Siewert-Rocks KM, Kim SS, Yao DW, Shi H, Price AL.

2022-03-03

doi:10.1016/j.ajhg.2022.01.005

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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

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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

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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

released

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

released

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

released

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

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

released

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

released

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

released

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

released

EagleC: A deep-learning framework for detecting a full range of structural variations from bulk and single-cell contact maps

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

released

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

released

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

released

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

released

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

released

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

released

High-throughput characterization of the role of non-B DNA motifs on promoter function

Yang D, Cho H, Tayyebi Z, Shukla A, Luo R, Dixon G, Ursu V, Stransky S, Tremmel DM, Sackett SD, Koche R, Kaplan SJ, Li QV, Park J, Zhu Z, Rosen BP, Pulecio J, Shi ZD, Bram Y, Schwartz RE, Odorico JS, Sidoli S, Wright CV, Leslie CS, Huangfu D.

doi:10.1038/s41556-022-00946-4

released

CRISPR screening uncovers a central requirement for HHEX in pancreatic lineage commitment and plasticity restriction

Luo C, Liu H, Xie F, Armand EJ, Siletti K, Bakken TE, Fang R, Doyle WI, Stuart T, Hodge RD, Hu L, Wang BA, Zhang Z, Preissl S, Lee DS, Zhou J, Niu SY, Castanon R, Bartlett A, Rivkin A, Wang X, Lucero J, Nery JR, Davis DA, Mash DC, Satija R, Dixon JR, Linnarsson S, Lein E, Behrens MM, Ren B, Mukamel EA, Ecker JR.

2022-03-09

doi:10.1016/j.xgen.2022.100107

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Single nucleus multi-omics identifies human cortical cell regulatory genome diversity