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  • 1
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    Techview: DNA sequencing. Sequencing the genome, fast (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-04-17
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mullikin, J C -- McMurragy, A A -- New York, N.Y. -- Science. 1999 Mar 19;283(5409):1867-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs, UK. jcm@sanger.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10206892" target="_blank"〉PubMed〈/a〉
    Keywords: Automation ; Base Sequence ; Fluorescence ; *Genome, Human ; Human Genome Project ; Humans ; Sequence Analysis, DNA/*instrumentation/methods ; Software
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Accurate whole human genome sequencing using reversible terminator chemistry (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-11-07
    Description: DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400-800 base pair) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intraspecies genetic variation. Here we report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from 〉30x average depth of paired 35-base reads. We characterize four million single-nucleotide polymorphisms and four hundred thousand structural variants, many of which were previously unknown. Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2581791/" 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/PMC2581791/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bentley, David R -- Balasubramanian, Shankar -- Swerdlow, Harold P -- Smith, Geoffrey P -- Milton, John -- Brown, Clive G -- Hall, Kevin P -- Evers, Dirk J -- Barnes, Colin L -- Bignell, Helen R -- Boutell, Jonathan M -- Bryant, Jason -- Carter, Richard J -- Keira Cheetham, R -- Cox, Anthony J -- Ellis, Darren J -- Flatbush, Michael R -- Gormley, Niall A -- Humphray, Sean J -- Irving, Leslie J -- Karbelashvili, Mirian S -- Kirk, Scott M -- Li, Heng -- Liu, Xiaohai -- Maisinger, Klaus S -- Murray, Lisa J -- Obradovic, Bojan -- Ost, Tobias -- Parkinson, Michael L -- Pratt, Mark R -- Rasolonjatovo, Isabelle M J -- Reed, Mark T -- Rigatti, Roberto -- Rodighiero, Chiara -- Ross, Mark T -- Sabot, Andrea -- Sankar, Subramanian V -- Scally, Aylwyn -- Schroth, Gary P -- Smith, Mark E -- Smith, Vincent P -- Spiridou, Anastassia -- Torrance, Peta E -- Tzonev, Svilen S -- Vermaas, Eric H -- Walter, Klaudia -- Wu, Xiaolin -- Zhang, Lu -- Alam, Mohammed D -- Anastasi, Carole -- Aniebo, Ify C -- Bailey, David M D -- Bancarz, Iain R -- Banerjee, Saibal -- Barbour, Selena G -- Baybayan, Primo A -- Benoit, Vincent A -- Benson, Kevin F -- Bevis, Claire -- Black, Phillip J -- Boodhun, Asha -- Brennan, Joe S -- Bridgham, John A -- Brown, Rob C -- Brown, Andrew A -- Buermann, Dale H -- Bundu, Abass A -- Burrows, James C -- Carter, Nigel P -- Castillo, Nestor -- Chiara E Catenazzi, Maria -- Chang, Simon -- Neil Cooley, R -- Crake, Natasha R -- Dada, Olubunmi O -- Diakoumakos, Konstantinos D -- Dominguez-Fernandez, Belen -- Earnshaw, David J -- Egbujor, Ugonna C -- Elmore, David W -- Etchin, Sergey S -- Ewan, Mark R -- Fedurco, Milan -- Fraser, Louise J -- Fuentes Fajardo, Karin V -- Scott Furey, W -- George, David -- Gietzen, Kimberley J -- Goddard, Colin P -- Golda, George S -- Granieri, Philip A -- Green, David E -- Gustafson, David L -- Hansen, Nancy F -- Harnish, Kevin -- Haudenschild, Christian D -- Heyer, Narinder I -- Hims, Matthew M -- Ho, Johnny T -- Horgan, Adrian M -- Hoschler, Katya -- Hurwitz, Steve -- Ivanov, Denis V -- Johnson, Maria Q -- James, Terena -- Huw Jones, T A -- Kang, Gyoung-Dong -- Kerelska, Tzvetana H -- Kersey, Alan D -- Khrebtukova, Irina -- Kindwall, Alex P -- Kingsbury, Zoya -- Kokko-Gonzales, Paula I -- Kumar, Anil -- Laurent, Marc A -- Lawley, Cynthia T -- Lee, Sarah E -- Lee, Xavier -- Liao, Arnold K -- Loch, Jennifer A -- Lok, Mitch -- Luo, Shujun -- Mammen, Radhika M -- Martin, John W -- McCauley, Patrick G -- McNitt, Paul -- Mehta, Parul -- Moon, Keith W -- Mullens, Joe W -- Newington, Taksina -- Ning, Zemin -- Ling Ng, Bee -- Novo, Sonia M -- O'Neill, Michael J -- Osborne, Mark A -- Osnowski, Andrew -- Ostadan, Omead -- Paraschos, Lambros L -- Pickering, Lea -- Pike, Andrew C -- Pike, Alger C -- Chris Pinkard, D -- Pliskin, Daniel P -- Podhasky, Joe -- Quijano, Victor J -- Raczy, Come -- Rae, Vicki H -- Rawlings, Stephen R -- Chiva Rodriguez, Ana -- Roe, Phyllida M -- Rogers, John -- Rogert Bacigalupo, Maria C -- Romanov, Nikolai -- Romieu, Anthony -- Roth, Rithy K -- Rourke, Natalie J -- Ruediger, Silke T -- Rusman, Eli -- Sanches-Kuiper, Raquel M -- Schenker, Martin R -- Seoane, Josefina M -- Shaw, Richard J -- Shiver, Mitch K -- Short, Steven W -- Sizto, Ning L -- Sluis, Johannes P -- Smith, Melanie A -- Ernest Sohna Sohna, Jean -- Spence, Eric J -- Stevens, Kim -- Sutton, Neil -- Szajkowski, Lukasz -- Tregidgo, Carolyn L -- Turcatti, Gerardo -- Vandevondele, Stephanie -- Verhovsky, Yuli -- Virk, Selene M -- Wakelin, Suzanne -- Walcott, Gregory C -- Wang, Jingwen -- Worsley, Graham J -- Yan, Juying -- Yau, Ling -- Zuerlein, Mike -- Rogers, Jane -- Mullikin, James C -- Hurles, Matthew E -- McCooke, Nick J -- West, John S -- Oaks, Frank L -- Lundberg, Peter L -- Klenerman, David -- Durbin, Richard -- Smith, Anthony J -- B05823/Biotechnology and Biological Sciences Research Council/United Kingdom -- G0701805/Medical Research Council/United Kingdom -- MOL04534/Biotechnology and Biological Sciences Research Council/United Kingdom -- Z01 HG200330-03/Intramural NIH HHS/ -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2008 Nov 6;456(7218):53-9. doi: 10.1038/nature07517.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Illumina Cambridge Ltd. (Formerly Solexa Ltd), Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex CB10 1XL, UK. dbentley@illumina.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18987734" target="_blank"〉PubMed〈/a〉
    Keywords: Chromosomes, Human, X/genetics ; Consensus Sequence/genetics ; Genome, Human/*genetics ; Genomics/economics/*methods ; Genotype ; Humans ; Male ; Nigeria ; Polymorphism, Single Nucleotide/genetics ; Sensitivity and Specificity ; Sequence Analysis, DNA/economics/*methods
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Mapping and sequencing of structural variation from eight human genomes (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-05-03
    Description: Genetic variation among individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single nucleotide changes. Here we explore variation on an intermediate scale--particularly insertions, deletions and inversions affecting from a few thousand to a few million base pairs. We employed a clone-based method to interrogate this intermediate structural variation in eight individuals of diverse geographic ancestry. Our analysis provides a comprehensive overview of the normal pattern of structural variation present in these genomes, refining the location of 1,695 structural variants. We find that 50% were seen in more than one individual and that nearly half lay outside regions of the genome previously described as structurally variant. We discover 525 new insertion sequences that are not present in the human reference genome and show that many of these are variable in copy number between individuals. Complete sequencing of 261 structural variants reveals considerable locus complexity and provides insights into the different mutational processes that have shaped the human genome. These data provide the first high-resolution sequence map of human structural variation--a standard for genotyping platforms and a prelude to future individual genome sequencing projects.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2424287/" 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/PMC2424287/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kidd, Jeffrey M -- Cooper, Gregory M -- Donahue, William F -- Hayden, Hillary S -- Sampas, Nick -- Graves, Tina -- Hansen, Nancy -- Teague, Brian -- Alkan, Can -- Antonacci, Francesca -- Haugen, Eric -- Zerr, Troy -- Yamada, N Alice -- Tsang, Peter -- Newman, Tera L -- Tuzun, Eray -- Cheng, Ze -- Ebling, Heather M -- Tusneem, Nadeem -- David, Robert -- Gillett, Will -- Phelps, Karen A -- Weaver, Molly -- Saranga, David -- Brand, Adrianne -- Tao, Wei -- Gustafson, Erik -- McKernan, Kevin -- Chen, Lin -- Malig, Maika -- Smith, Joshua D -- Korn, Joshua M -- McCarroll, Steven A -- Altshuler, David A -- Peiffer, Daniel A -- Dorschner, Michael -- Stamatoyannopoulos, John -- Schwartz, David -- Nickerson, Deborah A -- Mullikin, James C -- Wilson, Richard K -- Bruhn, Laurakay -- Olson, Maynard V -- Kaul, Rajinder -- Smith, Douglas R -- Eichler, Evan E -- 3 U54 HG002043/HG/NHGRI NIH HHS/ -- HG004120/HG/NHGRI NIH HHS/ -- P01 HG004120/HG/NHGRI NIH HHS/ -- P01 HG004120-01/HG/NHGRI NIH HHS/ -- U54 HG002043-07S1/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 May 1;453(7191):56-64. doi: 10.1038/nature06862.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18451855" target="_blank"〉PubMed〈/a〉
    Keywords: Chromosome Inversion/genetics ; Continental Population Groups/genetics ; Euchromatin/genetics ; Gene Deletion ; Genetic Variation/*genetics ; Genome, Human/*genetics ; Geography ; Haplotypes ; Humans ; Mutagenesis, Insertional/genetics ; *Physical Chromosome Mapping ; Polymorphism, Single Nucleotide/genetics ; Reproducibility of Results ; *Sequence Analysis, DNA
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
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    A draft sequence of the Neandertal genome (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-05-08
    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〉
    Keywords: African Continental Ancestry Group/genetics ; Animals ; Asian Continental Ancestry Group/genetics ; Base Sequence ; Bone and Bones ; DNA, Mitochondrial/genetics ; European Continental Ancestry Group/genetics ; Evolution, Molecular ; Extinction, Biological ; Female ; *Fossils ; Gene Dosage ; Gene Flow ; Genetic Variation ; *Genome ; *Genome, Human ; Haplotypes ; Hominidae/*genetics ; Humans ; Pan troglodytes/genetics ; Polymorphism, Single Nucleotide ; Selection, Genetic ; Sequence Alignment ; *Sequence Analysis, DNA ; Time
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-08-13
    Description: Antibody VRC01 is a human immunoglobulin that neutralizes about 90% of HIV-1 isolates. To understand how such broadly neutralizing antibodies develop, we used x-ray crystallography and 454 pyrosequencing to characterize additional VRC01-like antibodies from HIV-1-infected individuals. Crystal structures revealed a convergent mode of binding for diverse antibodies to the same CD4-binding-site epitope. A functional genomics analysis of expressed heavy and light chains revealed common pathways of antibody-heavy chain maturation, confined to the IGHV1-2*02 lineage, involving dozens of somatic changes, and capable of pairing with different light chains. Broadly neutralizing HIV-1 immunity associated with VRC01-like antibodies thus involves the evolution of antibodies to a highly affinity-matured state required to recognize an invariant viral structure, with lineages defined from thousands of sequences providing a genetic roadmap of their development.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516815/" 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/PMC3516815/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wu, Xueling -- Zhou, Tongqing -- Zhu, Jiang -- Zhang, Baoshan -- Georgiev, Ivelin -- Wang, Charlene -- Chen, Xuejun -- Longo, Nancy S -- Louder, Mark -- McKee, Krisha -- O'Dell, Sijy -- Perfetto, Stephen -- Schmidt, Stephen D -- Shi, Wei -- Wu, Lan -- Yang, Yongping -- Yang, Zhi-Yong -- Yang, Zhongjia -- Zhang, Zhenhai -- Bonsignori, Mattia -- Crump, John A -- Kapiga, Saidi H -- Sam, Noel E -- Haynes, Barton F -- Simek, Melissa -- Burton, Dennis R -- Koff, Wayne C -- Doria-Rose, Nicole A -- Connors, Mark -- NISC Comparative Sequencing Program -- Mullikin, James C -- Nabel, Gary J -- Roederer, Mario -- Shapiro, Lawrence -- Kwong, Peter D -- Mascola, John R -- 5U19 AI 067854-06/AI/NIAID NIH HHS/ -- R01 AI033292/AI/NIAID NIH HHS/ -- U19 AI067854/AI/NIAID NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2011 Sep 16;333(6049):1593-602. doi: 10.1126/science.1207532. Epub 2011 Aug 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21835983" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines ; Amino Acid Sequence ; Antibodies, Neutralizing/*chemistry/genetics/*immunology/isolation & purification ; Antibody Affinity ; Antibody Specificity ; Antigens, CD4/metabolism ; Base Sequence ; Binding Sites ; Binding Sites, Antibody ; Complementarity Determining Regions/genetics ; Crystallography, X-Ray ; Epitopes ; *Evolution, Molecular ; Genes, Immunoglobulin Heavy Chain ; HIV Antibodies/*chemistry/genetics/*immunology/isolation & purification ; HIV Envelope Protein gp120/chemistry/*immunology/metabolism ; HIV Infections/immunology ; HIV-1/chemistry/*immunology ; High-Throughput Nucleotide Sequencing ; Humans ; Immunoglobulin Fab Fragments/chemistry/immunology ; Immunoglobulin Heavy Chains/chemistry/immunology ; Immunoglobulin J-Chains/genetics ; Immunoglobulin Light Chains/chemistry/immunology ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-12-18
    Description: An understanding of ctenophore biology is critical for reconstructing events that occurred early in animal evolution. Toward this goal, we have sequenced, assembled, and annotated the genome of the ctenophore Mnemiopsis leidyi. Our phylogenomic analyses of both amino acid positions and gene content suggest that ctenophores rather than sponges are the sister lineage to all other animals. Mnemiopsis lacks many of the genes found in bilaterian mesodermal cell types, suggesting that these cell types evolved independently. The set of neural genes in Mnemiopsis is similar to that of sponges, indicating that sponges may have lost a nervous system. These results present a newly supported view of early animal evolution that accounts for major losses and/or gains of sophisticated cell types, including nerve and muscle cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3920664/" 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/PMC3920664/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ryan, Joseph F -- Pang, Kevin -- Schnitzler, Christine E -- Nguyen, Anh-Dao -- Moreland, R Travis -- Simmons, David K -- Koch, Bernard J -- Francis, Warren R -- Havlak, Paul -- NISC Comparative Sequencing Program -- Smith, Stephen A -- Putnam, Nicholas H -- Haddock, Steven H D -- Dunn, Casey W -- Wolfsberg, Tyra G -- Mullikin, James C -- Martindale, Mark Q -- Baxevanis, Andreas D -- ZIA HG000140-13/Intramural NIH HHS/ -- ZIA HG000140-14/Intramural NIH HHS/ -- ZIA HG000140-15/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2013 Dec 13;342(6164):1242592. doi: 10.1126/science.1242592.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genome Technology Branch, Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24337300" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; *Biological Evolution ; Cell Lineage/*genetics ; Ctenophora/classification/*cytology/*genetics ; *Genome ; Mesoderm/cytology ; Molecular Sequence Data ; Muscle Development/genetics ; Neurogenesis/genetics ; Phylogeny
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    The bonobo genome compared with the chimpanzee and human genomes (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-06-23
    Description: Two African apes are the closest living relatives of humans: the chimpanzee (Pan troglodytes) and the bonobo (Pan paniscus). Although they are similar in many respects, bonobos and chimpanzees differ strikingly in key social and sexual behaviours, and for some of these traits they show more similarity with humans than with each other. Here we report the sequencing and assembly of the bonobo genome to study its evolutionary relationship with the chimpanzee and human genomes. We find that more than three per cent of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other. These regions allow various aspects of the ancestry of the two ape species to be reconstructed. In addition, many of the regions that overlap genes may eventually help us understand the genetic basis of phenotypes that humans share with one of the two apes to the exclusion of the other.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3498939/" 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/PMC3498939/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Prufer, Kay -- Munch, Kasper -- Hellmann, Ines -- Akagi, Keiko -- Miller, Jason R -- Walenz, Brian -- Koren, Sergey -- Sutton, Granger -- Kodira, Chinnappa -- Winer, Roger -- Knight, James R -- Mullikin, James C -- Meader, Stephen J -- Ponting, Chris P -- Lunter, Gerton -- Higashino, Saneyuki -- Hobolth, Asger -- Dutheil, Julien -- Karakoc, Emre -- Alkan, Can -- Sajjadian, Saba -- Catacchio, Claudia Rita -- Ventura, Mario -- Marques-Bonet, Tomas -- Eichler, Evan E -- Andre, Claudine -- Atencia, Rebeca -- Mugisha, Lawrence -- Junhold, Jorg -- Patterson, Nick -- Siebauer, Michael -- Good, Jeffrey M -- Fischer, Anne -- Ptak, Susan E -- Lachmann, Michael -- Symer, David E -- Mailund, Thomas -- Schierup, Mikkel H -- Andres, Aida M -- Kelso, Janet -- Paabo, Svante -- 090532/Wellcome Trust/United Kingdom -- 090532/Z/09/Z/Wellcome Trust/United Kingdom -- 2R01GM077117-04A1/GM/NIGMS NIH HHS/ -- HG002385/HG/NHGRI NIH HHS/ -- MC_U137761446/Medical Research Council/United Kingdom -- R01 GM077117/GM/NIGMS NIH HHS/ -- R01 HG002385/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- Intramural NIH HHS/ -- England -- Nature. 2012 Jun 28;486(7404):527-31. doi: 10.1038/nature11128.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany. pruefer@eva.mpg.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22722832" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; DNA Transposable Elements/genetics ; *Evolution, Molecular ; Gene Duplication/genetics ; Genetic Variation/*genetics ; Genome/*genetics ; Genome, Human/*genetics ; Genotype ; Humans ; Molecular Sequence Data ; Pan paniscus/*genetics ; Pan troglodytes/*genetics ; Phenotype ; Phylogeny ; Species Specificity
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
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    Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies (2014)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2014-03-05
    Description: Antibodies capable of neutralizing HIV-1 often target variable regions 1 and 2 (V1V2) of the HIV-1 envelope, but the mechanism of their elicitation has been unclear. Here we define the developmental pathway by which such antibodies are generated and acquire the requisite molecular characteristics for neutralization. Twelve somatically related neutralizing antibodies (CAP256-VRC26.01-12) were isolated from donor CAP256 (from the Centre for the AIDS Programme of Research in South Africa (CAPRISA)); each antibody contained the protruding tyrosine-sulphated, anionic antigen-binding loop (complementarity-determining region (CDR) H3) characteristic of this category of antibodies. Their unmutated ancestor emerged between weeks 30-38 post-infection with a 35-residue CDR H3, and neutralized the virus that superinfected this individual 15 weeks after initial infection. Improved neutralization breadth and potency occurred by week 59 with modest affinity maturation, and was preceded by extensive diversification of the virus population. HIV-1 V1V2-directed neutralizing antibodies can thus develop relatively rapidly through initial selection of B cells with a long CDR H3, and limited subsequent somatic hypermutation. These data provide important insights relevant to HIV-1 vaccine development.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4395007/" 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/PMC4395007/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Doria-Rose, Nicole A -- Schramm, Chaim A -- Gorman, Jason -- Moore, Penny L -- Bhiman, Jinal N -- DeKosky, Brandon J -- Ernandes, Michael J -- Georgiev, Ivelin S -- Kim, Helen J -- Pancera, Marie -- Staupe, Ryan P -- Altae-Tran, Han R -- Bailer, Robert T -- Crooks, Ema T -- Cupo, Albert -- Druz, Aliaksandr -- Garrett, Nigel J -- Hoi, Kam H -- Kong, Rui -- Louder, Mark K -- Longo, Nancy S -- McKee, Krisha -- Nonyane, Molati -- O'Dell, Sijy -- Roark, Ryan S -- Rudicell, Rebecca S -- Schmidt, Stephen D -- Sheward, Daniel J -- Soto, Cinque -- Wibmer, Constantinos Kurt -- Yang, Yongping -- Zhang, Zhenhai -- NISC Comparative Sequencing Program -- Mullikin, James C -- Binley, James M -- Sanders, Rogier W -- Wilson, Ian A -- Moore, John P -- Ward, Andrew B -- Georgiou, George -- Williamson, Carolyn -- Abdool Karim, Salim S -- Morris, Lynn -- Kwong, Peter D -- Shapiro, Lawrence -- Mascola, John R -- P01 AI082362/AI/NIAID NIH HHS/ -- R01 AI100790/AI/NIAID NIH HHS/ -- UM1 AI100663/AI/NIAID NIH HHS/ -- Intramural NIH HHS/ -- Wellcome Trust/United Kingdom -- England -- Nature. 2014 May 1;509(7498):55-62. doi: 10.1038/nature13036. Epub 2014 Mar 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA [2]. ; 1] Department of Biochemistry, Columbia University, New York, New York 10032, USA [2]. ; 1] Center for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service (NHLS), Johannesburg, 2131, South Africa [2] Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2050, South Africa [3] Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Congella, 4013, South Africa [4]. ; 1] Center for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service (NHLS), Johannesburg, 2131, South Africa [2] Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2050, South Africa. ; Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA. ; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA. ; 1] Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA [2] Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California 92037, USA [3] IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California 92037, USA. ; Torrey Pines Institute, San Diego, California 92037, USA. ; Weill Medical College of Cornell University, New York, New York 10065, USA. ; Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Congella, 4013, South Africa. ; Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA. ; Center for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service (NHLS), Johannesburg, 2131, South Africa. ; Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town and NHLS, Cape Town 7701, South Africa. ; Department of Biochemistry, Columbia University, New York, New York 10032, USA. ; 1] NISC Comparative Sequencing program, National Institutes of Health, Bethesda, Maryland 20892, USA [2] NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA. ; Department of Medical Microbiology, Academic Medical Center, Amsterdam 1105 AZ, Netherlands. ; 1] Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA [2] Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California 92037, USA [3] IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California 92037, USA [4] Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA. ; 1] Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA [2] Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA [3] Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA. ; 1] Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Congella, 4013, South Africa [2] Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town and NHLS, Cape Town 7701, South Africa. ; 1] Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Congella, 4013, South Africa [2] Department of Epidemiology, Columbia University, New York, New York 10032, USA. ; 1] Center for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service (NHLS), Johannesburg, 2131, South Africa [2] Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2050, South Africa [3] Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Congella, 4013, South Africa. ; 1] Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA [2] Department of Biochemistry, Columbia University, New York, New York 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24590074" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines/chemistry/immunology ; Amino Acid Sequence ; Antibodies, Neutralizing/chemistry/genetics/*immunology/isolation & purification ; Antibody Affinity/genetics/immunology ; Antigens, CD4/immunology/metabolism ; B-Lymphocytes/cytology/immunology/metabolism ; Binding Sites/immunology ; Cell Lineage ; Complementarity Determining Regions/chemistry/genetics/immunology ; Epitope Mapping ; Epitopes, B-Lymphocyte/chemistry/immunology ; Evolution, Molecular ; HIV Antibodies/chemistry/genetics/*immunology/isolation & purification ; HIV Envelope Protein gp160/*chemistry/*immunology ; HIV Infections/immunology ; HIV-1/chemistry/immunology ; Humans ; Models, Molecular ; Molecular Sequence Data ; Neutralization Tests ; Protein Structure, Tertiary ; Somatic Hypermutation, Immunoglobulin/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 9
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    Complete Khoisan and Bantu genomes from southern Africa (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-02-19
    Description: The genetic structure of the indigenous hunter-gatherer peoples of southern Africa, the oldest known lineage of modern human, is important for understanding human diversity. Studies based on mitochondrial and small sets of nuclear markers have shown that these hunter-gatherers, known as Khoisan, San, or Bushmen, are genetically divergent from other humans. However, until now, fully sequenced human genomes have been limited to recently diverged populations. Here we present the complete genome sequences of an indigenous hunter-gatherer from the Kalahari Desert and a Bantu from southern Africa, as well as protein-coding regions from an additional three hunter-gatherers from disparate regions of the Kalahari. We characterize the extent of whole-genome and exome diversity among the five men, reporting 1.3 million novel DNA differences genome-wide, including 13,146 novel amino acid variants. In terms of nucleotide substitutions, the Bushmen seem to be, on average, more different from each other than, for example, a European and an Asian. Observed genomic differences between the hunter-gatherers and others may help to pinpoint genetic adaptations to an agricultural lifestyle. Adding the described variants to current databases will facilitate inclusion of southern Africans in medical research efforts, particularly when family and medical histories can be correlated with genome-wide data.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890430/" 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/PMC3890430/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schuster, Stephan C -- Miller, Webb -- Ratan, Aakrosh -- Tomsho, Lynn P -- Giardine, Belinda -- Kasson, Lindsay R -- Harris, Robert S -- Petersen, Desiree C -- Zhao, Fangqing -- Qi, Ji -- Alkan, Can -- Kidd, Jeffrey M -- Sun, Yazhou -- Drautz, Daniela I -- Bouffard, Pascal -- Muzny, Donna M -- Reid, Jeffrey G -- Nazareth, Lynne V -- Wang, Qingyu -- Burhans, Richard -- Riemer, Cathy -- Wittekindt, Nicola E -- Moorjani, Priya -- Tindall, Elizabeth A -- Danko, Charles G -- Teo, Wee Siang -- Buboltz, Anne M -- Zhang, Zhenhai -- Ma, Qianyi -- Oosthuysen, Arno -- Steenkamp, Abraham W -- Oostuisen, Hermann -- Venter, Philippus -- Gajewski, John -- Zhang, Yu -- Pugh, B Franklin -- Makova, Kateryna D -- Nekrutenko, Anton -- Mardis, Elaine R -- Patterson, Nick -- Pringle, Tom H -- Chiaromonte, Francesca -- Mullikin, James C -- Eichler, Evan E -- Hardison, Ross C -- Gibbs, Richard A -- Harkins, Timothy T -- Hayes, Vanessa M -- R01 GM087472/GM/NIGMS NIH HHS/ -- R01 HG004909/HG/NHGRI NIH HHS/ -- R01GM087472/GM/NIGMS NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- Intramural NIH HHS/ -- England -- Nature. 2010 Feb 18;463(7283):943-7. doi: 10.1038/nature08795.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, 310 Wartik Lab, University Park, Pennsylvania 16802, USA. scs@bx.psu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20164927" target="_blank"〉PubMed〈/a〉
    Keywords: African Continental Ancestry Group/*genetics ; Asian Continental Ancestry Group/genetics ; Ethnic Groups/*genetics ; European Continental Ancestry Group/genetics ; Exons/genetics ; Genetics, Medical ; Genome, Human/*genetics ; Humans ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; South Africa/ethnology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-04-05
    Description: Current human immunodeficiency virus-1 (HIV-1) vaccines elicit strain-specific neutralizing antibodies. However, cross-reactive neutralizing antibodies arise in approximately 20% of HIV-1-infected individuals, and details of their generation could provide a blueprint for effective vaccination. Here we report the isolation, evolution and structure of a broadly neutralizing antibody from an African donor followed from the time of infection. The mature antibody, CH103, neutralized approximately 55% of HIV-1 isolates, and its co-crystal structure with the HIV-1 envelope protein gp120 revealed a new loop-based mechanism of CD4-binding-site recognition. Virus and antibody gene sequencing revealed concomitant virus evolution and antibody maturation. Notably, the unmutated common ancestor of the CH103 lineage avidly bound the transmitted/founder HIV-1 envelope glycoprotein, and evolution of antibody neutralization breadth was preceded by extensive viral diversification in and near the CH103 epitope. These data determine the viral and antibody evolution leading to induction of a lineage of HIV-1 broadly neutralizing antibodies, and provide insights into strategies to elicit similar antibodies by vaccination.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3637846/" 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/PMC3637846/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liao, Hua-Xin -- Lynch, Rebecca -- Zhou, Tongqing -- Gao, Feng -- Alam, S Munir -- Boyd, Scott D -- Fire, Andrew Z -- Roskin, Krishna M -- Schramm, Chaim A -- Zhang, Zhenhai -- Zhu, Jiang -- Shapiro, Lawrence -- NISC Comparative Sequencing Program -- Mullikin, James C -- Gnanakaran, S -- Hraber, Peter -- Wiehe, Kevin -- Kelsoe, Garnett -- Yang, Guang -- Xia, Shi-Mao -- Montefiori, David C -- Parks, Robert -- Lloyd, Krissey E -- Scearce, Richard M -- Soderberg, Kelly A -- Cohen, Myron -- Kamanga, Gift -- Louder, Mark K -- Tran, Lillian M -- Chen, Yue -- Cai, Fangping -- Chen, Sheri -- Moquin, Stephanie -- Du, Xiulian -- Joyce, M Gordon -- Srivatsan, Sanjay -- Zhang, Baoshan -- Zheng, Anqi -- Shaw, George M -- Hahn, Beatrice H -- Kepler, Thomas B -- Korber, Bette T M -- Kwong, Peter D -- Mascola, John R -- Haynes, Barton F -- AI067854/AI/NIAID NIH HHS/ -- AI100645/AI/NIAID NIH HHS/ -- P30 AI050410/AI/NIAID NIH HHS/ -- UM1 AI100645/AI/NIAID NIH HHS/ -- Intramural NIH HHS/ -- England -- Nature. 2013 Apr 25;496(7446):469-76. doi: 10.1038/nature12053. Epub 2013 Apr 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Duke University Human Vaccine Institute, Departments of Medicine and Immunology, Duke University School of Medicine, Durham, North Carolina 27710, USA. hliao@duke.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23552890" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines/immunology ; Africa ; Amino Acid Sequence ; Antibodies, Monoclonal/chemistry/genetics/immunology ; Antibodies, Neutralizing/*chemistry/genetics/*immunology ; Antigens, CD4/chemistry/immunology ; Cell Lineage ; Cells, Cultured ; Clone Cells/cytology ; Cross Reactions/immunology ; Crystallography, X-Ray ; Epitopes/chemistry/immunology ; *Evolution, Molecular ; HIV Antibodies/*chemistry/genetics/*immunology ; HIV Envelope Protein gp120/chemistry/genetics/immunology/metabolism ; HIV-1/*chemistry/classification/*immunology ; Humans ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Neutralization Tests ; Phylogeny ; Protein Structure, Tertiary
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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