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Akademický článek

Single-molecule states link transcription factor binding to gene expression.

Autor: Doughty BR; Genetics Department, Stanford University, Stanford, CA, USA., Hinks MM; Bioengineering Department, Stanford University, Stanford, CA, USA., Schaepe JM; Bioengineering Department, Stanford University, Stanford, CA, USA., Marinov GK; Genetics Department, Stanford University, Stanford, CA, USA., Thurm AR; Biophysics Program, Stanford University, Stanford, CA, USA., Rios-Martinez C; Bioengineering Department, Stanford University, Stanford, CA, USA., Parks BE; Computer Science Department, Stanford University, Stanford, CA, USA., Tan Y; Computer Science Department, Stanford University, Stanford, CA, USA., Marklund E; Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden., Dubocanin D; Genetics Department, Stanford University, Stanford, CA, USA., Bintu L; Bioengineering Department, Stanford University, Stanford, CA, USA. lbintu@stanford.edu., Greenleaf WJ; Genetics Department, Stanford University, Stanford, CA, USA. wjg@stanford.edu.; Department of Applied Physics, Stanford University, Stanford, CA, USA. wjg@stanford.edu.

Publikováno v: Nature [Nature] 2024 Nov 20. Date of Electronic Publication: 2024 Nov 20.

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Akademický článek

DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools .

Autor: Jha A; Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA., Bohaczuk SC; Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA., Mao Y; Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA., Ranchalis J; Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA., Mallory BJ; Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA., Min AT; Department of Statistics, University of Washington, Seattle, Washington 98195, USA., Hamm MO; Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA., Swanson E; Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA., Dubocanin D; Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA., Finkbeiner C; Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA., Li T; Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA., Whittington D; Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, USA., Noble WS; Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.; Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA., Stergachis AB; Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; absterga@uw.edu mvollger@uw.edu.; Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA.; Brotman Baty Institute for Precision Medicine, Seattle, Washington 98195, USA., Vollger MR; Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; absterga@uw.edu mvollger@uw.edu.

Publikováno v: Genome research [Genome Res] 2024 Nov 20; Vol. 34 (11), pp. 1976-1986. Date of Electronic Publication: 2024 Nov 20.

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Akademický článek

Human Satellite 3 DNA encodes megabase-scale transcription factor binding platforms.

Autor: Franklin JM, Dubocanin D, Chittenden C, Barillas A, Lee RJ, Ghosh RP, Gerton JL, Guan KL, Altemose N

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 Oct 22. Date of Electronic Publication: 2024 Oct 22.

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Akademický článek

Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon.

Autor: Hartley GA; Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA., Okhovat M; Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA., Hoyt SJ; Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA., Fuller E; Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA., Pauloski N; Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA., Alexandre N; Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA., Alexandrov I; Department of Anatomy and Anthropology and Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Israel., Drennan R; Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA., Dubocanin D; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA., Gilbert DM; San Diego Biomedical Research Institute, San Diego, CA 92121, USA., Mao Y; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA., McCann C; Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA., Neph S; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA., Ryabov F; UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA.; Department of Biomolecular Engineering, University of California Santa Cruz, CA, USA., Sasaki T; San Diego Biomedical Research Institute, San Diego, CA 92121, USA., Storer JM; Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA., Svendsen D; Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA., Troy W; FormBio, Dallas, TX, USA., Wells J; Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA., Core L; Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA., Stergachis A; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA., Carbone L; Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR, USA.; Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA.; Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA.; Division of Genetics, Oregon National Primate Research Center, Portland, OR, USA., O'Neill RJ; Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 Aug 30. Date of Electronic Publication: 2024 Aug 30.

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Single-molecule chromatin configurations link transcription factor binding to expression in human cells.

Autor: Doughty BR; Genetics Department, Stanford University, Stanford, CA 94305, USA., Hinks MM; Bioengineering Department, Stanford University, Stanford, CA 94305, USA., Schaepe JM; Bioengineering Department, Stanford University, Stanford, CA 94305, USA., Marinov GK; Genetics Department, Stanford University, Stanford, CA 94305, USA., Thurm AR; Biophysics Graduate Program, Stanford University, Stanford, CA 94305, USA., Rios-Martinez C; Bioengineering Department, Stanford University, Stanford, CA 94305, USA., Parks BE; Computer Science Department, Stanford University, Stanford, CA 94305, USA., Tan Y; Computer Science Department, Stanford University, Stanford, CA 94305, USA., Marklund E; Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden., Dubocanin D; Genetics Department, Stanford University, Stanford, CA 94305, USA., Bintu L; Bioengineering Department, Stanford University, Stanford, CA 94305, USA., Greenleaf WJ; Genetics Department, Stanford University, Stanford, CA 94305, USA.; Department of Applied Physics, Stanford University, Stanford, CA 94205, USA.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 Feb 04. Date of Electronic Publication: 2024 Feb 04.

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