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Webb Miller

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George H Perry; Aakrosh Ratan; Stephan C Schuster; Oscar C Bedoya-Reina; Richard Burhans; Steig E Johnson; Runhua Lei; Edward E Louis; Webb Miller
Aye-aye population genomic analyses highlight an important center of endemism in northern Madagascar.
Aakrosh Ratan; Joseph Guillory; Webb Miller; Somasekar Seshagiri; Jeremy Stinson; Stephan C Schuster
Comparison of sequencing platforms for single nucleotide variant calls in a human sample.
Webb Miller; Rafael Montiel; Martyn Obbard; Elizabeth Peacock; Aakrosh Ratan; Karyn Rode; George K Sage; Stephan C Schuster; Sandra L Talbot; Lynn P Tomsho; Andreanna J Welch; Oystein Wiig; Nicola E Wittekindt; Fangqing Zhao; Jon Aars; Lutz Bachmann; Oscar C Bedoya-Reina; Richard Burhans; Daniela I Drautz; Sean Farley; Luis Herrera-Estrella; Enrique Ibarra-Laclette; Olafur Ingólfsson; Hie Lim Kim; Thomas Mailund; Charlotte Lindqvist
Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change.

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All Publications

2013: George H Perry; Aakrosh Ratan; Stephan C Schuster; Oscar C Bedoya-Reina; Richard Burhans; Steig E Johnson; Runhua Lei; Edward E Louis; Webb Miller
Aye-aye population genomic analyses highlight an important center of endemism in northern Madagascar.
Proceedings of the National Academy of Sciences of the United States of America 2013;110(15):5823-8.
2013: Aakrosh Ratan; Joseph Guillory; Webb Miller; Somasekar Seshagiri; Jeremy Stinson; Stephan C Schuster
Comparison of sequencing platforms for single nucleotide variant calls in a human sample.
PloS one 2013;8(2):e55089.
2012: Webb Miller; Rafael Montiel; Martyn Obbard; Elizabeth Peacock; Aakrosh Ratan; Karyn Rode; George K Sage; Stephan C Schuster; Sandra L Talbot; Lynn P Tomsho; Andreanna J Welch; Oystein Wiig; Nicola E Wittekindt; Fangqing Zhao; Jon Aars; Lutz Bachmann; Oscar C Bedoya-Reina; Richard Burhans; Daniela I Drautz; Sean Farley; Luis Herrera-Estrella; Enrique Ibarra-Laclette; Olafur Ingólfsson; Hie Lim Kim; Thomas Mailund; Charlotte Lindqvist
Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(36):E2382-90.
2012: Belinda Giardine; Aakrosh Ratan; Cathy Riemer; Richard Burhans; Webb Miller
Some phenotype association tools in Galaxy: looking for disease SNPs in a full genome.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2012;Chapter 15():Unit15.2.
2012: Ravi Gupta; Hie Lim Kim; Webb Miller; Changanamkandath Rajesh; Aakrosh Ratan; Sam Santhosh; Stephan C Schuster; Somasekar Seshagiri; Richard Burhans; Atul J Butte; Rong Chen; Ramana V Davuluri; George Thomas
Sequencing and analysis of a South Asian-Indian personal genome.
BMC genomics 2012;13():440.
2012: Giltae Song; Louxin Zhang; Yu Zhang; Cathy Riemer; Benjamin Dickins; Eric D Green; Ross C Hardison; Chih-Hao Hsu; Hie Lim Kim; Webb Miller
Revealing mammalian evolutionary relationships by comparative analysis of gene clusters.
Genome biology and evolution 2012;4(4):586-601.
2012: George H Perry; Jonathan K Pritchard; Aakrosh Ratan; Darryl Reeves; Edward E Louis; Christopher E Mason; Páll Melsted; Katelyn Michelini; Webb Miller; Yoav Gilad
A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar.
Genome biology and evolution 2012;4(2):126-35.
2011: Weisheng Wu; Yu Zhang; Gerd A Blobel; Kuan-Bei Chen; Yong Cheng; Francesca Chiaromonte; Gregory E Crawford; Christine M Dorman; Daniela Drautz; Jason Ernst; Terrence S Furey; Belinda Giardine; Cheryl A Keller; Manolis Kellis; Swathi Ashok Kumar; Webb Miller; Tejaswini Mishra; Christapher Morrissey; Max Pimkin; Stephan C Schuster; Yoichiro Shibata; Lingyun Song; James TAYLOR; Mitchell J Weiss; Ross C Hardison
Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration.
Genome research 2011;21(10):1659-71.
2011: Webb Miller; Nick Patterson; Desiree C Petersen; Thomas H Pringle; Stephen Pyecroft; Ji Qi; Aakrosh Ratan; Oscar C Bedoya-Reina; Mads Frost Bertelsen; Dale Dixon; Rae-Anne Hardie; Vanessa M Hayes; Kristofer M Helgen; Menna E Jones; Lindsay McClellan Kasson; Neerja Katiyar; James Knight; Alexandre Kreiss; Arthur M Lesk; Jason Miller; Elizabeth A Tindall; Lynn P Tomsho; Brian Walenz; Qingyu Wang; Nicola E Wittekindt; Paula Woodbridge; Gregory M Woods; Yu Zhang; Fangqing Zhao; Stephan C Schuster
Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil).
Proceedings of the National Academy of Sciences of the United States of America 2011;108(30):12348-53.
2011: Leila Taher; Ivy Aneas; Seneca L Bessling; Samantha Maragh; Andy McCallion; David M McGaughey; Webb Miller; Marcelo A Nobrega; Ivan Ovcharenko
Genome-wide identification of conserved regulatory function in diverged sequences.
Genome research 2011;21(7):1139-49.
2011: Giltae Song; Louxin Zhang; Yu Zhang; Cathy Riemer; Eric D Green; Ross C Hardison; Federico Hoffmann; Chih-Hao Hsu; Hie Lim Kim; Webb Miller
Conversion events in gene clusters.
BMC evolutionary biology 2011;11():226.
2011: Giltae Song; Chih-Hao Hsu; Cathy Riemer; Webb Miller
Evaluation of methods for detecting conversion events in gene clusters.
BMC bioinformatics 2011;12 Suppl 1():S45.
2010: Chih-Hao Hsu; Yu Zhang; Ross C Hardison; Eric D Green; Webb Miller
An effective method for detecting gene conversion events in whole genomes.
Journal of computational biology : a journal of computational molecular cell biology 2010;17(9):1281-97.
2010: Giltae Song; Louxin Zhang; Tomas Vinar; Webb Miller
CAGE: Combinatorial Analysis of Gene-cluster Evolution.
Journal of computational biology : a journal of computational molecular cell biology 2010;17(9):1227-42.
2010: Laura Elnitski; Richard Burhans; Cathy Riemer; Ross Hardison; Webb Miller
MultiPipMaker: a comparative alignment server for multiple DNA sequences.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2010;Chapter 10():Unit10.4.
2010: Charlotte Lindqvist; Stephan C Schuster; Yazhou Sun; Sandra L Talbot; Ji Qi; Aakrosh Ratan; Lynn P Tomsho; Lindsay Kasson; Eve ZEYL; Jon Aars; Webb Miller; Olafur Ingólfsson; Lutz Bachmann; Oystein Wiig
Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(11):5053-7.
2010: Aakrosh Ratan; Yu Zhang; Vanessa M Hayes; Stephan C Schuster; Webb Miller
Calling SNPs without a reference sequence.
BMC bioinformatics 2010;11():130.
2010: Elizabeth A Tindall; Desiree C Petersen; Stina Nikolaysen; Webb Miller; Stephan C Schuster; Vanessa M Hayes
Interpretation of custom designed Illumina genotype cluster plots for targeted association studies and next-generation sequence validation.
BMC research notes 2010;3():39.
2010: Webb Miller; Stephen J Wright; Yu Zhang; Stephan C Schuster; Vanessa M Hayes
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: Yong Cheng; Weisheng Wu; Swathi Ashok Kumar; Duonan Yu; Wulan Deng; Tamara Tripic; David C King; Kuan-Bei Chen; Ying Zhang; Daniela Drautz; Belinda Giardine; Stephan C Schuster; Webb Miller; Francesca Chiaromonte; Yu Zhang; Gerd A Blobel; Mitchell J Weiss; Ross C Hardison
Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression.
Genome research 2009;19(12):2172-84.
2009: Yu Zhang; Giltae Song; Tomás Vinar; Eric Green; Adam Siepel; Webb Miller
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: Webb Miller; Daniela I Drautz; Jan E Janecka; Arthur M Lesk; Aakrosh Ratan; Lynn P Tomsho; Mike Packard; Yeting Zhang; Lindsay R McClellan; Ji Qi; Fangqing Zhao; M Thomas P Gilbert; Love Dalén; Juan Luis Arsuaga; Per G P Ericson; Daniel H Huson; Kristofer M Helgen; William J Murphy; Anders Gotherstrom; Stephan C Schuster
The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus).
Genome research 2009;19(2):213-20.
2009: Eske Willerslev; M Thomas P Gilbert; Jonas Binladen; Simon Y W Ho; Paula F Campos; Aakrosh Ratan; Lynn P Tomsho; Rute R da Fonseca; Andrei Sher; Tatanya V Kuznetsova; Malgosia Nowak-Kemp; Terri L Roth; Webb Miller; Stephan C Schuster
Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution.
BMC evolutionary biology 2009;9():95.
2009: Yu Zhang; Giltae Song; Chih-Hao Hsu; Webb Miller
Simultaneous history reconstruction for complex gene clusters in multiple species.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2009;():162-73.
2008: Yong Cheng; David C King; Lou Dore; Xinmin Zhang; Yuepin Zhou; Ying Zhang; Christine Dorman; Demesew Abebe; Swathi A Kumar; Francesca Chiaromonte; Webb Miller; Roland D Green; Mitchell J Weiss; Ross C Hardison
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: Webb Miller; Daniela I Drautz; Aakrosh Ratan; Barbara Pusey; Ji Qi; Arthur M Lesk; Lynn P Tomsho; Michael D Packard; Fangqing Zhao; Andrei Sher; Alexei Tikhonov; Brian J Raney; Nick Patterson; Kerstin Lindblad-Toh; Eric S Lander; James R Knight; Gerard P Irzyk; Karin M Fredrikson; Timothy T Harkins; Sharon Sheridan; Tom Pringle; Stephan C Schuster
Sequencing the nuclear genome of the extinct woolly mammoth.
Nature 2008;456(7220):387-90.
2008: Jian Ma; Aakrosh Ratan; Brian J Raney; Bernard B Suh; Louxin Zhang; Webb Miller; David Haussler
DUPCAR: reconstructing contiguous ancestral regions with duplications.
Journal of computational biology : a journal of computational molecular cell biology 2008;15(8):1007-27.
2008: Jian Ma; Aakrosh Ratan; Brian J Raney; Bernard B Suh; Webb Miller; David Haussler
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: Mike Buckley; Angela Walker; Simon Y W Ho; Yue Yang; Colin Smith; Peter Ashton; Jane Thomas Oates; Enrico Cappellini; Hannah Koon; Kirsty Penkman; Ben Elsworth; David A Ashford; Caroline Solazzo; Philip C Andrews; John Strahler; Beth Shapiro; PH Ostrom; Hasand Gandhi; Webb Miller; Brian Raney; Maria Ines Zylber; M Thomas P Gilbert; Richard V Prigodich; Michael Ryan; Kenneth F Rijsdijk; Anwar Janoo; Matthew J Collins
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: Mathauieu Blanchette; Abdoulaye Baniré Diallo; Eric Green; Webb Miller; David Haussler
Computational reconstruction of ancestral DNA sequences.
Methods in molecular biology (Clifton, N.J.) 2008;422():171-84.
2008: Kate Rosenbloom; James TAYLOR; Stephen Schaeffer; W James Kent; David Haussler; Webb Miller
Phylogenomic resources at the UCSC Genome Browser.
Methods in molecular biology (Clifton, N.J.) 2008;422():133-44.
2008: Svitlana Tyekucheva; Kateryna D Makova; John E Karro; Ross C Hardison; Webb Miller; Francesca Chiaromonte
Human-macaque comparisons illuminate variation in neutral substitution rates.
Genome biology 2008;9(4):R76.
2008: Donna Karolchik; Robert M Kuhn; Robert Baertsch; Galt P Barber; Hiram Clawson; Mark Diekhans; Belinda Giardine; Rachel A Harte; Angie S Hinrichs; Fan Hsu; K M Kober; Webb Miller; Jan Skov Pedersen; Andy Pohl; Brian J Raney; Brooke L Rhead; Kate Rosenbloom; Kayla E Smith; M Stanke; A Thakkapallayil; Heather Trumbower; T Wang; Ann S Zweig; David Haussler; W James Kent
The UCSC Genome Browser Database: 2008 update.
Nucleic acids research 2008;36(Database issue):D773-9.
2007: Webb Miller; Kate Rosenbloom; Ross C Hardison; Minmei Hou; James TAYLOR; Brian J Raney; Richard Burhans; David C King; Robert Baertsch; Daniel Blankenberg; Sergei L Kosakovsky Pond; Anton Nekrutenko; Belinda Giardine; Robert S Harris; Svitlana Tyekucheva; Mark Diekhans; Tom H Pringle; William J Murphy; Arthur Lesk; George Weinstock; Kerstin Lindblad-Toh; Richard A Gibbs; Eric S Lander; Adam Siepel; David Haussler; W James Kent
28-way vertebrate alignment and conservation track in the UCSC Genome Browser.
Genome research 2007;17(12):1797-808.
2007: Jan E Janecka; Webb Miller; Thomas H Pringle; Frank Wiens; Annette Zitzmann; Kristofer M Helgen; Mark S Springer; William J Murphy
Molecular and genomic data identify the closest living relative of primates.
Science (New York, N.Y.) 2007;318(5851):792-4.
2007: Daniel Blankenberg; James TAYLOR; Ian Schenck; Jianbin He; Yi Zhang; Matthew Ghent; Narayanan Veeraraghavan; Istvan Albert; Webb Miller; Kateryna D Makova; Ross C Hardison; Anton Nekrutenko
A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly.
Genome research 2007;17(6):960-4.
2007: David C King; James TAYLOR; Ying Zhang; Yong Cheng; Heather A Lawson; Joel Martin; Francesca Chiaromonte; Webb Miller; Ross C Hardison
Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data.
Genome research 2007;17(6):775-86.
2007: Belinda Giardine; Cathy Riemer; Tim Hefferon; Daryl Thomas; Fan Hsu; Julian Zielenski; Yunhua Sang; Laura Elnitski; Garry R Cutting; Heather Trumbower; Andrew Kern; Robert Kuhn; George P Patrinos; Jim Hughes; Doug Higgs; David Chui; Charles R Scriver; Manyphong Phommarinh; Santosh K Patnaik; Olga O Blumenfeld; Bruce Gottlieb; Mauno Vihinen; Jouni Väliaho; W James Kent; Webb Miller; Ross C Hardison
PhenCode: connecting ENCODE data with mutations and phenotype.
Human mutation 2007;28(6):554-62.
2007: Kyudong Han; Miriam K Konkel; Jinchuan Xing; Hui Wang; Jungnam Lee; Thomas J Meyer; Charles T Huang; Erin Sandifer; Kristi Hebert; Erin W Barnes; Robert Hubley; Webb Miller; Arian F A Smit; Brygg Ullmer; Mark A Batzer
Mobile DNA in Old World monkeys: a glimpse through the rhesus macaque genome.
Science (New York, N.Y.) 2007;316(5822):238-40.
2007: William J Murphy; Thomas H Pringle; Tess A Crider; Mark S Springer; Webb Miller
Using genomic data to unravel the root of the placental mammal phylogeny.
Genome research 2007;17(4):413-21.
2007: Belinda Giardine; Sjozef van Baal; Polynikis Kaimakis; Cathy Riemer; Webb Miller; Maria Samara; Panagoula Kollia; Nicholas P Anagnou; David H K Chui; Henri Wajcman; Ross C Hardison; George P Patrinos
HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update.
Human mutation 2007;28(2):206.
2007: Donna Karolchik; Gill Bejerano; Angie S Hinrichs; Robert M Kuhn; Webb Miller; Kate Rosenbloom; Ann S Zweig; David Haussler; W James Kent
Comparative genomic analysis using the UCSC genome browser.
Methods in molecular biology (Clifton, N.J.) 2007;395():17-34.
2007: Christine P Bird; Barbara E Stranger; Maureen Liu; Daryl J Thomas; Catherine E Ingle; Claude Beazley; Webb Miller; Matthew E Hurles; Emmanouil T Dermitzakis
Fast-evolving noncoding sequences in the human genome.
Genome biology 2007;8(6):R118.
2007: M Thomas P Gilbert; Jonas Binladen; Webb Miller; Carsten Wiuf; Eske Willerslev; Hendrik Poinar; John E Carlson; Jim Leebens-Mack; Stephan C Schuster
Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis.
Nucleic acids research 2007;35(1):1-10.
2006: James TAYLOR; Svitlana Tyekucheva; David C King; Ross C Hardison; Webb Miller; Francesca Chiaromonte
ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements.
Genome research 2006;16(12):1596-604.
2006: Hao Wang; Ying Zhang; Yong Cheng; Yuepin Zhou; David C King; James TAYLOR; Francesca Chiaromonte; Jyotsna Kasturi; Hanna Petrykowska; Brian Gibb; Christine Dorman; Webb Miller; Lou Dore; john welch; Mitchell J Weiss; Ross C Hardison
Experimental validation of predicted mammalian erythroid cis-regulatory modules.
Genome research 2006;16(12):1480-92.
2006: Jian Ma; Louxin Zhang; Bernard B Suh; Brian J Raney; Richard Burhans; W James Kent; Mathieu Blanchette; David Haussler; Webb Miller
Reconstructing contiguous regions of an ancestral genome.
Genome research 2006;16(12):1557-65.
2006: Jan Skov Pedersen; Gill Bejerano; Adam Siepel; Kate Rosenbloom; Kerstin Lindblad-Toh; Eric S Lander; W James Kent; Webb Miller; David Haussler
Identification and classification of conserved RNA secondary structures in the human genome.
PLoS computational biology 2006;2(4):e33.
2006: Hendrik Poinar; Carsten Schwarz; Ji Qi; Beth Shapiro; Ross D E MacPhee; Bernard Buigues; Alexei N Tikhonov; Daniel H Huson; Lynn P Tomsho; Alexander Auch; Markus Rampp; Webb Miller; Stephan C Schuster
Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA.
Science (New York, N.Y.) 2006;311(5759):392-4.
2005: Belinda Giardine; Cathy Riemer; Ross C Hardison; Richard Burhans; Laura Elnitski; Prachi Shah; Yi Zhang; Daniel Blankenberg; Istvan Albert; James TAYLOR; Webb Miller; W James Kent; Anton Nekrutenko
Galaxy: a platform for interactive large-scale genome analysis.
Genome research 2005;15(10):1451-5.
2005: Adam Siepel; Gill Bejerano; Jan Skov Pedersen; Angie S Hinrichs; Minmei Hou; Kate Rosenbloom; Hiram Clawson; John Spieth; LaDeana W Hillier; Stephen Richards; George M Weinstock; Richard K Wilson; Richard A Gibbs; W James Kent; Webb Miller; David Haussler
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
Genome research 2005;15(8):1034-50.
2005: David C King; James TAYLOR; Laura Elnitski; Francesca Chiaromonte; Webb Miller; Ross C Hardison
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: Laura Elnitski; Cathy Riemer; Richard Burhans; Ross Hardison; Webb Miller
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: Elliott H Margulies; Jade P Vinson; Webb Miller; David B Jaffe; Kerstin Lindblad-Toh; Jean L Chang; Eric Green; Eric S Lander; James C Mullikin; Michele Clamp
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: Laura Elnitski; Belinda Giardine; Prachi Shah; Yi Zhang; Cathy Riemer; Matthew Weirauch; Richard Burhans; Webb Miller; Ross C Hardison
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: Ivan Ovcharenko; Gabriela G Loots; Marcelo A Nobrega; Ross C Hardison; Webb Miller; Lisa Stubbs
Evolution and functional classification of vertebrate gene deserts.
Genome research 2005;15(1):137-45.
2005: Ivan Ovcharenko; Gabriela G Loots; Belinda Giardine; Minmei Hou; Jian Ma; Ross C Hardison; Lisa Stubbs; Webb Miller
Mulan: multiple-sequence local alignment and visualization for studying function and evolution.
Genome research 2005;15(1):184-94.
2004: Mathieu Blanchette; Eric Green; Webb Miller; David Haussler
Reconstructing large regions of an ancestral mammalian genome in silico.
Genome research 2004;14(12):2412-23.
2004: Xinwei She; Julie E Horvath; Zhaoshi Jiang; Ge Liu; Terrence S Furey; Laurie A Christ; Royden Clark; Tina Graves; Cassy L Gulden; Can Alkan; Jeffrey A Bailey; Cenk Sahinalp; Mariano Rocchi; David Haussler; Richard K Wilson; Webb Miller; Stuart Schwartz; Evan E Eichler
The structure and evolution of centromeric transition regions within the human genome.
Nature 2004;430(7002):857-64.
2004: Mathieu Blanchette; W James Kent; Cathy Riemer; Laura Elnitski; Arian F A Smit; Krishna M Roskin; Robert Baertsch; Kate Rosenbloom; Hiram Clawson; Eric Green; David Haussler; Webb Miller
Aligning multiple genomic sequences with the threaded blockset aligner.
Genome research 2004;14(4):708-15.
2004: Diana Kolbe; James TAYLOR; Laura Elnitski; Pallavi Eswara; Jia Li; Webb Miller; Ross C Hardison; Francesca Chiaromonte
Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat.
Genome research 2004;14(4):700-7.
2004: Cristina Tufarelli; Ross Hardison; Webb Miller; Jim Hughes; Kevin Clark; Nicki Ventress; Anna-Maria Frischauf; Douglas R Higgs
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: Shan Yang; Arian F A Smit; Scott Schwartz; Francesca Chiaromonte; Krishna M Roskin; David Haussler; Webb Miller; Ross C Hardison
Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes.
Genome research 2004;14(4):517-27.
2004: Ivan Ovcharenko; Gabriela G Loots; Ross C Hardison; Webb Miller; Lisa Stubbs
zPicture: dynamic alignment and visualization tool for analyzing conservation profiles.
Genome research 2004;14(3):472-7.
2004: Webb Miller; Kateryna D Makova; Anton Nekrutenko; Ross C Hardison
Comparative genomics.
Annual review of genomics and human genetics 2004;5():15-56.
2004: George P Patrinos; Belinda Giardine; Cathy Riemer; Webb Miller; David H K Chui; Nicholas P Anagnou; Henri Wajcman; Ross C Hardison
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.
2003: Francesca Chiaromonte; Webb Miller; Eric E Bouhassira
Gene length and proximity to neighbors affect genome-wide expression levels.
Genome research 2003;13(12):2602-8.
2003: Hooman F Farhadi; Pierre Lepage; Reza Forghani; Hana C H Friedman; Wayel Orfali; Luc Jasmin; Webb Miller; Thomas J Hudson; Alan Peterson
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: monique rijnkels; Laura Elnitski; Webb Miller; Jeffrey M Rosen
Multispecies comparative analysis of a mammalian-specific genomic domain encoding secretory proteins.
Genomics 2003;82(4):417-32.
2003: W James Kent; Robert Baertsch; Angie S Hinrichs; Webb Miller; David Haussler
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: Liliana Florea; Michael McClelland; Cathy Riemer; Scott Schwartz; Webb Miller
EnteriX 2003: Visualization tools for genome alignments of Enterobacteriaceae.
Nucleic acids research 2003;31(13):3527-32.
2003: Scott Schwartz; Laura Elnitski; Mei Li; Matt Weirauch; Cathy Riemer; Arian Smit; Eric Green; Ross C Hardison; Webb Miller
MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences.
Nucleic acids research 2003;31(13):3518-24.
2003: Belinda Giardine; Laura Elnitski; Cathy Riemer; Izabela Makalowska; Scott Schwartz; Webb Miller; Ross C Hardison
GALA, a database for genomic sequence alignments and annotations.
Genome research 2003;13(4):732-41.
2003: Phil Green; Brent Ewing; Webb Miller; Pamela J Thomas; Eric Green
Transcription-associated mutational asymmetry in mammalian evolution.
Nature genetics 2003;33(4):514-7.
2003: Laura Elnitski; Cathy Riemer; Scott Schwartz; Ross Hardison; Webb Miller
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: Ross C Hardison; Francesca Chiaromonte; Diana Kolbe; H Wang; Hanna Petrykowska; Laura Elnitski; Shan Yang; Belinda Giardine; Yi Zhang; Cathy Riemer; Scott Schwartz; David Haussler; Krishna M Roskin; RJ Weber; Mark Diekhans; W James Kent; Mitchell J Weiss; john welch; Webb Miller
Global predictions and tests of erythroid regulatory regions.
Cold Spring Harbor symposia on quantitative biology 2003;68():335-44.
2003: C Yung Yu; Erwin K Chung; Yan Yang; Carol A Blanchong; Natalie Jacobsen; Kapil Saxena; Zhenyu Yang; Webb Miller; Lilian Varga; George Füst
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: Jia Li; Webb Miller
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.
2003: Scott Schwartz; W James Kent; Arian Smit; Zheng Zhang; Robert Baertsch; Ross C Hardison; David Haussler; Webb Miller
Human-mouse alignments with BLASTZ.
Genome research 2003;13(1):103-7.
2003: Laura Elnitski; Ross C Hardison; Jia Li; Shan Yang; Diana Kolbe; Pallavi Eswara; Michael J O'Connor; Scott Schwartz; Webb Miller; Francesca Chiaromonte
Distinguishing regulatory DNA from neutral sites.
Genome research 2003;13(1):64-72.
2003: Ross C Hardison; Krishna M Roskin; Shan Yang; Mark Diekhans; W James Kent; Ryan Weber; Laura Elnitski; Jia Li; Michael O'Connor; Diana Kolbe; Scott Schwartz; Terrence S Furey; Simon Whelan; Nick Goldman; Arian Smit; Webb Miller; Francesca Chiaromonte; David Haussler
Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution.
Genome research 2003;13(1):13-26.
2002: Laura Elnitski; Cathy Riemer; Hanna Petrykowska; Liliana Florea; Scott Schwartz; Webb Miller; Ross C Hardison
PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences.
Genomics 2002;80(6):681-90.
2002: Jude E Maul; jenny lilly; Liying Cui; Claude W dePamphilis; Webb Miller; Elizabeth H Harris; David B Stern
The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of repeats.
The Plant cell 2002;14(11):2659-79.
2002: Peter Agron; Madison Macht; Lyndsay Radnedge; Evan W Skowronski; Webb Miller; Gary L Andersen
Use of subtractive hybridization for comprehensive surveys of prokaryotic genome differences.
FEMS microbiology letters 2002;211(2):175-82.
2002: Ross C Hardison; David H K Chui; Belinda Giardine; Cathy Riemer; George P Patrinos; Nicholas P Anagnou; Webb Miller; Henri Wajcman
HbVar: A relational database of human hemoglobin variants and thalassemia mutations at the globin gene server.
Human mutation 2002;19(3):225-33.
2002: Laurie Jo Kurihara; Ekaterina Semenova; Webb Miller; Robert S Ingram; Xiao-Juan Guan; Shirley M Tilghman
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: Joseph M Molete; Hanna Petrykowska; Martin Sigg; Webb Miller; Ross C Hardison
Functional and binding studies of HS3.2 of the beta-globin locus control region.
Gene 2002;283(1-2):185-97.
2002: Kenta Sumiyama; Steven Q Irvine; David W Stock; Kenneth M Weiss; Kazuhiko Kawasaki; Nobuyoshi Shimizu; Cooduvalli S Shashikant; Webb Miller; Frank H Ruddle
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: Francesca Chiaromonte; V B Yap; Webb Miller
Scoring pairwise genomic sequence alignments.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2002;():115-26.
2002: Udaya DeSilva; Laura Elnitski; Jacquelyn R Idol; Johannah L Doyle; Weiniu Gan; James W Thomas; Scott Schwartz; Nicole L Dietrich; Stephen Beckstrom-Sternberg; Jennifer C McDowell; Robert W Blakesley; Gerald Bouffard; Pamela J Thomas; Jeffrey W Touchman; Webb Miller; Eric Green
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.
2001: Francesca Chiaromonte; Shan Yang; Laura Elnitski; V B Yap; Webb Miller; Ross C Hardison
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: Michael McClelland; K E Sanderson; John Spieth; Sandra W Clifton; P Latreille; L Courtney; Steffen Porwollik; J Ali; Mike Dante; F Du; S Hou; D Layman; S Leonard; C Nguyen; K Scott; A Holmes; N Grewal; E Mulvaney; E Ryan; H Sun; Liliana Florea; Webb Miller; T Stoneking; M Nhan; Robert H Waterston; Richard K Wilson
Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.
Nature 2001;413(6858):852-6.
2001: Ross C Hardison; David H K Chui; Cathy Riemer; Belinda Giardine; H Lehväslaiho; Henri Wajcman; Webb Miller
Databases of human hemoglobin variants and other resources at the globin gene server.
Hemoglobin 2001;25(2):183-93.
2001: J M Molete; Hanna Petrykowska; Eric E Bouhassira; Yong-Qing Feng; Webb Miller; Ross C Hardison
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: Laura Elnitski; J Li; Constance Tom Noguchi; Webb Miller; Ross C Hardison
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: Jonathan Flint; Cristina Tufarelli; JF Peden; Kevin Clark; Rachael J Daniels; Ross Hardison; Webb Miller; Sjaak Philipsen; Kian-Cheng Tan-Un; Tara McMorrow; Jon Frampton; BLANCHE ALTER; Anna-Maria Frischauf; Douglas R Higgs
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: Michael McClelland; Liliana Florea; K Sanderson; Sandra W Clifton; J Parkhill; C Churcher; G Dougan; Richard K Wilson; Webb Miller
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: Liliana Florea; Cathy Riemer; Scott Schwartz; Zhaolei Zhang; Nikola Stojanovic; Webb Miller; Michael McClelland
Web-based visualization tools for bacterial genome alignments.
Nucleic acids research 2000;28(18):3486-96.
2000: Chack Yung Yu; Z Yang; Carol A Blanchong; Webb Miller
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: Gabriela G Loots; Richard M Locksley; C M Blankespoor; Zhi-En Wang; Webb Miller; Edward M Rubin; Kelly A Frazer
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: Scott Schwartz; Zhaolei Zhang; K A Frazer; Arian Smit; Cathy Riemer; John Bouck; Richard Gibbs; Ross C Hardison; Webb Miller
PipMaker--a web server for aligning two genomic DNA sequences.
Genome research 2000;10(4):577-86.
2000: Chang-Bae Kim; Chris T Amemiya; W Bailey; Kazuhiko Kawasaki; JG Mezey; Webb Miller; S Minoshima; Nobuyoshi Shimizu; G Wagner; Frank H Ruddle
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: Piotr Berman; Zhaolei Zhang; Y I Wolf; Eugene V Koonin; Webb Miller
Winnowing sequences from a database search.
Journal of computational biology : a journal of computational molecular cell biology 2000;7(1-2):293-302.
2000: Zhaolei Zhang; S Schwartz; L Wagner; Webb Miller
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: Rachel E Ellsworth; DC Jamison; Jeffrey W Touchman; SL Chissoe; V V Braden Maduro; Gerald Bouffard; Nicole L Dietrich; Stephen Beckstrom-Sternberg; LM Iyer; LA Weintraub; M Cotton; L Courtney; J Edwards; R Maupin; Philip Ozersky; T Rohlfing; P Wohldmann; Tracie L Miner; K Kemp; J Kramer; Ian F Korf; Kymberlie H Pepin; L Antonacci-Fulton; Robert S Fulton; Patrick J Minx; L W Hillier; Richard K Wilson; Robert H Waterston; Webb Miller; Eric Green
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: J L Doyle; Udaya DeSilva; Webb Miller; Eric Green
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: Nikola Stojanovic; Liliana Florea; Cathy Riemer; Deborah L Gumucio; Jerry L Slightom; Morris Goodman; Webb Miller; Ross C Hardison
Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions.
Nucleic acids research 1999;27(19):3899-910.
1999: X Y Liu; Andrew W Dangel; Richard I Kelley; W Zhao; Paul Denny; M Botcherby; Bruce Cattanach; Jo Peters; P R Hunsicker; Ann-Marie Mallon; Mark A Strivens; R Bate; Webb Miller; M Rhodes; Steve D M Brown; Gail E Herman
The gene mutated in bare patches and striated mice encodes a novel 3beta-hydroxysteroid dehydrogenase.
Nature genetics 1999;22(2):182-7.
1999: W Jang; A Hua; Sandra V Spilson; Webb Miller; Bruce A Roe; Miriam H Meisler
Comparative sequence of human and mouse BAC clones from the mnd2 region of chromosome 2p13.
Genome research 1999;9(1):53-61.
1998: Cathy Riemer; A ElSherbini; Nikola Stojanovic; Scott Schwartz; P B Kwitkin; Webb Miller; Ross C Hardison
A database of experimental results on globin gene expression.
Genomics 1998;53(3):325-37.
1998: John Bouck; Webb Miller; JH Gorrell; Donna M Muzny; Richard A Gibbs
Analysis of the quality and utility of random shotgun sequencing at low redundancies.
Genome research 1998;8(10):1074-84.
1998: Liliana Florea; G Hartzell; Zhaolei Zhang; G M Rubin; Webb Miller
A computer program for aligning a cDNA sequence with a genomic DNA sequence.
Genome research 1998;8(9):967-74.
1998: Zhaolei Zhang; Alejandro A Schäffer; Webb Miller; Thomas L Madden; David Lipman; Eugene V Koonin; Stephen F Altschul
Protein sequence similarity searches using patterns as seeds.
Nucleic acids research 1998;26(17):3986-90.
1998: David H K Chui; Ross C Hardison; Cathy Riemer; Webb Miller; Melinda Carver; TP Molchanova; Georgi D Efremov; T H Huisman
An electronic database of human hemoglobin variants on the World Wide Web.
Blood 1998;91(8):2643-4.
1998: Ross C Hardison; David H K Chui; Cathy Riemer; Webb Miller; Melinda Carver; TP Molchanova; Georgi D Efremov; TH Huisman
Access to a syllabus of human hemoglobin variants (1996) via the World Wide Web.
Hemoglobin 1998;22(2):113-27.
1998: Ross C Hardison; Cathy Riemer; David H K Chui; TH Huisman; Webb Miller
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: Zhaolei Zhang; Piotr Berman; Webb Miller
Alignments without low-scoring regions.
Journal of computational biology : a journal of computational molecular cell biology 1998;5(2):197-210.
1998: MA Ansari-Lari; John C Oeltjen; S Schwartz; Zhengdong D Zhang; Donna M Muzny; J Lu; JH Gorrell; A Craig Chinault; John W Belmont; Webb Miller; Richard A Gibbs
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.
1997: Ross C Hardison; Jerry L Slightom; Deborah L Gumucio; Morris Goodman; Nikola Stojanovic; Webb Miller
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: Ross C Hardison; John C Oeltjen; Webb Miller
Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome.
Genome research 1997;7(10):959-66.
1997: Stephen F Altschul; Thomas L Madden; Alejandro A Schäffer; J Zhang; Zhaolei Zhang; Webb Miller; David Lipman
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Nucleic acids research 1997;25(17):3389-402.
1997: DA Shelton; Lauren D Stegman; Ross C Hardison; Webb Miller; JH Bock; Jerry L Slightom; Morris Goodman; Deborah L Gumucio
Phylogenetic footprinting of hypersensitive site 3 of the beta-globin locus control region.
Blood 1997;89(9):3457-69.
1997: John C Oeltjen; T M Malley; Donna M Muzny; Webb Miller; Richard A Gibbs; John W Belmont
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: Laura Elnitski; Webb Miller; Ross C Hardison
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: Zhaolei Zhang; W R Pearson; Webb Miller
Aligning a DNA sequence with a protein sequence.
Journal of computational biology : a journal of computational molecular cell biology 1997;4(3):339-49.
1997: Jerry L Slightom; JH Bock; D A Tagle; Deborah L Gumucio; Morris Goodman; Nikola Stojanovic; J Jackson; Webb Miller; Ross C Hardison
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.
1996: J D Jackson; Webb Miller; Ross C Hardison
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: J D Jackson; Hanna Petrykowska; S Philipsen; Webb Miller; Ross C Hardison
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: Kun-Mao Chao; J Zhang; James Ostell; Webb Miller
A local alignment tool for very long DNA sequences.
Computer applications in the biosciences : CABIOS 1995;11(2):147-53.
1994: Webb Miller; M Boguski
A note about computing all local alignments.
Computer applications in the biosciences : CABIOS 1994;10(4):455-6.
1994: Ross C Hardison; Kun-Mao Chao; S Schwartz; Nikola Stojanovic; M Ganetsky; Webb Miller
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: Kun-Mao Chao; Ross C Hardison; Webb Miller
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: Zhaolei Zhang; B Raghavachari; Ross C Hardison; Webb Miller
Chaining multiple-alignment blocks.
Journal of computational biology : a journal of computational molecular cell biology 1994;1(3):217-26.
1994: Webb Miller; M Boguski; B Raghavachari; Zhaolei Zhang; Ross C Hardison
Constructing aligned sequence blocks.
Journal of computational biology : a journal of computational molecular cell biology 1994;1(1):51-64.
1993: Kun-Mao Chao; Ross C Hardison; Webb Miller
Locating well-conserved regions within a pairwise alignment.
Computer applications in the biosciences : CABIOS 1993;9(4):387-96.
1993: Kun-Mao Chao; Ross C Hardison; Webb Miller
Constrained sequence alignment.
Bulletin of mathematical biology 1993;55(3):503-24.
1993: Webb Miller
Building multiple alignments from pairwise alignments.
Computer applications in the biosciences : CABIOS 1993;9(2):169-76.
1993: Ross C Hardison; J Xu; J Jackson; J Mansberger; O Selifonova; B Grotch; J Biesecker; Hanna Petrykowska; Webb Miller
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: Ross C Hardison; Webb Miller
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: Ross C Hardison; Kun-Mao Chao; M Adamkiewicz; D Price; J Jackson; T Zeigler; Nikola Stojanovic; Webb Miller
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: D K Price; J A Ayres; D Pasqualone; C H Cabell; Webb Miller; Ross C Hardison
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: Kun-Mao Chao; W R Pearson; Webb Miller
Aligning two sequences within a specified diagonal band.
Computer applications in the biosciences : CABIOS 1992;8(5):481-7.
1992: Mark S Boguski; R C Hardison; S Schwartz; Webb Miller
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: Ross C Hardison; D Krane; D Vandenbergh; J F Cheng; J Mansberger; J Taddie; S Schwartz; X Q Huang; Webb Miller
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: Webb Miller; J Barr; Kenneth E Rudd
Improved algorithms for searching restriction maps.
Computer applications in the biosciences : CABIOS 1991;7(4):447-56.
1991: S Schwartz; Webb Miller; C M Yang; Ross C Hardison
Software tools for analyzing pairwise alignments of long sequences.
Nucleic acids research 1991;19(17):4663-7.
1991: Kenneth E Rudd; Webb Miller; Craig Werner; James Ostell; C Tolstoshev; S G Satterfield
Mapping sequenced E.coli genes by computer: software, strategies and examples.
Nucleic acids research 1991;19(3):637-47.
1990: Stephen F Altschul; W Gish; Webb Miller; E W Myers; David Lipman
Basic local alignment search tool.
Journal of molecular biology 1990;215(3):403-10.
1990: Webb Miller; James Ostell; Kenneth E Rudd
An algorithm for searching restriction maps.
Computer applications in the biosciences : CABIOS 1990;6(3):247-52.
1990: Kenneth E Rudd; Webb Miller; James Ostell; Dennis A Benson
Alignment of Escherichia coli K12 DNA sequences to a genomic restriction map.
Nucleic acids research 1990;18(2):313-21.