Research Topics
| R HardisonSummaryAffiliation: 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...- Comparative genomicsRoss C Hardison
Center for Comparative Genomics and Bioinformatics at The Pennsylvania State University in University Park, Pennsylvania, USA
PLoS Biol 1:E58. 2003 - 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... - Globin genes on the moveRoss 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... - Locus control regions of mammalian beta-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insightsR 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... - Databases of human hemoglobin variants and other resources at the globin gene serverR 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... - Conserved noncoding sequences are reliable guides to regulatory elementsR 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... - Hemoglobins from bacteria to man: evolution of different patterns of gene expressionR 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... - Tree-guided Bayesian inference of population structuresYu 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... - Poisson approximation for significance in genome-wide ChIP-chip tiling arraysYu 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... - Bayesian epistasis association mapping via SNP imputationYu 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... - 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... - Calling SNPs without a reference sequenceAakrosh Ratan
Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, USA
BMC Bioinformatics 11:130. 2010.... - 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.... - 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/ ... - Bayesian inference of epistatic interactions in case-control studiesYu Zhang
Department of Statistics, The Pennsylvania State University, Thomas Building 422A, University Park, Pennsylvania 16802, USA
Nat Genet 39:1167-73. 2007.... - Efficient and reliable transfection of mouse erythroleukemia cells using cationic lipidsL 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... - A varying threshold method for ChIP peak-calling using multiple sources of informationKuan 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... - 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... - A negative cis-element regulates the level of enhancement by hypersensitive site 2 of the beta-globin locus control regionL 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... - 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... - 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... - Evolutionary and biomedical insights from the rhesus macaque genomeRichard 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... - Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectEwan Birney
Nature 447:799-816. 2007..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function... - A T-to-G transversion at nucleotide -567 upstream of HBG2 in a GATA-1 binding motif is associated with elevated hemoglobin FZhiyi 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... - 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/... - 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... - 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)... - 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/... - Computational prediction of cis-regulatory modules from multispecies alignments using Galaxy, Table Browser, and GALALaura 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/... - Cross-species sequence comparisons: a review of methods and available resourcesKelly 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... - 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... - 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... - 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... - Improvements in the HbVar database of human hemoglobin variants and thalassemia mutations for population and sequence variation studiesGeorge 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... - Genome sequence of the Brown Norway rat yields insights into mammalian evolutionRichard 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 <http://www.hgsc.bcm.tmc.edu
Nature 428:493-521. 2004.... - 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... - 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... - Mulan: multiple-sequence local alignment and visualization for studying function and evolutionIvan 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/... - 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... - 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... - 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/... - Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolutionLadeana W Hillier
Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
Nature 432:695-716. 2004..The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture... - Evolution and functional classification of vertebrate gene desertsIvan 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... - Initial sequencing and comparative analysis of the mouse genomeRobert 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.... - zPicture: dynamic alignment and visualization tool for analyzing conservation profilesIvan 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... - A complex chromatin landscape revealed by patterns of nuclease sensitivity and histone modification within the mouse beta-globin locusMichael 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... - 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... - 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....
Research Grants
- ORGANIZATION AND EXPRESSION OF GLOBIN GENE LOCIRoss 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...
- FUNCTION AND CONSERVATION IN GLOBIN LOCUS CONTROL REGIONRoss Hardison; Fiscal Year: 2001..5 and isolate the binding proteins. ..
- Global Predictions and Tests of Erythroid RegulationRoss 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. ..
- ORGANIZATION AND EXPRESSION OF GLOBIN GENE LOCIRoss 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...
- Global Predictions and Tests of Erythroid RegulationYu Zhang; Fiscal Year: 2010....