Comparative analysis of the transcriptome across distant species

Autor: Gerstein, MB, Rozowsky, J, Yan, KK, Wang, D, Cheng, C, Brown, JB, Davis, CA, Hillier, L, Sisu, C, Li, JJ, Pei, B, Harmanci, AO, Duff, MO, Djebali, S, Alexander, RP, Alver, BH, Auerbach, R, Bell, K, Bickel, PJ, Boeck, ME, Boley, NP, Booth, BW, Cherbas, L, Cherbas, P, Di, C, Dobin, A, Drenkow, J, Ewing, B, Fang, G, Fastuca, M, Feingold, EA, Frankish, A, Gao, G, Good, PJ, Guigó, R, Hammonds, A, Harrow, J, Hoskins, RA, Howald, C, Hu, L, Huang, H, Hubbard, TJP, Huynh, C, Jha, S, Kasper, D, Kato, M, Kaufman, TC, Kitchen, RR, Ladewig, E, Lagarde, J, Lai, E, Leng, J, Lu, Z, MacCoss, M, May, G, McWhirter, R, Merrihew, G, Miller, DM, Mortazavi, A, Murad, R, Oliver, B, Olson, S, Park, PJ, Pazin, MJ, Perrimon, N, Pervouchine, D, Reinke, V, Reymond, A, Robinson, G

Publikováno v: Gerstein, MB; Rozowsky, J; Yan, KK; Wang, D; Cheng, C; Brown, JB; et al.(2014). Comparative analysis of the transcriptome across distant species. Nature, 512(7515), 445-448. doi: 10.1038/nature13424. UC Berkeley: Retrieved from: http://www.escholarship.org/uc/item/7w33f659

The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data fo

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=od_______325::3715f93c4e6a4bf38a0b9dfb59e10efc
http://www.escholarship.org/uc/item/7w33f659

Transcriptomic analysis of the Myxococcus xanthus FruA regulon, and comparative developmental transcriptomic analysis of two fruiting body forming species, Myxococcus xanthus and Myxococcus stipitatus.

Autor: McLoon AL; Biology Department, Siena College, Loudonville, NY, USA., Boeck ME; Biology Department, Regis University, Denver, CO, USA., Bruckskotten M; Center of Medical Genetics and Human Genetics, Philipps-University, Marburg, Germany., Keyel AC; Department of Atmospheric and Environmental Sciences, University at Albany, Albany, NY, USA., Søgaard-Andersen L; Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany. sogaard@mpi-marburg.mpg.de.

Publikováno v: BMC genomics [BMC Genomics] 2021 Nov 01; Vol. 22 (1), pp. 784. Date of Electronic Publication: 2021 Nov 01.

Comparative analysis of the transcriptome across distant species.

Autor: Gerstein MB; 1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [3] Department of Computer Science, Yale University, 51 Prospect Street, New Haven, Connecticut 06511, USA [4] [5]., Rozowsky J; 1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [3]., Yan KK; 1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [3]., Wang D; 1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [3]., Cheng C; 1] Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA [2] Institute for Quantitative Biomedical Sciences, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03766, USA [3]., Brown JB; 1] Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA [2] Department of Statistics, University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA [3]., Davis CA; 1] Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA [2]., Hillier L; 1] Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA [2]., Sisu C; 1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [3]., Li JJ; 1] Department of Statistics, University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA [2] Department of Statistics, University of California, Los Angeles, California 90095-1554, USA [3] Department of Human Genetics, University of California, Los Angeles, California 90095-7088, USA [4]., Pei B; 1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [3]., Harmanci AO; 1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [3]., Duff MO; 1] Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA [2]., Djebali S; 1] Centre for Genomic Regulation, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain [2] Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain [3]., Alexander RP; 1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA., Alver BH; Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, Massachusetts 02115, USA., Auerbach R; 1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA., Bell K; Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA., Bickel PJ; Department of Statistics, University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA., Boeck ME; Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA., Boley NP; 1] Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA [2] Department of Biostatistics, University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA., Booth BW; Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA., Cherbas L; 1] Department of Biology, Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405-7005, USA [2] Center for Genomics and Bioinformatics, Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405-7005, USA., Cherbas P; 1] Department of Biology, Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405-7005, USA [2] Center for Genomics and Bioinformatics, Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405-7005, USA., Di C; MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China., Dobin A; Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA., Drenkow J; Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA., Ewing B; Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA., Fang G; 1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA., Fastuca M; Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA., Feingold EA; National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA., Frankish A; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK., Gao G; MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China., Good PJ; National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA., Guigó R; 1] Centre for Genomic Regulation, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain [2] Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain., Hammonds A; Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA., Harrow J; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK., Hoskins RA; Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA., Howald C; 1] Center for Integrative Genomics, University of Lausanne, Genopode building, Lausanne 1015, Switzerland [2] Swiss Institute of Bioinformatics, Genopode building, Lausanne 1015, Switzerland., Hu L; MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China., Huang H; Department of Statistics, University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA., Hubbard TJ; 1] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK [2] Medical and Molecular Genetics, King's College London, London WC2R 2LS, UK., Huynh C; Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA., Jha S; Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA., Kasper D; Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520-8005, USA., Kato M; Department of Molecular, Cellular and Developmental Biology, PO Box 208103, Yale University, New Haven, Connecticut 06520, USA., Kaufman TC; Department of Biology, Indiana University, 1001 East 3rd Street, Bloomington, Indiana 47405-7005, USA., Kitchen RR; 1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA., Ladewig E; Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, New York 10065, USA., Lagarde J; 1] Centre for Genomic Regulation, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain [2] Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain., Lai E; Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, New York 10065, USA., Leng J; 1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA., Lu Z; MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China., MacCoss M; Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA., May G; 1] Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA [2] Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 USA., McWhirter R; Department of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue South, Nashville, Tennessee 37232-8240, USA., Merrihew G; Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA., Miller DM; Department of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue South, Nashville, Tennessee 37232-8240, USA., Mortazavi A; 1] Developmental and Cell Biology, University of California, Irvine, California 92697, USA [2] Center for Complex Biological Systems, University of California, Irvine, California 92697, USA., Murad R; 1] Developmental and Cell Biology, University of California, Irvine, California 92697, USA [2] Center for Complex Biological Systems, University of California, Irvine, California 92697, USA., Oliver B; Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA., Olson S; Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA., Park PJ; Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, Massachusetts 02115, USA., Pazin MJ; National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Bethesda, Maryland 20892-9307, USA., Perrimon N; 1] Department of Genetics and Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA [2] Howard Hughes Medical Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA., Pervouchine D; 1] Centre for Genomic Regulation, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain [2] Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain., Reinke V; Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520-8005, USA., Reymond A; Center for Integrative Genomics, University of Lausanne, Genopode building, Lausanne 1015, Switzerland., Robinson G; Department of Statistics, University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA., Samsonova A; 1] Department of Genetics and Drosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA [2] Howard Hughes Medical Institute, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA., Saunders GI; 1] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK [2] European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK., Schlesinger F; Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA., Sethi A; 1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA., Slack FJ; Department of Molecular, Cellular and Developmental Biology, PO Box 208103, Yale University, New Haven, Connecticut 06520, USA., Spencer WC; Department of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue South, Nashville, Tennessee 37232-8240, USA., Stoiber MH; 1] Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA [2] Department of Biostatistics, University of California, Berkeley, 367 Evans Hall, Berkeley, California 94720-3860, USA., Strasbourger P; Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA., Tanzer A; 1] Bioinformatics and Genomics Programme, Center for Genomic Regulation, Universitat Pompeu Fabra (CRG-UPF), 08003 Barcelona, Catalonia, Spain [2] Institute for Theoretical Chemistry, Theoretical Biochemistry Group (TBI), University of Vienna, Währingerstrasse 17/3/303, A-1090 Vienna, Austria., Thompson OA; Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA., Wan KH; Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA., Wang G; Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520-8005, USA., Wang H; Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA., Watkins KL; Department of Cell and Developmental Biology, Vanderbilt University, 465 21st Avenue South, Nashville, Tennessee 37232-8240, USA., Wen J; Sloan-Kettering Institute, 1275 York Avenue, Box 252, New York, New York 10065, USA., Wen K; MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China., Xue C; Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA., Yang L; 1] Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA [2] Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China., Yip K; 1] Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong [2] 5 CUHK-BGI Innovation Institute of Trans-omics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong., Zaleski C; Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA., Zhang Y; 1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA., Zheng H; 1] Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA [2] Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA., Brenner SE; 1] Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA [2] Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA [3]., Graveley BR; 1] Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, Connecticut 06030, USA [2]., Celniker SE; 1] Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA [2]., Gingeras TR; 1] Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA [2]., Waterston R; 1] Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA [2].

Publikováno v: Nature [Nature] 2014 Aug 28; Vol. 512 (7515), pp. 445-8.

Automated analysis of embryonic gene expression with cellular resolution in C. elegans.

Autor: Murray JI; Department of Genome Sciences, University of Washington School of Medicine, 1705 NE Pacific Street, Seattle, Washington 98195, USA., Bao Z, Boyle TJ, Boeck ME, Mericle BL, Nicholas TJ, Zhao Z, Sandel MJ, Waterston RH

Publikováno v: Nature methods [Nat Methods] 2008 Aug; Vol. 5 (8), pp. 703-9. Date of Electronic Publication: 2008 Jun 29.