R Hardison

Summary

Affiliation: Pennsylvania State University
Country: USA

Publications

  1. pmc Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1
    Ying Zhang
    Center for Comparative Genomics and Bioinformatics, Huck Institutes of Life Sciences
    Nucleic Acids Res 37:7024-38. 2009
  2. pmc Evolution of hemoglobin and its genes
    Ross C Hardison
    Center for Comparative Genomics and Bioinformatics, Huck Institute of Genome Sciences, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Cold Spring Harb Perspect Med 2:a011627. 2012
  3. pmc Genome-wide epigenetic data facilitate understanding of disease susceptibility association studies
    Ross C Hardison
    Department of Biochemistry and Molecular Biology and Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16801, USA
    J Biol Chem 287:30932-40. 2012
  4. pmc Genomic approaches towards finding cis-regulatory modules in animals
    Ross C Hardison
    Department of Biochemistry and Molecular Biology, Center for Comparative Genomics and Bioinformatics, 304 Wartik Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Nat Rev Genet 13:469-83. 2012
  5. 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
  6. ncbi request reprint Locus control regions of mammalian beta-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insights
    R Hardison
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park 16802, USA
    Gene 205:73-94. 1997
  7. pmc Globin genes on the move
    Ross C Hardison
    Center for Comparative Genomics and Bioinformatics, Huck Institutes of Life Sciences, University Park, PA 16802, USA
    J Biol 7:35. 2008
  8. pmc Comparative genomics
    Ross C Hardison
    Center for Comparative Genomics and Bioinformatics at The Pennsylvania State University in University Park, Pennsylvania, USA
    PLoS Biol 1:E58. 2003
  9. 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
  10. ncbi request reprint Conserved noncoding sequences are reliable guides to regulatory elements
    R C Hardison
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Trends Genet 16:369-72. 2000

Research Grants

Detail Information

Publications54

  1. pmc Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1
    Ying Zhang
    Center for Comparative Genomics and Bioinformatics, Huck Institutes of Life Sciences
    Nucleic Acids Res 37:7024-38. 2009
    ....
  2. pmc Evolution of hemoglobin and its genes
    Ross C Hardison
    Center for Comparative Genomics and Bioinformatics, Huck Institute of Genome Sciences, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Cold Spring Harb Perspect Med 2:a011627. 2012
    ....
  3. pmc Genome-wide epigenetic data facilitate understanding of disease susceptibility association studies
    Ross C Hardison
    Department of Biochemistry and Molecular Biology and Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16801, USA
    J Biol Chem 287:30932-40. 2012
    ..Community efforts such as the ENCODE Project provide a wealth of data about epigenetic features associated with gene regulation. These data enable the prediction of testable functions for many phenotype-associated variants...
  4. pmc Genomic approaches towards finding cis-regulatory modules in animals
    Ross C Hardison
    Department of Biochemistry and Molecular Biology, Center for Comparative Genomics and Bioinformatics, 304 Wartik Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    Nat Rev Genet 13:469-83. 2012
    ..The validation rates for predictions indicate that identifying diagnostic biochemical marks is the most reliable method, and understanding is enhanced by the analysis of motifs and conservation patterns within those predicted CRMs...
  5. 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...
  6. ncbi request reprint Locus control regions of mammalian beta-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insights
    R Hardison
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park 16802, USA
    Gene 205:73-94. 1997
    ..Multiple HS units (at least three: HS2, HS3 and HS4 cores plus flanking DNAs) together establish a chromatin structure that allows the proper developmental regulation of genes within the cluster...
  7. pmc Globin genes on the move
    Ross C Hardison
    Center for Comparative Genomics and Bioinformatics, Huck Institutes of Life Sciences, University Park, PA 16802, USA
    J Biol 7:35. 2008
    ..This resolves some controversies about vertebrate globin gene evolution but ignites new ones...
  8. pmc Comparative genomics
    Ross C Hardison
    Center for Comparative Genomics and Bioinformatics at The Pennsylvania State University in University Park, Pennsylvania, USA
    PLoS Biol 1:E58. 2003
  9. 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...
  10. ncbi request reprint Conserved noncoding sequences are reliable guides to regulatory elements
    R C Hardison
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Trends Genet 16:369-72. 2000
    ..However, the choice of a species for most effective comparison differs among various loci...
  11. ncbi request reprint Hemoglobins from bacteria to man: evolution of different patterns of gene expression
    R Hardison
    Department of Biochemistry, Pennsylvania State University, University Park, PA 16802, USA
    J Exp Biol 201:1099-117. 1998
    ..Examples include a potential target for the hematopoietic transcription factor TAL1...
  12. ncbi request reprint Databases of human hemoglobin variants and other resources at the globin gene server
    R C Hardison
    Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park 16802, USA
    Hemoglobin 25:183-93. 2001
    ..These resources are reviewed in the context of a larger plan for providing related resources on hemoglobins, benign and pathological variation in these proteins and the genes that encode them, and the regulation of the globin genes...
  13. doi request reprint Tree-guided Bayesian inference of population structures
    Yu Zhang
    Department of Statistics, The Pennsylvania State University, State College, PA, USA
    Bioinformatics 24:965-71. 2008
    ..As a result, they can lose sensitivity and specificity in detecting subtle stratifications. In addition, when a large number of genetic markers are used, many existing algorithms perform rather inefficiently...
  14. doi request reprint Poisson approximation for significance in genome-wide ChIP-chip tiling arrays
    Yu Zhang
    Department of Statistics, The Pennsylvania State University, 325 Thomas Bldg, State College, PA, USA
    Bioinformatics 24:2825-31. 2008
    ..No accurate and efficient method exists for evaluating statistical significance in tiling arrays. The Bonferroni method is overly conservative and the permutation test is time consuming for genome-wide studies...
  15. 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
    ....
  16. 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...
  17. pmc Calling SNPs without a reference sequence
    Aakrosh Ratan
    Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, USA
    BMC Bioinformatics 11:130. 2010
    ....
  18. pmc Bayesian epistasis association mapping via SNP imputation
    Yu Zhang
    Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA
    Biostatistics 12:211-22. 2011
    ..We use a data set of inflammatory bowel disease to demonstrate the application of our method...
  19. 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/ ...
  20. ncbi request reprint Bayesian inference of epistatic interactions in case-control studies
    Yu Zhang
    Department of Statistics, The Pennsylvania State University, Thomas Building 422A, University Park, Pennsylvania 16802, USA
    Nat Genet 39:1167-73. 2007
    ....
  21. ncbi request reprint Efficient and reliable transfection of mouse erythroleukemia cells using cationic lipids
    L Elnitski
    Department of Biochemistry and Molecular Biology, The Center for Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
    Blood Cells Mol Dis 25:299-304. 1999
    ..This report describes an efficient and reliable method for transient transfection of MEL cells using commercially available cationic lipids...
  22. pmc A varying threshold method for ChIP peak-calling using multiple sources of information
    Kuan Bei Chen
    Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA 16802, USA
    Bioinformatics 26:i504-10. 2010
    ..We call the additional data related with the target protein binding as supporting tracks...
  23. 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...
  24. ncbi request reprint A negative cis-element regulates the level of enhancement by hypersensitive site 2 of the beta-globin locus control region
    L Elnitski
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    J Biol Chem 276:6289-98. 2001
    ..The novel negative element also functions after stable integration into MEL chromosomes. Smaller deletions at the 5' end of the HS2 core map the negative element within a 20-base pair region containing two conserved sequences...
  25. 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...
  26. 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...
  27. 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/...
  28. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  29. 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...
  30. pmc A T-to-G transversion at nucleotide -567 upstream of HBG2 in a GATA-1 binding motif is associated with elevated hemoglobin F
    Zhiyi Chen
    Center of Excellence in Sickle Cell Disease, Division of Hematology Oncology, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, USA
    Mol Cell Biol 28:4386-93. 2008
    ..The T-to-G mutation in this motif disrupts GATA-1 binding and the associated repressor complex, abolishing its silencing effect and resulting in the up-regulation of gamma-globin gene expression in adults...
  31. ncbi request reprint Evolutionary and biomedical insights from the rhesus macaque genome
    Richard A Gibbs
    Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
    Science 316:222-34. 2007
    ..The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species...
  32. ncbi request reprint Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002
    ....
  33. 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...
  34. 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...
  35. ncbi request reprint Genome sequence of the Brown Norway rat yields insights into mammalian evolution
    Richard A Gibbs
    Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA lt http www hgsc bcm tmc edu
    Nature 428:493-521. 2004
    ....
  36. pmc Improvements in the HbVar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studies
    George P Patrinos
    MGC Department of Cell Biology and Genetics, Erasmus MC, Faculty of Medicine and Health Sciences, PO Box 1738, 3000 DR, Rotterdam, The Netherlands
    Nucleic Acids Res 32:D537-41. 2004
    ..It also expands the capacity to view and analyze the data, using tools within GALA and the University of California at Santa Cruz (UCSC) Genome Browser...
  37. 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...
  38. 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...
  39. 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...
  40. pmc Cross-species sequence comparisons: a review of methods and available resources
    Kelly A Frazer
    Perlegen Sciences, Mountain View, California 94043, USA
    Genome Res 13:1-12. 2003
    ..In this review, we outline the strategy for choosing DNA sequences from different species for comparative analyses and describe the methods used and the resources publicly available for these studies...
  41. pmc Mulan: multiple-sequence local alignment and visualization for studying function and evolution
    Ivan Ovcharenko
    Energy, Environment, Biology and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
    Genome Res 15:184-94. 2005
    ..Source code for the aligners and the aligner-evaluation software can be freely downloaded from http://www.bx.psu.edu/miller_lab/...
  42. pmc Evolution and functional classification of vertebrate gene deserts
    Ivan Ovcharenko
    Energy, Environment, Biology, and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
    Genome Res 15:137-45. 2005
    ..Stable gene deserts resist chromosomal rearrangements and appear to harbor multiple distant regulatory elements physically linked to their neighboring genes, with the linearity of conservation invariant throughout vertebrate evolution...
  43. 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/...
  44. 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...
  45. 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...
  46. 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)...
  47. ncbi request reprint Computational prediction of cis-regulatory modules from multispecies alignments using Galaxy, Table Browser, and GALA
    Laura Elnitski
    Genome Technology Branch, National Institutes of Health, Rockville, MD, USA
    Methods Mol Biol 338:91-103. 2006
    ..Links to these servers can be accessed at http://www.bx.psu.edu/ and http://genome.ucsc.edu/...
  48. 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/...
  49. 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
    ....
  50. 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...
  51. pmc A complex chromatin landscape revealed by patterns of nuclease sensitivity and histone modification within the mouse beta-globin locus
    Michael Bulger
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
    Mol Cell Biol 23:5234-44. 2003
    ..Our results reveal a complex chromatin landscape for the active beta-globin locus and illustrate the complexity of broad structural changes that accompany gene activation...
  52. pmc zPicture: dynamic alignment and visualization tool for analyzing conservation profiles
    Ivan Ovcharenko
    Energy, Environment, Biology and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
    Genome Res 14:472-7. 2004
    ..Finally, we describe how this tool can be efficiently applied to the analysis of nonvertebrate genomes, including those of microbial organisms...
  53. 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...

Research Grants24

  1. ORGANIZATION AND EXPRESSION OF GLOBIN GENE LOCI
    Ross Hardison; Fiscal Year: 1993
    ..These conserved sequences will be tested for ability to affect expression of linked reporter genes and to bind nuclear proteins specifically. Novel proteins will be purified and characterized...
  2. FUNCTION AND CONSERVATION IN GLOBIN LOCUS CONTROL REGION
    Ross Hardison; Fiscal Year: 2001
    ..5 and isolate the binding proteins. ..
  3. Global Predictions and Tests of Erythroid Regulation
    Ross Hardison; Fiscal Year: 2007
    ..More broadly, the experimental and computational approaches generated by our work should provide valuable tools for analyzing the control of gene expression in other tissues during normal development and various pathological states. ..
  4. ORGANIZATION AND EXPRESSION OF GLOBIN GENE LOCI
    Ross Hardison; Fiscal Year: 1991
    ..6) The sequence of the entire rabbit Beta-like globin gene cluster (44 kb) will be completed and compared to the homologous region in humans and mice...
  5. Global Predictions and Tests of Erythroid Regulation
    Yu Zhang; Fiscal Year: 2010
    ....