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73 items
  • Publication
    doi:10.1016/j.ajhg.2022.01.005
    Leveraging gene co-regulation to identify gene sets enriched for disease heritability
    Alkes Price, Harvard
    Citation
    Siewert-Rocks KM, Kim SS, Yao DW, Shi H, Price AL. (2022, March 3). Leveraging gene co-regulation to identify gene sets enriched for disease heritability.  
    released
  • Publication
    doi:10.1186/s11689-022-09461-x
    Focus on your locus with a massively parallel reporter assay
    Hyejung Won, UNC
    Citation
    McAfee JC, Bell JL, Krupa O, Matoba N, Stein JL, Won H. (2022, September 9). Focus on your locus with a massively parallel reporter assay.  
    released
  • Publication
    doi:10.1016/j.devcel.2022.03.013
    Rapid and efficient degradation of endogenous proteins in vivo identifies stage-specific roles of RNA Pol II pausing in mammalian development
    Anna-Katerina Hadjantonakis, MSKCC
    Citation
    Abuhashem A, Lee AS, Joyner AL, Hadjantonakis AK. (2022, April 25). Rapid and efficient degradation of endogenous proteins in vivo identifies stage-specific roles of RNA Pol II pausing in mammalian development.  
    released
  • Publication
    doi:10.1101/gr.275870.121
    Chromatin interaction-aware gene regulatory modeling with graph attention networks
    Christina Leslie, MSKCC
    released
  • Publication
    doi:10.1038/s42255-022-00607-8
    Every islet matters: improving the impact of human islet research
    Maike Sander, UCSD
    released
  • Publication
    doi:10.1080/01621459.2021.1914634
    Large-Scale Hypothesis Testing for Causal Mediation Effects with Applications in Genome-wide Epigenetic Studies
    Xihong Lin, HSPH
    released
  • Publication
    doi:10.1038/s41586-022-05089-y
    A RORγt+ cell instructs gut microbiota-specific Treg cell differentiation
    Manuel Garber, UMass
    Citation
    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, September 7). A RORγt+ cell instructs gut microbiota-specific Treg cell differentiation.  
    released
  • Publication
    doi:10.1038/s41586-021-03211-0
    Systematic analysis of binding of transcription factors to noncoding variants
    Bing Ren, UCSD
    released
  • Publication
    doi:10.1038/s41592-022-01640-x
    A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies
    Xihong Lin, HSPH
    Citation
    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, December 19). A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies.  
    released
  • Publication
    doi:10.1142/9789811270611_0030
    Multi-objective prioritization of genes for high-throughput functional assays towards improved clinical variant classification
    Predrag Radivojac, Northeastern
    released
  • Publication
    doi:10.1186/s13059-022-02799-4
    Deciphering the impact of genetic variation on human polyadenylation using APARENT2
    Anshul Kundaje, Stanford
    Citation
    Linder J, Koplik SE, Kundaje A, Seelig G. (2022, December 5). Deciphering the impact of genetic variation on human polyadenylation using APARENT2.  
    released
  • Publication
    doi:10.1038/s41590-021-01086-x
    Hierarchical regulation of the resting and activated T cell epigenome by major transcription factor families
    Alexander Rudensky, MSKCC
    released
  • Publication
    doi:10.1038/nprot.2016.105
    Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes
    Anne Carpenter, Broad
    Citation
    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, November 9). Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes.  
    released
  • Publication
    doi:10.1038/s43018-022-00405-x
    Transition to a mesenchymal state in neuroblastoma confers resistance to anti-GD2 antibody via reduced expression of ST8SIA1
    Ansuman Satpathy, Stanford
    released
  • Publication
    doi:10.1126/sciadv.abn9215
    EagleC: A deep-learning framework for detecting a full range of structural variations from bulk and single-cell contact maps
    Feng Yue, WashU
    released
  • Publication
    doi:10.1091/mbc.E21-11-0538
    Cell Painting predicts impact of lung cancer variants
    Anne Carpenter, Broad
    Citation
    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, December 5). Cell Painting predicts impact of lung cancer variants.  
    released
  • Publication
    doi:10.1016/j.cell.2021.09.021
    A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development
    Ting Wang, WashU
    Citation
    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, October 28). A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development.  
    released
  • Publication
    doi:10.1158/0008-5472.CAN-21-4160
    Developmental Pathways Are Epigenetically Reprogrammed during Lung Cancer Brain Metastasis
    Ting Wang, WashU
    Citation
    Karlow JA, Devarakonda S, Xing X, Jang HS, Govindan R, Watson M, Wang T. (2022, August 3). Developmental Pathways Are Epigenetically Reprogrammed during Lung Cancer Brain Metastasis.  
    released
  • Publication
    doi:10.1038/s41586-022-04713-1
    Single-cell eQTL models reveal dynamic T cell state dependence of disease loci
    Soumya Raychaudhuri, Brigham and Women's Hospital
    released
  • Publication
    doi:10.1038/s41592-022-01550-y
    Exploring genomic data coupled with 3D chromatin structures using the WashU Epigenome Browser
    Ting Wang, WashU
    released
  • Publication
    doi:10.1001/jamapsychiatry.2022.1450
    Convergence and Divergence of Rare Genetic Disorders on Brain Phenotypes: A Review
    Hyejung Won, UNC
    released
  • Publication
    doi:10.1016/j.xcrm.2022.100857
    Determining asthma endotypes and outcomes: Complementing existing clinical practice with modern machine learning
    Jishnu Das, University of Pittsburgh
    Citation
    Ray A, Das J, Wenzel SE. (2022, December 20). Determining asthma endotypes and outcomes: Complementing existing clinical practice with modern machine learning.  
    released
  • Publication
    doi:10.1016/j.xgen.2022.100111
    High-throughput characterization of the role of non-B DNA motifs on promoter function
    Nadav Ahituv, UCSF
    released
  • Publication
    doi:10.1038/s41556-022-00946-4
    CRISPR screening uncovers a central requirement for HHEX in pancreatic lineage commitment and plasticity restriction
    Danwei Huangfu, MSKCC
    released
  • Publication
    doi:10.1016/j.xgen.2022.100107
    Single nucleus multi-omics identifies human cortical cell regulatory genome diversity
    Bing Ren, UCSD
    Citation
    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, March 9). Single nucleus multi-omics identifies human cortical cell regulatory genome diversity.  
    released