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Patterns of somatic structural variation in human cancer genomes (vol 578, pg 112, 2020)

NATURE 2023年第7948期614卷 E38-E38页

作者： Li, Yilong Roberts, Nicola D. Wala, Jeremiah A. Shapira, Ofer Schumacher, Steven E. Kumar, Kiran Khurana, Ekta Waszak, Sebastian Korbel, Jan O. Haber, James E. Imielinski, Marcin Weischenfeldt, Joachim Beroukhim, Rameen Campbell, Peter J. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK Totient Inc Cambridge MA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Haematology University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Korea Advanced Institute of Science and Technology Daejeon South Korea Department of Zoology Genetics and Physical Anthropology University of Santiago de Compostela Santiago de Compostela Spain Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) University of Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) University of Vigo Vigo Spain Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain Department of Zoology Genetics and Physical Anthropology (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) Universidade de Vigo Vigo Spain The Broad Institute of Harvard and MIT Cambridge MA USA Bioinformatics and Integrative Genomics Harvard University Cambridge MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Harvard Medical School Boston MA USA Massachusetts General Hospital Center for Cancer Research Charlestown MA USA Dana-Farber Cancer Institute Boston MA USA Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute and Harvard Medical School Boston MA USA Weill Cornell Medical College New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine Ne

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The need to implement FAIR principles in biomolecular simulations

arXiv

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arXiv 2024年

作者： Amaro, R. Åqvist, J. Bahar, I. Battistini, F. Bellaiche, A. Beltran, D. Biggin, P.C. Bonomi, M. Bowman, G.R. Bryce, R. Bussi, G. Carloni, P. Case, D. Cavalli, A. Chang, C.A. Cheatham, T.E. Cheung, M.S. Chipot, C. Chong, L.T. Choudhary, P. Cisneros, G.A. Clementi, C. Collepardo-Guevara, R. Coveney, P. Covino, R. Crawford, T.D. Dal Peraro, M. de Groot, B. Delemotte, L. De Vivo, M. Essex, J. Fraternali, F. Gao, J. Gelpí, J.L. Gervasio, F.L. Gonzalez-Nilo, F.D. Grubmüller, H. Guenza, M.G. Guzman, H.V. Harris, S. Head-Gordon, T. Hernandez, R. Hospital, A. Huang, N. Huang, X. Hummer, G. Iglesias-Fernández, J. Jensen, J.H. Jha, S. Jiao, W. Jorgensen, W.L. Kamerlin, S.C.L. Khalid, S. Laughton, C. Levitt, M. Limongelli, V. Lindahl, E. Lindorff-Larsen, K. Loverde, S. Lundborg, M. Luo, Y.L. Luque, F.J. Lynch, C.I. MacKerell, A. Magistrato, A. Marrink, S.J. Martin, H. McCammon, J.A. Merz, K. Moliner, V. Mulholland, A. Murad, S. Naganathan, A.N. Nangia, S. Noe, F. Noy, A. Oláh, J. O'Mara, M. Ondrechen, M.J. Onuchic, J.N. Onufriev, A. Osuna, S. Palermo, G. Panchenko, A.R. Pantano, S. Parish, C. Parrinello, M. Perez, A. Perez-Acle, T. Perilla, J.R. Pettitt, B.M. Pietropaolo, A. Piquemal, J.-P. Poma, A. Praprotnik, M. Ramos, M.J. Ren, P. Reuter, N. Roitberg, A. Rosta, E. Rovira, C. Roux, B. Röthlisberger, U. Sanbonmatsu, K. Schlick, T. Shaytan, A.K. Simmerling, C. Smith, J.C. Sugita, Y. Świderek, K. Taiji, M. Tao, P. Tikhonova, I.G. Tirado-Rives, J. Tuñón, I. Van Der Kamp, M.W. Van der Spoel, D. Velankar, S. Voth, G.A. Wade, R. Warshel, A. Welborn, V.V. Wetmore, S. Wong, C.F. Yang, L.-W. Zacharias, M. Orozco, M. Department of Molecular Biology University of California San DiegoCA United States Department of Cell and Molecular Biology Uppsala University Uppsala Sweden Laufer Center for Physical and Quantitative Biology Renaissance School of Medicine Stony Brook University Stony BrookNY United States Department of Biochemistry and Cell Biology Renaissance School of Medicine Stony Brook University Stony BrookNY United States Barcelona Spain European Molecular Biology Laboratory European Bioinformatics Institute Hinxton United Kingdom Structural Bioinformatics and Computational Biochemistry Department of Biochemistry University of Oxford Oxford United Kingdom Institut Pasteur Université Paris Cité CNRS UMR 3528 Computational Structural Biology Unit Paris France Department of Biochemistry and Biophysics University of Pennsylvania PhiladelphiaPA United States Division of Pharmacy and Optometry University of Manchester Manchester United Kingdom Scuola Internazionale Superiore di Studi Avanzati-SISSA Trieste Italy Computational Biomedicine Institute of Advanced Simulations IAS-5 Institute for Neuroscience and Medicine INM-9 Forschungszentrum Jülich GmbH Jülich Germany Department of Physics and Universitätsklinikum RWTH Aachen University Aachen Germany Department of Chemistry & Chemical Biology Rutgers University PiscatawayNJ United States Istituto Italiano di Tecnologia Drug Discovery and Development Bologna Italy Lausanne Switzerland Department of Chemistry University of California RiversideCA United States Department of Medicinal Chemistry College of Pharmacy University of Utah Salt Lake CityUT United States Department of Physics University of Washington SeattleWA United States Pacific Northwest National Laboratory RichlandWA United States LIA CNRS-UIUC UMR n°7019 Université de Lorraine Vandœuvre-lès-Nancy France Department of Physics University of Illinois at Urbana-Champaign UrbanaIL United States Department of Biochemistry and Molecular Biol

The communities that embraced data archiving efforts decades ago are now, in the era of data-driven biology, those gaining the most from the AI revolution. The structural biology community was a pioneer in this regard by establishing the Protein Data Bank (PDB) in 1971 and making data accessible using the FAIR (Findable, Accessible, Interoperable and Reusable) principles even before these were articulated [1, 2]. The genomics/bioinformatics community has followed the example, establishing many widely used databases [3, 4]. By contrast, molecular simulation has been anchored in usage paradigms dating back to the seventies, when molecular dynamics (MD) simulation was first applied to study biomacromolecules [5]. At that time, MD was used by theoretical physicists and chemists in "proof of concept" simulations. Still, fifty years later, MD has evolved into a cornerstone molecular biology technique that can provide accurate quantitative analysis and property prediction. MD is now employed by tens of thousands of researchers worldwide, accounting for roughly 15% of global supercomputer usage. Unfortunately, these rich and costly data are not systematically maintained, and when further analyses are required, simulations have to be rerun-an unacceptable situation from scientific, environmental and sustainability standpoints. In this letter, we argue for a collaborative endeavor to archive MD simulation data and describe ongoing efforts to establish cost-effective and sustainable data archiving strategies. © 2024, CC BY-NC-SA.

关键词： Biotic

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The evolutionary history of 2,658 cancers (vol 578, pg 122, 2020)

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NATURE 2023年第7948期614卷 E42-E42页

作者： Gerstung, Moritz Jolly, Clemency Leshchiner, Ignaty Dentro, Stefan C. Gonzalez, Santiago Rosebrock, Daniel Mitchell, Thomas J. Rubanova, Yulia Anur, Pavana Yu, Kaixian Tarabichi, Maxime Deshwar, Amit Wintersinger, Jeff Kleinheinz, Kortine Vazquez-Garcia, Ignacio Haase, Kerstin Jerman, Lara Sengupta, Subhajit Macintyre, Geoff Malikic, Salem Donmez, Nilgun Livitz, Dimitri G. Cmero, Marek Demeulemeester, Jonas Schumacher, Steven Fan, Yu Yao, Xiaotong Lee, Juhee Schlesner, Matthias Boutros, Paul C. Bowtell, David D. Zhu, Hongtu Getz, Gad Imielinski, Marcin Beroukhim, Rameen Sahinalp, S. Cenk Ji, Yuan Peifer, Martin Markowetz, Florian Mustonen, Ville Yuan, Ke Wang, Wenyi Morris, Quaid D. Spellman, Paul T. Wedge, David C. Van Loo, Peter European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Wellcome Sanger Institute Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany University of Ljubljana Ljubljana Slovenia The Francis Crick Institute London UK Big Data Institute University of Oxford Oxford UK Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Big Data Institute Li Ka Shing Centre University of Oxford Oxford UK University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Department of Applied Mathematics and Theoretical Physics Centre for Mathematical Sciences University of Cambridge Cambridge UK Department of Epidemiology and Biostatistics Memorial Sloan Kettering Cancer Center New York NY USA Department of Statistics Columbia University New York NY USA Department of Haematology University of Cambridge Cambridge UK University of Leuven Leuven Belgium Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Charlestown MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Dana-Farber Cancer Institute Boston MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Oxford NIHR Biomedical Research Centre Oxford UK Oxford NIHR Biomedical Research Centre University of Oxford Oxford UK University of Toronto Toronto Ontario Canada Vector Institute Toronto Ontario Canada Vector Institute Toronto ON Canada Department of Computer Science University of Toronto Toronto ON Canada Ontario Institute for Cancer Research Toronto Ontario Canada University of California Los Angeles

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Genomic basis for RNA alterations in cancer (vol 578, pg 129, 2020)

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NATURE 2023年第7948期614卷 E37-E37页

作者： Calabrese, Claudia Davidson, Natalie R. Demircioglu, Deniz Fonseca, Nuno A. He, Yao Lehmann, Kjong-Van Liu, Fenglin Shiraishi, Yuichi Soulette, Cameron M. Urban, Lara Greger, Liliana Li, Siliang Liu, Dongbing Perry, Marc D. Xiang, Qian Zhang, Fan Zhang, Junjun Bailey, Peter Erkek, Serap Hoadley, Katherine A. Hou, Yong Huska, Matthew R. Kilpinen, Helena Korbel, Jan O. Marin, Maximillian G. Markowski, Julia Nandi, Tannistha Pan-Hammarstrom, Qiang Pedamallu, Chandra Sekhar Siebert, Reiner Stark, Stefan G. Su, Hong Tan, Patrick Waszak, Sebastian M. Yung, Christina Zhu, Shida Awadalla, Philip Creighton, Chad J. Meyerson, Matthew Ouellette, B. F. Francis Wu, Kui Yang, Huanming Brazma, Alvis Brooks, Angela N. Goke, Jonathan Ratsch, Gunnar Schwarz, Roland F. Stegle, Oliver Zhang, Zemin European Molecular Biology Laboratory European Bioinformatics Institute Hinxton UK European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources Universidade do Porto Vairão Portugal Berlin Institute for Medical Systems Biology Max Delbruck Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) partner site Berlin Germany German Cancer Research Center (DKFZ) Heidelberg Germany Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) Partner site Berlin Berlin Germany European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Division of Computational Genomics and Systems Genetics German Cancer Research Center (DKFZ) Heidelberg Germany ETH Zurich Zurich Switzerland Memorial Sloan Kettering Cancer Center New York NY USA Weill Cornell Medical College New York NY USA SIB Swiss Institute of Bioinformatics Lausanne Switzerland University Hospital Zurich Zurich Switzerland Computational Biology Center Memorial Sloan Kettering Cancer Center New York NY USA Department of Biology ETH Zurich Zürich Switzerland Department of Computer Science ETH Zurich Zurich Switzerland Korea University Seoul South Korea Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA National University of Singapore Singapore Singapore Genome Institute of Singapore Singapore Singapore Computational and Systems Biology Genome Institute of Singap

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Author Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer (Dec, 10.1038/s41467-019-13824-9, 2022)

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NATURE COMMUNICATIONS 2022年第1期13卷 1-1页

作者： Sieverling, Lina Hong, Chen Koser, Sandra D. Ginsbach, Philip Kleinheinz, Kortine Hutter, Barbara Braun, Delia M. Cortes-Ciriano, Isidro Xi, Ruibin Kabbe, Rolf Park, Peter J. Eils, Roland Schlesner, Matthias Brors, Benedikt Rippe, Karsten Jones, David T. W. Feuerbach, Lars Division of Applied Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Faculty of Biosciences Heidelberg University 69120 Heidelberg Germany Division of Applied Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Biosciences Heidelberg University Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Department for Bioinformatics and Functional Genomics Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant 69120 Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Institute of Pharmacy and Molecular Biotechnology and BioQuant Heidelberg University Heidelberg Germany German Cancer Consortium (DKTK) Heidelberg Germany National Center for Tumor Diseases (NCT) Heidelberg Heidelberg Germany Heidelberg Center for Personalized Oncology (DKFZ-HIPO) German Cancer Research Center (DKFZ) Heidelberg Germany German Cancer Consortium (DKTK) German Cancer Research Center (DKFZ) Heidelberg Germany Division of Chromatin Networks German Cancer Research Center (DKFZ) and BioQuant 69120 Heidelberg Germany Department of Biomedical Informatics Harvard Medical School Boston Massachusetts 02115 USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge CB2 1EW UK Ludwig Center at Harvard Medical School Boston Massachusetts 02115 USA Department of Biomedical Informatics Harvard Medical School Boston MA USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge UK Ludwig Center at Harvard Medical School Boston MA USA School of Mathematical Sciences and Center for Statistical Science Peking University Beijing 100871 China Heidelberg University Heidelberg Germany New BIH Digital Health Center Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin Berlin Germany Bioi

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The Impact of Genomic Variation on Function (IGVF) Consortium

arXiv

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arXiv 2023年

作者： Shendure, Jay Ahituv, Nadav Kircher, Martin Agarwal, Vikram Blair, Andrew Chalkiadakis, Theofilos Chardon, Florence M. Dash, Pyaree M. Deng, Chengyu Hamazaki, Nobuhiko Keukeleire, Pia Kubo, Connor Lalanne, Jean-Benoît Maass, Thorben Martin, Beth McDiarmid, Troy Nobuhara, Mai Page, Nicholas F. Regalado, Sam Schubach, Max Sims, Jasmine Ushiki, Aki Zhao, Jingjing Starita, Lea M. Fowler, Douglas M. Best, Sabrina M. Boyle, Gabe Camp, Nathan Casadei, Silvia Da, Estelle Y. Dawood, Moez Dawson, Samantha C. Fayer, Shawn Hamm, Audrey James, Richard G. Jarvik, Gail P. McEwen, Abbye E. Moore, Nick Muffley, Lara A. Pendyala, Sriram Popp, Nicholas A. Post, Mason Rubin, Alan F. Shendure, Jay Smith, Nahum T. Rubin, Alan F. Stone, Jeremy Tejura, Malvika Wang, Ziyu R. Wheelock, Melinda K. Woo, Ivan Zapp, Brendan D. Engreitz, Jesse M. Quertermous, Thomas Amgalan, Dulguun Aradhana, Aradhana Arana, Sophia M. Bassik, Michael C. Bauman, Julia R. Bhattacharya, Asmita Cai, Xiangmeng Shawn Chen, Ziwei Conley, Stephanie Deshpande, Salil Doughty, Benjamin R. Du, Peter P. Gifford, Casey Greenleaf, William J. Gschwind, Andreas R. Guo, Katherine Isobe, Sarasa Jagoda, Evelyn Jain, Nimit Jones, Hank Kang, Helen Y. Kim, Samuel H. Kim, YeEun Klemm, Sandy Kundaje, Anshul Kundu, Soumya Lago-Docampo, Mauro Lee-Yow, Yannick C. Levin-Konigsberg, Roni Li, Daniel Y. Lindenhofer, Dominik Rosa Ma, X. Marinov, Georgi K. Martyn, Gabriella E. Metzl-Raz, Eyal Monteiro, Joao P. Montgomery, Michael T. Mualim, Kristy S. Munger, Chad Munson, Glen Nguyen, Tri C. Nguyen, Trieu Palmisano, Brian T. Pampari, Anusri Park, Chong Y. Rabinovitch, Marlene Ramste, Markus Ray, Judhajeet Roy, Kevin R. Rubio, Oriane M. Schaepe, Julia M. Schnitzler, Gavin Schreiber, Jacob Sharma, Disha Sheth, Maya U. Shi, Huitong Singh, Vasundhara Sinha, Riya Steinmetz, Lars M. Tan, Jason Tan, Anthony Tycko, Josh Valbuena, Raeline C. Pour Amiri, Valeh Valiollah van Kooten, Mariëlle J.F.M. Vaughan-Jackson, Alun Venida, Anthony Weldy, Chad S. Yao, David Zeng, Tony Zhou, Ronghao Vidal, Marc Calderw Department of Genome Sciences University of Washington SeattleWA United States Department of Bioengineering and Therapeutic Sciences Institute for Human Genetics University of California San Francisco San FranciscoCA United States Institute of Human Genetics University Medical Center Schleswig-Holstein University of Lübeck Lübeck23562 Germany Exploratory Diagnostic Sciences Berlin Institute of Health Charité-Universitätsmedizin Berlin Berlin10117 Germany Brotman Baty Institute for Precision Medicine SeattleWA United States Center of immunotherapy and Immunity Seattle Children's Research Institute SeattleWA United States Bioinformatics Division WEHI ParkvilleVIC Australia Human Genome Sequencing Center Baylor College of Medicine HoustonTX United States Department of Laboratory Medicine and Pathology University of Washington SeattleWA United States Department of Genetics Stanford University School of Medicine StanfordCA United States Basic Science and Engineering Initiative Stanford Children’s Health Betty Irene Moore Children’s Heart Center StanfordCA United States The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease Broad Institute of MIT and Harvard CambridgeMA United States Division of Cardiovascular Medicine School of Medicine Stanford University United States Department of Computer Science Stanford University School of Medicine StanfordCA United States Institute for Computational and Mathematical Engineering Stanford University StanfordCA United States Department of Pediatrics Stanford University School of Medicine StanfordCA United States Institute for Stem Cell Biology and Regenerative Medicine Stanford University School of Medicine StanfordCA United States Division of Pediatric Cardiology Cardiovascular Institute Stanford University School of Medicine Stanford University United States Genome Biology Unit Heidelberg Germany Department of Biology Stanford University StanfordCA United States Stanford Genome Techn

Our genomes influence nearly every aspect of human biology from molecular and cellular functions to phenotypes in health and disease. Human genetics studies have now associated hundreds of thousands of differences in our DNA sequence ("genomic variation") with disease risk and other phenotypes, many of which could reveal novel mechanisms of human biology and uncover the basis of genetic predispositions to diseases, thereby guiding the development of new diagnostics and therapeutics. Yet, understanding how genomic variation alters genome function to influence phenotype has proven challenging. To unlock these insights, we need a systematic and comprehensive catalog of genome function and the molecular and cellular effects of genomic variants. Toward this goal, the Impact of Genomic Variation on Function (IGVF) Consortium will combine approaches in single-cell mapping, genomic perturbations, and predictive modeling to investigate the relationships among genomic variation, genome function, and phenotypes. Through systematic comparisons and benchmarking of experimental and computational methods, we aim to create maps across hundreds of cell types and states describing how coding variants alter protein activity, how noncoding variants change the regulation of gene expression, and how both coding and noncoding variants may connect through gene regulatory and protein interaction networks. These experimental data, computational predictions, and accompanying standards and pipelines will be integrated into an open resource that will catalyze community efforts to explore genome function and the impact of genetic variation on human biology and disease across populations. © 2023, CC BY.

关键词： Genome

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Publisher Correction: The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles

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Genome biology 2025年第1期26卷 31页

作者： Jacob Matthew Schreiber Carles A Boix Jin Wook Lee Hongyang Li Yuanfang Guan Chun-Chieh Chang Jen-Chien Chang Alex Hawkins-Hooker Bernhard Schölkopf Gabriele Schweikert Mateo Rojas Carulla Arif Canakoglu Francesco Guzzo Luca Nanni Marco Masseroli Mark James Carman Pietro Pinoli Chenyang Hong Kevin Y Yip Jefrey P Spence Sanjit Singh Batra Yun S Song Shaun Mahony Zheng Zhang Wuwei Tan Yang Shen Yuanfei Sun Minyi Shi Jessika Adrian Richard S Sandstrom Nina P Farrell Jessica M Halow Kristen Lee Lixia Jiang Xinqiong Yang Charles B Epstein J Seth Strattan Bradley E Bernstein Michael P Snyder Manolis Kellis William S Noble Anshul Bharat Kundaje Department of Genetics Stanford University Stanford CA USA. jmschreiber91@***. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology Cambridge MA USA. Department of Genetics Stanford University Stanford CA USA. Department of Computational Medicine and Bioinformatics University of Michigan Ann Arbor MI USA. Department of Research and Development DeepSeq.AI San Francisco CA USA. RIKEN Center for Integrative Medical Sciences Yokohama Japan. Department of Empirical Inference Max Planck Institute for Intelligent Systems Stuttgart Germany. School of Life Sciences University of Dundee Dundee UK. Department of Electronics Information and Bioengineering Politecnico Di Milano Milan Italy. Department of Computational Biology University of Lausanne Lausanne Switzerland. Department of Computer Science and Engineering The Chinese University of Hong Kong Sha Tin Hong Kong. Sanford Burnham Prebys Medical Discovery Institute San Diego CA USA. Department of Electrical Engineering and Computer Sciences University of California Berkeley Berkeley CA USA. Department of Statistics University of California Berkeley Berkeley CA USA. Department of Biochemistry & Molecular Biology Center for Eukaryotic Gene Regulation Pennsylvania State University University Park PA USA. Department of Statistics Pennsylvania State University University Park PA USA. Department of Electrical and Computer Engineering Texas A&M University College Station TX USA. Altius Institute Seattle WA USA. Epigenomics Program The Broad Institute of MIT and Harvard Cambridge MA USA. Department of Genome Sciences University of Washington Seattle WA USA. Department of Computer Science Stanford University Stanford CA USA.

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Author Correction: Vaccine elicitation of HIV broadly neutralizing antibodies from engineered B cells

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Nature communications 2020年第1期11卷 6360页

作者： Deli Huang Jenny Tuyet Tran Alex Olson Thomas Vollbrecht Mary Tenuta Mariia V Guryleva Roberta P Fuller Torben Schiffner Justin R Abadejos Lauren Couvrette Tanya R Blane Karen Saye Wenjuan Li Elise Landais Alicia Gonzalez-Martin William Schief Ben Murrell Dennis R Burton David Nemazee James E Voss Department of Immunology and Microbiology The Scripps Research Institute La Jolla CA USA. Department of Medicine The University of California San Diego La Jolla CA USA. Department of Microbiology Tumor and Cell Biology Karolinska Institutet Stockholm Sweden. Faculty of Bioengineering and Bioinformatics Moscow Lomonosov State University Moscow Russia. Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD) The Scripps Research Institute La Jolla CA USA. IAVI Neutralizing Antibody Center (IAVI) The Scripps Research Institute La Jolla CA USA. Faculty of Science University of Ottawa Ottawa Canada. Department of Biochemistry Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM) Madrid Spain. Ragon Institute of Massachusetts General Hospital Massachusetts Institute of Technology and Harvard Cambridge MA USA. Department of Microbiology Tumor and Cell Biology Karolinska Institutet Stockholm Sweden. benjamin.murrell@ki.se. Department of Immunology and Microbiology The Scripps Research Institute La Jolla CA USA. burton@scripps.edu. Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD) The Scripps Research Institute La Jolla CA USA. burton@scripps.edu. IAVI Neutralizing Antibody Center (IAVI) The Scripps Research Institute La Jolla CA USA. burton@scripps.edu. Ragon Institute of Massachusetts General Hospital Massachusetts Institute of Technology and Harvard Cambridge MA USA. burton@scripps.edu. Department of Immunology and Microbiology The Scripps Research Institute La Jolla CA USA. nemazee@scripps.edu. Department of Immunology and Microbiology The Scripps Research Institute La Jolla CA USA. jvoss@scripps.edu.

A Correction to this paper has been published: https://***/10.1038/s41467-020-20304-y.

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137 ancient human genomes from across the Eurasian steppes (vol 557, pg 369, 2018)

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NATURE 2018年第7729期563卷 E16-E16页

作者： Damgaard, Peter de Barros Marchi, Nina Rasmussen, Simon Peyrot, Michael Renaud, Gabriel Korneliussen, Thorfinn Moreno-Mayar, J. Victor Pedersen, Mikkel Winther Goldberg, Amy Usmanova, Emma Baimukhanov, Nurbol Loman, Valeriy Hedeager, Lotte Pedersen, Anders Gorm Nielsen, Kasper Afanasiev, Gennady Akmatov, Kunbolot Aldashev, Almaz Alpaslan, Ashyk Baimbetov, Gabit Bazaliiskii, Vladimir I. Beisenov, Arman Boldbaatar, Bazartseren Boldgiv, Bazartseren Dorzhu, Choduraa Ellingvag, Sturla Erdenebaatar, Diimaajav Dajani, Rana Dmitriev, Evgeniy Evdokimov, Valeriy Frei, Karin M. Gromov, Andrey Goryachev, Alexander Hakonarson, Hakon Hegay, Tatyana Khachatryan, Zaruhi Khaskhanov, Ruslan Kitov, Egor Kolbina, Alina Kubatbek, Tabaldiev Kukushkin, Alexey Kukushkin, Igor Lau, Nina Margaryan, Ashot Merkyte, Inga Mertz, Ilya V. Mertz, Viktor K. Mijiddorj, Enkhbayar Moiyesev, Vyacheslav Mukhtarova, Gulmira Nurmukhanbetov, Bekmukhanbet Orozbekova, Z. Panyushkina, Irina Pieta, Karol Smrcka, Vaclav Shevnina, Irina Logvin, Andrey Sjogren, Karl-Goran Stolcova, Tereza Taravella, Angela M. Tashbaeva, Kadicha Tkachev, Alexander Tulegenov, Turaly Voyakin, Dmitriy Yepiskoposyan, Levon Undrakhbold, Sainbileg Varfolomeev, Victor Weber, Andrzej Sayres, Melissa A. Wilson Kradin, Nikolay Allentoft, Morten E. Orlando, Ludovic Nielsen, Rasmus Sikora, Martin Heyer, Evelyne Kristiansen, Kristian Willerslev, Eske Center for GeoGenetics Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark Eco-anthropologie et Ethnobiologie Muséum national d’Histoire naturelle CNRS Université Paris Diderot Paris France Department of Bio and Health Informatics Technical University of Denmark Lyngby Denmark Leiden University Centre for Linguistics Leiden University Leiden The Netherlands Department of Zoology University of Cambridge Cambridge UK Department of Biology Stanford University Stanford USA Buketov Karaganda State University Saryarka Archaeological Institute Karaganda Kazakhstan Shejire DNA Almaty Kazakhstan Department of Archaeology Conservation and History University of Oslo Oslo Norway Carlsberg Research Laboratory Copenhagen Denmark Department of Theory and Methods Institute of Archaeology Russian Academy of Sciences Moscow Russia Department of History Kyrgyzstan-Turkey Manas University Bishkek Kyrgyzstan National Academy of Sciences of Kyrgyzstan Bishkek Kyrgyzstan Department of History Irkutsk State University Irkutsk Russia A. Kh. Margulan Institute of Archaeology Almaty Kazakhstan Laboratory of Virology Institute of Veterinary Medicine Mongolian University of Life Sciences Ulaanbaatar Mongolia Department of Biology School of Arts and Sciences National University of Mongolia Ulaanbaatar Mongolia Departament of Biology and Ecology Tuvan State University Kyzyl Russia The Explico Foundation Floro Norway Department of Archaeology Ulaanbaatar State University Ulaanbaatar Mongolia Department of Biology and Biotechnology Hashemite University Zarqa Jordan Radcliffe Institute for Advanced Study Harvard University Cambridge USA Unit for Environmental Archaeology and Materials Science National Museum of Denmark Copenhagen Denmark Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS St. Petersburg Russia Archaeological Expertise LLC Almaty Kazakhstan Center for Applied Genomics The Children’s Hospital of Philadelphia Ph

with In this Article, Angela M. Taravella and Melissa A. Wilson Sayres have been added to the author list (associated with: School of Life Sciences, Center for Evolution and Medicine, The Biodesign institute, Arizona State University, Tempe, AZ, USA). The author list and Author Information section have been corrected online.

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Fluorescence color diversity of great barrier reef corals

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Journal of Innovative Optical Health Sciences 2015年第4期8卷 58-68页

作者： Grigory Lapshin Anya Salih Peter Kolosov Maria Golovkina Yuri Zavorotnyi Tatyana Ivashina Leonid Vinokurov Victor Bagratashvili Alexander Savitsky Physical Biochemistry Lab INBI RASLeninsky Prospekt 33Build.2 Moscow 119071Russia Faculty of Bioengineering and Bioinformatics Moscow State University Leninskiye Gory 1-73 MSU GSP-1 Moscow 119991Russia Confocal Bio-Imaging Facility(CBIF) Division Deputy Vice-Chancellor(Research&Development)University of Western SydneyLocked Bag 1797 Penrith South DCNSW 1797Australia Institute of Higher Nervous Activity and Neurophysiology The Russian Academy of Sciences 5A Butlerova St.Moscow 117485Russia Skobeltsyn Institute of Nuclear Physics Moscow State University 1(2)Leninskie Gory GSP-1Moscow 119991Russia Molecular Microbiology Lab Skryabin Institute of Biochemistry and Physiology of Micro-organisms RAS Prospect Nauki 5 Pushchino142290 Moscow RegionRussia Group of Bioengineering of Reporter Proteins Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences Prospekt Nauki 65 Pushchino 142290 Moscow RegionRussia Institute of Laser and Information Technologies RAS 2 Pionerskaya TroitskMoscow 142190Russia

A group of variously colored proteins belonging to the green fAuorescent protein(GFP)family are responsible for coloring coral *** of the Great Barrier Reef were studied with the custom-built fiber laser fluorescence *** analysis showed that most of the excarmined corals contained multiple fuorescent peaks ranging from 470 to *** obser-vation was attributed to the presence of multiple genes of GFP-like proteins in a single coral,as well as by the photo-induced post-translational modifcations of certain GFP-like *** isolated a novel photo-convertible fuorescent protein(FP)from one of the tested ***:propose that two processes may explain the observed diversity of the fuorescent spectra in corals:(1)dark post-translational modifcation(maturation),and(2)color photo-conversion of certain maturated proteins in response to sunlight.

关键词： Coral fuorescence GFP like proteins fuorophores Kaede

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