ALBERT

Description: We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3529199/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3529199/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Colbourne, John K -- Pfrender, Michael E -- Gilbert, Donald -- Thomas, W Kelley -- Tucker, Abraham -- Oakley, Todd H -- Tokishita, Shinichi -- Aerts, Andrea -- Arnold, Georg J -- Basu, Malay Kumar -- Bauer, Darren J -- Caceres, Carla E -- Carmel, Liran -- Casola, Claudio -- Choi, Jeong-Hyeon -- Detter, John C -- Dong, Qunfeng -- Dusheyko, Serge -- Eads, Brian D -- Frohlich, Thomas -- Geiler-Samerotte, Kerry A -- Gerlach, Daniel -- Hatcher, Phil -- Jogdeo, Sanjuro -- Krijgsveld, Jeroen -- Kriventseva, Evgenia V -- Kultz, Dietmar -- Laforsch, Christian -- Lindquist, Erika -- Lopez, Jacqueline -- Manak, J Robert -- Muller, Jean -- Pangilinan, Jasmyn -- Patwardhan, Rupali P -- Pitluck, Samuel -- Pritham, Ellen J -- Rechtsteiner, Andreas -- Rho, Mina -- Rogozin, Igor B -- Sakarya, Onur -- Salamov, Asaf -- Schaack, Sarah -- Shapiro, Harris -- Shiga, Yasuhiro -- Skalitzky, Courtney -- Smith, Zachary -- Souvorov, Alexander -- Sung, Way -- Tang, Zuojian -- Tsuchiya, Dai -- Tu, Hank -- Vos, Harmjan -- Wang, Mei -- Wolf, Yuri I -- Yamagata, Hideo -- Yamada, Takuji -- Ye, Yuzhen -- Shaw, Joseph R -- Andrews, Justen -- Crease, Teresa J -- Tang, Haixu -- Lucas, Susan M -- Robertson, Hugh M -- Bork, Peer -- Koonin, Eugene V -- Zdobnov, Evgeny M -- Grigoriev, Igor V -- Lynch, Michael -- Boore, Jeffrey L -- P42 ES004699/ES/NIEHS NIH HHS/ -- P42 ES004699-25/ES/NIEHS NIH HHS/ -- P42ES004699/ES/NIEHS NIH HHS/ -- R01 ES019324/ES/NIEHS NIH HHS/ -- R24 GM078274/GM/NIGMS NIH HHS/ -- R24 GM078274-01A1/GM/NIGMS NIH HHS/ -- R24GM07827401/GM/NIGMS NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2011 Feb 4;331(6017):555-61. doi: 10.1126/science.1197761.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Genomics and Bioinformatics, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA. jcolbour@indiana.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21292972" target="_blank"〉PubMed〈/a〉

Description: To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405904/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405904/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jarvis, Erich D -- Mirarab, Siavash -- Aberer, Andre J -- Li, Bo -- Houde, Peter -- Li, Cai -- Ho, Simon Y W -- Faircloth, Brant C -- Nabholz, Benoit -- Howard, Jason T -- Suh, Alexander -- Weber, Claudia C -- da Fonseca, Rute R -- Li, Jianwen -- Zhang, Fang -- Li, Hui -- Zhou, Long -- Narula, Nitish -- Liu, Liang -- Ganapathy, Ganesh -- Boussau, Bastien -- Bayzid, Md Shamsuzzoha -- Zavidovych, Volodymyr -- Subramanian, Sankar -- Gabaldon, Toni -- Capella-Gutierrez, Salvador -- Huerta-Cepas, Jaime -- Rekepalli, Bhanu -- Munch, Kasper -- Schierup, Mikkel -- Lindow, Bent -- Warren, Wesley C -- Ray, David -- Green, Richard E -- Bruford, Michael W -- Zhan, Xiangjiang -- Dixon, Andrew -- Li, Shengbin -- Li, Ning -- Huang, Yinhua -- Derryberry, Elizabeth P -- Bertelsen, Mads Frost -- Sheldon, Frederick H -- Brumfield, Robb T -- Mello, Claudio V -- Lovell, Peter V -- Wirthlin, Morgan -- Schneider, Maria Paula Cruz -- Prosdocimi, Francisco -- Samaniego, Jose Alfredo -- Vargas Velazquez, Amhed Missael -- Alfaro-Nunez, Alonzo -- Campos, Paula F -- Petersen, Bent -- Sicheritz-Ponten, Thomas -- Pas, An -- Bailey, Tom -- Scofield, Paul -- Bunce, Michael -- Lambert, David M -- Zhou, Qi -- Perelman, Polina -- Driskell, Amy C -- Shapiro, Beth -- Xiong, Zijun -- Zeng, Yongli -- Liu, Shiping -- Li, Zhenyu -- Liu, Binghang -- Wu, Kui -- Xiao, Jin -- Yinqi, Xiong -- Zheng, Qiuemei -- Zhang, Yong -- Yang, Huanming -- Wang, Jian -- Smeds, Linnea -- Rheindt, Frank E -- Braun, Michael -- Fjeldsa, Jon -- Orlando, Ludovic -- Barker, F Keith -- Jonsson, Knud Andreas -- Johnson, Warren -- Koepfli, Klaus-Peter -- O'Brien, Stephen -- Haussler, David -- Ryder, Oliver A -- Rahbek, Carsten -- Willerslev, Eske -- Graves, Gary R -- Glenn, Travis C -- McCormack, John -- Burt, Dave -- Ellegren, Hans -- Alstrom, Per -- Edwards, Scott V -- Stamatakis, Alexandros -- Mindell, David P -- Cracraft, Joel -- Braun, Edward L -- Warnow, Tandy -- Jun, Wang -- Gilbert, M Thomas P -- Zhang, Guojie -- DP1 OD000448/OD/NIH HHS/ -- DP1OD000448/OD/NIH HHS/ -- R24 GM092842/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Dec 12;346(6215):1320-31. doi: 10.1126/science.1253451.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA. jarvis@neuro.duke.edu tandywarnow@gmail.com mtpgilbert@gmail.com wangj@genomics.cn zhanggj@genomics.cn. ; Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA. ; Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany. ; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. College of Medicine and Forensics, Xi'an Jiaotong University Xi'an 710061, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark. ; Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA. ; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark. ; School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia. ; Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA. ; CNRS UMR 5554, Institut des Sciences de l'Evolution de Montpellier, Universite Montpellier II Montpellier, France. ; Department of Neurobiology, Howard Hughes Medical Institute (HHMI), and Duke University Medical Center, Durham, NC 27710, USA. ; Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala Sweden. ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark. ; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. ; Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA. Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Onna-son, Okinawa 904-0495, Japan. ; Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA. ; Laboratoire de Biometrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Universite de Lyon, F-69622 Villeurbanne, France. ; Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia. ; Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain. Institucio Catalana de Recerca i Estudis Avancats, Barcelona, Spain. ; Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Dr. Aiguader 88, 08003 Barcelona, Spain. Universitat Pompeu Fabra, Barcelona, Spain. ; Joint Institute for Computational Sciences, The University of Tennessee, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. ; Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark. ; The Genome Institute, Washington University School of Medicine, St Louis, MI 63108, USA. ; Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA. ; Department of Ecology and Evolutionary Biology, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA. ; Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University Cardiff CF10 3AX, Wales, UK. ; Organisms and Environment Division, Cardiff School of Biosciences, Cardiff University Cardiff CF10 3AX, Wales, UK. Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China. ; International Wildlife Consultants, Carmarthen SA33 5YL, Wales, UK. ; College of Medicine and Forensics, Xi'an Jiaotong University Xi'an, 710061, China. ; State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, China. ; Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA. Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA. ; Center for Zoo and Wild Animal Health, Copenhagen Zoo Roskildevej 38, DK-2000 Frederiksberg, Denmark. ; Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA. ; Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA. Brazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil. ; Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR 97239, USA. ; Brazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil. Institute of Biological Sciences, Federal University of Para, Belem, Para, Brazil. ; Brazilian Avian Genome Consortium (CNPq/FAPESPA-SISBIO Aves), Federal University of Para, Belem, Para, Brazil. Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro RJ 21941-902, Brazil. ; Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark Kemitorvet 208, 2800 Kgs Lyngby, Denmark. ; Breeding Centre for Endangered Arabian Wildlife, Sharjah, United Arab Emirates. ; Dubai Falcon Hospital, Dubai, United Arab Emirates. ; Canterbury Museum Rolleston Avenue, Christchurch 8050, New Zealand. ; Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia. ; Department of Integrative Biology, University of California, Berkeley, CA 94720, USA. ; Laboratory of Genomic Diversity, National Cancer Institute Frederick, MD 21702, USA. Institute of Molecular and Cellular Biology, SB RAS and Novosibirsk State University, Novosibirsk, Russia. ; Smithsonian Institution National Museum of Natural History, Washington, DC 20013, USA. ; BGI-Shenzhen, Shenzhen 518083, China. ; Department of Biological Sciences, National University of Singapore, Republic of Singapore. ; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Suitland, MD 20746, USA. ; Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark. ; Bell Museum of Natural History, University of Minnesota, Saint Paul, MN 55108, USA. ; Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark. Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK. Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK. ; Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA. ; Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC 20008, USA. ; Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia 199004. Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA. ; Center for Biomolecular Science and Engineering, UCSC, Santa Cruz, CA 95064, USA. ; San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA. ; Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark. Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK. ; Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen O, Denmark. Department of Vertebrate Zoology, MRC-116, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA. ; Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA. ; Moore Laboratory of Zoology and Department of Biology, Occidental College, Los Angeles, CA 90041, USA. ; Department of Genomics and Genetics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK. ; Swedish Species Information Centre, Swedish University of Agricultural Sciences Box 7007, SE-750 07 Uppsala, Sweden. Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China. ; Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA. ; Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany. Institute of Theoretical Informatics, Department of Informatics, Karlsruhe Institute of Technology, D- 76131 Karlsruhe, Germany. ; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA. ; Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA. ; Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA. ; Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA. Departments of Bioengineering and Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. jarvis@neuro.duke.edu tandywarnow@gmail.com mtpgilbert@gmail.com wangj@genomics.cn zhanggj@genomics.cn. ; BGI-Shenzhen, Shenzhen 518083, China. Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia. Macau University of Science and Technology, Avenida Wai long, Taipa, Macau 999078, China. Department of Medicine, University of Hong Kong, Hong Kong. jarvis@neuro.duke.edu tandywarnow@gmail.com mtpgilbert@gmail.com wangj@genomics.cn zhanggj@genomics.cn. ; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oster Voldgade 5-7, 1350 Copenhagen, Denmark. Trace and Environmental DNA Laboratory Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102, Australia. jarvis@neuro.duke.edu tandywarnow@gmail.com mtpgilbert@gmail.com wangj@genomics.cn zhanggj@genomics.cn. ; China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark. jarvis@neuro.duke.edu tandywarnow@gmail.com mtpgilbert@gmail.com wangj@genomics.cn zhanggj@genomics.cn.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25504713" target="_blank"〉PubMed〈/a〉

Description: A DNA sequence coding for the immunogenic capsid protein VP3 of foot-and-mouth disease virus A12, prepared from the virion RNA, was ligated to a plasmid designed to express a chimeric protein from the Escherichia coli tryptophan promoter-operator system. When Escherichia coli transformed with this plasmid was grown in tryptophan-depleted media, approximately 17 percent of the total cellular protein was found to be an insoluble and stable chimeric protein. The purified chimeric protein competed equally on a molar basis with VP3 for specific antibodies to foot-and-mouth disease virus. When inoculated into six cattle and two swine, this protein elicited high levels of neutralizing antibody and protection against challenge with foot-and-mouth disease virus.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kleid, D G -- Yansura, D -- Small, B -- Dowbenko, D -- Moore, D M -- Grubman, M J -- McKercher, P D -- Morgan, D O -- Robertson, B H -- Bachrach, H L -- New York, N.Y. -- Science. 1981 Dec 4;214(4525):1125-9.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6272395" target="_blank"〉PubMed〈/a〉

Description: Passive transfer of broadly neutralizing HIV antibodies can prevent infection, which suggests that vaccines that elicit such antibodies would be protective. Thus far, however, few broadly neutralizing HIV antibodies that occur naturally have been characterized. To determine whether these antibodies are part of a larger group of related molecules, we cloned 576 new HIV antibodies from four unrelated individuals. All four individuals produced expanded clones of potent broadly neutralizing CD4-binding-site antibodies that mimic binding to CD4. Despite extensive hypermutation, the new antibodies shared a consensus sequence of 68 immunoglobulin H (IgH) chain amino acids and arise independently from two related IgH genes. Comparison of the crystal structure of one of the antibodies to the broadly neutralizing antibody VRC01 revealed conservation of the contacts to the HIV spike.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3351836/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3351836/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scheid, Johannes F -- Mouquet, Hugo -- Ueberheide, Beatrix -- Diskin, Ron -- Klein, Florian -- Oliveira, Thiago Y K -- Pietzsch, John -- Fenyo, David -- Abadir, Alexander -- Velinzon, Klara -- Hurley, Arlene -- Myung, Sunnie -- Boulad, Farid -- Poignard, Pascal -- Burton, Dennis R -- Pereyra, Florencia -- Ho, David D -- Walker, Bruce D -- Seaman, Michael S -- Bjorkman, Pamela J -- Chait, Brian T -- Nussenzweig, Michel C -- P01 AI081677/AI/NIAID NIH HHS/ -- P30 AI060354/AI/NIAID NIH HHS/ -- R01 AI033292/AI/NIAID NIH HHS/ -- RR00862/RR/NCRR NIH HHS/ -- RR022220/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Sep 16;333(6049):1633-7. doi: 10.1126/science.1207227. Epub 2011 Jul 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21764753" target="_blank"〉PubMed〈/a〉

Description: Interpreting variants, especially noncoding ones, in the increasing number of personal genomes is challenging. We used patterns of polymorphisms in functionally annotated regions in 1092 humans to identify deleterious variants; then we experimentally validated candidates. We analyzed both coding and noncoding regions, with the former corroborating the latter. We found regions particularly sensitive to mutations ("ultrasensitive") and variants that are disruptive because of mechanistic effects on transcription-factor binding (that is, "motif-breakers"). We also found variants in regions with higher network centrality tend to be deleterious. Insertions and deletions followed a similar pattern to single-nucleotide variants, with some notable exceptions (e.g., certain deletions and enhancers). On the basis of these patterns, we developed a computational tool (FunSeq), whose application to ~90 cancer genomes reveals nearly a hundred candidate noncoding drivers.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3947637/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3947637/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Khurana, Ekta -- Fu, Yao -- Colonna, Vincenza -- Mu, Xinmeng Jasmine -- Kang, Hyun Min -- Lappalainen, Tuuli -- Sboner, Andrea -- Lochovsky, Lucas -- Chen, Jieming -- Harmanci, Arif -- Das, Jishnu -- Abyzov, Alexej -- Balasubramanian, Suganthi -- Beal, Kathryn -- Chakravarty, Dimple -- Challis, Daniel -- Chen, Yuan -- Clarke, Declan -- Clarke, Laura -- Cunningham, Fiona -- Evani, Uday S -- Flicek, Paul -- Fragoza, Robert -- Garrison, Erik -- Gibbs, Richard -- Gumus, Zeynep H -- Herrero, Javier -- Kitabayashi, Naoki -- Kong, Yong -- Lage, Kasper -- Liluashvili, Vaja -- Lipkin, Steven M -- MacArthur, Daniel G -- Marth, Gabor -- Muzny, Donna -- Pers, Tune H -- Ritchie, Graham R S -- Rosenfeld, Jeffrey A -- Sisu, Cristina -- Wei, Xiaomu -- Wilson, Michael -- Xue, Yali -- Yu, Fuli -- 1000 Genomes Project Consortium -- Dermitzakis, Emmanouil T -- Yu, Haiyuan -- Rubin, Mark A -- Tyler-Smith, Chris -- Gerstein, Mark -- 085532/Wellcome Trust/United Kingdom -- 090532/Wellcome Trust/United Kingdom -- 095908/Wellcome Trust/United Kingdom -- 098051/Wellcome Trust/United Kingdom -- CA167824/CA/NCI NIH HHS/ -- G12 MD007579/MD/NIMHD NIH HHS/ -- G12 RR003050/RR/NCRR NIH HHS/ -- GM104424/GM/NIGMS NIH HHS/ -- HG005718/HG/NHGRI NIH HHS/ -- HG007000/HG/NHGRI NIH HHS/ -- P20 MD006899/MD/NIMHD NIH HHS/ -- R01 CA166661/CA/NCI NIH HHS/ -- R01 HG002898/HG/NHGRI NIH HHS/ -- R01CA152057/CA/NCI NIH HHS/ -- R01HG4719/HG/NHGRI NIH HHS/ -- U01 CA111275/CA/NCI NIH HHS/ -- U01 HG005718/HG/NHGRI NIH HHS/ -- U01HG6513/HG/NHGRI NIH HHS/ -- U41 HG007000/HG/NHGRI NIH HHS/ -- U54 HG003079/HG/NHGRI NIH HHS/ -- UL1 TR000457/TR/NCATS NIH HHS/ -- WT085532/Wellcome Trust/United Kingdom -- WT095908/Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2013 Oct 4;342(6154):1235587. doi: 10.1126/science.1235587.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24092746" target="_blank"〉PubMed〈/a〉

Description: Artemisinin is a plant natural product produced by Artemisia annua and the active ingredient in the most effective treatment for malaria. Efforts to eradicate malaria are increasing demand for an affordable, high-quality, robust supply of artemisinin. We performed deep sequencing on the transcriptome of A. annua to identify genes and markers for fast-track breeding. Extensive genetic variation enabled us to build a detailed genetic map with nine linkage groups. Replicated field trials resulted in a quantitative trait loci (QTL) map that accounts for a significant amount of the variation in key traits controlling artemisinin yield. Enrichment for positive QTLs in parents of new high-yielding hybrids confirms that the knowledge and tools to convert A. annua into a robust crop are now available.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Graham, Ian A -- Besser, Katrin -- Blumer, Susan -- Branigan, Caroline A -- Czechowski, Tomasz -- Elias, Luisa -- Guterman, Inna -- Harvey, David -- Isaac, Peter G -- Khan, Awais M -- Larson, Tony R -- Li, Yi -- Pawson, Tanya -- Penfield, Teresa -- Rae, Anne M -- Rathbone, Deborah A -- Reid, Sonja -- Ross, Joe -- Smallwood, Margaret F -- Segura, Vincent -- Townsend, Theresa -- Vyas, Darshna -- Winzer, Thilo -- Bowles, Dianna -- New York, N.Y. -- Science. 2010 Jan 15;327(5963):328-31. doi: 10.1126/science.1182612.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5YW, UK. iag1@york.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20075252" target="_blank"〉PubMed〈/a〉

Description: Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Green, Richard E -- Krause, Johannes -- Briggs, Adrian W -- Maricic, Tomislav -- Stenzel, Udo -- Kircher, Martin -- Patterson, Nick -- Li, Heng -- Zhai, Weiwei -- Fritz, Markus Hsi-Yang -- Hansen, Nancy F -- Durand, Eric Y -- Malaspinas, Anna-Sapfo -- Jensen, Jeffrey D -- Marques-Bonet, Tomas -- Alkan, Can -- Prufer, Kay -- Meyer, Matthias -- Burbano, Hernan A -- Good, Jeffrey M -- Schultz, Rigo -- Aximu-Petri, Ayinuer -- Butthof, Anne -- Hober, Barbara -- Hoffner, Barbara -- Siegemund, Madlen -- Weihmann, Antje -- Nusbaum, Chad -- Lander, Eric S -- Russ, Carsten -- Novod, Nathaniel -- Affourtit, Jason -- Egholm, Michael -- Verna, Christine -- Rudan, Pavao -- Brajkovic, Dejana -- Kucan, Zeljko -- Gusic, Ivan -- Doronichev, Vladimir B -- Golovanova, Liubov V -- Lalueza-Fox, Carles -- de la Rasilla, Marco -- Fortea, Javier -- Rosas, Antonio -- Schmitz, Ralf W -- Johnson, Philip L F -- Eichler, Evan E -- Falush, Daniel -- Birney, Ewan -- Mullikin, James C -- Slatkin, Montgomery -- Nielsen, Rasmus -- Kelso, Janet -- Lachmann, Michael -- Reich, David -- Paabo, Svante -- GM40282/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 May 7;328(5979):710-22. doi: 10.1126/science.1188021.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany. green@eva.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20448178" target="_blank"〉PubMed〈/a〉

Description: We generated a high-resolution whole-genome sequence and individually deleted 5100 genes in Sigma1278b, a Saccharomyces cerevisiae strain closely related to reference strain S288c. Similar to the variation between human individuals, Sigma1278b and S288c average 3.2 single-nucleotide polymorphisms per kilobase. A genome-wide comparison of deletion mutant phenotypes identified a subset of genes that were conditionally essential by strain, including 44 essential genes unique to Sigma1278b and 13 unique to S288c. Genetic analysis indicates the conditional phenotype was most often governed by complex genetic interactions, depending on multiple background-specific modifiers. Our comprehensive analysis suggests that the presence of a complex set of modifiers will often underlie the phenotypic differences between individuals.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4412269/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4412269/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dowell, Robin D -- Ryan, Owen -- Jansen, An -- Cheung, Doris -- Agarwala, Sudeep -- Danford, Timothy -- Bernstein, Douglas A -- Rolfe, P Alexander -- Heisler, Lawrence E -- Chin, Brian -- Nislow, Corey -- Giaever, Guri -- Phillips, Patrick C -- Fink, Gerald R -- Gifford, David K -- Boone, Charles -- DK076284/DK/NIDDK NIH HHS/ -- GM035010/GM/NIGMS NIH HHS/ -- GM069676/GM/NIGMS NIH HHS/ -- P01 NS055923/NS/NINDS NIH HHS/ -- R01 GM035010/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Apr 23;328(5977):469. doi: 10.1126/science.1189015.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Computer Science and Artificial Intelligence Laboratory, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20413493" target="_blank"〉PubMed〈/a〉

Description: Salicylate, a plant product, has been in medicinal use since ancient times. More recently, it has been replaced by synthetic derivatives such as aspirin and salsalate, both of which are rapidly broken down to salicylate in vivo. At concentrations reached in plasma after administration of salsalate or of aspirin at high doses, salicylate activates adenosine monophosphate-activated protein kinase (AMPK), a central regulator of cell growth and metabolism. Salicylate binds at the same site as the synthetic activator A-769662 to cause allosteric activation and inhibition of dephosphorylation of the activating phosphorylation site, threonine-172. In AMPK knockout mice, effects of salicylate to increase fat utilization and to lower plasma fatty acids in vivo were lost. Our results suggest that AMPK activation could explain some beneficial effects of salsalate and aspirin in humans.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3399766/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3399766/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hawley, Simon A -- Fullerton, Morgan D -- Ross, Fiona A -- Schertzer, Jonathan D -- Chevtzoff, Cyrille -- Walker, Katherine J -- Peggie, Mark W -- Zibrova, Darya -- Green, Kevin A -- Mustard, Kirsty J -- Kemp, Bruce E -- Sakamoto, Kei -- Steinberg, Gregory R -- Hardie, D Grahame -- 080982/Wellcome Trust/United Kingdom -- 097726/Wellcome Trust/United Kingdom -- MC_U127088492/Medical Research Council/United Kingdom -- Canadian Institutes of Health Research/Canada -- Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2012 May 18;336(6083):918-22. doi: 10.1126/science.1215327. Epub 2012 Apr 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Cell Signalling and Immunology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22517326" target="_blank"〉PubMed〈/a〉

Description: Bacterial biofilms are structured multicellular communities involved in a broad range of infections. Knowing how free-swimming bacteria adapt their motility mechanisms near surfaces is crucial for understanding the transition between planktonic and biofilm phenotypes. By translating microscopy movies into searchable databases of bacterial behavior, we identified fundamental type IV pili-driven mechanisms for Pseudomonas aeruginosa surface motility involved in distinct foraging strategies. Bacteria stood upright and "walked" with trajectories optimized for two-dimensional surface exploration. Vertical orientation facilitated surface detachment and could influence biofilm morphology.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gibiansky, Maxsim L -- Conrad, Jacinta C -- Jin, Fan -- Gordon, Vernita D -- Motto, Dominick A -- Mathewson, Margie A -- Stopka, Wiktor G -- Zelasko, Daria C -- Shrout, Joshua D -- Wong, Gerard C L -- New York, N.Y. -- Science. 2010 Oct 8;330(6001):197. doi: 10.1126/science.1194238.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Bioengineering, California Nano Systems Institute,University of California, Los Angeles, CA 90024, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20929769" target="_blank"〉PubMed〈/a〉