Miller Lab: Publications and Supplementary Materials

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

• 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).

• Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions: publication, associated materials and software, test servers.
• Post-processing long pairwise alignments: publication, software.

• Sim4: publication, instructions, software (revised 13 June 2003).
• Alignments without low-scoring regions: pre-print.

• Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome: publication.