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78 items
Siewert-Rocks KM, Kim SS, Yao DW, Shi H, Price AL.
2022-03-03
doi:10.1016/j.ajhg.2022.01.005
released
Leveraging gene co-regulation to identify gene sets enriched for disease heritability
McAfee JC, Bell JL, Krupa O, Matoba N, Stein JL, Won H.
2022-09-09
doi:10.1186/s11689-022-09461-x
released
Focus on your locus with a massively parallel reporter assay
Abuhashem A, Lee AS, Joyner AL, Hadjantonakis AK.
2022-04-25
doi:10.1016/j.devcel.2022.03.013
released
Rapid and efficient degradation of endogenous proteins in vivo identifies stage-specific roles of RNA Pol II pausing in mammalian development
Karbalayghareh A, Sahin M, Leslie CS.
doi:10.1101/gr.275870.121
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Chromatin interaction-aware gene regulatory modeling with graph attention networks
Gloyn AL, Ibberson M, Marchetti P, Powers AC, Rorsman P, Sander M, Solimena M.
doi:10.1038/s42255-022-00607-8
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Every islet matters: improving the impact of human islet research
Liu Z, Shen J, Barfield R, Schwartz J, Baccarelli AA, Lin X.
doi:10.1080/01621459.2021.1914634
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Large-Scale Hypothesis Testing for Causal Mediation Effects with Applications in Genome-wide Epigenetic Studies
Kedmi R, Najar TA, Mesa KR, Grayson A, Kroehling L, Hao Y, Hao S, Pokrovskii M, Xu M, Talbot J, Wang J, Germino J, Lareau CA, Satpathy AT, Anderson MS, Laufer TM, Aifantis I, Bartleson JM, Allen PM, Paidassi H, Gardner JM, Stoeckius M, Littman DR.
2022-09-07
doi:10.1038/s41586-022-05089-y
released
A RORγt+ cell instructs gut microbiota-specific Treg cell differentiation
doi:10.1096/fj.01-0995fje, PMID:11967234
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Preferential transformation of human neuronal cells by human adenoviruses and the origin of HEK 293 cells
Yan J, Qiu Y, Ribeiro Dos Santos AM, Yin Y, Li YE, Vinckier N, Nariai N, Benaglio P, Raman A, Li X, Fan S, Chiou J, Chen F, Frazer KA, Gaulton KJ, Sander M, Taipale J, Ren B.
doi:10.1038/s41586-021-03211-0
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Systematic analysis of binding of transcription factors to noncoding variants
Li Z, Li X, Zhou H, Gaynor SM, Selvaraj MS, Arapoglou T, Quick C, Liu Y, Chen H, Sun R, Dey R, Arnett DK, Auer PL, Bielak LF, Bis JC, Blackwell TW, Blangero J, Boerwinkle E, Bowden DW, Brody JA, Cade BE, Conomos MP, Correa A, Cupples LA, Curran JE, de Vries PS, Duggirala R, Franceschini N, Freedman BI, Göring HHH, Guo X, Kalyani RR, Kooperberg C, Kral BG, Lange LA, Lin BM, Manichaikul A, Manning AK, Martin LW, Mathias RA, Meigs JB, Mitchell BD, Montasser ME, Morrison AC, Naseri T, O'Connell JR, Palmer ND, Peyser PA, Psaty BM, Raffield LM, Redline S, Reiner AP, Reupena MS, Rice KM, Rich SS, Smith JA, Taylor KD, Taub MA, Vasan RS, Weeks DE, Wilson JG, Yanek LR, Zhao W; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; TOPMed Lipids Working Group; Rotter JI, Willer CJ, Natarajan P, Peloso GM, Lin X.
2022-12-19
doi:10.1038/s41592-022-01640-x
released
A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies
Yile Chen, Shantanu Jain, Daniel Zeiberg, Lilia M. Iakoucheva, Sean D. Mooney, Predrag Radivojac, and Vikas Pejaver
doi:10.1142/9789811270611_0030
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Multi-objective prioritization of genes for high-throughput functional assays towards improved clinical variant classification
Linder J, Koplik SE, Kundaje A, Seelig G.
2022-12-05
doi:10.1186/s13059-022-02799-4
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Deciphering the impact of genetic variation on human polyadenylation using APARENT2
Zhong Y, Walker SK, Pritykin Y, Leslie CS, Rudensky AY, van der Veeken J.
doi:10.1038/s41590-021-01086-x
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Hierarchical regulation of the resting and activated T cell epigenome by major transcription factor families
Mark-Anthony Bray, Shantanu Singh,1 Han Han, Chadwick T. Davis, Blake Borgeson,2 Cathy Hartland, Maria Kost-Alimova, Sigrun M. Gustafsdottir, Christopher C. Gibson and Anne E. Carpenter
2016-11-09
doi:10.1038/nprot.2016.105
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Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes
Mabe NW, Huang M, Dalton GN, Alexe G, Schaefer DA, Geraghty AC, Robichaud AL, Conway AS, Khalid D, Mader MM, Belk JA, Ross KN, Sheffer M, Linde MH, Ly N, Yao W, Rotiroti MC, Smith BAH, Wernig M, Bertozzi CR, Monje M, Mitsiades CS, Majeti R, Satpathy AT, Stegmaier K, Majzner RG.
doi:10.1038/s43018-022-00405-x
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Transition to a mesenchymal state in neuroblastoma confers resistance to anti-GD2 antibody via reduced expression of ST8SIA1
Wang X, Luan Y, Yue F.
doi:10.1126/sciadv.abn9215
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EagleC: A deep-learning framework for detecting a full range of structural variations from bulk and single-cell contact maps
Jean-Benoît Lalanne, Samuel G. Regalado, Silvia Domcke, Diego Calderon, Beth Martin, Tony Li, Chase C. Suiter, Choli Lee, Cole Trapnell, Jay Shendure
bioRxiv
2022-12-10
doi:10.1101/2022.12.10.519236
released
Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters
Juan C. Caicedo, John Arevalo, Federica Piccioni, Mark-Anthony Bray, Cathy L. Hartland, Xiaoyun Wu, Angela N. Brooks, Alice H. Berger, Jesse S. Boehm, Anne E. Carpenter, and Shantanu Singh
2022-12-05
doi:10.1091/mbc.E21-11-0538
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Cell Painting predicts impact of lung cancer variants
Modzelewski AJ, Shao W, Chen J, Lee A, Qi X, Noon M, Tjokro K, Sales G, Biton A, Anand A, Speed TP, Xuan Z, Wang T, Risso D, He L.
2021-10-28
doi:10.1016/j.cell.2021.09.021
released
A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development
Karlow JA, Devarakonda S, Xing X, Jang HS, Govindan R, Watson M, Wang T.
2022-08-03
doi:10.1158/0008-5472.CAN-21-4160
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Developmental Pathways Are Epigenetically Reprogrammed during Lung Cancer Brain Metastasis
Nathan A, Asgari S, Ishigaki K, Valencia C, Amariuta T, Luo Y, Beynor JI, Baglaenko Y, Suliman S, Price AL, Lecca L, Murray MB, Moody DB, Raychaudhuri S.
doi:10.1038/s41586-022-04713-1
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Single-cell eQTL models reveal dynamic T cell state dependence of disease loci
Li D, Harrison JK, Purushotham D, Wang T.
doi:10.1038/s41592-022-01550-y
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Exploring genomic data coupled with 3D chromatin structures using the WashU Epigenome Browser
Raznahan A, Won H, Glahn DC, Jacquemont S.
doi:10.1001/jamapsychiatry.2022.1450
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Convergence and Divergence of Rare Genetic Disorders on Brain Phenotypes: A Review
Ray A, Das J, Wenzel SE.
2022-12-20
doi:10.1016/j.xcrm.2022.100857
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Determining asthma endotypes and outcomes: Complementing existing clinical practice with modern machine learning
Georgakopoulos-Soares I, Victorino J, Parada GE, Agarwal V, Zhao J, Wong HY, Umar MI, Elor O, Muhwezi A, An JY, Sanders SJ, Kwok CK, Inoue F, Hemberg M, Ahituv N.
doi:10.1016/j.xgen.2022.100111
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High-throughput characterization of the role of non-B DNA motifs on promoter function