Cole Trapnell - Related publications

Affiliations: 
2010 Computer Science University of Maryland, College Park, College Park, MD 
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50 most relevant papers in past 60 days:
Year Citation  Score
2021 Schumacher A, Rookmaaker MB, Joles JA, Kramann R, Nguyen TQ, van Griensven M, LaPointe VLS. Defining the variety of cell types in developing and adult human kidneys by single-cell RNA sequencing. Npj Regenerative Medicine. 6: 45. PMID 34381054 DOI: 10.1038/s41536-021-00156-w   
2021 Li YE, Preissl S, Hou X, Zhang Z, Zhang K, Qiu Y, Poirion OB, Li B, Chiou J, Liu H, Pinto-Duarte A, Kubo N, Yang X, Fang R, Wang X, et al. An atlas of gene regulatory elements in adult mouse cerebrum. Nature. 598: 129-136. PMID 34616068 DOI: 10.1038/s41586-021-03604-1   
2021 Oh S, Gray DHD, Chong MMW. Single-Cell RNA Sequencing Approaches for Tracing T Cell Development. Journal of Immunology (Baltimore, Md. : 1950). 207: 363-370. PMID 34644259 DOI: 10.4049/jimmunol.2100408   
2021 Lohoff T, Ghazanfar S, Missarova A, Koulena N, Pierson N, Griffiths JA, Bardot ES, Eng CL, Tyser RCV, Argelaguet R, Guibentif C, Srinivas S, Briscoe J, Simons BD, Hadjantonakis AK, et al. Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis. Nature Biotechnology. PMID 34489600 DOI: 10.1038/s41587-021-01006-2   
2021 Yao Z, Liu H, Xie F, Fischer S, Adkins RS, Aldridge AI, Ament SA, Bartlett A, Behrens MM, Van den Berge K, Bertagnolli D, de Bézieux HR, Biancalani T, Booeshaghi AS, Bravo HC, et al. A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature. 598: 103-110. PMID 34616066 DOI: 10.1038/s41586-021-03500-8   
2021 Shrestha S, Singhal S, Kalonick M, Guyer R, Volkert A, Somji S, Garrett SH, Sens DA, Singhal SK. Role of HRTPT in kidney proximal epithelial cell regeneration: Integrative differential expression and pathway analyses using microarray and scRNA-seq. Journal of Cellular and Molecular Medicine. PMID 34626063 DOI: 10.1111/jcmm.16976   
2021 Sarropoulos I, Sepp M, Frömel R, Leiss K, Trost N, Leushkin E, Okonechnikov K, Joshi P, Giere P, Kutscher LM, Cardoso-Moreira M, Pfister SM, Kaessmann H. Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells. Science (New York, N.Y.). 373. PMID 34446581 DOI: 10.1126/science.abg4696   
2021 Ziffra RS, Kim CN, Ross JM, Wilfert A, Turner TN, Haeussler M, Casella AM, Przytycki PF, Keough KC, Shin D, Bogdanoff D, Kreimer A, Pollard KS, Ament SA, Eichler EE, et al. Single-cell epigenomics reveals mechanisms of human cortical development. Nature. 598: 205-213. PMID 34616060 DOI: 10.1038/s41586-021-03209-8   
2021 Sun Z, Tang Y, Zhang Y, Fang Y, Jia J, Zeng W, Fang D. Joint single-cell multiomic analysis in Wnt3a induced asymmetric stem cell division. Nature Communications. 12: 5941. PMID 34642323 DOI: 10.1038/s41467-021-26203-0   
2021 Denoth-Lippuner A, Jaeger BN, Liang T, Royall LN, Chie SE, Buthey K, Machado D, Korobeynyk VI, Kruse M, Munz CM, Gerbaulet A, Simons BD, Jessberger S. Visualization of individual cell division history in complex tissues using iCOUNT. Cell Stem Cell. PMID 34525348 DOI: 10.1016/j.stem.2021.08.012   
2021 Gebert N, Rahman S, Lewis CA, Ori A, Cheng CW. Identifying Cell-Type-Specific Metabolic Signatures Using Transcriptome and Proteome Analyses. Current Protocols. 1: e245. PMID 34516047 DOI: 10.1002/cpz1.245   
2021 Inoue Y, Hasegawa S, Hasebe Y, Kawagishi-Hotta M, Okuno R, Yamada T, Adachi H, Miyachi K, Ishii Y, Sugiura K, Akamatsu H. Establishment of Three Types of Immortalized Human Skin Stem Cell Lines Derived from the Single Donor. Biological & Pharmaceutical Bulletin. 44: 1403-1412. PMID 34602549 DOI: 10.1248/bpb.b21-00058   
2021 Lin SZ, Zhou XY, Wang WQ, Jiang K. Autism with dysphasia accompanied by mental retardation caused by exon deletion: A case report. World Journal of Clinical Cases. 9: 6858-6866. PMID 34447835 DOI: 10.12998/wjcc.v9.i23.6858   
2021 Zhang J, Pang J, Bai Y, Lin Z, Huang J, Songyang Z, Shi G. Global molecular features in transcription and chromatin accessibility in human extended pluripotent stem cells. Biochemical and Biophysical Research Communications. 574: 63-69. PMID 34438348 DOI: 10.1016/j.bbrc.2021.08.047   
2021 Liu H, Zhou J, Tian W, Luo C, Bartlett A, Aldridge A, Lucero J, Osteen JK, Nery JR, Chen H, Rivkin A, Castanon RG, Clock B, Li YE, Hou X, et al. DNA methylation atlas of the mouse brain at single-cell resolution. Nature. 598: 120-128. PMID 34616061 DOI: 10.1038/s41586-020-03182-8   
2021 Yildirim E, Bora G, Onel T, Talas N, Yaba A. Cell fate determination and Hippo signaling pathway in preimplantation mouse embryo. Cell and Tissue Research. PMID 34586506 DOI: 10.1007/s00441-021-03530-8   
2021 Bonora G, Ramani V, Singh R, Fang H, Jackson DL, Srivatsan S, Qiu R, Lee C, Trapnell C, Shendure J, Duan Z, Deng X, Noble WS, Disteche CM. Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation. Genome Biology. 22: 279. PMID 34579774 DOI: 10.1186/s13059-021-02432-w   
2021 Zhu Y, Cheng C, Chen L, Zhang L, Pan H, Hou L, Sun Z, Zhang L, Fu X, Chan KY, Zhang J. Cell cycle heterogeneity directs spontaneous 2C state entry and exit in mouse embryonic stem cells. Stem Cell Reports. PMID 34624246 DOI: 10.1016/j.stemcr.2021.09.003   
2021 Sun X, Li L, Wu B, Ge J, Zheng Y, Yu T, Zhou L, Zhang T, Yang A, Liu Z. Cell type diversity in scallop adductor muscles revealed by single-cell RNA-Seq. Genomics. PMID 34425225 DOI: 10.1016/j.ygeno.2021.08.015   
2021 Wang J, Tu C, Zhang H, Huo Y, Menu E, Liu J. Single-cell analysis at the protein level delineates intracellular signaling dynamic during hematopoiesis. Bmc Biology. 19: 201. PMID 34503511 DOI: 10.1186/s12915-021-01138-6   
2021 Lencer E, Prekeris R, Artinger KB. Single-cell RNA analysis identifies pre-migratory neural crest cells expressing markers of differentiated derivatives. Elife. 10. PMID 34397384 DOI: 10.7554/eLife.66078   
2021 Dey A, Uppal S, Giri J, Misra HS. Emerging roles of Bromodomain protein 4 in regulation of stem cell identity. Stem Cells (Dayton, Ohio). PMID 34520583 DOI: 10.1002/stem.3454   
2021 Koduru SV, Leberfinger A, Ozbolat IT, Ravnic DJ. Navigating genomic landscape of human adipose stem cell derived β-cells. Stem Cells and Development. PMID 34514867 DOI: 10.1089/scd.2021.0160   
2021 Lubanska D, Qemo I, Byrne M, Matthews KN, Fifield BA, Brown J, da Silva EF, Porter LA. The Cyclin-Like Protein SPY1 overrides Reprogramming Induced Senescence Through EZH2 Mediated H3K27me3. Stem Cells (Dayton, Ohio). PMID 34486784 DOI: 10.1002/stem.3453   
2021 Jiang Y, Chen C, Randolph LN, Ye S, Zhang X, Bao X, Lian XL. Generation of pancreatic progenitors from human pluripotent stem cells by small molecules. Stem Cell Reports. PMID 34450037 DOI: 10.1016/j.stemcr.2021.07.021   
2021 Zhao K, Wang M, Gao S, Chen J. Chromatin architecture reorganization during somatic cell reprogramming. Current Opinion in Genetics & Development. 70: 104-113. PMID 34530248 DOI: 10.1016/j.gde.2021.07.006   
2021 Rebuzzini P, Zuccotti M, Garagna S. Building Pluripotency Identity in the Early Embryo and Derived Stem Cells. Cells. 10. PMID 34440818 DOI: 10.3390/cells10082049   
2021 Gonzalez NM, Zou D, Gu A, Chen W. Schrödinger's T Cells: Molecular Insights Into Stemness and Exhaustion. Frontiers in Immunology. 12: 725618. PMID 34512656 DOI: 10.3389/fimmu.2021.725618   
2021 Mitchell JM, Sucharov J, Pulvino AT, Brooks EP, Gillen AE, Nichols JT. The alx3 gene shapes the zebrafish neurocranium by regulating frontonasal neural crest cell differentiation timing. Development (Cambridge, England). 148. PMID 34437690 DOI: 10.1242/dev.197483   
2021 Lehnertz B, Chagraoui J, MacRae T, Tomellini E, Corneau S, Mayotte N, Boivin I, Durand A, Gracias D, Sauvageau G. HLF Expression Defines the Human Hematopoietic Stem Cell State. Blood. PMID 34499717 DOI: 10.1182/blood.2021010745   
2021 Nakhaei-Nejad M, Trinity L, Jabbari H, Pasdar M, Jahroudi N. In Silico Analysis to Explore Lineage-Independent and -Dependent Transcriptional Programs Associated with the Process of Endothelial and Neural Differentiation of Human Induced Pluripotent Stem Cells. Journal of Clinical Medicine. 10. PMID 34575270 DOI: 10.3390/jcm10184161   
2021 Kay M, Soltani BM, Nemir M, Aghagolzadeh P, Pezzuto I, Chouvardas P, Ruberto F, Movahedi F, Ansari H, Baharvand H, Pedrazzini T. The conserved long noncoding RNA CARMA regulates cardiomyocyte differentiation. Cardiovascular Research. PMID 34459880 DOI: 10.1093/cvr/cvab281   
2021 Ferreira MJS, Mancini FE, Humphreys PA, Ogene L, Buckley M, Domingos MAN, Kimber SJ. Pluripotent stem cells for skeletal tissue engineering. Critical Reviews in Biotechnology. 1-20. PMID 34488516 DOI: 10.1080/07388551.2021.1968785   
2021 Echeagaray O, Kim T, Casillas A, Monsanto M, Sussman M. Transcriptional features of biological age maintained in human cultured cardiac interstitial cells. Genomics. 113: 3705-3717. PMID 34509618 DOI: 10.1016/j.ygeno.2021.09.004   
2021 López AE, Bauzá MDR, Cuniberti L, Crottogini AJ, Olea FD, Locatelli P. Gene Therapy: Targeting Cardiomyocyte Proliferation to Repopulate the Ischemic Heart. Journal of Cardiovascular Pharmacology. 78: 346-360. PMID 34516452 DOI: 10.1097/FJC.0000000000001072   
2021 Chan K, Li X. Current Epigenetic Insights in Kidney Development. Genes. 12. PMID 34440455 DOI: 10.3390/genes12081281   
2021 Winkley KM, Reeves WM, Veeman MT. Single-cell analysis of cell fate bifurcation in the chordate Ciona. Bmc Biology. 19: 180. PMID 34465302 DOI: 10.1186/s12915-021-01122-0   
2021 Hou Z, Liu Y, Zhang M, Zhao L, Jin X, Liu L, Su Z, Cai H, Qin Y. High-throughput single-cell transcriptomics reveals the female germline differentiation trajectory in Arabidopsis thaliana. Communications Biology. 4: 1149. PMID 34599277 DOI: 10.1038/s42003-021-02676-z   
2021 Park S, Mali NM, Kim R, Choi JW, Lee J, Lim J, Park JM, Park JW, Kim D, Kim T, Yi K, Choi JH, Kwon SG, Hong JH, Youk J, et al. Clonal dynamics in early human embryogenesis inferred from somatic mutation. Nature. PMID 34433967 DOI: 10.1038/s41586-021-03786-8   
2021 Brown G. Oncogenes, Proto-Oncogenes, and Lineage Restriction of Cancer Stem Cells. International Journal of Molecular Sciences. 22. PMID 34575830 DOI: 10.3390/ijms22189667   
2021 Little MH, Howden SE, Lawlor KT, Vanslambrouck JM. Determining lineage relationships in kidney development and disease. Nature Reviews. Nephrology. PMID 34594045 DOI: 10.1038/s41581-021-00485-5   
2021 Chow LS, Bosnakovski D, Mashek DG, Kyba M, Perlingeiro RCR, Magli A. Chromatin accessibility profiling identifies evolutionary conserved loci in activated human satellite cells. Stem Cell Research. 55: 102496. PMID 34411972 DOI: 10.1016/j.scr.2021.102496   
2021 Hogrebe NJ, Maxwell KG, Augsornworawat P, Millman JR. Generation of insulin-producing pancreatic β cells from multiple human stem cell lines. Nature Protocols. PMID 34349281 DOI: 10.1038/s41596-021-00560-y   
2021 Ni X, Geng B, Zheng H, Shi J, Hu G, Gao J. Accurate estimation of single-cell differentiation potency based on network topology and gene ontology information. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 34529570 DOI: 10.1109/TCBB.2021.3112951   
2021 Sebastião MJ, Serra M, Gomes-Alves P, Alves PM. Stem cells characterization: OMICS reinforcing analytics. Current Opinion in Biotechnology. 71: 175-181. PMID 34425321 DOI: 10.1016/j.copbio.2021.07.021   
2021 Bleckwehl T, Crispatzu G, Schaaf K, Respuela P, Bartusel M, Benson L, Clark SJ, Dorighi KM, Barral A, Laugsch M, van IJcken WFJ, Manzanares M, Wysocka J, Reik W, Rada-Iglesias Á. Enhancer-associated H3K4 methylation safeguards in vitro germline competence. Nature Communications. 12: 5771. PMID 34599190 DOI: 10.1038/s41467-021-26065-6   
2021 Chhabra S, Warmflash A. BMP-treated human embryonic stem cells transcriptionally resemble amnion cells in the monkey embryo. Biology Open. PMID 34435204 DOI: 10.1242/bio.058617   
2021 Kim YJ, Tamadon A, Kim YY, Kang BC, Ku SY. Epigenetic Regulation of Cardiomyocyte Differentiation from Embryonic and Induced Pluripotent Stem Cells. International Journal of Molecular Sciences. 22. PMID 34445302 DOI: 10.3390/ijms22168599   
2021 Sundaravadivelu PK, Raina K, Thool M, Ray A, Joshi JM, Kaveeshwar V, Sudhagar S, Lenka N, Thummer RP. Tissue-Restricted Stem Cells as Starting Cell Source for Efficient Generation of Pluripotent Stem Cells: An Overview. Advances in Experimental Medicine and Biology. PMID 34611861 DOI: 10.1007/5584_2021_660   
2021 Zuch DT, Doyle SM, Majda M, Smith RS, Robert S, Torii KU. Cell biology of the leaf epidermis: Fate specification, morphogenesis and coordination. The Plant Cell. PMID 34623438 DOI: 10.1093/plcell/koab250