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List of works by Webb Miller

28-way vertebrate alignment and conservation track in the UCSC Genome Browser

scientific article (publication date: December 2007)

A file comparison program

A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly

scientific article

A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar

scientific article (publication date: 2012)

Aligning two sequences within a specified diagonal band

scientific article published in October 1992

An effective method for detecting gene conversion events in whole genomes

scientific article

An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing

scientific article (publication date: 29 March 2005)

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

scientific article published in June 2007

Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution

scientific article (publication date: 11 May 2009)

Author Correction: Comparative and demographic analysis of orang-utan genomes

correction of a scholarly article

Aye-aye population genomic analyses highlight an important center of endemism in northern Madagascar

scientific article published on 25 March 2013

BLAST algorithm

algorithm in bioinformatics that finds regions of local similarity between molecular sequences

Basic local alignment search tool

scientific article

CAGE: Combinatorial Analysis of Gene-cluster Evolution

scientific article

Calling SNPs without a reference sequence

scientific article

Candidate genes required for embryonic development: a comparative analysis of distal mouse chromosome 14 and human chromosome 13q22.

scientific article

CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets

scientific article

Comparative Genomic Analysis Using the UCSC Genome Browser

Comparative analysis of the alpha-like globin clusters in mouse, rat, and human chromosomes indicates a mechanism underlying breaks in conserved synteny

scientific article published on April 2004

Comparative and demographic analysis of orang-utan genomes

scientific article

Comparative and population mitogenomic analyses of Madagascar's extinct, giant 'subfossil' lemurs

scientific article published on 16 December 2014

Comparative genome sequence analysis of the Bpa/Str region in mouse and Man

scientific article

Comparative genomic analysis using the UCSC genome browser

scientific article published in January 2007

Comparative genomics

scientific article published in January 2004

Comparative sequence of human and mouse BAC clones from the mnd2 region of chromosome 2p13

scientific article

Comparison of sequencing platforms for single nucleotide variant calls in a human sample

scientific article

Complete Khoisan and Bantu genomes from southern Africa

scientific article

Complete genome sequence of Salmonella enterica serovar Typhimurium LT2

scientific article

Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear

scientific article

Computational reconstruction of ancestral DNA sequences

scientific article published in January 2008

Conversion events in gene clusters

scientific article

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

scientific article

DUPCAR: reconstructing contiguous ancestral regions with duplications

scientific article

Dancing with Complement C4 and the RP-C4-CYP21-TNX (RCCX) Modules of the Major Histocompatibility Complex ⬇️

scientific article published on January 1, 2003

Distinguishing regulatory DNA from neutral sites

scientific article published on January 2003

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

scientific article

ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements

scientific article

Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic

scientific article

EnteriX 2003: Visualization tools for genome alignments of Enterobacteriaceae

scientific article

Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression

scientific article

Evaluation of methods for detecting conversion events in gene clusters ⬇️

scientific article published on February 15, 2011

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

scientific article

Evolution and functional classification of vertebrate gene deserts

scientific article

Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes

scientific article

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

scientific article

Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

scientific article

Evolutionary history reconstruction for Mammalian complex gene clusters

scientific article

Experimental validation of predicted mammalian erythroid cis-regulatory modules

scientific article

Fast-evolving noncoding sequences in the human genome

scientific article

Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data

scientific article

Functional and binding studies of HS3.2 of the beta-globin locus control region

scientific article (publication date: 23 January 2002)

Functional architecture of deleterious genetic variants in the Wrangel Island mammoth genome

GALA, a database for genomic sequence alignments and annotations

scientific article

Galaxy: a platform for interactive large-scale genome analysis

scientific article

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs ⬇️

scientific article published on September 1, 1997

Gene Length and Proximity to Neighbors Affect Genome-Wide Expression Levels ⬇️

scientific article published on November 12, 2003

Generation and annotation of the DNA sequences of human chromosomes 2 and 4

scientific article

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

scientific article

Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil)

scientific article

Genome analysis of the platypus reveals unique signatures of evolution

scientific article

Genome analysis of the platypus reveals unique signatures of evolution

scientific article published in Nature

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

scientific article

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

scientific article published on 10 July 2015

Genome-wide identification of conserved regulatory function in diverged sequences

scientific article

Genomic structure and functional control of the Dlx3-7 bigene cluster

scientific article

HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update

scientific article published in February 2007

Human-macaque comparisons illuminate variation in neutral substitution rates

scientific article published on 30 April 2008

Human-mouse alignments with BLASTZ

scientific article

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

scientific article published in June 2007

Identification and classification of conserved RNA secondary structures in the human genome

scientific article

Identification of indels in next-generation sequencing data

scientific article

Improvements in the HbVar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studies

scientific article

Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results

scientific article

Inferring the Recent Duplication History of a Gene Cluster

article

Initial sequencing and comparative analysis of the mouse genome

scientific article

Interpretation of custom designed Illumina genotype cluster plots for targeted association studies and next-generation sequence validation

scientific article

Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes

scientific article (publication date: 17 June 2008)

Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history

scientific article

Mobile DNA in Old World monkeys: a glimpse through the rhesus macaque genome

scientific article published in April 2007

Molecular and genomic data identify the closest living relative of primates

scientific article

Mulan: multiple-sequence local alignment and visualization for studying function and evolution

scientific article

MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences

scientific article

MultiPipMaker: comparative alignment server for multiple DNA sequences

scientific article published in April 2005

Optimal alignments in linear space

scientific article published in 1988

Optimization methods for selecting founder individuals for captive breeding or reintroduction of endangered species.

scientific article

Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes

scientific article published on April 2004

PhenCode: connecting ENCODE data with mutations and phenotype

scientific article

Phylogenomic resources at the UCSC Genome Browser

scientific article published in January 2008

PipMaker: a World Wide Web server for genomic sequence alignments

scientific article published in February 2003

PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences

scientific article published in December 2002

Polar bears exhibit genome-wide signatures of bioenergetic adaptation to life in the arctic environment

scientific article published on February 2014

Prepublication data sharing

scientific article

Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis

scientific article (publication date: 2007)

Reconstructing contiguous regions of an ancestral genome

scientific article

Reconstructing large regions of an ancestral mammalian genome in silico

scientific article

Reconstructing the Evolutionary History of Complex Human Gene Clusters

article

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

scientific article published on April 2004

Revealing mammalian evolutionary relationships by comparative analysis of gene clusters

scientific article

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

scientific article

Sequence conservation at human and mouse orthologous common fragile regions, FRA3B/FHIT and Fra14A2/Fhit

scientific article

Sequencing and analysis of a South Asian-Indian personal genome

scientific article

Sequencing the nuclear genome of the extinct woolly mammoth

scientific article

Sex determination by SRY PCR and sequencing of Tasmanian devil facial tumour cell lines reveals non-allograft transmission

scientific article published on 12 April 2016

Significance of interspecies matches when evolutionary rate varies

scientific article published in January 2003

Some Phenotype Association Tools in Galaxy: Looking for Disease SNPs in a Full Genome ⬇️

scientific article published on September 1, 2012

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

scientific article

The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of repeats

scientific article published in November 2002

The infinite sites model of genome evolution

scholarly article

The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)

scientific article published in February 2009

Transcription-associated mutational asymmetry in mammalian evolution

scientific article

Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif.

scientific article published on 25 September 2008

Updates of the HbVar database of human hemoglobin variants and thalassemia mutations

scientific article

Use of subtractive hybridization for comprehensive surveys of prokaryotic genome differences

scientific article published on June 2002

Using genomic data to unravel the root of the placental mammal phylogeny

scientific article

Whole-genome shotgun sequencing of mitochondria from ancient hair shafts

scientific article

zPicture: dynamic alignment and visualization tool for analyzing conservation profiles

scientific article

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