Research Topics
| WEBB COLBY MILLERSummaryAffiliation: Pennsylvania State University Country: USA Publications
Research Grants
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Detail Information
Publications
Human-macaque comparisons illuminate variation in neutral substitution ratesSvitlana Tyekucheva
Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA
Genome Biol 9:R76. 2008..Here we investigate the human-macaque neutral substitution rate as a function of a number of genomic parameters...- Interpretation of custom designed Illumina genotype cluster plots for targeted association studies and next-generation sequence validationElizabeth A Tindall
Cancer Genetics Group, Children s Cancer Institute Australia for Medical Research, Sydney Children s Hospital, High Street, Randwick, NSW 2031, Australia
BMC Res Notes 3:39. 2010..We highlight applications for interpretation of Illumina generated genotype cluster plots to maximise data inclusion and reduce genotyping errors... - Conversion events in gene clustersGiltae Song
Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802 USA
BMC Evol Biol 11:226. 2011..In particular, conversion events can mislead inferences about the relationships among these regions, as traced by traditional methods such as construction of phylogenetic trees or multi-species alignments... - Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolutionEske Willerslev
Centre for Ancient Genetics, University of Copenhagen, Universitetsparken 15, DK 2100, Denmark
BMC Evol Biol 9:95. 2009..One notable example concerns the rhinoceroses, a group for which several contradictory phylogenies were proposed on the basis of morphology, then apparently resolved using mitochondrial DNA fragments... - Evaluation of methods for detecting conversion events in gene clustersGiltae Song
Center for Comparative Genomics and Bioinformatics, 506 Wartik Lab, Pennsylvania State University, University Park, PA 16802, USA
BMC Bioinformatics 12:S45. 2011..Many computational methods for detecting gene conversion events have been released, but their performance has not been assessed for wide deployment in evolutionary history studies due to a lack of accurate evaluation methods... - Calling SNPs without a reference sequenceAakrosh Ratan
Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, USA
BMC Bioinformatics 11:130. 2010.... - Sequencing the nuclear genome of the extinct woolly mammothWebb Miller
Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, 310 Wartik Building, University Park, Pennsylvania 16802, USA
Nature 456:387-90. 2008..This study shows that nuclear genome sequencing of extinct species can reveal population differences not evident from the fossil record, and perhaps even discover genetic factors that affect extinction... - 28-way vertebrate alignment and conservation track in the UCSC Genome BrowserWebb Miller
Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania 16802, USA
Genome Res 17:1797-808. 2007..Each functional class has a distinctive period of stringent constraint, followed by decays that allow (for the case of regulatory regions) or reject (for coding regions and ultraconserved elements) insertions and deletions... - The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)Webb Miller
Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, University Park, Pennsylvania 16802, USA
Genome Res 19:213-20. 2009..This study therefore adds to the growing evidence that extensive sequencing of museum collections is both feasible and desirable, and can yield complete genomes... - Comparative genomicsWebb Miller
The Center for Comparative Genomics and Bioinformatics, The Huck Institutes of Life Sciences, Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
Annu Rev Genomics Hum Genet 5:15-56. 2004..Internet resources for accessing and analyzing the treasure trove of sequence alignments and annotations are reviewed, and we discuss critical problems to address in new bioinformatic developments in comparative genomics... - Distinguishing regulatory DNA from neutral sitesLaura Elnitski
Departments of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Genome Res 13:64-72. 2003..Such scoring functions should aid in the identification of putative regulatory regions throughout the human genome... - Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomesShan Yang
Department of Biochemistry and Molecular Biology, Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Genome Res 14:517-27. 2004..The correlations are explained only in part by the GC content, indicating that other factors also contribute to the inherent tendency of DNA segments to change over evolutionary time... - MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequencesScott Schwartz
Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
Nucleic Acids Res 31:3518-24. 2003..Analysis of the alignments also confirms the phylogenetic inference that horses are more closely related to cats than to cows... - Regulatory potential scores from genome-wide three-way alignments of human, mouse, and ratDiana Kolbe
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Genome Res 14:700-7. 2004..A variant of the RP scoring scheme that accounts for local variation in neutral mutational patterns further improves our predictions... - Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequencesDavid C King
Center for Comparative Genomics and Bioinformatics, Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Genome Res 15:1051-60. 2005..78 and a true discovery rate of approximately 0.6. The performance is better on other reference sets; both phastCons and RP scores can capture almost all regulatory elements in those sets along with approximately 7% of the human genome... - Significance of interspecies matches when evolutionary rate variesJia Li
Statistics Department, Penn State, University Park, PA 16802, USA
J Comput Biol 10:537-54. 2003..Our methods are illustrated in detail using a 1.49 Mb genomic region. Results obtained from the analysis of human chromosome 22 using these techniques are also provided... - Functional and binding studies of HS3.2 of the beta-globin locus control regionJoseph M Molete
Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 206 Althouse Laboratory, University Park, PA 16802, USA
Gene 283:185-97. 2002..GATA1 and Oct1 also bind in the HS cores of the LCR and to promoters in HBBC. Their binding to this minor HS suggests that they may be used in assembly of a large complex containing multiple regulatory sequences... - PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequencesLaura Elnitski
Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
Genomics 80:681-90. 2002.... - Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolutionRoss C Hardison
Department of Biochemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Genome Res 13:13-26. 2003..Regional variation in all processes is correlated with, but not completely accounted for, by GC content in human and the difference between GC content in human and mouse... - PipMaker: a World Wide Web server for genomic sequence alignmentsLaura Elnitski
The Pennsylvania State University, University Park, Pennsylvania, USA
Curr Protoc Bioinformatics . 2003..Optional annotations on the pip provide additional information to assist in the interpretation of the alignment. The default parameters of the underlying blastz alignment program are tuned for human-mouse alignments... - GALA, a database for genomic sequence alignments and annotationsBelinda Giardine
Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Genome Res 13:732-41. 2003..The database is available online at http://globin.cse.psu.edu/ and http://bio.cse.psu.edu/... - Evolutionary history reconstruction for Mammalian complex gene clustersYu Zhang
Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, PA 16802, USA
J Comput Biol 16:1051-70. 2009.... - Complete Khoisan and Bantu genomes from southern AfricaStephan C Schuster
Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, 310 Wartik Lab, University Park, Pennsylvania 16802, USA
Nature 463:943-7. 2010..Adding the described variants to current databases will facilitate inclusion of southern Africans in medical research efforts, particularly when family and medical histories can be correlated with genome-wide data... - Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental resultsLaura Elnitski
Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
Nucleic Acids Res 33:D466-70. 2005..Improved hardware and tuning has reduced response times and increased querying capacity, while simplified query interfaces will help direct new users through the querying process. Links are available at http://www.bx.psu.edu/... - ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elementsJames Taylor
Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Genome Res 16:1596-604. 2006..Our software, training data, and genome-wide predictions are available from our Web site (http://www.bx.psu.edu/projects/esperr)... - CAGE: Combinatorial Analysis of Gene-cluster EvolutionGiltae Song
Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, PA 16802, USA
J Comput Biol 17:1227-42. 2010..We describe a new method for reconstructing the recent evolutionary history of gene clusters, and evaluate its performance on both simulated data and actual human gene clusters... - Reconstructing contiguous regions of an ancestral genomeJian Ma
Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania 16802, USA
Genome Res 16:1557-65. 2006..Our methods were developed as part of a project to reconstruct the genome sequence of the last ancestor of human, dogs, and most other placental mammals... - MultiPipMaker: comparative alignment server for multiple DNA sequencesLaura Elnitski
The Pennsylvania State University, University Park, Pennsylvania, USA
Curr Protoc Bioinformatics . 2005..Alignments can include unordered, unoriented secondary sequences... - An effective method for detecting gene conversion events in whole genomesChih Hao Hsu
Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802, USA
J Comput Biol 17:1281-97. 2010..Our approach is illustrated using conversion events in primate CCL gene clusters. Source code for our program is included in the 3SEQ_2D package, which is freely available at www.bx.psu.edu/miller_lab/ ... - MultiPipMaker: a comparative alignment server for multiple DNA sequencesLaura Elnitski
The Pennsylvania State University, University Park, Pennsylvania, USA
Curr Protoc Bioinformatics . 2010..Input sequences other than the reference can be fragmented, unordered, and unoriented... - Human-mouse alignments with BLASTZScott Schwartz
Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Genome Res 13:103-7. 2003..This work describes BLASTZ, its modifications, the hardware environment on which we run it, and several empirical studies to validate its results... - A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendlyDaniel Blankenberg
Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802, USA
Genome Res 17:960-4. 2007..Every section of the manuscript is supplemented with QuickTime screencasts. Galaxy2(ENCODE) and the screencasts can be accessed at http://g2.bx.psu.edu... - Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE dataDavid C King
Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Genome Res 17:775-86. 2007..Some of the putative regulatory regions show evidence for recent selection, including a primate-specific, distal promoter that may play a novel role in regulation... - Experimental validation of predicted mammalian erythroid cis-regulatory modulesHao Wang
Center for Comparative Genomics and Bioinformatics of the Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Genome Res 16:1480-92. 2006..Genome-wide predictions based on RP and a large set of well-defined transcription factor binding sites are available through servers at http://www.bx.psu.edu/... - Galaxy: a platform for interactive large-scale genome analysisBelinda Giardine
Center for Comparative Genomics and Bioinformatics, Huck Institutes for Life Sciences, Penn State University, University Park, Pennsylvania 16802, USA
Genome Res 15:1451-5. 2005..Galaxy can be accessed at http://g2.bx.psu.edu... - Gene length and proximity to neighbors affect genome-wide expression levelsFrancesca Chiaromonte
Department of Statistics and Department of Health Evaluation Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
Genome Res 13:2602-8. 2003..This confirms that transcriptional and posttranscriptional processes are highly interrelated and implies that transcriptional interference plays a role in determining steady-state levels of mRNA in cells... - Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motifYong Cheng
Center for Comparative Genomics and Bioinformatics of the Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Genome Res 18:1896-905. 2008..Thus, GATA1 binding sites that regulate gene expression during erythroid maturation are under strong selective constraint, while nonconstrained binding may have only a limited or indirect role in regulation... - PhenCode: connecting ENCODE data with mutations and phenotypeBelinda Giardine
Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
Hum Mutat 28:554-62. 2007..We present several examples illustrating the power of these connections for exploring phenotypes associated with functional elements, and for identifying genomic data that could help to explain clinical phenotypes... - HbVar database of human hemoglobin variants and thalassemia mutations: 2007 updateBelinda Giardine
The Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, University Park, Pennsylvania, USA
Hum Mutat 28:206. 2007.... - HbVar: A relational database of human hemoglobin variants and thalassemia mutations at the globin gene serverRoss C Hardison
Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
Hum Mutat 19:225-33. 2002..quot; This new database should be useful for clinical diagnosis as well as in fundamental studies of hemoglobin biochemistry, globin gene regulation, and human sequence variation at these loci... - CleaveLand: a pipeline for using degradome data to find cleaved small RNA targetsCharles Addo-Quaye
Department of Computer Science and Engineering and Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
Bioinformatics 25:130-1. 2009..AVAILABILITY: The code and documentation for CleaveLand is freely available under a GNU license at http://www.bio.psu.edu/people/faculty/Axtell/AxtellLab/Software.html.. - Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expressionYong Cheng
Center for Comparative Genomics and Bioinformatics of the Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Genome Res 19:2172-84. 2009..More broadly, these studies illustrate how a "master regulator" transcription factor coordinates tissue differentiation through a panoply of DNA and protein interactions... - EST clustering error evaluation and correctionJi Ping Z Wang
Department of Statistics, Northwestern University, Evanston, IL 60208, USA
Bioinformatics 20:2973-84. 2004..A novel statistical approach is proposed to correct ISO error to provide more accurate estimates of the true gene cluster profile...
Research Grants
- SOFTWARE FOR ANALYZING BIOSEQUENCE DATAWebb Miller; Fiscal Year: 2006..abstract_text> ..
- SOFTWARE FOR ANALYZING BIOSEQUENCE DATAWEBB COLBY MILLER; Fiscal Year: 2010..We will produce data and computational methods that will greatly increase our understanding of these differences, which may assist with selection of biomedical models for progression of infectious diseases. ..