Miller Lab: Publications and Supplementary Materials

2011 2010 2009 2008
  • Sequencing the nuclear genome of the extinct woolly mammoth: publication.
  • Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif: publication.
  • Response to comment on "Whole-genome shotgun sequencing of mitochondria from ancient hair shafts": publication.
  • The infinite sites model of genome evolution: publication.
  • DUPCAR: reconstructing contiguous ancestral regions with duplication: publication.
  • Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes: publication.
  • Human-macaque comparisons illuminate variation in neutral substitution rates: publication.
  • Genome analysis of the platypus reveals unique signatures of evolution: publication.
  • Computational reconstruction of ancestral DNA sequences: publication.
  • Phylogenomic resources at the UCSC Genome Browser: publication.
  • Comment on "Protein sequences from mastodon and tyrannosaurus rex revealed by mass spectrometry": publication.
  • The UCSC Genome Browser Database: 2008 update: publication.
  • 28-way vertebrate alignment and conservation track in the UCSC Genome Browser: publication, supplement, sample source code (for testing the "indel clock" hypothesis)..
  • Molecular and genomic data identify the closest living relative of primates: publication, supplement.
  • Whole-genome shotgun sequencing of mitochondria from ancient hair shafts: publication, supplement.
  • A heuristic algorithm for reconstructing ancestral gene orders with duplications: publication.
  • Fast-evolving non-coding sequences in the human genome: publication.
  • Evolutionary and biomedical insights from the rhesus macaque genome: publication.
  • Mobile DNA in Old World monkeys: a glimpse through the rhesus macaque genome: publication.
  • HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update: publication.
  • PhenCode: Connecting ENCODE data with mutations and phenotype: publication.
  • A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly: publication.
  • Finding cis-regulatory elements using comparative genomics: Some lessons from the ENCODE data: publication.
  • Analyses of deep mammalian sequence alignments and constraint predictions in 1% of the human genome: publication.
  • Using genomic data to unravel the root of the placental mammal phylogeny: publication and software.
  • Experimental validation of predicted mammalian erythroid cis-regulatory modules: publication.
  • ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements: publication.
  • Controlling size when aligning multiple genomic sequences with duplications: publication.
  • Reconstructing contiguous regions of an ancestral genome: publication, data and software.
  • Recharacterizationi of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis: publication.
  • Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA: publication.
  • Identification and classification of conserved RNA secondary structures in the human genome: publication
  • Galaxy: a platform for interactive large-scale genome analysis: publication, supplemental data.
  • Evolutionarily conserved element in vertebrate, insect, worm and yeast genomes: publication.
  • Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences: publication.
  • Generation and annotation of the DNA sequence of human chromosomes 2 and 4: publication.
  • An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing: publication.
  • Mulan: multiple-sequence local alignment and visualization for studying function and evolution: publication, software.
  • Evolution and functional classification of vertebrate gene deserts: publication.
  • Improvements to GALA and dbERGEII: databases featuring genomic sequence alignment, annotation and experimental results: publication.
  • Sequence and comparative analysis of the chicken genome provide unique perspecitives on vertebrate evolution: publication.
  • Reconstructing large regions of an ancestral mammalian genome in silico: publication.
  • Comparative genomics: publication.
  • The ENCODE (ENCyclopedia Of DNA Elements) Project: publication.
  • Patterns of insertions and their covaration with substitutions in the rat, mouse, and human genomes: publication.
  • Comparative analysis of the alpha-like globin clusters in mouse, rat and human chromosomes indicates a mechanism underlying breaks in conserved synteny: publication.
  • Regulatory potential scores for genome-wide three-way alignments of human, mouse, and rat: publication.
  • Aligning multiple genomic sequences with the threaded blockset aligner: publication.
  • Genome sequence of the Brown Norway rat yields insights into mammalian evolution: publication.
  • Improvements in the HbVar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studies:
  • zPicture: dynamic alignment and visualization tool for anlayzing conservation profiles: publication.
  • Global predictions and tests of erythroid regulation: publication.
  • A combinatorial network of evolutionarily conserved Myelin Basic Protein regulatory sequences confers distinct glial-specific phenotypes: publication.
  • Comparative analyses of multi-species sequences from targeted genomic regions: publication.
  • Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution: publication.
  • Cross-species sequence comparison: a review of methods and available resources: publication.
  • Distinguishing regulatory DNA from neutral sites: publication.
  • EnteriX 2003: visualization tools for genome alignments of Enterobacteriaceae: publication.
  • Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes: publication, supplementary data.
  • GALA, a database for genomic sequence alignments and annotations: publication.
  • Gene length and proximity to neighbors affect genome-wide expression levels: publication, supplementary data.
  • Human-mouse alignments with BLASTZ: publication.
  • MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences: publication, supplement, software.
  • Multispecies comparative analysis of mammalian-specific genomic domain encoding secretory proteins: publication.
  • Significance of interspecies matches when evolutionary rate varies: publication.
  • Transcription-associated mutational asymmetry in mammalian evolution: publication.
  • Aligning two fragmented sequences: publication.
  • Candidate genes required for embryonic development: a comparative analysis of distal mouse chromosome 14 and human chromosome 13q22: abstract, publication, data and PIPs.
  • 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: publication, electronic supplement.
  • Initial sequencing and comparative analysis of the mouse genome: publication.
  • PipTools: A computational toolkit to prepare and evaluate annotated pairwise comparisons of genomic sequences: publication, software.
  • Scoring pairwise genomic sequence alignments: publication (Pacific Symposium on Biocomputing, 2002).
  • Use of subtractive hybridization for comprehensive surveys of prokaryotic genome differences (comparison of two Helicobacter pylori strains): publication, Figure 1, Figure 2, Table 1, pip of J99 vs. 26695, pip of 26695 vs. J99.
  • Association between divergence and interspersed repeats in mammalian noncoding genomic DNA: abstract, publication.
  • Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5: publication, web site.
  • Comparative genome analysis delimits a chromosomal domain and identifies key regulatory elements in the alpha globin cluster: publication.
  • Comparison of genomic DNA sequences: solved and unsolved problems: publication.
  • Sequence conservation at human and mouse orthologous common fragile regions, FRA3B/FHIT and Fra14A2/Fhit: publication, data and PIPs.
  • A greedy algorithm for aligning DNA sequences: publication.
  • Comparative structural and functional analysis of the olfactory receptor genes flanking the human and mouse beta-globin gene clusters: publication, supplement.
  • Comparison of the Escherichia coli K-12 genome with sampled genomes of Klebsiella pneumoniae and three Salmonella enterica serovars, Typhimurium, Typhi and Paratyphi: publication, data.
  • PipMaker -- a web server for aligning two genomic DNA sequences: publication.
  • Sequence and comparative analysis of the mouse 1-megabase region orthologous to the human 11p15 imprinted domain: abstract, data and PIPs.
  • So many genomes, so little time: manuscript. An edited version appeared in Nature Biotechnology 18:148-149 (February, 2000).
  • Web-based visualization tools for bacterial genome alignments: publication, code (Enteric) (tested on Solaris 7).
1999 1998 1997
  • Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome: publication.

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