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824 results on '"Miller,Webb"'

101. Giraffe genome sequence reveals clues to its unique morphology and physiology

Author

Agaba, Morris, primary, Ishengoma, Edson, additional, Miller, Webb C., additional, McGrath, Barbara C., additional, Hudson, Chelsea N., additional, Bedoya Reina, Oscar C., additional, Ratan, Aakrosh, additional, Burhans, Rico, additional, Chikhi, Rayan, additional, Medvedev, Paul, additional, Praul, Craig A., additional, Wu-Cavener, Lan, additional, Wood, Brendan, additional, Robertson, Heather, additional, Penfold, Linda, additional, and Cavener, Douglas R., additional

Published
2016
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103. Experimental validation of predicted mammalian erythroid cis-regulatory modules

Author

Hao Wang; Ying Zhang; Yong Cheng and Gibb, Brian; Dorman, Christine; Miller, Webb

Subjects
Mammals -- Genetic aspects, Mammals -- Physiological aspects, Genetic transcription -- Research, Genetic research, Health
Abstract

The cis-regulatory modules (CRMs) are predicted for mammalian genes expressed in red blood cells by combining two properties obtained from aligned, noncoding genome sequences, such as a positive regulatory potential (RP) score and conservation of a binding site motif for the essential erythroid transcription factor GATA-1. The results have shown that high RP in combination with another feature of a CRM, such as a conserved transcription factor-binding site, is a good predictor of functional CRMs.

Published
2006

104. ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements

Author

Chiaromonte, Francesca, Miller, Webb, and King, David C.; Hardison, Ross C.

Subjects
Nucleotide sequence -- Research, Genetic code -- Research, Genetic research, Health
Abstract

A computational method ESPERR (evolutionary and sequence pattern extraction through reduced representations) is developed, which uses training examples to learn encoding of multispecies alignments into reduced forms tailored for the prediction of chosen classes of functional elements. The results have shown that ESPERR could greatly improve the effectiveness of the strategy used to select regions to be tested for developmental enhancer activity.

Published
2006

105. Reconstructing contiguous regions of an ancestral genome

Author

Burhans, Richard C., Ma, Jian, Haussler, David, Blanchette, Mathieu, Kent, W. James, Zhang, Louxin, and Miller, Webb

Subjects
Genetic research -- Forecasts and trends, Nucleotide sequence -- Chemical properties, Eutherians -- Genetic aspects, Market trend/market analysis, Health
Abstract

Mammalian genome rearrangements are analyzed at higher resolution and a new method is described for predicting ancestral order and orientation of those intervals from their observed adjacencies in modern species. These methods are developed as part of a project to reconstruct the genome sequence of the last ancestor of human, dogs and most other placental mammals.

Published
2006

106. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genome

Author

Siepel, Adam, Bejerano, Gill, Pedersen, Jakob S., Hinrichs, Angie S., Hou, Minmei, Rosenbloom, Kate, Clawson, Hiram, Spieth, John, Hiller, LaDeana W., Richards, Stephen, Weinstock, George M., Wilson, Richard K., Gibbs, Richard A., Kent, W.James, Miller, Webb, and Haussler, David

Subjects
Vertebrates -- Genetic aspects, Genomes -- Research, Nucleotide sequence -- Research, Health
Abstract

A comprehensive search for conserved elements in vertebrate genomes using genome-wide multiple alignments of five vertebrate species and four insect species is done. It is found that in all species groups, the most highly conserved elements (HCEs) are hundreds or thousands of bases long and show extreme levels of conservation.

Published
2005

107. Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences

Author

King, David C., Taylor, James, Elnitski, Laura, Chiaromonte, Francesca, Miller, Webb, and Hardison, Ross C.

Subjects
Nucleotide sequence -- Research, Mammals -- Genetic aspects, Genomes -- Research, Health
Abstract

Different analytical methods score distinctive features of whole-genome alignments among human, mouse, and rat to predict functional regions. Three of the methods used for their ability to identify the positions of known regulatory regions in the well-studied 'HBB' gene complex are evaluated.

Published
2005

108. Supporting California condor conservation management through analysis of species-wide whole genome sequence variation

Author

Ryder, Oliver, Chemnick, Leona G., Thomas, Steven, Martin, Jessica, Romanov, Michael N, Ralls, Katherine, Ballou, Jonathan D., Mace, Michael, Ratan, Aakrosh, Miller, Webb, and Schuster, Stephan

Subjects
QL, QH75, QH426
Abstract

The critically endangered California condor (Gymnogyps californianus) has been the focus of intensive conservation efforts for several decades. Reduced to a population size of twenty-three birds in 1985, the entire surviving population was brought under captive management for recovery. Founded by fourteen individuals, the surviving California condor gene pool has been managed through captive breeding of individuals paired through pedigree analysis. As of August, 2013, there were 424 California condor individuals; 223 are flying in the wild in four re-introduced populations in California, Arizona and Baja California, Mexico. All condors have their sex identified via amplification of sex chromosome specific markers and DNA samples are stored for every individual of the species. Microsatellite genotyping has confirmed parentage in captive and wild condor chicks, corrected switched identities, and identified successful extra-pair copulation in the wild population. Whole genome sequencing using data generated on multiple platforms has been used to produce a de novo genome assembly for a founder male condor and thirty additional condors that together encompass the entire genetic variation of the species, perhaps the first time such a comprehensive effort has been conducted for any species. Studbook-based kinship relationships between founder birds and kinship estimates from genome-wide genetic variation can be compared and evaluated in the context of retention of genetic diversity in the generations of California condors. Genomic studies of California condors are providing a model system for avian conservation genomics and allow empirical evaluation of basic facets of transmission genetics, including segregation, linkage, recombination and mutation.

Published
2014

109. Aligning multiple genomic sequences with the threaded blockset aligner

Author

Blanchette, Mathieu, Riemer, Cathy, Kent, W. James, Elnitski, Laura;, Roskin, Krishna M., Smit, Arian F.A., Baertsch, Robert, Rosenbloom, Kate, Clawson, Hiram, Green, Eric D., Haussler, David, and Miller, Webb

Subjects
Genomics -- Analysis, Nucleotide sequence -- Analysis, Mammals -- Genetic aspects, Mammals -- Analysis, Health
Abstract

Threaded blockset, a novel generalization of the classic notion of a multiple alignment, is defined. A new computer program called threaded blockset aligner(TBA) builds a threaded blockset and is designed to be appropriate for aligning many megabase-sized regions of multiple mammalian genomes.

Published
2004

110. Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat

Author

Kolbe, Diana;, Taylor, James, Elnitski, Laura, Eswara, Pallavi, Li, Jia, Miller, Webb, and Chiaromonte, Francesca

Subjects
Genomics -- Analysis, Mice -- Genetic aspects, Mice -- Analysis, Human genetics -- Analysis, Chromosome mapping -- Analysis, Health
Abstract

A computational method for identifying regulatory regions within three-way DNA alignments of human, mouse, and rat is developed. The resulting Regulatory Potential(RP) score is generalized.

Published
2004

111. zPicture: dynamic alignment and visualization tool for analyzing conservation profiles

Author

Ovcharenko, Ivan, Loots, Gabriela G., Hardison, Ross C, Miller, Webb, and Stubbs, Lisa

Subjects
Phylogeny -- Research, Nucleotide sequence -- Research, Genetic research, Health
Abstract

zPicture, an interactive Web-based sequence alignment and visualization tool for dynamically generating conservation profiles and identifying evolutionary conserved regions (ECRs) is introduced. zPicture is highly flexible, because critical parameters can be modified interactively, allowing users to differentially predict ECRs in comparisons of sequences of different phylogenetic distances and evolutionary rates.

Published
2004

115. Gene length and proximity to neighbors affect genome-wide expression levels

Author

Chiaromonte, Francesca, Miller, Webb, and Bouhassira, Eric E.

Subjects
Chromatin -- Genetic aspects, Gene expression -- Physiological aspects, Genetic research -- Analysis, Genetic transcription -- Physiological aspects, Genomes -- Physiological aspects, Genomes -- Research, Messenger RNA -- Genetic aspects, Health
Abstract

Research has been conducted on gene length and proximity to neighbors. The results have demonstrated that on genome-wide scale highly expressed genes are smaller and produce shorter mRNA.

Published
2003

116. GALA, a database for genomic sequence alignments and annotations

Author

Giardine, Belinda, Elnitski, Laura, Riemer, Cathy, Makalowska, Izabela, Schwartz, Scott, Miller, Webb, and Hardison, Ross C.

Subjects
Genetic research -- Analysis, Genetic research -- Methods, Genomes -- Research, Gene expression -- Physiological aspects, DNA -- Genetic aspects, Methodology -- Analysis, Health
Abstract

The authors discuss the development of a relational database, GALA. They report that this database contains whole genome sequence alignments between human and mouse, and that it is useful in searching across data tracks supplied by databases, alignment resources and current browsers.

Published
2003

117. Human-mouse alignments with BLASTZ

Author

Schwartz, Scott, Kent, W. James, Smit, Arian, Zhang, Zheng, Baertsch, Robert, Hardison, Ross C., Haussler, David, and Miller, Webb

Subjects
Genomes -- Research, Genetic research -- Analysis, Methodology -- Analysis, Gene mutations -- Physiological aspects, Genetic algorithms -- Analysis, Genetic algorithms -- Usage, Health
Abstract

Research has been conducted on genome evolution. The use of program BLASTZ, an algorithm designed for aligning long genomic sequences, the modifications of the program and the hardware environment on which it runs are described.

Published
2003

118. Distinguishing regulatory DNA from neutral sites

Author

Elnitski, Laura, Hardison, Ross C., Li, Jia, Yang, Shan, Kolbe, Diana, Eswara, Pallavi, O'Connor, Michael J., Schwartz, Scott, Miller, Webb, and Chiaromonte, Francesca

Subjects
Genetic research -- Analysis, Genomes -- Research, Genetic regulation -- Analysis, DNA -- Genetic aspects, Nucleotides -- Genetic aspects, Health
Abstract

Research has been conducted on genome discrimination. Results demonstrate that discrimination based on individual nucleotide pair frequencies are partially successful.

Published
2003

119. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution

Author

Hardison, Ross C., Roskin, Krishna M., Yang, Shan, Diekhans, Mark, Kent, W. James, Weber, Ryan, Elnitski, Laura, Li, Jia, O'Connor, Michael, Kolbe, Diana, Schwartz, Scott, Furey, Terrence S., Whelan, Simon, Goldman, Nick, Smit, Arian, Miller, Webb, Chiaromonte, Francesca, and Haussler, David

Subjects
Genomes -- Research, Genetic research -- Analysis, DNA -- Genetic aspects, Gene mutations -- Physiological aspects, Health
Abstract

Research has been conducted on human genome evolution. Results demonstrate that some regions of genome are changed slowly by the same processes that alter DNA, and some are changed faster.

Published
2003

125. Generation and comparative analysis of ~3.3 Mb of mouse genomic sequence orthologous to the region of human chromosome 7qll.23 implicated in Williams syndrome

Author

DeSilva, Udaya, Elnitski, Laura, Idol, Jacquelyn R., Doyle, Johannah L., Gan, Weiniu; ., Green, Eric D., Miller, Webb, Touchman, Jeffrey W., Thomas, Pamela J., Bouffard, Gerard G., Blakesley, Robert W., McDowell, Jennifer C., Beckstrom-Sternberg, Stephen M., Dietriich, Nicole L, Schwartz, Scott;, and Thomas, James W.

Subjects
Developmental disabilities -- Research, Child development deviations -- Research, Human chromosomes -- Research, Williams syndrome -- Research, Genetic research, Health
Abstract

Williams syndrome is a complex developmental disorder that results from the heterozygous deletion of a ~1.6-Mb segment of human chromosome 7qll.23. The results from a study in this context provided an important comparative sequence resource to develop mouse models of the disorder.

Published
2002

127. The Genome 10K Project:a way forward

Author

Koepfli, Klaus-Peter, Paten, Benedict, O'Brien, Stephen J., Antunes, Agostinho, Belov, Kathy, Bustamante, Carlos, Castoe, Todd A., Clawson, Hiram, Crawford, Andrew J., Diekhans, Mark, Distel, Dan, Durbin, Richard, Earl, Dent, Fujita, Matthew K., Gamble, Tony, Georges, Arthur, Gemmell, Neil, Gilbert, M Thomas P, Graves, Jennifer Marshall, Green, Richard E, Hickey, Glenn, Jarvis, Erich D., Johnson, Warren, Komissarov, Aleksey, Korf, Ian, Kuhn, Robert, Larkin, Denis M., Lewin, Harris, Lopez, Jose V., Ma, Jian, Marques-Bonet, Tomas, Miller, Webb, Murphy, Robert, Pevzner, Pavel, Shapiro, Beth, Steiner, Cynthia, Tamazian, Gaik, Venkatesh, Byrappa, Wang, Jun, Wayne, Robert, Wiley, Edward, Yang, Huanming, Zhang, Guojie, Haussler, David, Ryder, Oliver, Koepfli, Klaus-Peter, Paten, Benedict, O'Brien, Stephen J., Antunes, Agostinho, Belov, Kathy, Bustamante, Carlos, Castoe, Todd A., Clawson, Hiram, Crawford, Andrew J., Diekhans, Mark, Distel, Dan, Durbin, Richard, Earl, Dent, Fujita, Matthew K., Gamble, Tony, Georges, Arthur, Gemmell, Neil, Gilbert, M Thomas P, Graves, Jennifer Marshall, Green, Richard E, Hickey, Glenn, Jarvis, Erich D., Johnson, Warren, Komissarov, Aleksey, Korf, Ian, Kuhn, Robert, Larkin, Denis M., Lewin, Harris, Lopez, Jose V., Ma, Jian, Marques-Bonet, Tomas, Miller, Webb, Murphy, Robert, Pevzner, Pavel, Shapiro, Beth, Steiner, Cynthia, Tamazian, Gaik, Venkatesh, Byrappa, Wang, Jun, Wayne, Robert, Wiley, Edward, Yang, Huanming, Zhang, Guojie, Haussler, David, and Ryder, Oliver

Published
2015

128. Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools

Author

Fuller, Zachary L., primary, Niño, Elina L., additional, Patch, Harland M., additional, Bedoya-Reina, Oscar C., additional, Baumgarten, Tracey, additional, Muli, Elliud, additional, Mumoki, Fiona, additional, Ratan, Aakrosh, additional, McGraw, John, additional, Frazier, Maryann, additional, Masiga, Daniel, additional, Schuster, Stephen, additional, Grozinger, Christina M., additional, and Miller, Webb, additional

Published
2015
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131. Weighing the mass spectrometric evidence for authentic Tyrannosaurus rex collagen

Author

Buckley, Mike, Walker, Angela, Ho, Simon Y. W., Yang, Yue, Smith, Colin, Ashton, Peter, Oates, Jane Thomas, Cappellini, Enrico, Koon, Hannah, Penkman, Kirsty, Elsworth, Ben, Ashford, Dave, Solazzo, Caroline, Andrews, Phil, Strahler, John, Shapiro, Beth, Ostrom, Peggy, Gandhi, Hasand, Miller, Webb, Raney, Brian, Zylber, Maria Ines, Gilbert, M. Thomas P., Prigodich, Richard V., Ryan, Michael, Rijsdijk, Kenneth F., Janoo, Anwar, and Collins, Matthew J.

Subjects
viruses, biochemical phenomena, metabolism, and nutrition, Article
Abstract

We use authentication tests developed for ancient DNA to evaluate claims by Asara et al. of collagen peptide sequences recovered from mastodon and Tyrannosaurus rex fossils. Although the mastodon passes, absence of amino acid composition data, lack of evidence for peptide deamidation, and association of the α1(I) peptide sequences with amphibians not birds, suggests that T. rex does not.

Published
2008

132. HbVar Database of Human Hemoglobin Variants and Thalassemia Mutations: 2007 Update

Author

Giardine, Belinda van Baal, Sjozef Kaimakis, Polynikis and Riemer, Cathy Miller, Webb Samara, Maria Kollia, Panagoula and Anagnou, Nicholas P. Chui, David H. K. Wajcman, Henri and Hardison, Ross C. Patrinos, George P.

Abstract

HbVar (http://globin.bx.psu.edu/hbvar) is a locus-specific database (LSDB) developed in 2001 by a multi-center academic effort to provide timely information on the genomic sequence changes leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Database records include extensive phenotypic descriptions, biochemical and hematological effects, associated pathology, and ethnic occurrence, accompanied by mutation frequencies and references. In addition to the regular updates to entries, we report significant advances and updates, which can be useful not only for HbVar users but also for other LSDB development and curation in general. The query page provides more functionality but in a simpler, more user-friendly format and known single nucleotide polymorphisms in the human alpha- and beta-globin loci are provided automatically. Populationspecific beta-thalassemia mutation frequencies for 31 population groups have been added and/or modified and the previously reported delta- and alpha-thalassemia mutation frequency data from 10 population groups have also been incorporated. In addition, an independent flat-file database, named XPRbase (http://www.goldenhelix.org/xprbase), has been developed and linked to the main HbVar web page to provide a succinct listing of 51 experimental protocols available for globin gene mutation screening. These updates significantly augment the database profile and quality of information provided, which should increase the already high impact of the HbVar database, while its combination with the UCSC powerful genome browser and the ITHANET web portal paves the way for drawing connections of clinical importance, that is from genome to function to phenotype. (C) 2007 Wiley-Liss, Inc.

Published
2007

138. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

Author

Hillier, LaDeana W, Miller, Webb, Birney, Ewan, Warren, Wesley, Hardison, Ross C, Ponting, Chris P, Bork, Peer, Burt, Peer, Groenen, Martien A M, Delany, Mary E, Dodgson, Jerry B, Chinwalla, Asif, Cliften, Paul F, Clifton, Sandra W, Delehaunty, Kimberly D, Fronick, Catrina, Fulton, Robert S, Graves, Tina A, Kremitzki, Colin, Layman, Dan, Magrini, Vincent, McPherson, John D, Miner, Tracie L, Minx, Patrick, Nash, William E, Nhan, Michael N, Nelson, Joanne O, Oddy, Lachlan G, Pohl, Craig S, Randall-Maher, Jennifer, Smith, Scott M, Wallis, John W, Yang, Shiaw-Pyng, Romanov, Michael N, Rondelli, Catherine M, Paton, Bob, Smith, Jacqueline, Morrice, David, Daniels, Laura, Tempest, Helen G, Robertson, Lindsay, Masabanda, Julio S, Griffin, Darren K., Vignal, Alain, Fillon, Valerie, Jacobbson, Lina, Kerje, Susanne, Andersson, Leif, Crooijmans, Richard P M A, Aerts, Jan, van der Poel, Jan J, Ellegren, Hans, Caldwell, Randolph B, Hubbard, Simon J, Grafham, Darren V, Kierzek, Andrzej M, McLaren, Stuart R, Overton, Ian M, Arakawa, Hiroshi, Beattie, Kevin J, Bezzubov, Yuri, Boardman, Paul E, Bonfield, James K, Croning, Michael D R, Davies, Robert M, Francis, Matthew D, Humphray, Sean J, Scott, Carol E, Taylor, Ruth G, Tickle, Cheryll, Brown, William R A, Rogers, Jane, Buerstedde, Jean-Marie, Wilson, Stuart A, Stubbs, Lisa, Ovcharenko, Ivan, Gordon, Laurie, Lucas, Susan, Miller, Marcia M, Inoko, Hidetoshi, Shiina, Takashi, Kaufman, Jim, Salomonsen, Jan, Skjoedt, Karsten, Wong, Gane Ka-Shu, Wang, Jun, Liu, Bin, Wang, Jian, Yu, Jun, Yang, Huanming, Nefedov, Mikhail, Koriabine, Maxim, de Jong, Pieter J, Goodstadt, Leo, Webber, Caleb, Dickens, Nicholas J, Letunic, Ivica, Suyama, Mikita, Torrents, David, von Mering, Christian, Zdobnov, Evgeny M, Makova, Kateryna, Nekrutenko, Anton, Elnitski, Laura, Eswara, Pallavi, King, David C, Yang, Shan, Tyekucheva, Svitlana, Radakrishnan, Anusha, Harris, Robert S, Chiaromonte, Francesca, Taylor, James, He, Jianbin, Rijnkels, Monique, Griffiths-Jones, Sam, Ureta-Vidal, Abe, Hoffman, Michael M, Severin, Jessica, Searle, Stephen M J, Law, Andy S, Speed, David, Waddington, David, Cheng, Ze, Tuzun, Eray, Eichler, Evan, Bao, Zhirong, Flicek, Paul, Shteynberg, David D, Brent, Michael R, Bye, Jacqueline M, Huckle, Elizabeth J, Chatterjee, Sourav, Dewey, Colin, Pachter, Lior, Kouranov, Andrei, Mourelatos, Zissimos, Hatzigeorgiou, Artemis G, Paterson, Andrew H, Ivarie, Robert, Brandstrom, Mikael, Axelsson, Erik, Backström, Niclas, Berlin, Sofia, Webster, Matthew T, Pourquie, Olivier, Reymond, Alexandre, Ucla, Catherine, Antonarakis, Stylianos E, Long, Manyuan, Emerson, J J, Betran, Esther, Dupanloup, Isabelle, Kaessmann, Henrik, Hinrichs, Angie S, Bejerano, Gill, Furey, Terrence S, Harte, Rachel A, Raney, Brian, Siepel, Adam, Kent, W James, Haussler, David, Eyras, Eduardo, Castelo, Robert, Abril, Josep F, Castellano, Sergi, Camara, Francisco, Parra, Genis, Guigo, Roderic, Bourque, Guillaume, Tesler, Glenn, Pevzner, Pavel A., Smit, Arian F. A., Fulton, Lucinda A., Mardis, Elaine R., Wilson, Richard K., International Chicken Genome Sequencing Consortium, ProdInra, Migration, Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and Zdobnov, Evgeny

Subjects
RNA, Untranslated, olfactory receptor, [SDV]Life Sciences [q-bio], mouse genome, QH75, Genome, 0302 clinical medicine, Gene Duplication, Coding region, ddc:576.5, Conserved Sequence, ComputingMilieux_MISCELLANEOUS, Short Interspersed Nucleotide Elements, Genetics, 0303 health sciences, Multidisciplinary, CHICKENS, recent segmental duplications, Untranslated, GENOME SEQUENCE, International Chicken Genome Sequencing Consortium, Genomics, Physical Chromosome Mapping, major histocompatibility complex, mammalian evolution, [SDV] Life Sciences [q-bio], Multigene Family, Vertebrates, SEQUENCE DU GENOME, Sequence Analysis, Pseudogenes, Biotechnology, brown-norway rat, animal structures, Evolution, General Science & Technology, Sequence analysis, Biology, Animal Breeding and Genomics, Synteny, Evolution, Molecular, Avian Proteins, 03 medical and health sciences, non-ltr retrotransposons, Animals, Humans, alcohol-dehydrogenase, Fokkerij en Genomica, SF, QP506, Gene, QH426, 030304 developmental biology, Whole genome sequencing, QL, phylogenetic analysis, QH, Human Genome, Molecular, Sequence Analysis, DNA, DNA, tissue-specific genes, EVOLUTION, Retroviridae, Long Interspersed Nucleotide Elements, Genes, Mutagenesis, Evolutionary biology, DNA Transposable Elements, Microchromosome, WIAS, RNA, Chickens, 030217 neurology & neurosurgery
Abstract

We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.

Published
2004

144. Row replacement algorithms for screen editors

Author

Myers, Eugene W. and Miller, Webb

Subjects
Technology, Algorithm Analysis, Software Complexity, Nonnumerical Algorithms, Discrete Mathematics, Dynamic Programming, Screen Editors, Efficiency
Published
1989

145. Dynamics of the Epigenetic Landscape During Erythroid Differentiation after Gata1 Restoration

Author

Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Kellis, Manolis, Ernst, Jason, Wu, Weisheng, Cheng, Yong, Keller, Cheryl A., Kumar, Swathi Ashok, Mishra, Tejaswini, Morrissey, Christapher, Dorman, Christine M., Chen, Kuan-Bei, Drautz, Daniela, Giardine, Belinda, Shibata, Yoichiro, Song, Lingyun, Pimkin, Max, Crawford, Gregory E., Furey, Terrence S., Miller, Webb, Taylor, James, Schuster, Stephan C., Zhang, Yu, Chiaromonte, Francesca, Blobel, Gerd A., Weiss, Mitchell J., Hardison, Ross C., Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Kellis, Manolis, Ernst, Jason, Wu, Weisheng, Cheng, Yong, Keller, Cheryl A., Kumar, Swathi Ashok, Mishra, Tejaswini, Morrissey, Christapher, Dorman, Christine M., Chen, Kuan-Bei, Drautz, Daniela, Giardine, Belinda, Shibata, Yoichiro, Song, Lingyun, Pimkin, Max, Crawford, Gregory E., Furey, Terrence S., Miller, Webb, Taylor, James, Schuster, Stephan C., Zhang, Yu, Chiaromonte, Francesca, Blobel, Gerd A., Weiss, Mitchell J., and Hardison, Ross C.

Abstract

Interplays among lineage-specific nuclear proteins, chromatin modifying enzymes, and the basal transcription machinery govern cellular differentiation, but their dynamics of action and coordination with transcriptional control are not fully understood. Alterations in chromatin structure appear to establish a permissive state for gene activation at some loci, but they play an integral role in activation at other loci. To determine the predominant roles of chromatin states and factor occupancy in directing gene regulation during differentiation, we mapped chromatin accessibility, histone modifications, and nuclear factor occupancy genome-wide during mouse erythroid differentiation dependent on the master regulatory transcription factor GATA1. Notably, despite extensive changes in gene expression, the chromatin state profiles (proportions of a gene in a chromatin state dominated by activating or repressive histone modifications) and accessibility remain largely unchanged during GATA1-induced erythroid differentiation. In contrast, gene induction and repression are strongly associated with changes in patterns of transcription factor occupancy. Our results indicate that during erythroid differentiation, the broad features of chromatin states are established at the stage of lineage commitment, largely independently of GATA1. These determine permissiveness for expression, with subsequent induction or repression mediated by distinctive combinations of transcription factors, National Institutes of Health (U.S.) (Grant number RC1HG005334), National Science Foundation (U.S.). (Award 0905968)

Published
2012

146. Systematic documentation and analysis of human genetic variation in hemoglobinopathies using the microattribution approach

Author

Giardine, Belinda, Borg, Joseph, Higgs, Douglas R., Peterson, Kenneth R., Philipsen, Sjaak, Maglott, Donna, Singleton, Belinda K., Anstee, David J., Basak, A. Nazli, Clark, Barnaby, Costa, Flavia C., Faustino, Paula, Fedosyuk, Halyna, Felice, Alex E., Francina, Alain, Galanello, Renzo, Gallivan, Monica V. E., Georgitsi, Marianthi, Gibbons, Richard J., Giordano, Piero C., Harteveld, Cornelis L., Hoyer, James D., Jarvis, Martin, Joly, Philippe, Kanavakis, Emmanuel, Kollia, Panagoula, Menzel, Stephan, Miller, Webb, Moradkhani, Kamran, Old, John, Papachatzopoulou, Adamantia, Papadakis, Manoussos N., Papadopoulos, Petros, Pavlović, Sonja, Perseu, Lucia, Radmilović Milena, Riemer, Cathy, Satta, Stefania, Schrijver, Iris, Stojiljković, Maja, Thein, Swee Lay, Traeger-Synodinos, Jan, Tully, Ray, Wada, Takahito, Waye, John S., Wiemann, Claudia, Zukić, Branka, Chui, David H. K., Wajcman, Henri, Hardison, Ross C., Patrinos, George P., Giardine, Belinda, Borg, Joseph, Higgs, Douglas R., Peterson, Kenneth R., Philipsen, Sjaak, Maglott, Donna, Singleton, Belinda K., Anstee, David J., Basak, A. Nazli, Clark, Barnaby, Costa, Flavia C., Faustino, Paula, Fedosyuk, Halyna, Felice, Alex E., Francina, Alain, Galanello, Renzo, Gallivan, Monica V. E., Georgitsi, Marianthi, Gibbons, Richard J., Giordano, Piero C., Harteveld, Cornelis L., Hoyer, James D., Jarvis, Martin, Joly, Philippe, Kanavakis, Emmanuel, Kollia, Panagoula, Menzel, Stephan, Miller, Webb, Moradkhani, Kamran, Old, John, Papachatzopoulou, Adamantia, Papadakis, Manoussos N., Papadopoulos, Petros, Pavlović, Sonja, Perseu, Lucia, Radmilović Milena, Riemer, Cathy, Satta, Stefania, Schrijver, Iris, Stojiljković, Maja, Thein, Swee Lay, Traeger-Synodinos, Jan, Tully, Ray, Wada, Takahito, Waye, John S., Wiemann, Claudia, Zukić, Branka, Chui, David H. K., Wajcman, Henri, Hardison, Ross C., and Patrinos, George P.

Abstract

We developed a series of interrelated locus-specific databases to store all published and unpublished genetic variation related to hemoglobinopathies and thalassemia and implemented microattribution to encourage submission of unpublished observations of genetic variation to these public repositories. A total of 1,941 unique genetic variants in 37 genes, encoding globins and other erythroid proteins, are currently documented in these databases, with reciprocal attribution of microcitations to data contributors. Our project provides the first example of implementing microattribution to incentivise submission of all known genetic variation in a defined system. It has demonstrably increased the reporting of human variants, leading to a comprehensive online resource for systematically describing human genetic variation in the globin genes and other genes contributing to hemoglobinopathies and thalassemias. The principles established here will serve as a model for other systems and for the analysis of other common and/or complex human genetic diseases.

Published
2011

147. Prepublication data sharing

Author

Birney, Ewan, Hudson, Thomas J., Green, Eric D., Gunter, Chris, Eddy, Sean, Rogers, Jane, Harris, Jennifer R., Ehrlich, S. Dusko, Apweiler, Rolf, Austin, Christopher P., Berglund, Lisa, Bobrow, Martin, Bountra, Chas, Brookes, Anthony J., Cambon-Thomsen, Anne, Carter, Nigel P., Chisholm, Rex L., Contreras, Jorge L., Cooke, Robert M., Crosby, William L., Dewar, Ken, Durbin, Richard, Dyke, Stephanie O. M., Ecker, Joseph R., El Emam, Khaled, Feuk, Lars, Gabriel, Stacey B., Gallacher, John, Gelbart, William M., Granell, Antoni, Guarner, Francisco, Hubbard, Tim, Jackson, Scott A., Jennings, Jennifer L., Joly, Yann, Jones, Steven M., Kaye, Jane, Kennedy, Karen L., Knoppers, Bartha Maria, Kyrpides, Nikos C., Lowrance, William W., Luo, Jingchu, MacKay, John J., Martín-Rivera, Luis, McCombie, W. Richard, McPherson, John D., Miller, Linda, Miller, Webb, Moerman, Don, Mooser, Vincent, Morton, Cynthia C., Ostell, James M., Ouellette, B. F. Francis, Parkhill, Julian, Raina, Parminder S., Rawlings, Christopher, Scherer, Steven E., Scherer, Stephen W., Schofield, Paul N., Sensen, Christoph W., Stodden, Victoria C., Sussman, Michael R., Tanaka, Toshihiro, Thornton, Janet, Tsunoda, Tatsuhiko, Valle, David, Vuorio, Eero I., Walker, Neil M., Wallace, Susan, Weinstock, George, Whitman, William B., Worley, Kim C., Wu, Cathy, Wu, Jiayan, Yu, Jun, Birney, Ewan, Hudson, Thomas J., Green, Eric D., Gunter, Chris, Eddy, Sean, Rogers, Jane, Harris, Jennifer R., Ehrlich, S. Dusko, Apweiler, Rolf, Austin, Christopher P., Berglund, Lisa, Bobrow, Martin, Bountra, Chas, Brookes, Anthony J., Cambon-Thomsen, Anne, Carter, Nigel P., Chisholm, Rex L., Contreras, Jorge L., Cooke, Robert M., Crosby, William L., Dewar, Ken, Durbin, Richard, Dyke, Stephanie O. M., Ecker, Joseph R., El Emam, Khaled, Feuk, Lars, Gabriel, Stacey B., Gallacher, John, Gelbart, William M., Granell, Antoni, Guarner, Francisco, Hubbard, Tim, Jackson, Scott A., Jennings, Jennifer L., Joly, Yann, Jones, Steven M., Kaye, Jane, Kennedy, Karen L., Knoppers, Bartha Maria, Kyrpides, Nikos C., Lowrance, William W., Luo, Jingchu, MacKay, John J., Martín-Rivera, Luis, McCombie, W. Richard, McPherson, John D., Miller, Linda, Miller, Webb, Moerman, Don, Mooser, Vincent, Morton, Cynthia C., Ostell, James M., Ouellette, B. F. Francis, Parkhill, Julian, Raina, Parminder S., Rawlings, Christopher, Scherer, Steven E., Scherer, Stephen W., Schofield, Paul N., Sensen, Christoph W., Stodden, Victoria C., Sussman, Michael R., Tanaka, Toshihiro, Thornton, Janet, Tsunoda, Tatsuhiko, Valle, David, Vuorio, Eero I., Walker, Neil M., Wallace, Susan, Weinstock, George, Whitman, William B., Worley, Kim C., Wu, Cathy, Wu, Jiayan, and Yu, Jun

Abstract

Rapid release of prepublication data has served the field of genomics well. Attendees at a workshop in Toronto recommend extending the practice to other biological data sets.

Published
2009
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148. The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)

Author

Miller, Webb, Drautz, Daniela I., Janecka, Jan E., Lesk, Arthur M., Ratan, Aakrosh, Tomsho, Lynn P., Packard, Mike, Zhang, Yeting, McClellan, Lindsay R., Qi, Ji, Zhao, Fangqing, Gilbert, M. Thomas P., Dalen, Love, Arsuaga, Juan Luis, Ericson, Per G. P., Huson, Daniel H., Helgen, Kristofer M., Murphy, William J., Götherström, Anders, Schuster, Stephan C., Miller, Webb, Drautz, Daniela I., Janecka, Jan E., Lesk, Arthur M., Ratan, Aakrosh, Tomsho, Lynn P., Packard, Mike, Zhang, Yeting, McClellan, Lindsay R., Qi, Ji, Zhao, Fangqing, Gilbert, M. Thomas P., Dalen, Love, Arsuaga, Juan Luis, Ericson, Per G. P., Huson, Daniel H., Helgen, Kristofer M., Murphy, William J., Götherström, Anders, and Schuster, Stephan C.

Abstract

We report the first two complete mitochondrial genome sequences of the thylacine (Thylacinus cynocephalus), or so-called Tasmanian tiger, extinct since 1936. The thylacine's phylogenetic position within australidelphian marsupials has long been debated, and here we provide strong support for the thylacine's basal position in Dasyuromorphia, aided by mitochondrial genome sequence that we generated from the extant numbat (Myrmecobius fasciatus). Surprisingly, both of our thylacine sequences differ by 11%-15% from putative thylacine mitochondrial genes in GenBank, with one of our samples originating from a direct offspring of the previously sequenced individual. Our data sample each mitochondrial nucleotide an average of 50 times, thereby providing the first high-fidelity reference sequence for thylacine population genetics. Our two sequences differ in only five nucleotides out of 15,452, hinting at a very low genetic diversity shortly before extinction. Despite the samples' heavy contamination with bacterial and human DNA and their temperate storage history, we estimate that as much as one-third of the total DNA in each sample is from the thylacine. The microbial content of the two thylacine samples was subjected to metagenomic analysis, and showed striking differences between a wild-captured individual and a born-in-captivity one. This study therefore adds to the growing evidence that extensive sequencing of museum collections is both feasible and desirable, and can yield complete genomes.

Published
2009
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149. Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution

Author

Willerslev, Eske, Gilbert, M Thomas, Binladen, Jonas, Ho, Simon, Campos, Paula F, Ratan, Aakrosh, Tomsho, Lynn P, da Fonseca, Rute R, Sher, Andrei, Kuznetsova, Tatanya V, Nowak-Kemp, Malgosia, Roth, Terri L, Miller, Webb, Schuster, Stephan C, Willerslev, Eske, Gilbert, M Thomas, Binladen, Jonas, Ho, Simon, Campos, Paula F, Ratan, Aakrosh, Tomsho, Lynn P, da Fonseca, Rute R, Sher, Andrei, Kuznetsova, Tatanya V, Nowak-Kemp, Malgosia, Roth, Terri L, Miller, Webb, and Schuster, Stephan C

Abstract

BACKGROUND: The scientific literature contains many examples where DNA sequence analyses have been used to provide definitive answers to phylogenetic problems that traditional (non-DNA based) approaches alone have failed to resolve. One notable example concerns the rhinoceroses, a group for which several contradictory phylogenies were proposed on the basis of morphology, then apparently resolved using mitochondrial DNA fragments. RESULTS: In this study we report the first complete mitochondrial genome sequences of the extinct ice-age woolly rhinoceros (Coelodonta antiquitatis), and the threatened Javan (Rhinoceros sondaicus), Sumatran (Dicerorhinus sumatrensis), and black (Diceros bicornis) rhinoceroses. In combination with the previously published mitochondrial genomes of the white (Ceratotherium simum) and Indian (Rhinoceros unicornis) rhinoceroses, this data set putatively enables reconstruction of the rhinoceros phylogeny. While the six species cluster into three strongly supported sister-pairings: (i) The black/white, (ii) the woolly/Sumatran, and (iii) the Javan/Indian, resolution of the higher-level relationships has no statistical support. The phylogenetic signal from individual genes is highly diffuse, with mixed topological support from different genes. Furthermore, the choice of outgroup (horse vs tapir) has considerable effect on reconstruction of the phylogeny. The lack of resolution is suggestive of a hard polytomy at the base of crown-group Rhinocerotidae, and this is supported by an investigation of the relative branch lengths. CONCLUSION: Satisfactory resolution of the rhinoceros phylogeny may not be achievable without additional analyses of substantial amounts of nuclear DNA. This study provides a compelling demonstration that, in spite of substantial sequence length, there are significant limitations with single-locus phylogenetics. We expect further examples of this to appear as next-generation, largescale sequencing of complete mitochondrial gen

Published
2009

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