Webb Miller

Pennsylvania State University

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DOI: 10.1002/0471250953.bi1002s00
·
2003
Cited 10 times
PipMaker: A World Wide Web Server for Genomic Sequence Alignments
Webb Miller
DOI: 10.1002/0471250953.bi1004s9
·
2005
Cited 10 times
MultiPipMaker: Comparative Alignment Server for Multiple DNA Sequences
Webb Miller
DOI: 10.1002/0471250953.bi1502s39
·
2012
Some Phenotype Association Tools in Galaxy: Looking for Disease SNPs in a Full Genome
Webb Miller
DOI: 10.1002/humu.10044
·
2002
Cited 331 times
HbVar: A relational database of human hemoglobin variants and thalassemia mutations at the globin gene server
Webb Miller
DOI: 10.1002/humu.20484
·
2007
Cited 76 times
PhenCode: connecting ENCODE data with mutations and phenotype
Webb Miller
DOI: 10.1002/humu.9479
·
2007
Cited 170 times
HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update
Webb Miller
DOI: 10.1002/j.1097-024x.1986.tb00012.x
·
1986
Side‐effects in Automatic File Updating
Webb Miller
DOI: 10.1002/spe.4380151102
·
1985
Cited 173 times
A file comparison program
Webb Miller
DOI: 10.1002/spe.4380180703
·
1988
Cited 3 times
A simple row-replacement method
Webb Miller
DOI: 10.1006/geno.1994.1275
·
1994
Cited 32 times
Globin Gene Server: A Prototype E-Mail Database Server Featuring Extensive Multiple Alignments and Data Compilation for Electronic Genetic Analysis
Webb Miller
DOI: 10.1006/geno.1996.4458
·
1997
Cited 31 times
The Complete Sequences of the Galago and Rabbit β-Globin Locus Control Regions: Extended Sequence and Functional Conservation Outside the Cores of DNase Hypersensitive Sites
Webb Miller
DOI: 10.1006/geno.1997.4995
·
1997
Cited 556 times
Comparison of DNA Sequences with Protein Sequences
Webb Miller
DOI: 10.1006/geno.1997.5147
·
1998
Cited 35 times
PROGRAM DESCRIPTION
Webb Miller
DOI: 10.1006/geno.1998.5524
·
1998
Cited 16 times
A Database of Experimental Results on Globin Gene Expression
Webb Miller
DOI: 10.1006/geno.1999.5910
·
1999
Cited 38 times
Comparative Sequence Analysis of the Mouse and Human Lgn1/SMA Interval
Webb Miller
DOI: 10.1006/geno.1999.5976
·
1999
Cited 141 times
Characterization of the Human and Mouse Unconventional Myosin XV Genes Responsible for Hereditary Deafness DFNB3 and Shaker 2
Webb Miller
DOI: 10.1006/geno.2002.6692
·
2002
Cited 18 times
Candidate Genes Required for Embryonic Development: A Comparative Analysis of Distal Mouse Chromosome 14 and Human Chromosome 13q22
Webb Miller
DOI: 10.1006/geno.2002.7018
·
2002
Cited 35 times
PipTools: A Computational Toolkit to Annotate and Analyze Pairwise Comparisons of Genomic Sequences
Webb Miller
DOI: 10.1007/11851561_13
·
2006
Cited 8 times
Controlling Size When Aligning Multiple Genomic Sequences with Duplications
Webb Miller
DOI: 10.1007/3-540-07170-9_24
·
1975
The error in interval arithmetic
Webb Miller
DOI: 10.1007/3-540-58094-8_8
·
1994
Cited 13 times
Parametric recomputing in alignment graphs
Webb Miller
DOI: 10.1007/3-540-63307-3_53
·
1997
Cited 34 times
A linear-time algorithm for the 1-mismatch problem
Webb Miller
DOI: 10.1007/978-1-59745-514-5_2
·
2007
Cited 22 times
Comparative Genomic Analysis Using the UCSC Genome Browser
Webb Miller
DOI: 10.1007/978-1-59745-581-7_11
·
2008
Cited 23 times
Computational Reconstruction of Ancestral DNA Sequences
Webb Miller
DOI: 10.1007/978-1-59745-581-7_9
·
2008
Cited 8 times
Phylogenomic Resources at the UCSC Genome Browser
Webb Miller
DOI: 10.1007/978-3-540-74960-8_10
·
2007
A Heuristic Algorithm for Reconstructing Ancestral Gene Orders with Duplications
Webb Miller
DOI: 10.1007/978-3-540-78839-3_4
·
2008
Cited 11 times
Reconstructing the Evolutionary History of Complex Human Gene Clusters
Webb Miller
DOI: 10.1007/978-3-642-04744-2_10
·
2009
Inferring the Recent Duplication History of a Gene Cluster
Webb Miller
DOI: 10.1007/978-3-642-04744-2_15
·
2009
Cited 3 times
Whole-Genome Analysis of Gene Conversion Events
Webb Miller
DOI: 10.1007/978-3-642-04744-2_9
·
2009
Aligning Two Genomic Sequences That Contain Duplications
Webb Miller
DOI: 10.1007/bf01188583
·
1995
Cited 39 times
Linear-space algorithms that build local alignments from fragments
Webb Miller
DOI: 10.1007/bf01404925
·
1972
Cited 6 times
On the stability of finite numerical procedures
Webb Miller
DOI: 10.1007/bf01932300
·
1972
Cited 15 times
Quadratic convergence in interval arithmetic, part I
Webb Miller
DOI: 10.1007/bf01932301
·
1972
Cited 5 times
Quadratic convergence in interval arithmetic, part II
Webb Miller
DOI: 10.1007/bf01932816
·
1972
Cited 8 times
On an interval-arithmetic matrix method
Webb Miller
DOI: 10.1007/bf01933525
·
1973
Cited 13 times
More on quadratic convergence in interval arithmetic
Webb Miller
DOI: 10.1007/bf01939411
·
1971
Cited 4 times
A note on the instability of Gaussian elimination
Webb Miller
DOI: 10.1007/bf02460648
·
1993
Cited 20 times
Constrained sequence alignment
Webb Miller
DOI: 10.1007/s004270050234
·
1999
Cited 14 times
The mouse cornichon gene family
Webb Miller
DOI: 10.1016/0020-0190(90)90035-v
·
1990
Cited 105 times
An O(NP) sequence comparison algorithm
Webb Miller
DOI: 10.1016/0022-2836(91)90209-o
·
1991
Cited 37 times
Sequence and comparative analysis of the rabbit α-like globin gene cluster reveals a rapid mode of evolution in a G + C-rich region of mammalian genomes
Webb Miller
DOI: 10.1016/0076-6879(92)10029-d
·
1992
Cited 91 times
[27] Dynamic programming algorithms for biological sequence comparison
Webb Miller
DOI: 10.1016/0196-8858(91)90017-d
·
1991
Cited 876 times
A time-efficient, linear-space local similarity algorithm
Webb Miller
DOI: 10.1016/j.bbrc.2016.04.052
·
2016
Sex determination by SRY PCR and sequencing of Tasmanian devil facial tumour cell lines reveals non-allograft transmission
Webb Miller
DOI: 10.1016/j.bcmd.2006.10.109
·
2007
HbVar database for human hemoglobin variants and thalassemia mutations
Webb Miller
DOI: 10.1016/j.bcmd.2006.10.158
·
2007
Validation of predicted erythroid cis-regulatory modules
Webb Miller
DOI: 10.1016/j.celrep.2015.06.027
·
2015
Cited 112 times
Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic
Webb Miller
DOI: 10.1016/j.jhevol.2014.06.016
·
2015
Cited 75 times
Comparative and population mitogenomic analyses of Madagascar's extinct, giant ‘subfossil’ lemurs
Webb Miller
DOI: 10.1016/s0022-0000(70)80043-5
·
1970
Cited 16 times
Recursive function theory and numerical analysis
Webb Miller
DOI: 10.1016/s0022-2836(05)80360-2
·
1990
Cited 71,750 times
Basic local alignment search tool
Webb Miller
DOI: 10.1016/s0079-6603(03)75007-7
·
2003
Cited 51 times
Dancing with Complement C4 and the RP-C4-CYP21-TNX (RCCX) Modules of the Major Histocompatibility Complex
Webb Miller
DOI: 10.1016/s0092-8240(88)80016-8
·
1988
Cited 97 times
Sequence comparison with concave weighting functions
Webb Miller
DOI: 10.1016/s0092-8240(89)80046-1
·
1989
Cited 111 times
Approximate matching of regular expressions
Webb Miller
DOI: 10.1016/s0166-218x(02)00289-5
·
2003
Cited 7 times
Aligning two fragmented sequences
Webb Miller
DOI: 10.1016/s0166-218x(96)00072-8
·
1996
Cited 8 times
Local multiple alignment via subgraph enumeration
Webb Miller
DOI: 10.1016/s0167-5699(00)01664-9
·
2000
Cited 42 times
The human and mouse MHC class III region: a parade of 21 genes at the centromeric segment
Webb Miller
DOI: 10.1016/s0378-1119(00)00510-2
·
2000
Cited 56 times
Levels of GATA-1/GATA-2 transcription factors modulate expression of embryonic and fetal hemoglobins
Webb Miller
DOI: 10.1016/s0378-1119(01)00858-7
·
2002
Cited 12 times
Functional and binding studies of HS3.2 of the beta-globin locus control region
Webb Miller
DOI: 10.1016/s0378-1119(97)00474-5
·
1997
Cited 228 times
Locus control regions of mammalian β-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insights
Webb Miller
DOI: 10.1016/s0888-7543(03)00114-9
·
2003
Cited 72 times
Multispecies comparative analysis of a mammalian-specific genomic domain encoding secretory proteins
Webb Miller
DOI: 10.1016/s0888-7543(05)80222-8
·
1992
Cited 15 times
The 5′ ends of LINE1 repeats in rabbit DNA define subfamilies and reveal a short sequence conserved between rabbits and humans
Webb Miller
DOI: 10.1038/35101614
·
2001
Cited 1,674 times
Complete genome sequence of Salmonella enterica serovar Typhimurium LT2
Webb Miller
DOI: 10.1038/461168a
·
2009
Cited 226 times
Prepublication data sharing
Webb Miller
DOI: 10.1038/72588
·
2000
Cited 19 times
So many genomes, so little time
Webb Miller
DOI: 10.1038/9700
·
1999
Cited 145 times
The gene mutated in bare patches and striated mice encodes a novel 3β-hydroxysteroid dehydrogenase
Webb Miller
DOI: 10.1038/nature01262
·
2002
Cited 6,199 times
Initial sequencing and comparative analysis of the mouse genome
Webb Miller
DOI: 10.1038/nature01858
·
2003
Cited 589 times
Comparative analyses of multi-species sequences from targeted genomic regions
Webb Miller
DOI: 10.1038/nature02426
·
2004
Cited 1,912 times
Genome sequence of the Brown Norway rat yields insights into mammalian evolution
Webb Miller
DOI: 10.1038/nature02806
·
2004
Cited 172 times
The structure and evolution of centromeric transition regions within the human genome
Webb Miller
DOI: 10.1038/nature03394
·
2005
Cited 10 times
Erratum: Corrigendum: Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
Webb Miller
DOI: 10.1038/nature03466
·
2005
Cited 74 times
Generation and annotation of the DNA sequences of human chromosomes 2 and 4
Webb Miller
DOI: 10.1038/nature05874
·
2007
Cited 4,561 times
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
Webb Miller
DOI: 10.1038/nature06936
·
2008
Cited 635 times
Genome analysis of the platypus reveals unique signatures of evolution
Webb Miller
DOI: 10.1038/nature07446
·
2008
Cited 293 times
Sequencing the nuclear genome of the extinct woolly mammoth
Webb Miller
DOI: 10.1038/nature08795
·
2010
Cited 418 times
Complete Khoisan and Bantu genomes from southern Africa
Webb Miller
DOI: 10.1038/nature09687
·
2011
Cited 516 times
Comparative and demographic analysis of orang-utan genomes
Webb Miller
DOI: 10.1038/ncomms11519
·
2016
Cited 40 times
Giraffe genome sequence reveals clues to its unique morphology and physiology
Webb Miller
DOI: 10.1038/ncomms6692
·
2014
Cited 59 times
Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history
Webb Miller
DOI: 10.1038/ng.785
·
2011
Cited 136 times
Systematic documentation and analysis of human genetic variation in hemoglobinopathies using the microattribution approach
Webb Miller
DOI: 10.1038/ng1103
·
2003
Cited 280 times
Transcription-associated mutational asymmetry in mammalian evolution
Webb Miller
DOI: 10.1038/s41598-020-69101-z
·
2020
Cited 14 times
STAGdb: a 30K SNP genotyping array and Science Gateway for Acropora corals and their dinoflagellate symbionts
Webb Miller
DOI: 10.1073/pnas.012584999
·
2002
Cited 68 times
Genomic structure and functional control of the Dlx3-7 bigene cluster
Webb Miller
DOI: 10.1073/pnas.030539697
·
2000
Cited 105 times
Hox cluster genomics in the horn shark, Heterodontus francisci
Webb Miller
DOI: 10.1073/pnas.0409882102
·
2005
Cited 110 times
An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing
Webb Miller
DOI: 10.1073/pnas.0802315105
·
2008
Cited 155 times
Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes
Webb Miller
DOI: 10.1073/pnas.0805217105
·
2008
Cited 78 times
The infinite sites model of genome evolution
Webb Miller
DOI: 10.1073/pnas.091095898
·
2001
Cited 65 times
Sequence conservation at human and mouse orthologous common fragile regions, FRA3B/FHIT and Fra14A2/Fhit
Webb Miller
DOI: 10.1073/pnas.0914266107
·
2010
Cited 128 times
Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear
Webb Miller
DOI: 10.1073/pnas.1102838108
·
2011
Cited 181 times
Genetic diversity and population structure of the endangered marsupial <i>Sarcophilus harrisii</i> (Tasmanian devil)
Webb Miller
DOI: 10.1073/pnas.1210506109
·
2012
Cited 284 times
Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change
Webb Miller
DOI: 10.1073/pnas.1211990110
·
2013
Cited 32 times
Aye-aye population genomic analyses highlight an important center of endemism in northern Madagascar
Webb Miller
DOI: 10.1073/pnas.1217345109
·
2012
Correction for Miller et al., Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil)
Webb Miller
DOI: 10.1073/pnas.1932072100
·
2003
Cited 731 times
Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes
Webb Miller
DOI: 10.1073/pnas.251423898
·
2001
Cited 39 times
Association between divergence and interspersed repeats in mammalian noncoding genomic DNA
Webb Miller
DOI: 10.1073/pnas.97.3.1172
·
2000
Cited 68 times
Comparative genomic sequence analysis of the human and mouse cystic fibrosis transmembrane conductance regulator genes
Webb Miller
DOI: 10.1074/jbc.271.20.11871
·
1996
Cited 54 times
Role of DNA Sequences Outside the Cores of DNase Hypersensitive Sites (HSs) in Functions of the β-Globin Locus Control Region
Webb Miller
DOI: 10.1074/jbc.272.1.369
·
1997
Cited 79 times
Conserved E Boxes Function as Part of the Enhancer in Hypersensitive Site 2 of the β-Globin Locus Control Region
Webb Miller
DOI: 10.1074/jbc.273.17.10202
·
1998
Cited 25 times
Multiple Regulatory Elements in the 5′-Flanking Sequence of the Human ε-Globin Gene
Webb Miller
DOI: 10.1074/jbc.m009624200
·
2001
Cited 16 times
A Negative Cis-element Regulates the Level of Enhancement by Hypersensitive Site 2 of the β-Globin Locus Control Region
Webb Miller
DOI: 10.1081/hem-100104027
·
2001
Cited 30 times
DATABASES OF HUMAN HEMOGLOBIN VARIANTS AND OTHER RESOURCES AT THE GLOBIN GENE SERVER
Webb Miller
DOI: 10.1089/10665270050081478
·
2000
Cited 3,858 times
A Greedy Algorithm for Aligning DNA Sequences
Webb Miller
DOI: 10.1089/10665270050081531
·
2000
Cited 6 times
Winnowing Sequences from a Database Search
Webb Miller
DOI: 10.1089/10665270360688174
·
2003
Cited 12 times
Significance of Interspecies Matches when Evolutionary Rate Varies
Webb Miller
DOI: 10.1089/1066527041410427
·
2004
Special RECOMB 2003 Issue
Webb Miller
DOI: 10.1089/cmb.1994.1.217
·
1994
Cited 23 times
Chaining Multiple-Alignment Blocks
Webb Miller
DOI: 10.1089/cmb.1994.1.271
·
1994
Cited 57 times
Recent Developments in Linear-Space Alignment Methods: A Survey
Webb Miller
DOI: 10.1089/cmb.1994.1.51
·
1994
Cited 11 times
Constructing Aligned Sequence Blocks
Webb Miller
DOI: 10.1089/cmb.1996.3.563
·
1996
Cited 21 times
Progressive Multiple Alignment with Constraints
Webb Miller
DOI: 10.1089/cmb.1997.4.339
·
1997
Cited 25 times
Aligning a DNA Sequence with a Protein Sequence
Webb Miller
DOI: 10.1089/cmb.1998.5.197
·
1998
Cited 41 times
Alignments Without Low-Scoring Regions
Webb Miller
DOI: 10.1089/cmb.2008.0069
·
2008
Cited 55 times
DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications
Webb Miller
DOI: 10.1089/cmb.2009.0040
·
2009
Cited 5 times
Evolutionary History Reconstruction for Mammalian Complex Gene Clusters
Webb Miller
DOI: 10.1089/cmb.2010.0094
·
2010
Cited 8 times
CAGE: Combinatorial Analysis of Gene-Cluster Evolution
Webb Miller
DOI: 10.1089/cmb.2010.0103
·
2010
Cited 11 times
An Effective Method for Detecting Gene Conversion Events in Whole Genomes
Webb Miller
DOI: 10.1093/bib/1.4.381
·
2000
Cited 23 times
Genome sequence comparisons: Hurdles in the fast lane to functional genomics
Webb Miller
DOI: 10.1093/bioinformatics/10.4.455
·
1994
A note about computing all local alignments
Webb Miller
DOI: 10.1093/bioinformatics/11.2.147
·
1995
Cited 31 times
A local alignment tool for very long DNA sequences
Webb Miller
DOI: 10.1093/bioinformatics/13.1.75
·
1997
Cited 18 times
A tool for aligning very similar DNA sequences
Webb Miller
DOI: 10.1093/bioinformatics/15.12.1012
·
1999
Cited 52 times
Post-processing long pairwise alignments
Webb Miller
DOI: 10.1093/bioinformatics/17.5.391
·
2001
Cited 113 times
Comparison of genomic DNA sequences: solved and unsolved problems
Webb Miller
DOI: 10.1093/bioinformatics/4.1.11
·
1988
Cited 722 times
Optimal alignments in linear space
Webb Miller
DOI: 10.1093/bioinformatics/6.3.247
·
1990
Cited 7 times
An algorithm for searching restriction maps
Webb Miller
DOI: 10.1093/bioinformatics/6.4.373
·
1990
Cited 98 times
A space-efficient algorithm for local similarities
Webb Miller
DOI: 10.1093/bioinformatics/7.4.447
·
1991
Cited 6 times
Improved algorithms for searching restriction maps
Webb Miller
DOI: 10.1093/bioinformatics/8.2.155
·
1992
Cited 15 times
Parallelization of a local similarity algorithm
Webb Miller
DOI: 10.1093/bioinformatics/8.5.481
·
1992
Cited 90 times
Aligning two sequences within a specified diagonal band
Webb Miller
DOI: 10.1093/bioinformatics/9.2.169
·
1993
Cited 20 times
Building multiple alignments from pairwise alignments
Webb Miller
DOI: 10.1093/bioinformatics/9.4.387
·
1993
Cited 16 times
Locating well-conserved regions within a pairwise alignment
Webb Miller
DOI: 10.1093/bioinformatics/bth342
·
2004
Cited 69 times
EST clustering error evaluation and correction
Webb Miller
DOI: 10.1093/bioinformatics/btn604
·
2009
Cited 476 times
CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets
Webb Miller
DOI: 10.1093/gbe/evr132
·
2012
Cited 52 times
A Genome Sequence Resource for the Aye-Aye (Daubentonia madagascariensis), a Nocturnal Lemur from Madagascar
Webb Miller
DOI: 10.1093/gbe/evs032
·
2012
Cited 8 times
Revealing Mammalian Evolutionary Relationships by Comparative Analysis of Gene Clusters
Webb Miller
DOI: 10.1093/gbe/evu025
·
2014
Cited 49 times
Polar Bears Exhibit Genome-Wide Signatures of Bioenergetic Adaptation to Life in the Arctic Environment
Webb Miller
DOI: 10.1093/gbe/evz279
·
2020
Cited 6 times
Functional Architecture of Deleterious Genetic Variants in the Genome of a Wrangel Island Mammoth
Webb Miller
DOI: 10.1093/hmg/10.4.371
·
2001
Cited 156 times
Comparative genome analysis delimits a chromosomal domain and identifies key regulatory elements in the alpha globin cluster
Webb Miller
DOI: 10.1093/jhered/esp086
·
2009
Cited 469 times
Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species
Webb Miller
DOI: 10.1093/nar/18.2.313
·
1990
Cited 106 times
Alignment of Escherichia coli K12 DNA sequences to a genomic restriction map
Webb Miller
DOI: 10.1093/nar/19.17.4663
·
1991
Cited 34 times
Software tools for analyzing pairwise alignments of long sequences
Webb Miller
DOI: 10.1093/nar/19.3.637
·
1991
Cited 83 times
Mapping sequencedE.coligenes by computer: software, strategies and examples
Webb Miller
DOI: 10.1093/nar/21.5.1265
·
1993
Cited 43 times
Comparative analysis of the locus control region of the rabbit β-like globin gene cluster: HS3 increases transient expression of an embryonic ε-globin gene
Webb Miller
DOI: 10.1093/nar/24.21.4327
·
1996
Cited 25 times
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
Webb Miller
DOI: 10.1093/nar/25.17.3389
·
1997
Cited 64,067 times
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Webb Miller
DOI: 10.1093/nar/26.17.3986
·
1998
Cited 301 times
Protein sequence similarity searches using patterns as seeds
Webb Miller
DOI: 10.1093/nar/27.19.3899
·
1999
Cited 105 times
Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions
Webb Miller
DOI: 10.1093/nar/28.18.3486
·
2000
Cited 31 times
Web-based visualization tools for bacterial genome alignments
Webb Miller
DOI: 10.1093/nar/28.24.4974
·
2000
Cited 108 times
Comparison of the Escherichia coli K-12 genome with sampled genomes of a Klebsiella pneumoniae and three Salmonella enterica serovars, Typhimurium, Typhi and Paratyphi
Webb Miller
DOI: 10.1093/nar/29.6.1352
·
2001
Cited 50 times
Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5
Webb Miller
DOI: 10.1093/nar/gkg551
·
2003
Cited 24 times
EnteriX 2003: visualization tools for genome alignments of Enterobacteriaceae
Webb Miller
DOI: 10.1093/nar/gkg579
·
2003
Cited 223 times
MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences
Webb Miller
DOI: 10.1093/nar/gkh006
·
2004
Cited 272 times
Improvements in the HbVar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studies
Webb Miller
DOI: 10.1093/nar/gki045
·
2004
Cited 9 times
Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results
Webb Miller
DOI: 10.1093/nar/gkl483
·
2006
Cited 136 times
Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis
Webb Miller
DOI: 10.1093/nar/gkm966
·
2007
Cited 458 times
The UCSC Genome Browser Database: 2008 update
Webb Miller
DOI: 10.1093/nar/gkt911
·
2014
Cited 305 times
Updates of the HbVar database of human hemoglobin variants and thalassemia mutations
Webb Miller
DOI: 10.1093/oxfordjournals.molbev.a039991
·
1993
Cited 36 times
Use of long sequence alignments to study the evolution and regulation of mammalian globin gene clusters.
Webb Miller
DOI: 10.1101/018366
·
2015
Elephantid genomes reveal the molecular bases of Woolly Mammoth adaptations to the arctic
Webb Miller
DOI: 10.1101/047498
·
2016
Cited 7 times
Genome-wide evidence for a hybrid origin of modern polar bears
Webb Miller
DOI: 10.1101/137455
·
2018
Functional architecture of deleterious genetic variants in the Wrangel Island mammoth genome
Webb Miller
DOI: 10.1101/2020.01.21.914424
·
2020
STAGdb: a 30K SNP genotyping array and Science Gateway for Acropora corals and their dinoflagellate symbionts
Webb Miller
DOI: 10.1101/349910
·
2018
Cited 5 times
Genomic variants among threatened<i>Acropora</i>corals
Webb Miller
DOI: 10.1101/397356
·
2018
Relaxed constraint and thermal desensitization of the cold-sensing ion channel TRPM8 in mammoths
Webb Miller
DOI: 10.1101/gr.082628.108
·
2009
Cited 99 times
The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)
Webb Miller
DOI: 10.1101/gr.083089.108
·
2008
Cited 29 times
Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif
Webb Miller
DOI: 10.1101/gr.098921.109
·
2009
Cited 189 times
Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression
Webb Miller
DOI: 10.1101/gr.10.4.577
·
2000
Cited 1,119 times
PipMaker—A Web Server for Aligning Two Genomic DNA Sequences
Webb Miller
DOI: 10.1101/gr.10.6.758
·
2000
Cited 49 times
Comparative Genome Sequence Analysis of the Bpa/Str Region in Mouse and Man
Webb Miller
DOI: 10.1101/gr.10.8.1095
·
2000
Cited 57 times
Genomic Sequence Analysis of the Mouse Naip Gene Array
Webb Miller
DOI: 10.1101/gr.1169203
·
2003
Cited 70 times
Gene Length and Proximity to Neighbors Affect Genome-Wide Expression Levels
Webb Miller
DOI: 10.1101/gr.119016.110
·
2011
Cited 65 times
Genome-wide identification of conserved regulatory function in diverged sequences
Webb Miller
DOI: 10.1101/gr.125088.111
·
2011
Cited 109 times
Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration
Webb Miller
DOI: 10.1101/gr.161800
·
2000
Cited 106 times
Sequence and Comparative Analysis of the Mouse 1-Megabase Region Orthologous to the Human 11p15 Imprinted Domain
Webb Miller
DOI: 10.1101/gr.1933104
·
2004
Cited 1,229 times
Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner
Webb Miller
DOI: 10.1101/gr.1976004
·
2004
Cited 108 times
Regulatory Potential Scores From Genome-Wide Three-Way Alignments of Human, Mouse, and Rat
Webb Miller
DOI: 10.1101/gr.1984404
·
2004
Cited 75 times
Patterns of Insertions and Their Covariation With Substitutions in the Rat, Mouse, and Human Genomes
Webb Miller
DOI: 10.1101/gr.2129504
·
2004
Cited 131 times
zPicture: Dynamic Alignment and Visualization Tool for Analyzing Conservation Profiles
Webb Miller
DOI: 10.1101/gr.2143604
·
2004
Cited 28 times
Comparative Analysis of the -Like Globin Clusters in Mouse, Rat, and Human Chromosomes Indicates a Mechanism Underlying Breaks in Conserved Synteny
Webb Miller
DOI: 10.1101/gr.214802
·
2002
Cited 72 times
Generation and Comparative Analysis of 3.3 Mb of Mouse Genomic Sequence Orthologous to the Region of Human Chromosome 7q11.23 Implicated in Williams Syndrome
Webb Miller
DOI: 10.1101/gr.2800104
·
2004
Cited 136 times
Reconstructing large regions of an ancestral mammalian genome in silico
Webb Miller
DOI: 10.1101/gr.3007205
·
2005
Cited 230 times
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
Webb Miller
DOI: 10.1101/gr.3015505
·
2005
Cited 216 times
Evolution and functional classification of vertebrate gene deserts
Webb Miller
DOI: 10.1101/gr.3642605
·
2005
Cited 202 times
Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences
Webb Miller
DOI: 10.1101/gr.3715005
·
2005
Cited 3,210 times
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Webb Miller
DOI: 10.1101/gr.4086505
·
2005
Cited 1,804 times
Galaxy: A platform for interactive large-scale genome analysis
Webb Miller
DOI: 10.1101/gr.4537706
·
2006
Cited 115 times
ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements
Webb Miller
DOI: 10.1101/gr.5353806
·
2006
Cited 58 times
Experimental validation of predicted mammalian erythroid cis-regulatory modules
Webb Miller
DOI: 10.1101/gr.5383506
·
2006
Cited 255 times
Reconstructing contiguous regions of an ancestral genome
Webb Miller
DOI: 10.1101/gr.5578007
·
2007
Cited 131 times
A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly
Webb Miller
DOI: 10.1101/gr.5592107
·
2007
Cited 77 times
Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data
Webb Miller
DOI: 10.1101/gr.5918807
·
2007
Cited 403 times
Using genomic data to unravel the root of the placental mammal phylogeny
Webb Miller
DOI: 10.1101/gr.603103
·
2003
Cited 44 times
GALA, a Database for Genomic Sequence Alignments and Annotations
Webb Miller
DOI: 10.1101/gr.6034307
·
2007
Cited 197 times
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
Webb Miller
DOI: 10.1101/gr.6761107
·
2007
Cited 252 times
28-Way vertebrate alignment and conservation track in the UCSC Genome Browser
Webb Miller
DOI: 10.1101/gr.7.10.959
·
1997
Cited 301 times
Long Human–Mouse Sequence Alignments Reveal Novel Regulatory Elements: A Reason to Sequence the Mouse Genome
Webb Miller
DOI: 10.1101/gr.7.4.315
·
1997
Cited 136 times
Large-Scale Comparative Sequence Analysis of the Human and Murine Bruton’s Tyrosine Kinase Loci Reveals Conserved Regulatory Domains
Webb Miller
DOI: 10.1101/gr.8.10.1074
·
1998
Cited 59 times
Analysis of the Quality and Utility of Random Shotgun Sequencing at Low Redundancies
Webb Miller
DOI: 10.1101/gr.8.9.967
·
1998
Cited 700 times
A Computer Program for Aligning a cDNA Sequence with a Genomic DNA Sequence
Webb Miller
DOI: 10.1101/gr.809403
·
2003
Cited 1,137 times
Human–Mouse Alignments with BLASTZ
Webb Miller
DOI: 10.1101/gr.817703
·
2003
Cited 131 times
Distinguishing Regulatory DNA From Neutral Sites
Webb Miller
DOI: 10.1101/gr.844103
·
2003
Cited 277 times
Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian Evolution
Webb Miller
DOI: 10.1101/gr.9.1.53
·
1999
Cited 40 times
Comparative Sequence of Human and Mouse BAC Clones from the mnd2 Region of Chromosome 2p13
Webb Miller
DOI: 10.1101/sqb.2003.68.335
·
2003
Cited 7 times
Global Predictions and Tests of Erythroid Regulatory Regions
Webb Miller
DOI: 10.1105/tpc.006155
·
2002
Cited 372 times
The<i>Chlamydomonas reinhardtii</i>Plastid Chromosome
Webb Miller
DOI: 10.1109/99.295375
·
1994
Cited 7 times
A point of contact between computer science and molecular biology
Webb Miller
DOI: 10.1109/hicss.1995.375350
·
1995
A database for globin gene expression data
Webb Miller
DOI: 10.1109/ipdps.2002.1016591
·
2002
Aligning two fragmented sequences
Webb Miller
DOI: 10.1111/j.1574-6968.2002.tb11221.x
·
2002
Cited 49 times
Use of subtractive hybridization for comprehensive surveys of prokaryotic genome differences
Webb Miller
DOI: 10.1126/science.1105136
·
2004
Cited 1,903 times
The ENCODE (ENCyclopedia Of DNA Elements) Project
Webb Miller
DOI: 10.1126/science.1123360
·
2006
Cited 527 times
Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA
Webb Miller
DOI: 10.1126/science.1139247
·
2007
Cited 1,168 times
Evolutionary and Biomedical Insights from the Rhesus Macaque Genome
Webb Miller
DOI: 10.1126/science.1139462
·
2007
Cited 118 times
Mobile DNA in Old World Monkeys: A Glimpse Through the Rhesus Macaque Genome
Webb Miller
DOI: 10.1126/science.1146971
·
2007
Cited 229 times
Whole-Genome Shotgun Sequencing of Mitochondria from Ancient Hair Shafts
Webb Miller
DOI: 10.1126/science.1147046
·
2008
Cited 120 times
Comment on "Protein Sequences from Mastodon and Tyrannosaurus rex Revealed by Mass Spectrometry"
Webb Miller
DOI: 10.1126/science.1147555
·
2007
Cited 266 times
Molecular and Genomic Data Identify the Closest Living Relative of Primates
Webb Miller
DOI: 10.1126/science.1158565
·
2008
Cited 3 times
Response to Comment on "Whole-Genome Shotgun Sequencing of Mitochondria from Ancient Hair Shafts"
Webb Miller
DOI: 10.1126/science.288.5463.136
·
2000
Cited 752 times
Identification of a Coordinate Regulator of Interleukins 4, 13, and 5 by Cross-Species Sequence Comparisons
Webb Miller
DOI: 10.1128/mcb.21.9.2969-2980.2001
·
2001
Cited 48 times
Sequences Flanking Hypersensitive Sites of the β-Globin Locus Control Region Are Required for Synergistic Enhancement
Webb Miller
DOI: 10.1137/0204009
·
1975
Cited 50 times
Computational Complexity and Numerical Stability
Webb Miller
DOI: 10.1137/0205017
·
1976
Cited 10 times
Graph Transformations for Roundoff Analysis
Webb Miller
DOI: 10.1137/070682150
·
2008
Cited 32 times
Approximating the Spanning Star Forest Problem and Its Application to Genomic Sequence Alignment
Webb Miller
DOI: 10.1142/9789812799623_0012
·
2001
Cited 102 times
SCORING PAIRWISE GENOMIC SEQUENCE ALIGNMENTS
Webb Miller
DOI: 10.1142/9789812836939_0011
·
2008
COMPUTATIONAL CHALLENGES IN COMPARATIVE GENOMICS: GENE FAMILY EVOLUTION, ANCESTRAL GENOME RECONSTRUCTION, AND APPLICATIONS TO HUMAN GENETICS – SESSION INTRODUCTION
Webb Miller
DOI: 10.1142/9789812836939_0016
·
2008
Cited 4 times
SIMULTANEOUS HISTORY RECONSTRUCTION FOR COMPLEX GENE CLUSTERS IN MULTIPLE SPECIES
Webb Miller
DOI: 10.1142/9789814295291_0001
·
2009
COMPUTATIONAL CHALLENGES IN COMPARATIVE GENOMICS – Session Introduction
Webb Miller
DOI: 10.1142/9789814295291_0006
·
2010
Cited 9 times
OPTIMIZATION METHODS FOR SELECTING FOUNDER INDIVIDUALS FOR CAPTIVE BREEDING OR REINTRODUCTION OF ENDANGERED SPECIES
Webb Miller
DOI: 10.1142/s012905419600004x
·
1996
ALIGNMENT-TO-ALIGNMENT EDITING WITH “MOVE GAP” OPERATIONS
Webb Miller
DOI: 10.1145/267521.267758
·
1997
Cited 22 times
Progressive multiple alignment with constraints
Webb Miller
DOI: 10.1145/267521.267893
·
1997
Cited 23 times
Aligning a DNA sequence with a protein sequence
Webb Miller
DOI: 10.1145/279069.279137
·
1998
Cited 11 times
Alignments without low-scoring regions
Webb Miller
DOI: 10.1145/299432.299451
·
1999
Cited 4 times
Winnowing sequences from a database search
Webb Miller
DOI: 10.1145/321765.321772
·
1973
Cited 4 times
Toward Abstract Numerical Analysis
Webb Miller
DOI: 10.1145/321906.321916
·
1975
Cited 15 times
Computer Search for Numerical Instability
Webb Miller
DOI: 10.1145/340358.340390
·
1999
My adventure using computer science on the Genome project
Webb Miller
DOI: 10.1145/355637.355639
·
1975
Cited 39 times
Software for Roundoff Analysis
Webb Miller
DOI: 10.1145/565196.565224
·
2002
Cited 6 times
Significance Of inter-species matches when evolutionary rate varies
Webb Miller
DOI: 10.1145/59287.59290
·
1989
Cited 16 times
Row replacement algorithms for screen editors
Webb Miller
DOI: 10.1145/800119.803910
·
1974
Computational complexity and numerical stability
Webb Miller
DOI: 10.1159/000056790
·
2000
Cited 19 times
Divergent human and mouse orthologs of a novel gene (WBSCR15/<i>Wbscr15</i>) reside within the genomic interval commonly deleted in Williams syndrome
Webb Miller
DOI: 10.1159/000056803
·
2000
Subject Index Vol. 90, 2000
Webb Miller
DOI: 10.1159/000056804
·
2000
Contents Vol. 90, 2000
Webb Miller
DOI: 10.1182/blood.v89.9.3457
·
1997
Cited 30 times
Phylogenetic Footprinting of Hypersensitive Site 3 of the β-Globin Locus Control Region
Webb Miller
DOI: 10.1182/blood.v91.8.2643.2643_2643_2644
·
1998
Cited 8 times
An Electronic Database of Human Hemoglobin Variants on the World Wide Web
Webb Miller
DOI: 10.1186/1471-2105-11-130
·
2010
Cited 42 times
Calling SNPs without a reference sequence
Webb Miller
DOI: 10.1186/1471-2105-12-s1-s45
·
2011
Cited 7 times
Evaluation of methods for detecting conversion events in gene clusters
Webb Miller
DOI: 10.1186/1471-2148-11-226
·
2011
Cited 11 times
Conversion events in gene clusters
Webb Miller
DOI: 10.1186/1471-2148-9-95
·
2009
Cited 97 times
Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution
Webb Miller
DOI: 10.1186/1471-2164-13-440
·
2012
Cited 27 times
Sequencing and analysis of a South Asian-Indian personal genome
Webb Miller
DOI: 10.1186/1756-0500-3-39
·
2010
Cited 25 times
Interpretation of custom designed Illumina genotype cluster plots for targeted association studies and next-generation sequence validation
Webb Miller
DOI: 10.1186/2047-217x-2-17
·
2013
Cited 19 times
Galaxy tools to study genome diversity
Webb Miller
DOI: 10.1186/gb-2007-8-6-r118
·
2007
Cited 146 times
Fast-evolving noncoding sequences in the human genome
Webb Miller
DOI: 10.1186/gb-2008-9-4-r76
·
2008
Cited 55 times
Human-macaque comparisons illuminate variation in neutral substitution rates
Webb Miller
DOI: 10.1186/s12859-015-0483-6
·
2015
Cited 37 times
Identification of indels in next-generation sequencing data
Webb Miller
DOI: 10.1186/s12864-015-1712-0
·
2015
Cited 32 times
Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools
Webb Miller
DOI: 10.1186/s12954-017-0188-4
·
2017
Cited 11 times
Characteristics of persons who inject drugs and who witness opioid overdoses in Vietnam: a cross-sectional analysis to inform future overdose prevention programs
Webb Miller
DOI: 10.1198/jasa.2006.s110
·
2006
Cited 8 times
An Introduction to Bioinformatics Algorithms
Webb Miller
DOI: 10.1371/journal.pbio.1001046
·
2011
Cited 1,206 times
A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
Webb Miller
DOI: 10.1371/journal.pcbi.0020033
·
2005
Cited 447 times
Identification and Classification of Conserved RNA Secondary Structures in the Human Genome
Webb Miller
DOI: 10.1371/journal.pone.0055089
·
2013
Cited 76 times
Comparison of Sequencing Platforms for Single Nucleotide Variant Calls in a Human Sample
Webb Miller
DOI: 10.1371/journal.pone.0055089.g003
·
2013
Venn diagram showing the overlap in the SNP calls made using data from the three sequencing technologies.
Webb Miller
DOI: 10.1523/jneurosci.23-32-10214.2003
·
2003
Cited 75 times
A Combinatorial Network of Evolutionarily Conserved<i>Myelin Basic Protein</i>Regulatory Sequences Confers Distinct Glial-Specific Phenotypes
Webb Miller
DOI: 10.1534/g3.119.400125
·
2019
Cited 18 times
Genomic Variants Among Threatened<i>Acropora</i>Corals
Webb Miller
DOI: 10.2174/1389202003351733
·
2000
Cited 6 times
Validating Computer Programs for Functional Genomics in Gene Regulatory Regions
Webb Miller
DOI: 10.2307/2008110
·
1984
Cited 7 times
The Engineering of Numerical Software.
Webb Miller
DOI: 10.3109/03630269809092136
·
1998
Cited 60 times
Access to a Syllabus of Human Hemoglobin Variants (1996) Via the World Wide Web
Webb Miller
DOI: 10.3109/10425179309015629
·
1993
Cited 26 times
Positive and negative regulatory elements of the rabbit embryonic ϵ-globin gene revealed by an improved multiple alignment program and functional analysis
Webb Miller
DOI: 10.5555/1283383.1283453
·
2007
Cited 6 times
Approximating the spanning star forest problem and its applications to genomic sequence alignment
Webb Miller
DOI: 10.5555/313651.313661
·
1995
Cited 15 times
Chaining multiple-alignment fragments in sub-quadratic time
Webb Miller
MAG: 88305068
·
1987
Cited 3 times
A software tools sampler
Webb Miller
MAG: 192140180
·
2010
Optimization Methods for Selecting Founder Populations for Captive Breeding of Endangered Species.
Webb Miller
MAG: 1521665908
·
2006
An Introduction to Bioinformatics Algorithms. Neil C. Jones and Pavel A. Pevzner
Webb Miller
MAG: 2120044673
·
1998
Cited 70 times
Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6.
Webb Miller
MAG: 2168148721
·
2004
Cited 465 times
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
Webb Miller
MAG: 2187242998
·
2010
Cited 5 times
Complete Khoisan and Bantu genomes from southern
Webb Miller
MAG: 2223431248
·
2009
Computational pipeline for the empirical detection of cleaved targets of small silencing rnas using degradome sequencing data
Webb Miller
MAG: 2231796970
·
2008
Genome analysis of the platypus reveals unique signatures of evolution | NOVA. The University of Newcastle's Digital Repository
Webb Miller
MAG: 2236118579
·
2014
Supporting California condor conservation management through analysis of species-wide whole genome sequence variation
Webb Miller
MAG: 2240456256
·
2009
Computational Challenges In Comparative Genomics: Gene Family Evolution, Ancestral Genome Reconstruction, And Applications To Human Genetics
Webb Miller
MAG: 2249421042
·
2013
Aye-aye population genomics: Signatures of natural selection
Webb Miller
MAG: 2340118742
·
2016
Whole genome sequencing of California condors is now utilized for guiding genetic management
Webb Miller
MAG: 2410463669
·
1992
Cited 26 times
Analysis of conserved domains and sequence motifs in cellular regulatory proteins and locus control regions using new software tools for multiple alignment and visualization.
Webb Miller
MAG: 2418703643
·
1997
Algorithms for locating conserved regions in alignments
Webb Miller
MAG: 2421755884
·
2011
Automating analysis of gene cluster evolution
Webb Miller
MAG: 2430590882
·
2000
Archeological Evidence of Parasitic Infection from the 19th Century Company Town of Fayette, Michigan
Webb Miller
MAG: 2472705729
·
1997
Software tools for pairwise sequence alignment
Webb Miller
MAG: 2472766040
·
2016
The Use of Genetic Databases in Population Screening Programs for Hemoglobinopathies
Webb Miller
MAG: 2480165257
·
2010
Correction for Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear
Webb Miller
MAG: 2503082614
·
2000
Detecting functional regions in dna with sequence comparison methods: program development and evaluation
Webb Miller
MAG: 2519244818
·
2012
Cited 322 times
An integrated encyclopedia of DNA elements in the human genome
Webb Miller
MAG: 2593215742
·
1972
Error analysis of a five-station P-wave location technique
Webb Miller
MAG: 2619529347
·
2001
Cited 6 times
Erratum: Sequence and comparative analysis of the mouse 1-megabase region orthologous to the human 11p15 imprinted domain (Genome Reasearch (2000) vol. 10 (1697-1710))
Webb Miller
MAG: 2738023245
·
2013
Ancient DNA genomics of Madagascar’s extinct subfossil lemurs: Palaeopropithecus ingens genetic diversity
Webb Miller
MAG: 2740387130
·
2008
Supporting Online Material for Comment on "Protein Sequences from Mastodon and Tyrannosaurus rex Revealed by Mass Spectrometry"
Webb Miller
MAG: 2769157931
·
1999
Functional genomics of the beta-globin gene cluster reveals novel regulatory elements in the locus control region
Webb Miller
MAG: 2784619191
·
1990
Cited 220 times
Basic local alignment search tool. Journal of Molecular Biology
Webb Miller
MAG: 2805324484
·
2004
Genome sequence of the Brown Norway rat yields insights into mammalian evolutionRat Genome Sequencing Project ConsortiumNature200442849352115057822
Webb Miller
MAG: 2912531335
·
2003
Proceedings of the seventh annual international conference on Research in computational molecular biology
Webb Miller
MAG: 2915215879
·
2012
Aye-aye demography and conservation genomics
Webb Miller
MAG: 2996433824
·
2008
Genome analysis of the platypus reveals unique signatures of evolution (vol 453, pg 175, 2008)
Webb Miller
MAG: 3172516730
·
2015
Nuclear genome sequences from the extinct subfossil lemurs Palaeopropithecus ingens and Megaladapis edwardsi
Webb Miller
MAG: 3178533926
·
2004
Erratum: Human-mouse alignments with BLASTZ (Genome Research (2003) vol. 13 (103-107))
Webb Miller
MAG: 3217138381
·
2020
Evolutionary and phylogenetic insights from a nuclear genome of the extinct giant koala lemur Megaladapis edwardsi
Webb Miller