WEBB COLBY MILLER

Summary

Affiliation: Pennsylvania State University
Country: USA

Publications

  1. pmc Sequencing and analysis of a South Asian-Indian personal genome
    Ravi Gupta
    SciGenom Labs Pvt Ltd, Kakkanad, Cochin, Kerala, India
    BMC Genomics 13:440. 2012
  2. pmc Human-macaque comparisons illuminate variation in neutral substitution rates
    Svitlana Tyekucheva
    Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA
    Genome Biol 9:R76. 2008
  3. pmc Interpretation of custom designed Illumina genotype cluster plots for targeted association studies and next-generation sequence validation
    Elizabeth 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
  4. pmc Conversion events in gene clusters
    Giltae Song
    Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802 USA
    BMC Evol Biol 11:226. 2011
  5. pmc Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution
    Eske Willerslev
    Centre for Ancient Genetics, University of Copenhagen, Universitetsparken 15, DK 2100, Denmark
    BMC Evol Biol 9:95. 2009
  6. pmc Evaluation of methods for detecting conversion events in gene clusters
    Giltae Song
    Center for Comparative Genomics and Bioinformatics, 506 Wartik Lab, Pennsylvania State University, University Park, PA 16802, USA
    BMC Bioinformatics 12:S45. 2011
  7. pmc Calling SNPs without a reference sequence
    Aakrosh Ratan
    Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, USA
    BMC Bioinformatics 11:130. 2010
  8. doi request reprint Sequencing the nuclear genome of the extinct woolly mammoth
    Webb Miller
    Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, 310 Wartik Building, University Park, Pennsylvania 16802, USA
    Nature 456:387-90. 2008
  9. ncbi request reprint Comparative genomics
    Webb 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
  10. pmc 28-way vertebrate alignment and conservation track in the UCSC Genome Browser
    Webb Miller
    Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania 16802, USA
    Genome Res 17:1797-808. 2007

Research Grants

  1. SOFTWARE FOR ANALYZING BIOSEQUENCE DATA
    Webb Miller; Fiscal Year: 2009
  2. SOFTWARE FOR ANALYZING BIOSEQUENCE DATA
    Webb Miller; Fiscal Year: 2006
  3. SOFTWARE FOR ANALYZING BIOSEQUENCE DATA
    Webb Miller; Fiscal Year: 2005
  4. SOFTWARE FOR ANALYZING BIOSEQUENCE DATA
    Webb Miller; Fiscal Year: 2004
  5. SOFTWARE FOR ANALYZING BIOSEQUENCE DATA
    Webb Miller; Fiscal Year: 2003
  6. SOFTWARE FOR ANALYZING BIOSEQUENCE DATA
    WEBB COLBY MILLER; Fiscal Year: 2010

Collaborators

Detail Information

Publications44

  1. pmc Sequencing and analysis of a South Asian-Indian personal genome
    Ravi Gupta
    SciGenom Labs Pvt Ltd, Kakkanad, Cochin, Kerala, India
    BMC Genomics 13:440. 2012
    ..In this study we have sequenced and analyzed the genome of a South Asian Indian female (SAIF) from the Indian state of Kerala...
  2. pmc Human-macaque comparisons illuminate variation in neutral substitution rates
    Svitlana 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...
  3. pmc Interpretation of custom designed Illumina genotype cluster plots for targeted association studies and next-generation sequence validation
    Elizabeth 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...
  4. pmc Conversion events in gene clusters
    Giltae 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...
  5. pmc Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution
    Eske 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...
  6. pmc Evaluation of methods for detecting conversion events in gene clusters
    Giltae 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...
  7. pmc Calling SNPs without a reference sequence
    Aakrosh Ratan
    Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, USA
    BMC Bioinformatics 11:130. 2010
    ....
  8. doi request reprint Sequencing the nuclear genome of the extinct woolly mammoth
    Webb 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...
  9. ncbi request reprint Comparative genomics
    Webb 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...
  10. pmc 28-way vertebrate alignment and conservation track in the UCSC Genome Browser
    Webb 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...
  11. pmc 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...
  12. pmc Distinguishing regulatory DNA from neutral sites
    Laura 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...
  13. pmc MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences
    Scott 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...
  14. pmc Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes
    Shan 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...
  15. pmc Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat
    Diana 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...
  16. pmc Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences
    David 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...
  17. pmc Complete Khoisan and Bantu genomes from southern Africa
    Stephan 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...
  18. pmc CAGE: Combinatorial Analysis of Gene-cluster Evolution
    Giltae 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...
  19. doi request reprint MultiPipMaker: comparative alignment server for multiple DNA sequences
    Laura Elnitski
    The Pennsylvania State University, University Park, Pennsylvania, USA
    Curr Protoc Bioinformatics . 2005
    ..Alignments can include unordered, unoriented secondary sequences...
  20. doi request reprint PipMaker: a World Wide Web server for genomic sequence alignments
    Laura 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...
  21. pmc An effective method for detecting gene conversion events in whole genomes
    Chih 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/ ...
  22. pmc Reconstructing contiguous regions of an ancestral genome
    Jian 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...
  23. pmc GALA, a database for genomic sequence alignments and annotations
    Belinda 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/...
  24. ncbi request reprint Significance of interspecies matches when evolutionary rate varies
    Jia 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...
  25. ncbi request reprint Functional and binding studies of HS3.2 of the beta-globin locus control region
    Joseph 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...
  26. pmc ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements
    James 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)...
  27. pmc Evolutionary history reconstruction for Mammalian complex gene clusters
    Yu Zhang
    Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, PA 16802, USA
    J Comput Biol 16:1051-70. 2009
    ....
  28. pmc Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution
    Ross 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...
  29. ncbi request reprint PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences
    Laura Elnitski
    Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
    Genomics 80:681-90. 2002
    ....
  30. pmc Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results
    Laura 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/...
  31. pmc Human-mouse alignments with BLASTZ
    Scott 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...
  32. ncbi request reprint MultiPipMaker: a comparative alignment server for multiple DNA sequences
    Laura 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...
  33. pmc Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data
    David 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...
  34. pmc A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly
    Daniel 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...
  35. pmc Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif
    Yong 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...
  36. pmc Experimental validation of predicted mammalian erythroid cis-regulatory modules
    Hao 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/...
  37. pmc Gene length and proximity to neighbors affect genome-wide expression levels
    Francesca 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...
  38. pmc Galaxy: a platform for interactive large-scale genome analysis
    Belinda 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...
  39. ncbi request reprint HbVar: A relational database of human hemoglobin variants and thalassemia mutations at the globin gene server
    Ross 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...
  40. pmc CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets
    Charles 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
    ..CleaveLand can thus be applied to degradome data from any species provided a set of mRNA transcripts and a set of query miRNAs or other small RNAs are available...
  41. ncbi request reprint HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update
    Belinda Giardine
    The Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, University Park, Pennsylvania, USA
    Hum Mutat 28:206. 2007
    ....
  42. ncbi request reprint PhenCode: connecting ENCODE data with mutations and phenotype
    Belinda 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...
  43. pmc Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression
    Yong 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...
  44. ncbi request reprint EST clustering error evaluation and correction
    Ji Ping Z Wang
    Department of Statistics, Northwestern University, Evanston, IL 60208, USA
    Bioinformatics 20:2973-84. 2004
    ..The EST clustering error structure, the relationship between clustering error and clustering criteria, and possible error correction methods need to be systematically investigated...

Research Grants11

  1. SOFTWARE FOR ANALYZING BIOSEQUENCE DATA
    Webb Miller; Fiscal Year: 2009
    ..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. ..
  2. SOFTWARE FOR ANALYZING BIOSEQUENCE DATA
    Webb Miller; Fiscal Year: 2006
    ..abstract_text> ..
  3. SOFTWARE FOR ANALYZING BIOSEQUENCE DATA
    Webb Miller; Fiscal Year: 2005
    ..abstract_text> ..
  4. SOFTWARE FOR ANALYZING BIOSEQUENCE DATA
    Webb Miller; Fiscal Year: 2004
    ..abstract_text> ..
  5. SOFTWARE FOR ANALYZING BIOSEQUENCE DATA
    Webb Miller; Fiscal Year: 2003
    ..abstract_text> ..
  6. SOFTWARE FOR ANALYZING BIOSEQUENCE DATA
    WEBB 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. ..