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Mapping Bisulfite-Treated Short DNA Reads

Autor: Porter, Jacob Stuart

Epigenetics are stable heritable traits that are not a result of the DNA sequence. Epigenetic modification of DNA cytosine plays a role in development and disease. The covalent bonding of a methyl group or a hydroxymethyl group to the 5-carbon of cyt

Externí odkaz: http://hdl.handle.net/10919/82870

Critical Assessment of Metagenome Interpretation: the second round of challenges.

Autor: Meyer F; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany., Fritz A; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.; German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany., Deng ZL; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany., Koslicki D; Pennsylvania State University, State College, PA, USA., Lesker TR; German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany.; Helmholtz Centre for Infection Research, Braunschweig, Germany., Gurevich A; Saint Petersburg State University, Saint Petersburg, Russia., Robertson G; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany., Alser M; Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland., Antipov D; Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia., Beghini F; Department CIBIO, University of Trento, Trento, Italy., Bertrand D; Genome Institute of Singapore, Singapore, Singapore., Brito JJ; University of Southern California, Los Angeles, CA, USA., Brown CT; University of California, Davis, Davis, CA, USA., Buchmann J; Institute for Biological Data Science, Heinrich-Heine-University, Düsseldorf, Germany., Buluç A; Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; University of California, Berkeley, Berkeley, CA, USA., Chen B; Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; University of California, Berkeley, Berkeley, CA, USA., Chikhi R; Institut Pasteur, Paris, France., Clausen PTLC; National Food Institute, Division of Global Surveillance, Technical University of Denmark, Lyngby, Denmark., Cristian A; Drexel University, Philadelphia, PA, USA.; Google Inc., Philadelphia, PA, USA., Dabrowski PW; Robert Koch-Institut, Berlin, Germany.; Hochschule für Technik und Wirtschaft Berlin, Berlin, Germany., Darling AE; University of Technology Sydney, Sydney, Australia., Egan R; DOE Joint Genome Institute, Berkeley, CA, USA.; Lawrence Berkeley National Laboratories, Berkeley, CA, USA., Eskin E; University of California, Los Angeles, Los Angeles, CA, USA., Georganas E; Intel Corporation, Santa Clara, CA, USA., Goltsman E; DOE Joint Genome Institute, Berkeley, CA, USA.; Lawrence Berkeley National Laboratories, Berkeley, CA, USA., Gray MA; Drexel University, Philadelphia, PA, USA.; Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Philadelphia, PA, USA., Hansen LH; University of Copenhagen, Department of Plant and Environmental Science, Frederiksberg, Denmark., Hofmeyr S; Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; University of California, Berkeley, Berkeley, CA, USA., Huang P; School of Computer Science, Fudan University, Shanghai, China., Irber L; University of California, Davis, Davis, CA, USA., Jia H; BGI-Shenzhen, Shenzhen, China.; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen, China., Jørgensen TS; Technical University of Denmark, Novo Nordisk Foundation Center for Biosustainability, Lyngby, Denmark.; Aarhus University, Department of Environmental Science, Roskilde, Denmark., Kieser SD; Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland.; Swiss Institute of Bioinformatics, Geneva, Switzerland., Klemetsen T; The Arctic University of Norway, Tromsø, Norway., Kola A; Charité-Universitätsmedizin Berlin, Berlin, Germany., Kolmogorov M; Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA., Korobeynikov A; Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia.; Department of Statistical Modelling, Saint Petersburg State University, Saint Petersburg, Russia., Kwan J; University of Wisconsin-Madison, Madison, WI, USA., LaPierre N; University of California, Los Angeles, Los Angeles, CA, USA., Lemaitre C; Univ. Rennes, Inria, CNRS, IRISA, Rennes, France., Li C; Genome Institute of Singapore, Singapore, Singapore., Limasset A; Université Lille, CNRS, CRIStAL, Lille, France., Malcher-Miranda F; Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany., Mangul S; University of Southern California, Los Angeles, CA, USA., Marcelino VR; Sydney Medical School, The University of Sydney, Sydney, Australia.; Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Australia., Marchet C; Université Lille, CNRS, CRIStAL, Lille, France., Marijon P; Department of Computer Science, Inria, University of Lille, CNRS, Lille, France., Meleshko D; Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia., Mende DR; Amsterdam University Medical Center, Amsterdam, the Netherlands., Milanese A; Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland.; Structural and Computational Biology Unit, EMBL, Heidelberg, Germany., Nagarajan N; Genome Institute of Singapore, A*STAR, Singapore, Singapore.; National University of Singapore, Singapore, Singapore., Nissen J; DTU Health Tech, Kongens, Lyngby, Denmark., Nurk S; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA., Oliker L; Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; University of California, Berkeley, Berkeley, CA, USA., Paoli L; Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland., Peterlongo P; Univ. Rennes, Inria, CNRS, IRISA, Rennes, France., Piro VC; Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany., Porter JS; University of Virginia, Charlottesville, VA, USA., Rasmussen S; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark., Rees ER; University of Wisconsin-Madison, Madison, WI, USA., Reinert K; Institute for Bioinformatics, FU Berlin, Berlin, Germany., Renard B; Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany.; Bioinformatics Unit (MF1), Robert Koch Institute, Berlin, Germany., Robertsen EM; The Arctic University of Norway, Tromsø, Norway., Rosen GL; Drexel University, Philadelphia, PA, USA.; Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Philadelphia, PA, USA.; Center for Biological Discovery from Big Data, Philadelphia, PA, USA., Ruscheweyh HJ; Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland., Sarwal V; University of California, Los Angeles, Los Angeles, CA, USA., Segata N; Department CIBIO, University of Trento, Trento, Italy., Seiler E; Institute for Bioinformatics, FU Berlin, Berlin, Germany., Shi L; Florida Polytechnic University, Lakeland, FL, USA., Sun F; Quantitative and Computational Biology Department, University of Southern California, Los Angeles, CA, USA., Sunagawa S; Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland., Sørensen SJ; University of Copenhagen, Copenhagen, Denmark., Thomas A; DOE Joint Genome Institute, Berkeley, CA, USA.; University of British Columbia, Vancouver, British Columbia, Canada., Tong C; Genome Institute of Singapore, Singapore, Singapore., Trajkovski M; Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland.; Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland., Tremblay J; Energy, Mining and Environment, National Research Council Canada, Montreal, Quebec, Canada., Uritskiy G; Phase Genomics, Seattle, WA, USA., Vicedomini R; Institut Pasteur, Paris, France., Wang Z; School of Computer Science, Fudan University, Shanghai, China., Wang Z; School of Mathematical Sciences, Fudan University, Shanghai, China., Wang Z; Department of Energy Joint Genome Institute, Berkeley, CA, USA.; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; School of Natural Sciences, University of California at Merced, Merced, CA, USA., Warren A; University of Virginia, Charlottesville, VA, USA., Willassen NP; The Arctic University of Norway, Tromsø, Norway., Yelick K; Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; University of California, Berkeley, Berkeley, CA, USA., You R; School of Computer Science, Fudan University, Shanghai, China., Zeller G; Structural and Computational Biology Unit, EMBL, Heidelberg, Germany., Zhao Z; Drexel University, Philadelphia, PA, USA., Zhu S; Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China., Zhu J; BGI-Shenzhen, Shenzhen, China.; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen, China., Garrido-Oter R; Max Planck Institute for Plant Breeding Research, Köln, Germany., Gastmeier P; Charité-Universitätsmedizin Berlin, Berlin, Germany., Hacquard S; Max Planck Institute for Plant Breeding Research, Köln, Germany., Häußler S; Helmholtz Centre for Infection Research, Braunschweig, Germany., Khaledi A; Helmholtz Centre for Infection Research, Braunschweig, Germany., Maechler F; Charité-Universitätsmedizin Berlin, Berlin, Germany., Mesny F; Max Planck Institute for Plant Breeding Research, Köln, Germany., Radutoiu S; Aarhus University, Aarhus, Denmark., Schulze-Lefert P; Max Planck Institute for Plant Breeding Research, Köln, Germany., Smit N; Helmholtz Centre for Infection Research, Braunschweig, Germany., Strowig T; Helmholtz Centre for Infection Research, Braunschweig, Germany., Bremges A; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.; German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany., Sczyrba A; Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany., McHardy AC; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany. amc14@helmholtz-hzi.de.; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany. amc14@helmholtz-hzi.de.; German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany. amc14@helmholtz-hzi.de.; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany. amc14@helmholtz-hzi.de.

Publikováno v: Nature methods [Nat Methods] 2022 Apr; Vol. 19 (4), pp. 429-440. Date of Electronic Publication: 2022 Apr 08.