Fine-mapping causal tissues and genes at disease-associated loci.

Autor: Strober BJ; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA., Zhang MJ; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.; Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA., Amariuta T; Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA.; Department of Medicine, University of California San Diego, La Jolla, CA, USA., Rossen J; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA., Price AL; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.

Publikováno v: MedRxiv : the preprint server for health sciences [medRxiv] 2024 Jun 17. Date of Electronic Publication: 2024 Jun 17.

SURGE: uncovering context-specific genetic-regulation of gene expression from single-cell RNA sequencing using latent-factor models.

Autor: Strober BJ; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA., Tayeb K; Department of Human Genetics, University of Chicago, Chicago, IL, USA., Popp J; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA., Qi G; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA., Gordon MG; Biological and Medical Informatics Graduate Program, University of California, San Francisco, CA, USA.; Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA.; Institute for Human Genetics, University of California, San Francisco, CA, USA.; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA., Perez R; Institute for Human Genetics, University of California, San Francisco, CA, USA., Ye CJ; Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA.; Institute for Human Genetics, University of California, San Francisco, CA, USA.; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.; Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA.; Chan-Zuckerberg Biohub, San Francisco, CA, USA., Battle A; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA. ajbattle@jhu.edu.; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA. ajbattle@jhu.edu.; Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA. ajbattle@jhu.edu.

Publikováno v: Genome biology [Genome Biol] 2024 Jan 22; Vol. 25 (1), pp. 28. Date of Electronic Publication: 2024 Jan 22.

Pervasive correlations between causal disease effects of proximal SNPs vary with functional annotations and implicate stabilizing selection.

Autor: Zhang MJ; Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Durvasula A; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California., Chiang C; Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA., Koch EM; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.; Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA., Strober BJ; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA., Shi H; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA., Barton AR; Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America., Kim SS; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA., Weissbrod O; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA., Loh PR; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA., Gazal S; Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California.; Department of Quantitative and Computational Biology, University of Southern California.; Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California., Sunyaev S; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.; Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA., Price AL; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.

Publikováno v: MedRxiv : the preprint server for health sciences [medRxiv] 2023 Dec 04. Date of Electronic Publication: 2023 Dec 04.

The functional impact of rare variation across the regulatory cascade.

Autor: Li T; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA., Ferraro N; Biomedical Informatics Training Program, Stanford University, Stanford, CA, USA., Strober BJ; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.; Harvard School of Public Health, Epidemiology Department, Boston, MA, USA., Aguet F; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Kasela S; New York Genome Center, New York, NY, USA.; Department of Systems Biology, Columbia University, New York, NY, USA., Arvanitis M; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.; Department of Medicine, Division of Cardiology, Johns Hopkins School of Medicine, Baltimore, MD, USA., Ni B; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA., Wiel L; Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA., Hershberg E; Department of Genetics, Stanford University, Stanford, CA, USA., Ardlie K; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Arking DE; McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA., Beer RL; National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA., Brody J; Cardiovascular Health Research Unit, Departments of Medicine and Epidemiology, University of Washington, Seattle, WA, USA., Blackwell TW; Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA., Clish C; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Gabriel S; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Gerszten R; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Cardiovascular Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA., Guo X; The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA., Gupta N; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Johnson WC; Collaborative Health Studies Coordinating Center, University of Washington, Seattle, WA, USA., Lappalainen T; New York Genome Center, New York, NY, USA.; Department of Systems Biology, Columbia University, New York, NY, USA., Lin HJ; The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA., Liu Y; Department of Medicine, Duke University School of Medicine, Durham, NC, USA., Nickerson DA; Department of Genome Sciences, University of Washington, Seattle, WA, USA., Papanicolaou G; National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA., Pritchard JK; Department of Genetics and Biology, Stanford University, Palo Alto, CA, USA., Qasba P; National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA., Shojaie A; Department of Biostatistics, University of Washington School of Public Health, Seattle, WA, USA., Smith J; Department of Genome Sciences, University of Washington, Seattle, WA, USA., Sotoodehnia N; Cardiovascular Health Research Unit, Departments of Medicine and Epidemiology, University of Washington, Seattle, WA, USA., Taylor KD; The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA., Tracy RP; Laboratory for Clinical Biochemistry Research, University of Vermont, Burlington, VT, USA., Van Den Berg D; Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA., Wheeler MT; Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA., Rich SS; Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA., Rotter JI; The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA., Battle A; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.; McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.; Malone Center for Engineering of Healthcare, Johns Hopkins University, Baltimore, MD, USA., Montgomery SB; Department of Genetics, Stanford University, Stanford, CA, USA.; Department of Pathology, Stanford University, Stanford, CA, USA.

Publikováno v: Cell genomics [Cell Genom] 2023 Sep 06; Vol. 3 (10), pp. 100401. Date of Electronic Publication: 2023 Sep 06 (Print Publication: 2023).

Redefining tissue specificity of genetic regulation of gene expression in the presence of allelic heterogeneity.

Autor: Arvanitis M; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21211, USA; Department of Medicine, Division of Cardiology, Johns Hopkins University, Baltimore, MD 21205, USA., Tayeb K; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21211, USA., Strober BJ; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21211, USA., Battle A; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21211, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD 21211, USA; Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, USA. Electronic address: ajbattle@jhu.edu.

Publikováno v: American journal of human genetics [Am J Hum Genet] 2022 Feb 03; Vol. 109 (2), pp. 223-239. Date of Electronic Publication: 2022 Jan 31.