Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species

Basic Information

Latin Name: Homo sapiens
Common Name: Human
Kingdom: Animalia
Division: Primates
Taxonomy ID: 9606
Parent Taxonomy ID: 9605

Datasets

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#

Publications

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)
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)
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)
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)
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)
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)
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
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)
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
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)
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)
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)
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)
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)
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)
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)
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)
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
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)
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)
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)
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;
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)
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)
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)
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)
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
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)
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)
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)
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;
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)
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)
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)
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)
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)
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)
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
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)
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
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)
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
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)
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)
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)
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
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)
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)
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)
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)
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)
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
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)
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)
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;
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)
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)
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
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
Single-cell transcriptomics of the human placenta: inferring the cell communication network of the maternal-fetal interface.
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