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Webb Miller

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

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Publications

TOP 3
Miller Webb; Wright Stephen J; Zhang Yu; Schuster Stephan C; Hayes Vanessa M
Optimization methods for selecting founder individuals for captive breeding or reintroduction of endangered species.
Zhang Yu; Song Giltae; Vinar Tomás; Green Eric D; Siepel Adam; Miller Webb
Evolutionary history reconstruction for Mammalian complex gene clusters.
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; Dalén Love; Arsuaga Juan Luis; Ericson Per G P; Huson Daniel H; Helgen Kristofer M; Murphy William J; Götherström Anders; Schuster Stephan C
The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus).

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All Publications

2010: Miller Webb; Wright Stephen J; Zhang Yu; Schuster Stephan C; Hayes Vanessa M
Optimization methods for selecting founder individuals for captive breeding or reintroduction of endangered species.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2010;():43-53.
2009: Zhang Yu; Song Giltae; Vinar Tomás; Green Eric D; Siepel Adam; Miller Webb
Evolutionary history reconstruction for Mammalian complex gene clusters.
Journal of computational biology : a journal of computational molecular cell biology 2009;16(8):1051-70.
2009: 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; Dalén Love; Arsuaga Juan Luis; Ericson Per G P; Huson Daniel H; Helgen Kristofer M; Murphy William J; Götherström Anders; Schuster Stephan C
The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus).
Genome research 2009;19(2):213-20.
2009: Willerslev Eske; Gilbert M Thomas P; Binladen Jonas; Ho Simon Y W; 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
Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution.
BMC evolutionary biology 2009;9():95.
2009: Zhang Yu; Song Giltae; Hsu Chih-Hao; Miller Webb
Simultaneous history reconstruction for complex gene clusters in multiple species.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2009;():162-73.
2008: Cheng Yong; King David C; Dore Louis C; Zhang Xinmin; Zhou Yuepin; Zhang Ying; Dorman Christine; Abebe Demesew; Kumar Swathi A; Chiaromonte Francesca; Miller Webb; Green Roland D; Weiss Mitchell J; Hardison Ross C
Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif.
Genome research 2008;18(12):1896-905.
2008: Miller Webb; Drautz Daniela I; Ratan Aakrosh; Pusey Barbara; Qi Ji; Lesk Arthur M; Tomsho Lynn P; Packard Michael D; Zhao Fangqing; Sher Andrei; Tikhonov Alexei; Raney Brian; Patterson Nick; Lindblad-Toh Kerstin; Lander Eric S; Knight James R; Irzyk Gerard P; Fredrikson Karin M; Harkins Timothy T; Sheridan Sharon; Pringle Tom; Schuster Stephan C
Sequencing the nuclear genome of the extinct woolly mammoth.
Nature 2008;456(7220):387-90.
2008: Ma Jian; Ratan Aakrosh; Raney Brian J; Suh Bernard B; Zhang Louxin; Miller Webb; Haussler David
DUPCAR: reconstructing contiguous ancestral regions with duplications.
Journal of computational biology : a journal of computational molecular cell biology 2008;15(8):1007-27.
2008: Ma Jian; Ratan Aakrosh; Raney Brian J; Suh Bernard B; Miller Webb; Haussler David
The infinite sites model of genome evolution.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(38):14254-61.
2008: 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 Phillip; 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; Collins Matthew J
Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry".
Science (New York, N.Y.) 2008;319(5859):33; author reply 33.
2008: Karolchik D; Kuhn R M; Baertsch R; Barber G P; Clawson H; Diekhans M; Giardine B; Harte R A; Hinrichs A S; Hsu F; Kober K M; Miller W; Pedersen J S; Pohl A; Raney B J; Rhead B; Rosenbloom K R; Smith K E; Stanke M; Thakkapallayil A; Trumbower H; Wang T; Zweig A S; Haussler D; Kent W J
The UCSC Genome Browser Database: 2008 update.
Nucleic acids research 2008;36(Database issue):D773-9.
2008: Blanchette Mathauieu; Diallo Abdoulaye Baniré; Green Eric D; Miller Webb; Haussler David
Computational reconstruction of ancestral DNA sequences.
Methods in molecular biology (Clifton, N.J.) 2008;422():171-84.
2008: Rosenbloom Kate; Taylor James; Schaeffer Stephen; Kent Jim; Haussler David; Miller Webb
Phylogenomic resources at the UCSC Genome Browser.
Methods in molecular biology (Clifton, N.J.) 2008;422():133-44.
2007: Miller Webb; Rosenbloom Kate; Hardison Ross C; Hou Minmei; Taylor James; Raney Brian; Burhans Richard; King David C; Baertsch Robert; Blankenberg Daniel; Kosakovsky Pond Sergei L; Nekrutenko Anton; Giardine Belinda; Harris Robert S; Tyekucheva Svitlana; Diekhans Mark; Pringle Thomas H; Murphy William J; Lesk Arthur; Weinstock George M; Lindblad-Toh Kerstin; Gibbs Richard A; Lander Eric S; Siepel Adam; Haussler David; Kent W James
28-way vertebrate alignment and conservation track in the UCSC Genome Browser.
Genome research 2007;17(12):1797-808.
2007: Janecka Jan E; Miller Webb; Pringle Thomas H; Wiens Frank; Zitzmann Annette; Helgen Kristofer M; Springer Mark S; Murphy William J
Molecular and genomic data identify the closest living relative of primates.
Science (New York, N.Y.) 2007;318(5851):792-4.
2007: Blankenberg Daniel; Taylor James; Schenck Ian; He Jianbin; Zhang Yi; Ghent Matthew; Veeraraghavan Narayanan; Albert Istvan; Miller Webb; Makova Kateryna D; Hardison Ross C; Nekrutenko Anton
A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly.
Genome research 2007;17(6):960-4.
2007: King David C; Taylor James; Zhang Ying; Cheng Yong; Lawson Heather A; Martin Joel; Chiaromonte Francesca; Miller Webb; Hardison Ross C
Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data.
Genome research 2007;17(6):775-86.
2007: Giardine Belinda; Riemer Cathy; Hefferon Tim; Thomas Daryl; Hsu Fan; Zielenski Julian; Sang Yunhua; Elnitski Laura; Cutting Garry; Trumbower Heather; Kern Andrew; Kuhn Robert; Patrinos George P; Hughes Jim; Higgs Doug; Chui David; Scriver Charles; Phommarinh Manyphong; Patnaik Santosh K; Blumenfeld Olga; Gottlieb Bruce; Vihinen Mauno; Väliaho Jouni; Kent Jim; Miller Webb; Hardison Ross C
PhenCode: connecting ENCODE data with mutations and phenotype.
Human mutation 2007;28(6):554-62.
2007: Han Kyudong; Konkel Miriam K; Xing Jinchuan; Wang Hui; Lee Jungnam; Meyer Thomas J; Huang Charles T; Sandifer Erin; Hebert Kristi; Barnes Erin W; Hubley Robert; Miller Webb; Smit Arian F A; Ullmer Brygg; Batzer Mark A
Mobile DNA in Old World monkeys: a glimpse through the rhesus macaque genome.
Science (New York, N.Y.) 2007;316(5822):238-40.
2007: Murphy William J; Pringle Thomas H; Crider Tess A; Springer Mark S; Miller Webb
Using genomic data to unravel the root of the placental mammal phylogeny.
Genome research 2007;17(4):413-21.
2007: Giardine Belinda; van Baal Sjozef; Kaimakis Polynikis; Riemer Cathy; Miller Webb; Samara Maria; Kollia Panagoula; Anagnou Nicholas P; Chui David H K; Wajcman Henri; Hardison Ross C; Patrinos George P
HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update.
Human mutation 2007;28(2):206.
2007: Karolchik Donna; Bejerano Gill; Hinrichs Angie S; Kuhn Robert M; Miller Webb; Rosenbloom Kate R; Zweig Ann S; Haussler David; Kent W James
Comparative genomic analysis using the UCSC genome browser.
Methods in molecular biology (Clifton, N.J.) 2007;395():17-34.
2007: Bird Christine P; Stranger Barbara E; Liu Maureen; Thomas Daryl J; Ingle Catherine E; Beazley Claude; Miller Webb; Hurles Matthew E; Dermitzakis Emmanouil T
Fast-evolving noncoding sequences in the human genome.
Genome biology 2007;8(6):R118.
2007: Gilbert M Thomas P; Binladen Jonas; Miller Webb; Wiuf Carsten; Willerslev Eske; Poinar Hendrik; Carlson John E; Leebens-Mack James H; Schuster Stephan C
Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis.
Nucleic acids research 2007;35(1):1-10.
2006: Taylor James; Tyekucheva Svitlana; King David C; Hardison Ross C; Miller Webb; Chiaromonte Francesca
ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements.
Genome research 2006;16(12):1596-604.
2006: Wang Hao; Zhang Ying; Cheng Yong; Zhou Yuepin; King David C; Taylor James; Chiaromonte Francesca; Kasturi Jyotsna; Petrykowska Hanna; Gibb Brian; Dorman Christine; Miller Webb; Dore Louis C; Welch John; Weiss Mitchell J; Hardison Ross C
Experimental validation of predicted mammalian erythroid cis-regulatory modules.
Genome research 2006;16(12):1480-92.
2006: Ma Jian; Zhang Louxin; Suh Bernard B; Raney Brian J; Burhans Richard C; Kent W James; Blanchette Mathieu; Haussler David; Miller Webb
Reconstructing contiguous regions of an ancestral genome.
Genome research 2006;16(12):1557-65.
2006: Pedersen Jakob Skou; Bejerano Gill; Siepel Adam; Rosenbloom Kate; Lindblad-Toh Kerstin; Lander Eric S; Kent Jim; Miller Webb; Haussler David
Identification and classification of conserved RNA secondary structures in the human genome.
PLoS computational biology 2006;2(4):e33.
2006: Poinar Hendrik N; Schwarz Carsten; Qi Ji; Shapiro Beth; Macphee Ross D E; Buigues Bernard; Tikhonov Alexei; Huson Daniel H; Tomsho Lynn P; Auch Alexander; Rampp Markus; Miller Webb; Schuster Stephan C
Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA.
Science (New York, N.Y.) 2006;311(5759):392-4.
2005: Giardine Belinda; Riemer Cathy; Hardison Ross C; Burhans Richard; Elnitski Laura; Shah Prachi; Zhang Yi; Blankenberg Daniel; Albert Istvan; Taylor James; Miller Webb; Kent W James; Nekrutenko Anton
Galaxy: a platform for interactive large-scale genome analysis.
Genome research 2005;15(10):1451-5.
2005: Siepel Adam; Bejerano Gill; Pedersen Jakob S; Hinrichs Angie S; Hou Minmei; Rosenbloom Kate; Clawson Hiram; Spieth John; Hillier Ladeana W; Richards Stephen; Weinstock George M; Wilson Richard K; Gibbs Richard A; Kent W James; Miller Webb; Haussler David
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
Genome research 2005;15(8):1034-50.
2005: King David C; Taylor James; Elnitski Laura; Chiaromonte Francesca; Miller Webb; Hardison Ross C
Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences.
Genome research 2005;15(8):1051-60.
2005: Elnitski Laura; Riemer Cathy; Burhans Richard; Hardison Ross; Miller Webb
MultiPipMaker: comparative alignment server for multiple DNA sequences.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2005;Chapter 10():Unit10.4.
2005: Margulies Elliott H; Vinson Jade P; Miller Webb; Jaffe David B; Lindblad-Toh Kerstin; Chang Jean L; Green Eric D; Lander Eric S; Mullikin James C; Clamp Michele
An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(13):4795-800.
2005: Elnitski Laura; Giardine Belinda; Shah Prachi; Zhang Yi; Riemer Cathy; Weirauch Matthew; Burhans Richard; Miller Webb; Hardison Ross C
Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results.
Nucleic acids research 2005;33(Database issue):D466-70.
2005: Ovcharenko Ivan; Loots Gabriela G; Nobrega Marcelo A; Hardison Ross C; Miller Webb; Stubbs Lisa
Evolution and functional classification of vertebrate gene deserts.
Genome research 2005;15(1):137-45.
2005: Ovcharenko Ivan; Loots Gabriela G; Giardine Belinda M; Hou Minmei; Ma Jian; Hardison Ross C; Stubbs Lisa; Miller Webb
Mulan: multiple-sequence local alignment and visualization for studying function and evolution.
Genome research 2005;15(1):184-94.
2004: Blanchette Mathieu; Green Eric D; Miller Webb; Haussler David
Reconstructing large regions of an ancestral mammalian genome in silico.
Genome research 2004;14(12):2412-23.
2004: She Xinwei; Horvath Julie E; Jiang Zhaoshi; Liu Ge; Furey Terrence S; Christ Laurie; Clark Royden; Graves Tina; Gulden Cassy L; Alkan Can; Bailey Jeff A; Sahinalp Cenk; Rocchi Mariano; Haussler David; Wilson Richard K; Miller Webb; Schwartz Stuart; Eichler Evan E
The structure and evolution of centromeric transition regions within the human genome.
Nature 2004;430(7002):857-64.
2004: Blanchette Mathieu; Kent W James; Riemer Cathy; Elnitski Laura; Smit Arian F A; Roskin Krishna M; Baertsch Robert; Rosenbloom Kate; Clawson Hiram; Green Eric D; Haussler David; Miller Webb
Aligning multiple genomic sequences with the threaded blockset aligner.
Genome research 2004;14(4):708-15.
2004: Kolbe Diana; Taylor James; Elnitski Laura; Eswara Pallavi; Li Jia; Miller Webb; Hardison Ross; Chiaromonte Francesca
Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat.
Genome research 2004;14(4):700-7.
2004: Tufarelli Cristina; Hardison Ross; Miller Webb; Hughes Jim; Clark Kevin; Ventress Nicki; Frischauf Anna Maria; Higgs Douglas R
Comparative analysis of the alpha-like globin clusters in mouse, rat, and human chromosomes indicates a mechanism underlying breaks in conserved synteny.
Genome research 2004;14(4):623-30.
2004: Yang Shan; Smit Arian F; Schwartz Scott; Chiaromonte Francesca; Roskin Krishna M; Haussler David; Miller Webb; Hardison Ross C
Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes.
Genome research 2004;14(4):517-27.
2004: Ovcharenko Ivan; Loots Gabriela G; Hardison Ross C; Miller Webb; Stubbs Lisa
zPicture: dynamic alignment and visualization tool for analyzing conservation profiles.
Genome research 2004;14(3):472-7.
2004: Patrinos George P; Giardine Belinda; Riemer Cathy; Miller Webb; Chui David H K; Anagnou Nicholas P; Wajcman Henri; Hardison Ross C
Improvements in the HbVar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studies.
Nucleic acids research 2004;32(Database issue):D537-41.
2004: Miller Webb; Makova Kateryna D; Nekrutenko Anton; Hardison Ross C
Comparative genomics.
Annual review of genomics and human genetics 2004;5():15-56.
2003: Chiaromonte Francesca; Miller Webb; Bouhassira Eric E
Gene length and proximity to neighbors affect genome-wide expression levels.
Genome research 2003;13(12):2602-8.
2003: Farhadi Hooman F; Lepage Pierre; Forghani Reza; Friedman Hana C H; Orfali Wayel; Jasmin Luc; Miller Webb; Hudson Thomas J; Peterson Alan C
A combinatorial network of evolutionarily conserved myelin basic protein regulatory sequences confers distinct glial-specific phenotypes.
The Journal of neuroscience : the official journal of the Society for Neuroscience 2003;23(32):10214-23.
2003: Rijnkels Monique; Elnitski Laura; Miller Webb; Rosen Jeffrey M
Multispecies comparative analysis of a mammalian-specific genomic domain encoding secretory proteins.
Genomics 2003;82(4):417-32.
2003: Kent W James; Baertsch Robert; Hinrichs Angie; Miller Webb; Haussler David
Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(20):11484-9.
2003: Florea Liliana; McClelland Michael; Riemer Cathy; Schwartz Scott; Miller Webb
EnteriX 2003: Visualization tools for genome alignments of Enterobacteriaceae.
Nucleic acids research 2003;31(13):3527-32.
2003: Schwartz Scott; Elnitski Laura; Li Mei; Weirauch Matt; Riemer Cathy; Smit Arian; Green Eric D; Hardison Ross C; Miller Webb
MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences.
Nucleic acids research 2003;31(13):3518-24.
2003: Giardine Belinda; Elnitski Laura; Riemer Cathy; Makalowska Izabela; Schwartz Scott; Miller Webb; Hardison Ross C
GALA, a database for genomic sequence alignments and annotations.
Genome research 2003;13(4):732-41.
2003: Green Phil; Ewing Brent; Miller Webb; Thomas Pamela J; Green Eric D
Transcription-associated mutational asymmetry in mammalian evolution.
Nature genetics 2003;33(4):514-7.
2003: Elnitski Laura; Riemer Cathy; Schwartz Scott; Hardison Ross; Miller Webb
PipMaker: a World Wide Web server for genomic sequence alignments.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2003;Chapter 10():Unit 10.2.
2003: Schwartz Scott; Kent W James; Smit Arian; Zhang Zheng; Baertsch Robert; Hardison Ross C; Haussler David; Miller Webb
Human-mouse alignments with BLASTZ.
Genome research 2003;13(1):103-7.
2003: Elnitski Laura; Hardison Ross C; Li Jia; Yang Shan; Kolbe Diana; Eswara Pallavi; O'Connor Michael J; Schwartz Scott; Miller Webb; Chiaromonte Francesca
Distinguishing regulatory DNA from neutral sites.
Genome research 2003;13(1):64-72.
2003: 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; Haussler David
Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution.
Genome research 2003;13(1):13-26.
2003: Hardison R C; Chiaromonte F; Kolbe D; Wang H; Petrykowska H; Elnitski L; Yang S; Giardine B; Zhang Y; Riemer C; Schwartz S; Haussler D; Roskin K M; Weber R J; Diekhans M; Kent W J; Weiss M J; Welch J; Miller W
Global predictions and tests of erythroid regulatory regions.
Cold Spring Harbor symposia on quantitative biology 2003;68():335-44.
2003: Yu C Yung; Chung Erwin K; Yang Yan; Blanchong Carol A; Jacobsen Natalie; Saxena Kapil; Yang Zhenyu; Miller Webb; Varga Lilian; Fust George
Dancing with complement C4 and the RP-C4-CYP21-TNX (RCCX) modules of the major histocompatibility complex.
Progress in nucleic acid research and molecular biology 2003;75():217-92.
2003: Li Jia; Miller Webb
Significance of interspecies matches when evolutionary rate varies.
Journal of computational biology : a journal of computational molecular cell biology 2003;10(3-4):537-54.
2002: Elnitski Laura; Riemer Cathy; Petrykowska Hanna; Florea Liliana; Schwartz Scott; Miller Webb; Hardison Ross
PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences.
Genomics 2002;80(6):681-90.
2002: Maul Jude E; Lilly Jason W; Cui Liying; dePamphilis Claude W; Miller Webb; Harris Elizabeth H; Stern David B
The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of repeats.
The Plant cell 2002;14(11):2659-79.
2002: Agron Peter G; Macht Madison; Radnedge Lyndsay; Skowronski Evan W; Miller Webb; Andersen Gary L
Use of subtractive hybridization for comprehensive surveys of prokaryotic genome differences.
FEMS microbiology letters 2002;211(2):175-82.
2002: Hardison Ross C; Chui David H K; Giardine Belinda; Riemer Cathy; Patrinos George P; Anagnou Nicholas; Miller Webb; Wajcman Henri
HbVar: A relational database of human hemoglobin variants and thalassemia mutations at the globin gene server.
Human mutation 2002;19(3):225-33.
2002: Kurihara Laurie Jo; Semenova Ekaterina; Miller Webb; Ingram Robert S; Guan Xiao-Juan; Tilghman Shirley M
Candidate genes required for embryonic development: a comparative analysis of distal mouse chromosome 14 and human chromosome 13q22.
Genomics 2002;79(2):154-61.
2002: Molete Joseph M; Petrykowska Hanna; Sigg Martin; Miller Webb; Hardison Ross
Functional and binding studies of HS3.2 of the beta-globin locus control region.
Gene 2002;283(1-2):185-97.
2002: Sumiyama Kenta; Irvine Steven Q; Stock David W; Weiss Kenneth M; Kawasaki Kazuhiko; Shimizu Nobuyoshi; Shashikant Cooduvalli S; Miller Webb; Ruddle Frank H
Genomic structure and functional control of the Dlx3-7 bigene cluster.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(2):780-5.
2002: DeSilva Udaya; Elnitski Laura; Idol Jacquelyn R; Doyle Johannah L; Gan Weiniu; Thomas James W; Schwartz Scott; Dietrich Nicole L; Beckstrom-Sternberg Stephen M; McDowell Jennifer C; Blakesley Robert W; Bouffard Gerard G; Thomas Pamela J; Touchman Jeffrey W; Miller Webb; Green Eric D
Generation and comparative analysis of approximately 3.3 Mb of mouse genomic sequence orthologous to the region of human chromosome 7q11.23 implicated in Williams syndrome.
Genome research 2002;12(1):3-15.
2002: Chiaromonte F; Yap V B; Miller W
Scoring pairwise genomic sequence alignments.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2002;():115-26.
2001: Chiaromonte F; Yang S; Elnitski L; Yap V B; Miller W; Hardison R C
Association between divergence and interspersed repeats in mammalian noncoding genomic DNA.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(25):14503-8.
2001: McClelland M; Sanderson K E; Spieth J; Clifton S W; Latreille P; Courtney L; Porwollik S; Ali J; Dante M; Du F; Hou S; Layman D; Leonard S; Nguyen C; Scott K; Holmes A; Grewal N; Mulvaney E; Ryan E; Sun H; Florea L; Miller W; Stoneking T; Nhan M; Waterston R; Wilson R K
Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.
Nature 2001;413(6858):852-6.
2001: Hardison R C; Chui D H; Riemer C; Giardine B; Lehväslaiho H; Wajcman H; Miller W
Databases of human hemoglobin variants and other resources at the globin gene server.
Hemoglobin 2001;25(2):183-93.
2001: Molete J M; Petrykowska H; Bouhassira E E; Feng Y Q; Miller W; Hardison R C
Sequences flanking hypersensitive sites of the beta-globin locus control region are required for synergistic enhancement.
Molecular and cellular biology 2001;21(9):2969-80.
2001: Elnitski L; Li J; Noguchi C T; Miller W; Hardison R
A negative cis-element regulates the level of enhancement by hypersensitive site 2 of the beta-globin locus control region.
The Journal of biological chemistry 2001;276(9):6289-98.
2001: Flint J; Tufarelli C; Peden J; Clark K; Daniels R J; Hardison R; Miller W; Philipsen S; Tan-Un K C; McMorrow T; Frampton J; Alter B P; Frischauf A M; Higgs D R
Comparative genome analysis delimits a chromosomal domain and identifies key regulatory elements in the alpha globin cluster.
Human molecular genetics 2001;10(4):371-82.
2000: McClelland M; Florea L; Sanderson K; Clifton S W; Parkhill J; Churcher C; Dougan G; Wilson R K; Miller W
Comparison of the Escherichia coli K-12 genome with sampled genomes of a Klebsiella pneumoniae and three salmonella enterica serovars, Typhimurium, Typhi and Paratyphi.
Nucleic acids research 2000;28(24):4974-86.
2000: Florea L; Riemer C; Schwartz S; Zhang Z; Stojanovic N; Miller W; McClelland M
Web-based visualization tools for bacterial genome alignments.
Nucleic acids research 2000;28(18):3486-96.
2000: Yung Yu C; Yang Z; Blanchong C A; Miller W
The human and mouse MHC class III region: a parade of 21 genes at the centromeric segment.
Immunology today 2000;21(7):320-8.
2000: Schwartz S; Zhang Z; Frazer K A; Smit A; Riemer C; Bouck J; Gibbs R; Hardison R; Miller W
PipMaker--a web server for aligning two genomic DNA sequences.
Genome research 2000;10(4):577-86.
2000: Loots G G; Locksley R M; Blankespoor C M; Wang Z E; Miller W; Rubin E M; Frazer K A
Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons.
Science (New York, N.Y.) 2000;288(5463):136-40.
2000: Berman P; Zhang Z; Wolf Y I; Koonin E V; Miller W
Winnowing sequences from a database search.
Journal of computational biology : a journal of computational molecular cell biology 2000;7(1-2):293-302.
2000: Zhang Z; Schwartz S; Wagner L; Miller W
A greedy algorithm for aligning DNA sequences.
Journal of computational biology : a journal of computational molecular cell biology 2000;7(1-2):203-14.
2000: Kim C B; Amemiya C; Bailey W; Kawasaki K; Mezey J; Miller W; Minoshima S; Shimizu N; Wagner G; Ruddle F
Hox cluster genomics in the horn shark, Heterodontus francisci.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(4):1655-60.
2000: Ellsworth R E; Jamison D C; Touchman J W; Chissoe S L; Braden Maduro V V; Bouffard G G; Dietrich N L; Beckstrom-Sternberg S M; Iyer L M; Weintraub L A; Cotton M; Courtney L; Edwards J; Maupin R; Ozersky P; Rohlfing T; Wohldmann P; Miner T; Kemp K; Kramer J; Korf I; Pepin K; Antonacci-Fulton L; Fulton R S; Minx P; Hillier L W; Wilson R K; Waterston R H; Miller W; Green E D
Comparative genomic sequence analysis of the human and mouse cystic fibrosis transmembrane conductance regulator genes.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(3):1172-7.
2000: Doyle J L; DeSilva U; Miller W; Green E D
Divergent human and mouse orthologs of a novel gene (WBSCR15/Wbscr15) reside within the genomic interval commonly deleted in Williams syndrome.
Cytogenetics and cell genetics 2000;90(3-4):285-90.
1999: Stojanovic N; Florea L; Riemer C; Gumucio D; Slightom J; Goodman M; Miller W; Hardison R
Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions.
Nucleic acids research 1999;27(19):3899-910.
1999: Liu X Y; Dangel A W; Kelley R I; Zhao W; Denny P; Botcherby M; Cattanach B; Peters J; Hunsicker P R; Mallon A M; Strivens M A; Bate R; Miller W; Rhodes M; Brown S D; Herman G E
The gene mutated in bare patches and striated mice encodes a novel 3beta-hydroxysteroid dehydrogenase.
Nature genetics 1999;22(2):182-7.
1999: Jang W; Hua A; Spilson S V; Miller W; Roe B A; Meisler M H
Comparative sequence of human and mouse BAC clones from the mnd2 region of chromosome 2p13.
Genome research 1999;9(1):53-61.
1998: Riemer C; ElSherbini A; Stojanovic N; Schwartz S; Kwitkin P B; Miller W; Hardison R
A database of experimental results on globin gene expression.
Genomics 1998;53(3):325-37.
1998: Bouck J; Miller W; Gorrell J H; Muzny D; Gibbs R A
Analysis of the quality and utility of random shotgun sequencing at low redundancies.
Genome research 1998;8(10):1074-84.
1998: Florea L; Hartzell G; Zhang Z; Rubin G M; Miller W
A computer program for aligning a cDNA sequence with a genomic DNA sequence.
Genome research 1998;8(9):967-74.
1998: Zhang Z; Schäffer A A; Miller W; Madden T L; Lipman D J; Koonin E V; Altschul S F
Protein sequence similarity searches using patterns as seeds.
Nucleic acids research 1998;26(17):3986-90.
1998: Chui D H; Hardison R; Riemer C; Miller W; Carver M F; Molchanova T P; Efremov G D; Huisman T H
An electronic database of human hemoglobin variants on the World Wide Web.
Blood 1998;91(8):2643-4.
1998: Hardison R C; Chui D H; Riemer C R; Miller W; Carver M F; Molchanova T P; Efremov G D; Huisman T H
Access to a syllabus of human hemoglobin variants (1996) via the World Wide Web.
Hemoglobin 1998;22(2):113-27.
1998: Hardison R; Riemer C; Chui D H; Huisman T H; Miller W
Electronic access to sequence alignments, experimental results, and human mutations as an aid to studying globin gene regulation.
Genomics 1998;47(3):429-37.
1998: Ansari-Lari M A; Oeltjen J C; Schwartz S; Zhang Z; Muzny D M; Lu J; Gorrell J H; Chinault A C; Belmont J W; Miller W; Gibbs R A
Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6.
Genome research 1998;8(1):29-40.
1998: Zhang Z; Berman P; Miller W
Alignments without low-scoring regions.
Journal of computational biology : a journal of computational molecular cell biology 1998;5(2):197-210.
1997: Hardison R; Slightom J L; Gumucio D L; Goodman M; Stojanovic N; Miller W
Locus control regions of mammalian beta-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insights.
Gene 1997;205(1-2):73-94.
1997: Hardison R C; Oeltjen J; Miller W
Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome.
Genome research 1997;7(10):959-66.
1997: Altschul S F; Madden T L; Schäffer A A; Zhang J; Zhang Z; Miller W; Lipman D J
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Nucleic acids research 1997;25(17):3389-402.
1997: Shelton D A; Stegman L; Hardison R; Miller W; Bock J H; Slightom J L; Goodman M; Gumucio D L
Phylogenetic footprinting of hypersensitive site 3 of the beta-globin locus control region.
Blood 1997;89(9):3457-69.
1997: Oeltjen J C; Malley T M; Muzny D M; Miller W; Gibbs R A; Belmont J W
Large-scale comparative sequence analysis of the human and murine Bruton's tyrosine kinase loci reveals conserved regulatory domains.
Genome research 1997;7(4):315-29.
1997: Slightom J L; Bock J H; Tagle D A; Gumucio D L; Goodman M; Stojanovic N; Jackson J; Miller W; Hardison R
The complete sequences of the galago and rabbit beta-globin locus control regions: extended sequence and functional conservation outside the cores of DNase hypersensitive sites.
Genomics 1997;39(1):90-4.
1997: Elnitski L; Miller W; Hardison R
Conserved E boxes function as part of the enhancer in hypersensitive site 2 of the beta-globin locus control region. Role of basic helix-loop-helix proteins.
The Journal of biological chemistry 1997;272(1):369-78.
1997: Zhang Z; Pearson W R; Miller W
Aligning a DNA sequence with a protein sequence.
Journal of computational biology : a journal of computational molecular cell biology 1997;4(3):339-49.
1996: Jackson J D; Miller W; Hardison R C
Sequences within and flanking hypersensitive sites 3 and 2 of the beta-globin locus control region required for synergistic versus additive interaction with the epsilon-globin gene promoter.
Nucleic acids research 1996;24(21):4327-35.
1996: Jackson J D; Petrykowska H; Philipsen S; Miller W; Hardison R
Role of DNA sequences outside the cores of DNase hypersensitive sites (HSs) in functions of the beta-globin locus control region. Domain opening and synergism between HS2 and HS3.
The Journal of biological chemistry 1996;271(20):11871-8.
1995: Chao K M; Zhang J; Ostell J; Miller W
A local alignment tool for very long DNA sequences.
Computer applications in the biosciences : CABIOS 1995;11(2):147-53.
1994: Miller W; Boguski M
A note about computing all local alignments.
Computer applications in the biosciences : CABIOS 1994;10(4):455-6.
1994: Hardison R; Chao K M; Schwartz S; Stojanovic N; Ganetsky M; Miller W
Globin gene server: a prototype E-mail database server featuring extensive multiple alignments and data compilation for electronic genetic analysis.
Genomics 1994;21(2):344-53.
1994: Chao K M; Hardison R C; Miller W
Recent developments in linear-space alignment methods: a survey.
Journal of computational biology : a journal of computational molecular cell biology 1994;1(4):271-91.
1994: Zhang Z; Raghavachari B; Hardison R C; Miller W
Chaining multiple-alignment blocks.
Journal of computational biology : a journal of computational molecular cell biology 1994;1(3):217-26.
1994: Miller W; Boguski M; Raghavachari B; Zhang Z; Hardison R C
Constructing aligned sequence blocks.
Journal of computational biology : a journal of computational molecular cell biology 1994;1(1):51-64.
1993: Chao K M; Hardison R C; Miller W
Locating well-conserved regions within a pairwise alignment.
Computer applications in the biosciences : CABIOS 1993;9(4):387-96.
1993: Chao K M; Hardison R C; Miller W
Constrained sequence alignment.
Bulletin of mathematical biology 1993;55(3):503-24.
1993: Miller W
Building multiple alignments from pairwise alignments.
Computer applications in the biosciences : CABIOS 1993;9(2):169-76.
1993: Hardison R; Xu J; Jackson J; Mansberger J; Selifonova O; Grotch B; Biesecker J; Petrykowska H; Miller W
Comparative analysis of the locus control region of the rabbit beta-like gene cluster: HS3 increases transient expression of an embryonic epsilon-globin gene.
Nucleic acids research 1993;21(5):1265-72.
1993: Hardison R; Miller W
Use of long sequence alignments to study the evolution and regulation of mammalian globin gene clusters.
Molecular biology and evolution 1993;10(1):73-102.
1993: Hardison R; Chao K M; Adamkiewicz M; Price D; Jackson J; Zeigler T; Stojanovic N; Miller W
Positive and negative regulatory elements of the rabbit embryonic epsilon-globin gene revealed by an improved multiple alignment program and functional analysis.
DNA sequence : the journal of DNA sequencing and mapping 1993;4(3):163-76.
1992: Price D K; Ayres J A; Pasqualone D; Cabell C H; Miller W; Hardison R C
The 5' ends of LINE1 repeats in rabbit DNA define subfamilies and reveal a short sequence conserved between rabbits and humans.
Genomics 1992;14(2):320-31.
1992: Chao K M; Pearson W R; Miller W
Aligning two sequences within a specified diagonal band.
Computer applications in the biosciences : CABIOS 1992;8(5):481-7.
1992: Boguski M S; Hardison R C; Schwartz S; Miller W
Analysis of conserved domains and sequence motifs in cellular regulatory proteins and locus control regions using new software tools for multiple alignment and visualization.
The New biologist 1992;4(3):247-60.
1991: Hardison R; Krane D; Vandenbergh D; Cheng J F; Mansberger J; Taddie J; Schwartz S; Huang X Q; Miller W
Sequence and comparative analysis of the rabbit alpha-like globin gene cluster reveals a rapid mode of evolution in a G + C-rich region of mammalian genomes.
Journal of molecular biology 1991;222(2):233-49.
1991: Miller W; Barr J; Rudd K E
Improved algorithms for searching restriction maps.
Computer applications in the biosciences : CABIOS 1991;7(4):447-56.
1991: Schwartz S; Miller W; Yang C M; Hardison R C
Software tools for analyzing pairwise alignments of long sequences.
Nucleic acids research 1991;19(17):4663-7.
1991: Rudd K E; Miller W; Werner C; Ostell J; Tolstoshev C; Satterfield S G
Mapping sequenced E.coli genes by computer: software, strategies and examples.
Nucleic acids research 1991;19(3):637-47.
1990: Altschul S F; Gish W; Miller W; Myers E W; Lipman D J
Basic local alignment search tool.
Journal of molecular biology 1990;215(3):403-10.
1990: Miller W; Ostell J; Rudd K E
An algorithm for searching restriction maps.
Computer applications in the biosciences : CABIOS 1990;6(3):247-52.
1990: Rudd K E; Miller W; Ostell J; Benson D A
Alignment of Escherichia coli K12 DNA sequences to a genomic restriction map.
Nucleic acids research 1990;18(2):313-21.

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