Yi Z, Sun Z, Chan L, Chung M, Chancay J, Vy HMT, Nadkarni G, Wong JS, Fu J, Lee K, Zhang W, He JC, Campbell KN.
Kidney Med. 2021-04-28; 3 (4)
PMID: 33942030 DOI: 10.1016/j.xkme.2021.02.012
|
The NF-κB Transcriptional Footprint Is Essential for SARS-CoV-2 Replication.
Nilsson-Payant BE, Uhl S, Grimont A, Doane AS, Cohen P, Patel RS, Higgins CA, Acklin JA, Bram Y, Chandar V, Blanco-Melo D, Panis M, Lim JK, Elemento O, Schwartz RE, Rosenberg BR, Chandwani R, tenOever BR.
J Virol. 2021-09-15; 95 (23)
PMID: 34523966 DOI: 10.1128/jvi.01257-21
|
Single cell analysis of human foetal liver captures the transcriptional profile of hepatobiliary hybrid progenitors.
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.
Nat Commun. 2019-07-26; 10 (1)
PMID: 31350390 DOI: 10.1038/s41467-019-11266-x
|
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
|
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
|
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
|
SARS-CoV-2 infection induces beta cell transdifferentiation.
Tang X, Uhl S, Zhang T, Xue D, Li B, Vandana JJ, Acklin JA, Bonnycastle LL, Narisu N, Erdos MR, Bram Y, Chandar V, Chong ACN, Lacko LA, Min Z, Lim JK, Borczuk AC, Xiang J, Naji A, Collins FS, Evans T, Liu C, tenOever BR, Schwartz RE, Chen S.
Cell Metab. 2021-05-19; 33 (8)
PMID: 34081913 DOI: 10.1016/j.cmet.2021.05.015
|
A radiogenomic dataset of non-small cell lung cancer.
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.
Sci Data. 2018-10-16; 5
PMID: 30325352 DOI: 10.1038/sdata.2018.202
|
Electrical and synaptic integration of glioma into neural circuits.
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.
Nature. 2019-09-18; 573 (7775)
PMID: 31534222 DOI: 10.1038/s41586-019-1563-y
|
Single-Cell RNA Sequencing Reveals Expanded Clones of Islet Antigen-Reactive CD4+ T Cells in Peripheral Blood of Subjects with Type 1 Diabetes.
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.
J Immunol. 2017-05-31; 199 (1)
PMID: 28566371 DOI: 10.4049/jimmunol.1700172
|
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
|
Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing.
Han X, Chen H, Huang D, Chen H, Fei L, Cheng C, Huang H, Yuan GC, Guo G.
Genome Biol. 2018-04-05; 19 (1)
PMID: 29622030 DOI: 10.1186/s13059-018-1426-0
|
Metabolic reprogramming and epigenetic changes of vital organs in SARS-CoV-2-induced systemic toxicity.
Li S, Ma F, Yokota T, Garcia G, Palermo A, Wang Y, Farrell C, Wang YC, Wu R, Zhou Z, Pan C, Morselli M, Teitell MA, Ryazantsev S, Fishbein GA, Hoeve JT, Arboleda VA, Bloom J, Dillon B, Pellegrini M, Lusis AJ, Graeber TG, Arumugaswami V, Deb A.
JCI Insight. 2021-01-25; 6 (2)
PMID: 33284134 DOI: 10.1172/jci.insight.145027
|
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
|
Genetic and transcriptional evolution alters cancer cell line drug response.
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.
Nature. 2018-08-08; 560 (7718)
PMID: 30089904 DOI: 10.1038/s41586-018-0409-3
|
Maternal respiratory SARS-CoV-2 infection in pregnancy is associated with a robust inflammatory response at the maternal-fetal interface.
Lu-Culligan A, Chavan AR, Vijayakumar P, Irshaid L, Courchaine EM, Milano KM, Tang Z, Pope SD, Song E, Vogels CBF, Lu-Culligan WJ, Campbell KH, Casanovas-Massana A, Bermejo S, Toothaker JM, Lee HJ, Liu F, Schulz W, Fournier J, Muenker MC, Moore AJ, Yale IMPACT Team, Konnikova L, Neugebauer KM, Ring A, Grubaugh ND, Ko AI, Morotti R, Guller S, Kliman HJ, Iwasaki A, Farhadian SF.
Med (N Y). 2021-04-30; 2 (5)
PMID: 33969332 DOI: 10.1016/j.medj.2021.04.016
|
Transcriptome Analysis of Peripheral Blood Mononuclear Cells Reveals Distinct Immune Response in Asymptomatic and Re-Detectable Positive COVID-19 Patients.
Zhang J, Lin D, Li K, Ding X, Li L, Liu Y, Liu D, Lin J, Teng X, Li Y, Liu M, Shen J, Wang X, He D, Shi Y, Wang D, Xu J.
Front Immunol. 2021-07-29; 12
PMID: 34394120 DOI: 10.3389/fimmu.2021.716075
|
Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells.
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.
Nat Struct Mol Biol. 2013-08-11; 20 (9)
PMID: 23934149 DOI: 10.1038/nsmb.2660
|
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
|
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
|
Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells.
Kim KT, Lee HW, Lee HO, Kim SC, Seo YJ, Chung W, Eum HH, Nam DH, Kim J, Joo KM, Park WY.
Genome Biol. 2015-06-19; 16
PMID: 26084335 DOI: 10.1186/s13059-015-0692-3
|
Vascular Damage, Thromboinflammation, Plasmablast Activation, T-Cell Dysregulation and Pathological Histiocytic Response in Pulmonary Draining Lymph Nodes of COVID-19.
Haslbauer JD, Zinner C, Stalder AK, Schneeberger J, Menter T, Bassetti S, Mertz KD, Went P, Matter MS, Tzankov A.
Front Immunol. 2021-12-13; 12
PMID: 34966385 DOI: 10.3389/fimmu.2021.763098
|
Regulatory KIR+ RA+ T cells accumulate with age and are highly activated during viral respiratory disease.
Pieren DKJ, Smits NAM, Hoeboer J, Kandiah V, Postel RJ, Mariman R, van Beek J, van Baarle D, de Wit J, Guichelaar T.
Aging Cell. 2021-05-27; 20 (6)
PMID: 34043881 DOI: 10.1111/acel.13372
|
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
|
Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells.
Xie S, Duan J, Li B, Zhou P, Hon GC.
Mol Cell. 2017-04-13; 66 (2)
PMID: 28416141 DOI: 10.1016/j.molcel.2017.03.007
|
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
|
RNA-sequencing of the brain transcriptome implicates dysregulation of neuroplasticity, circadian rhythms and GTPase binding in bipolar disorder.
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.
Mol Psychiatry. 2014-01-07; 19 (11)
PMID: 24393808 DOI: 10.1038/mp.2013.170
|
Single-Cell Transcriptomic Profiling of Pluripotent Stem Cell-Derived SCGB3A2+ Airway Epithelium.
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.
Stem Cell Reports. 2018-04-12; 10 (5)
PMID: 29657097 DOI: 10.1016/j.stemcr.2018.03.013
|
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 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
|
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
|
Airway Smooth Muscle-Specific Transcriptomic Signatures of Glucocorticoid Exposure.
Kan M, Koziol-White C, Shumyatcher M, Johnson M, Jester W, Panettieri RA, Himes BE.
Am J Respir Cell Mol Biol. 2019-07-01; 61 (1)
PMID: 30694689 DOI: 10.1165/rcmb.2018-0385oc
|
SARS-CoV-2 infection and replication in human gastric organoids.
Giobbe GG, Bonfante F, Jones BC, Gagliano O, Luni C, Zambaiti E, Perin S, Laterza C, Busslinger G, Stuart H, Pagliari M, Bortolami A, Mazzetto E, Manfredi A, Colantuono C, Di Filippo L, Pellegata AF, Panzarin V, Thapar N, Li VSW, Eaton S, Cacchiarelli D, Clevers H, Elvassore N, De Coppi P.
Nat Commun. 2021-11-16; 12 (1)
PMID: 34785679 DOI: 10.1038/s41467-021-26762-2
|
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
|