PubRank

Webb Miller

Author PubWeight™ 570.08‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Initial sequencing and comparative analysis of the mouse genome. Nature 2002 96.15
2 Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007 75.09
3 Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 2005 44.08
4 Galaxy: a platform for interactive large-scale genome analysis. Genome Res 2005 35.75
5 Human-mouse alignments with BLASTZ. Genome Res 2003 35.49
6 Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 2004 24.52
7 Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 2004 24.40
8 Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A 2003 16.58
9 Evolutionary and biomedical insights from the rhesus macaque genome. Science 2007 16.21
10 Prepublication data sharing. Nature 2009 12.24
11 Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res 2003 11.12
12 Complete Khoisan and Bantu genomes from southern Africa. Nature 2010 9.06
13 Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science 2005 8.14
14 Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. Genome Res 2005 7.09
15 Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res 2007 7.05
16 Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol 2006 6.73
17 A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res 2007 5.97
18 Genome analysis of the platypus reveals unique signatures of evolution. Nature 2008 5.74
19 Distinguishing regulatory DNA from neutral sites. Genome Res 2003 5.63
20 MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Res 2003 4.97
21 Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis. Nucleic Acids Res 2006 4.70
22 Using genomic data to unravel the root of the placental mammal phylogeny. Genome Res 2007 4.52
23 An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing. Proc Natl Acad Sci U S A 2005 4.38
24 zPicture: dynamic alignment and visualization tool for analyzing conservation profiles. Genome Res 2004 4.26
25 Comparative and demographic analysis of orang-utan genomes. Nature 2011 3.83
26 Reconstructing contiguous regions of an ancestral genome. Genome Res 2006 3.68
27 HbVar: A relational database of human hemoglobin variants and thalassemia mutations at the globin gene server. Hum Mutat 2002 3.65
28 Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat. Genome Res 2004 3.53
29 Transcription-associated mutational asymmetry in mammalian evolution. Nat Genet 2003 3.52
30 Evolution and functional classification of vertebrate gene deserts. Genome Res 2004 2.92
31 Mulan: multiple-sequence local alignment and visualization for studying function and evolution. Genome Res 2004 2.91
32 Whole-genome shotgun sequencing of mitochondria from ancient hair shafts. Science 2007 2.85
33 The structure and evolution of centromeric transition regions within the human genome. Nature 2004 2.78
34 ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements. Genome Res 2006 2.65
35 Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. Genome Res 2009 2.64
36 CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. Bioinformatics 2008 2.58
37 Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. Proc Natl Acad Sci U S A 2010 2.57
38 GALA, a database for genomic sequence alignments and annotations. Genome Res 2003 2.56
39 Systematic documentation and analysis of human genetic variation in hemoglobinopathies using the microattribution approach. Nat Genet 2011 2.51
40 The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of repeats. Plant Cell 2002 2.36
41 Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature 2005 2.27
42 Molecular and genomic data identify the closest living relative of primates. Science 2007 2.26
43 Improvements in the HbVar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studies. Nucleic Acids Res 2004 2.24
44 HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update. Hum Mutat 2007 2.22
45 Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Res 2011 2.07
46 Reconstructing large regions of an ancestral mammalian genome in silico. Genome Res 2004 2.01
47 The infinite sites model of genome evolution. Proc Natl Acad Sci U S A 2008 1.89
48 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 Res 2002 1.80
49 PhenCode: connecting ENCODE data with mutations and phenotype. Hum Mutat 2007 1.75
50 Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data. Genome Res 2007 1.75
51 Experimental validation of predicted mammalian erythroid cis-regulatory modules. Genome Res 2006 1.71
52 Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes. Genome Res 2004 1.70
53 Fast-evolving noncoding sequences in the human genome. Genome Biol 2007 1.64
54 Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif. Genome Res 2008 1.58
55 Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes. Proc Natl Acad Sci U S A 2008 1.53
56 DUPCAR: reconstructing contiguous ancestral regions with duplications. J Comput Biol 2008 1.50
57 Gene length and proximity to neighbors affect genome-wide expression levels. Genome Res 2003 1.47
58 Mobile DNA in Old World monkeys: a glimpse through the rhesus macaque genome. Science 2007 1.47
59 Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry". Science 2008 1.41
60 Human-macaque comparisons illuminate variation in neutral substitution rates. Genome Biol 2008 1.41
61 Calling SNPs without a reference sequence. BMC Bioinformatics 2010 1.36
62 Multispecies comparative analysis of a mammalian-specific genomic domain encoding secretory proteins. Genomics 2003 1.29
63 Comparison of sequencing platforms for single nucleotide variant calls in a human sample. PLoS One 2013 1.28
64 Use of subtractive hybridization for comprehensive surveys of prokaryotic genome differences. FEMS Microbiol Lett 2002 1.24
65 A combinatorial network of evolutionarily conserved myelin basic protein regulatory sequences confers distinct glial-specific phenotypes. J Neurosci 2003 1.23
66 Updates of the HbVar database of human hemoglobin variants and thalassemia mutations. Nucleic Acids Res 2013 1.23
67 Genomic structure and functional control of the Dlx3-7 bigene cluster. Proc Natl Acad Sci U S A 2002 1.22
68 Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results. Nucleic Acids Res 2005 1.21
69 EnteriX 2003: Visualization tools for genome alignments of Enterobacteriaceae. Nucleic Acids Res 2003 1.20
70 Genome-wide identification of conserved regulatory function in diverged sequences. Genome Res 2011 1.07
71 Significance of interspecies matches when evolutionary rate varies. J Comput Biol 2003 1.07
72 Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution. BMC Evol Biol 2009 1.07
73 A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar. Genome Biol Evol 2011 1.07
74 PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences. Genomics 2002 1.01
75 Computational reconstruction of ancestral DNA sequences. Methods Mol Biol 2008 1.00
76 PipMaker: a World Wide Web server for genomic sequence alignments. Curr Protoc Bioinformatics 2003 0.98
77 Comparative genomic analysis using the UCSC genome browser. Methods Mol Biol 2007 0.98
78 MultiPipMaker: a comparative alignment server for multiple DNA sequences. Curr Protoc Bioinformatics 2010 0.97
79 Dancing with complement C4 and the RP-C4-CYP21-TNX (RCCX) modules of the major histocompatibility complex. Prog Nucleic Acid Res Mol Biol 2003 0.96
80 Comparative analysis of the alpha-like globin clusters in mouse, rat, and human chromosomes indicates a mechanism underlying breaks in conserved synteny. Genome Res 2004 0.96
81 Interpretation of custom designed Illumina genotype cluster plots for targeted association studies and next-generation sequence validation. BMC Res Notes 2010 0.93
82 Evolutionary history reconstruction for Mammalian complex gene clusters. J Comput Biol 2009 0.92
83 Sequencing and analysis of a South Asian-Indian personal genome. BMC Genomics 2012 0.91
84 Functional and binding studies of HS3.2 of the beta-globin locus control region. Gene 2002 0.88
85 CAGE: Combinatorial Analysis of Gene-cluster Evolution. J Comput Biol 2010 0.86
86 Aye-aye population genomic analyses highlight an important center of endemism in northern Madagascar. Proc Natl Acad Sci U S A 2013 0.85
87 An effective method for detecting gene conversion events in whole genomes. J Comput Biol 2010 0.84
88 MultiPipMaker: comparative alignment server for multiple DNA sequences. Curr Protoc Bioinformatics 2005 0.83
89 Conversion events in gene clusters. BMC Evol Biol 2011 0.83
90 Phylogenomic resources at the UCSC Genome Browser. Methods Mol Biol 2008 0.83
91 Revealing mammalian evolutionary relationships by comparative analysis of gene clusters. Genome Biol Evol 2012 0.82
92 Polar bears exhibit genome-wide signatures of bioenergetic adaptation to life in the arctic environment. Genome Biol Evol 2014 0.82
93 Simultaneous history reconstruction for complex gene clusters in multiple species. Pac Symp Biocomput 2009 0.81
94 Candidate genes required for embryonic development: a comparative analysis of distal mouse chromosome 14 and human chromosome 13q22. Genomics 2002 0.78
95 Evaluation of methods for detecting conversion events in gene clusters. BMC Bioinformatics 2011 0.78
96 Some phenotype association tools in Galaxy: looking for disease SNPs in a full genome. Curr Protoc Bioinformatics 2012 0.75