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Perspectives on Human Population Structure at the Cusp of the Sequencing Era

Genomics and Human Genetics 1000年第1期12卷 245-274页

作者： John Novembre Sohini Ramachandran *Both authors contributed equally. 1Department of Ecology and Evolutionary Biology and Interdepartmental Program on Bioinformatics University of California Los Angeles California 90403 email: jnovembre@ucla.edu 2Department of Ecology and Evolutionary Biology and Center for Computational Molecular Biology Brown University Providence Rhode Island 02912 email: sramachandran@brown.edu

Human groups show structured levels of genetic similarity as a consequence of factors such as geographical subdivision and genetic drift. Surveying this structure gives us a scientific perspective on human origins, sheds light on evolutionary processes that shape both human adaptation and disease, and is integral to effectively carrying out the mission of global medical genetics and personalized medicine. Surveys of population structure have been ongoing for decades, but in the past three years, single-nucleotide-polymorphism (SNP) array technology has provided unprecedented detail on human population structure at global and regional scales. These studies have confirmed well-known relationships between distantly related populations and uncovered previously unresolvable relationships among closely related human groups. SNPs represent the first dense genome-wide markers, and as such, their analysis has raised many challenges and insights relevant to the study of population genetics with whole-genome sequences. Here we draw on the lessons from these studies to anticipate the directions that will be most fruitful to pursue during the emerging whole-genome sequencing era.

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Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models

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Journal of Structural and Functional Genomics 2011年第2期12卷 137-147页

作者： Zimmermann, Michael T. Leelananda, Sumudu P. Gniewek, Pawel Feng, Yaping Jernigan, Robert L. Kloczkowski, Andrzej Department of Biochemistry Biophysics and Molecular Biology Iowa State University Ames IA 50011-0320 United States L.H.Baker Center for Bioinformatics and Biological Statistics Iowa State University Ames IA 50011-3020 United States Bioinformatics and Computational Biology Interdepartmental Graduate Program Iowa State University Ames IA 50011 United States Laboratory of Theory of Biopolymers Faculty of Chemistry University of Warsaw 02-093 Warsaw Pasteura 1 Poland Battelle Center for Mathematical Medicine Research Institute at Nationwide Children's Hospital Columbus OH 43205 United States Department of Pediatrics Ohio State University College of Medicine Columbus OH 43205 United States

We propose a novel method of calculation of free energy for coarse grained models of proteins by combining our newly developed multibody potentials with entropies computed from elastic network models of proteins. Multi-body potentials have been of much interest recently because they take into account three dimensional interactions related to residue packing and capture the cooperativity of these interactions in protein structures. Combining four-body non-sequential, four-body sequential and pairwise short range potentials with optimized weights for each term, our coarse-grained potential improved recognition of native structure among misfolded decoys, outperforming all other contact potentials for CASP8 decoy sets and performance comparable to the fully atomic empirical DFIRE potentials. By combing statistical contact potentials with entropies from elastic network models of the same structures we can compute free energy changes and improve coarse-grained modeling of protein structure and dynamics. The consideration of protein flexibility and dynamics should improve protein structure prediction and refinement of computational models. This work is the first to combine coarse-grained multibody potentials with an entropic model that takes into account contributions of the entire structure, investigating native-like decoy selection. © 2011 Springer Science+Business Media B.V.

关键词： 4-Body potentials Elastic network models Multibody potentials Protein dynamics Protein structure prediction Protein structure refinement

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PS2-108. Infection with Hepatitis C down-regulates the expression of cytokine genes in peripheral blood

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Cytokine 2011年第1期56卷 94-94页

作者： Milton W. Taylor Christopher R. Bolen Steven H. Kleinstein Leonid Brodsky Department of Biology Indiana University Bloomington IN 47401 USA 1Interdepartmental Program in Computational Biology and Bioinformatics Yale University 300 George St. Suite 501 New Haven CT 06511 USA Department of Pathology Yale University School of Medicine New Haven CT USA Institute of Evolution University of Haifa Mount Carmel Haifa 31905 Israel

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Author Correction: Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing

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Nature communications 2020年第1期11卷 4499页

作者： Igor Mandric Jeremy Rotman Harry Taegyun Yang Nicolas Strauli Dennis J Montoya William Van Der Wey Jiem R Ronas Benjamin Statz Douglas Yao Velislava Petrova Alex Zelikovsky Roberto Spreafico Sagiv Shifman Noah Zaitlen Maura Rossetti K Mark Ansel Eleazar Eskin Serghei Mangul Department of Computer Science University of California Los Angeles 404 Westwood Plaza Los Angeles CA 90095 USA. Department of Clinical Pharmacy School of Pharmacy University of Southern California 1540 Alcazar Street Los Angeles CA 90033 USA. Bioinformatics Interdepartmental Ph.D. Program University of California Los Angeles 611 Charles E. Young Drive East Los Angeles CA 90095-1570 USA. Biomedical Sciences Graduate Program University of California San Francisco 1675 Owens Street Suite 310 San Francisco CA 94143-0523 USA. Department of Molecular Cell and Developmental Biology University of California Los Angeles 610 Charles E. Young Drive South Los Angeles CA 90095 USA. Department of Microbiology Immunology and Molecular Genetics University of California Los Angeles 609 Charles E. Young Drive East Los Angeles CA 90095 USA. Program in Bioinformatics and Integrative Genomics Harvard Medical School 10 Shattuck Street Suite 514 Boston MA 02115 USA. Wellcome Trust Sanger Institute Wellcome Genome Campus Hinxton Cambridge CB10 1SA UK. Department of Computer Science Georgia State University 33 Gilmer Street SE Atlanta GA 30303 USA. The Laboratory of Bioinformatics I.M. Sechenov First Moscow State Medical University Moscow 119991 Russia. Institute for Quantitative and Computational Biosciences University of California Los Angeles 611 Charles E. Young Drive East Los Angeles CA 90095 USA. Department of Genetics The Institute of Life Sciences The Hebrew University of Jerusalem Jerusalem 9190401 Israel. Department of Medicine University of California San Francisco 533 Parnassus Avenue San Francisco CA 94143 USA. Immunogenetics Center Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California Los Angeles 1000 Veteran Avenue Los Angeles CA 90095-1652 USA. Sandler Asthma Basic Research Center Department of Microbiology and Immunology University of California San Francisco 513 Parnass

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

关键词： computational biology and bioinformatics Adaptive immunity Immunogenetics B cells

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Author Correction: Universal DNA methylation age across mammalian tissues

Nature aging

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Nature aging 2023年第11期3卷 1462页

作者： A T Lu Z Fei A Haghani T R Robeck J A Zoller C Z Li R Lowe Q Yan J Zhang H Vu J Ablaeva V A Acosta-Rodriguez D M Adams J Almunia A Aloysius R Ardehali A Arneson C S Baker G Banks K Belov N C Bennett P Black D T Blumstein E K Bors C E Breeze R T Brooke J L Brown G G Carter A Caulton J M Cavin L Chakrabarti I Chatzistamou H Chen K Cheng P Chiavellini O W Choi S M Clarke L N Cooper M L Cossette J Day J DeYoung S DiRocco C Dold E E Ehmke C K Emmons S Emmrich E Erbay C Erlacher-Reid C G Faulkes S H Ferguson C J Finno J E Flower J M Gaillard E Garde L Gerber V N Gladyshev V Gorbunova R G Goya M J Grant C B Green E N Hales M B Hanson D W Hart M Haulena K Herrick A N Hogan C J Hogg T A Hore T Huang J C Izpisua Belmonte A J Jasinska G Jones E Jourdain O Kashpur H Katcher E Katsumata V Kaza H Kiaris M S Kobor P Kordowitzki W R Koski M Krützen S B Kwon B Larison S G Lee M Lehmann J F Lemaitre A J Levine C Li X Li A R Lim D T S Lin D M Lindemann T J Little N Macoretta D Maddox C O Matkin J A Mattison M McClure J Mergl J J Meudt G A Montano K Mozhui J Munshi-South A Naderi M Nagy P Narayan P W Nathanielsz N B Nguyen C Niehrs J K O'Brien P O'Tierney Ginn D T Odom A G Ophir S Osborn E A Ostrander K M Parsons K C Paul M Pellegrini K J Peters A B Pedersen J L Petersen D W Pietersen G M Pinho J Plassais J R Poganik N A Prado P Reddy B Rey B R Ritz J Robbins M Rodriguez J Russell E Rydkina L L Sailer A B Salmon A Sanghavi K M Schachtschneider D Schmitt T Schmitt L Schomacher L B Schook K E Sears A W Seifert A Seluanov A B A Shafer D Shanmuganayagam A V Shindyapina M Simmons K Singh I Sinha J Slone R G Snell E Soltanmaohammadi M L Spangler M C Spriggs L Staggs N Stedman K J Steinman D T Stewart V J Sugrue B Szladovits J S Takahashi M Takasugi E C Teeling M J Thompson B Van Bonn S C Vernes D Villar H V Vinters M C Wallingford N Wang R K Wayne G S Wilkinson C K Williams R W Williams X W Yang M Yao B G Young B Zhang Z Zhang P Zhao Y Zhao W Zhou J Zimmermann J Ernst K Raj S Horvath Department of Human Genetics David Geffen School of Medicine University of California Los Angeles Los Angeles CA USA. Altos Labs San Diego Institute of Science San Diego CA USA. Department of Biostatistics Fielding School of Public Health University of California Los Angeles Los Angeles CA USA. Department of Statistics University of California Riverside Riverside CA USA. Zoological SeaWorld Parks and Entertainment Orlando FL USA. Altos Labs Cambridge Institute of Science Cambridge UK. Bioinformatics Interdepartmental Program University of California Los Angeles CA USA. Department of Biological Chemistry University of California Los Angeles Los Angeles CA USA. Department of Biology University of Rochester Rochester NY USA. Department of Neuroscience Peter O'Donnell Jr. Brain Institute University of Texas Southwestern Medical Center Dallas TX USA. Department of Biology University of Maryland College Park MD USA. Loro Parque Fundacion Puerto de la Cruz Spain. Department of Biology University of Kentucky Lexington KY USA. Division of Cardiology Department of Internal Medicine David Geffen School of Medicine University of California Los Angeles Los Angeles CA USA. Marine Mammal Institute Oregon State University Newport OR USA. School of Science and Technology Clifton Campus Nottingham Trent University Nottingham UK. School of Life and Environmental Sciences the University of Sydney Sydney New South Wales Australia. Department of Zoology and Entomology University of Pretoria Hatfield South Africa. Busch Gardens Tampa Tampa FL USA. Department of Ecology and Evolutionary Biology University of California Los Angeles Los Angeles CA USA. Rocky Mountain Biological Laboratory Crested Butte CO USA. Altius Institute for Biomedical Sciences Seattle WA USA. Epigenetic Clock Development Foundation Los Angeles CA USA. Center for Species Survival Smithsonian Conservation Biology Institute Front Royal VA USA. Department of Evolution Eco

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