Ross Hardison

Ross Hardison

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Interrogating Histone Acetylation and BRD4 as Mitotic Bookmarks of Transcription.

Cell Rep 2019 Apr;27(2):400-415.e5

Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.03.057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6664437PMC
April 2019

Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation.

Mol Cell 2019 02 13;73(3):519-532.e4. Epub 2018 Dec 13.

Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2018.11.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6368450PMC
February 2019

The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions.

Genome Biol 2018 10 4;19(1):151. Epub 2018 Oct 4.

Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, 16802, USA.

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http://dx.doi.org/10.1186/s13059-018-1519-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6172833PMC
October 2018

Evolution of hemoglobin loci and their regulatory elements.

Blood Cells Mol Dis 2018 05 9;70:2-12. Epub 2017 Aug 9.

Department of Biochemistry and Molecular Biology, Huck Institute for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA. Electronic address:

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http://dx.doi.org/10.1016/j.bcmd.2017.08.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5807248PMC
May 2018

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient.

Genome Res 2017 11 30;27(11):1939-1949. Epub 2017 Aug 30.

Bioinformatics and Genomics Program, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.220640.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5668950PMC
November 2017

Between form and function: the complexity of genome folding.

Hum Mol Genet 2017 10;26(R2):R208-R215

MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK.

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http://dx.doi.org/10.1093/hmg/ddx306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5886466PMC
October 2017

Accurate and reproducible functional maps in 127 human cell types via 2D genome segmentation.

Nucleic Acids Res 2017 Sep;45(17):9823-9836

Department of Biochemistry and Molecular Biology, the Pennsylvania State University, University Park, PA 16802, USA.

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http://academic.oup.com/nar/article/45/17/9823/4056234
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http://dx.doi.org/10.1093/nar/gkx659DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5622376PMC
September 2017

The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries.

Mol Cell 2017 Apr;66(1):102-116.e7

Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2017.02.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5393350PMC
April 2017

Jointly characterizing epigenetic dynamics across multiple human cell types.

Nucleic Acids Res 2016 08 19;44(14):6721-31. Epub 2016 Apr 19.

Dept. of Biochemistry and Molecular Biology, Penn State University, 304 Wartik Laboratory, University Park, PA 16802, USA.

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http://dx.doi.org/10.1093/nar/gkw278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5772166PMC
August 2016

A guide to translation of research results from model organisms to human.

Authors:
Ross C Hardison

Genome Biol 2016 07 26;17(1):161. Epub 2016 Jul 26.

Department of Biochemistry and Molecular Biology, Huck Institute for Genome Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.

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http://dx.doi.org/10.1186/s13059-016-1026-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4962550PMC
July 2016

A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition.

Genes Dev 2016 06;30(12):1423-39

Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.

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http://dx.doi.org/10.1101/gad.280859.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4926865PMC
June 2016

Unlinking an lncRNA from Its Associated cis Element.

Mol Cell 2016 Apr 31;62(1):104-10. Epub 2016 Mar 31.

Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2016.02.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4877494PMC
April 2016

Finding partners to play the music of regulation.

Authors:
Ross C Hardison

Blood 2016 Mar;127(13):1624-6

PENNSYLVANIA STATE UNIVERSITY.

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http://dx.doi.org/10.1182/blood-2016-02-697169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4817306PMC
March 2016

Genome-Wide Organization of GATA1 and TAL1 Determined at High Resolution.

Mol Cell Biol 2016 Jan 26;36(1):157-72. Epub 2015 Oct 26.

Center for Eukaryotic Gene Regulation, Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA

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http://dx.doi.org/10.1128/MCB.00806-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702602PMC
January 2016

SBR-Blood: systems biology repository for hematopoietic cells.

Nucleic Acids Res 2016 Jan 20;44(D1):D925-31. Epub 2015 Nov 20.

National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.

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http://dx.doi.org/10.1093/nar/gkv1263DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702891PMC
January 2016

Dynamics of GATA1 binding and expression response in a GATA1-induced erythroid differentiation system.

Genom Data 2015 Jun;4:1-7

Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania 16802, USA ; Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S22135960150001
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http://dx.doi.org/10.1016/j.gdata.2015.01.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4338950PMC
June 2015

Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility.

Epigenetics Chromatin 2015 23;8:16. Epub 2015 Apr 23.

Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 304 Wartik Laboratory, University Park, PA 16802 USA.

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http://dx.doi.org/10.1186/s13072-015-0009-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4432502PMC
May 2015

Functions of BET proteins in erythroid gene expression.

Blood 2015 Apr 18;125(18):2825-34. Epub 2015 Feb 18.

Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA; Perelman School of Medicine, University of Pennsylvania, Philadelphia PA; and.

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http://dx.doi.org/10.1182/blood-2014-10-607309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4424630PMC
April 2015

The effects of chromatin organization on variation in mutation rates in the genome.

Nat Rev Genet 2015 Apr 3;16(4):213-23. Epub 2015 Mar 3.

Department of Biochemistry and Molecular Biology, Huck Institute for Genome Sciences, The Pennsylvania State University, University Park, State College, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1038/nrg3890DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4500049PMC
April 2015

Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution.

BMC Genomics 2015 Feb 14;16:87. Epub 2015 Feb 14.

Department of Mathematics and Computer Science, Emory University, Atlanta, GA, 30322, USA.

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http://www.biomedcentral.com/1471-2164/16/87
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http://dx.doi.org/10.1186/s12864-015-1245-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333152PMC
February 2015

Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis.

Genome Res 2014 Dec 15;24(12):1945-62. Epub 2014 Oct 15.

Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA;

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http://dx.doi.org/10.1101/gr.164830.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4248312PMC
December 2014

A comparative encyclopedia of DNA elements in the mouse genome.

Authors:
Feng Yue Yong Cheng Alessandra Breschi Jeff Vierstra Weisheng Wu Tyrone Ryba Richard Sandstrom Zhihai Ma Carrie Davis Benjamin D Pope Yin Shen Dmitri D Pervouchine Sarah Djebali Robert E Thurman Rajinder Kaul Eric Rynes Anthony Kirilusha Georgi K Marinov Brian A Williams Diane Trout Henry Amrhein Katherine Fisher-Aylor Igor Antoshechkin Gilberto DeSalvo Lei-Hoon See Meagan Fastuca Jorg Drenkow Chris Zaleski Alex Dobin Pablo Prieto Julien Lagarde Giovanni Bussotti Andrea Tanzer Olgert Denas Kanwei Li M A Bender Miaohua Zhang Rachel Byron Mark T Groudine David McCleary Long Pham Zhen Ye Samantha Kuan Lee Edsall Yi-Chieh Wu Matthew D Rasmussen Mukul S Bansal Manolis Kellis Cheryl A Keller Christapher S Morrissey Tejaswini Mishra Deepti Jain Nergiz Dogan Robert S Harris Philip Cayting Trupti Kawli Alan P Boyle Ghia Euskirchen Anshul Kundaje Shin Lin Yiing Lin Camden Jansen Venkat S Malladi Melissa S Cline Drew T Erickson Vanessa M Kirkup Katrina Learned Cricket A Sloan Kate R Rosenbloom Beatriz Lacerda de Sousa Kathryn Beal Miguel Pignatelli Paul Flicek Jin Lian Tamer Kahveci Dongwon Lee W James Kent Miguel Ramalho Santos Javier Herrero Cedric Notredame Audra Johnson Shinny Vong Kristen Lee Daniel Bates Fidencio Neri Morgan Diegel Theresa Canfield Peter J Sabo Matthew S Wilken Thomas A Reh Erika Giste Anthony Shafer Tanya Kutyavin Eric Haugen Douglas Dunn Alex P Reynolds Shane Neph Richard Humbert R Scott Hansen Marella De Bruijn Licia Selleri Alexander Rudensky Steven Josefowicz Robert Samstein Evan E Eichler Stuart H Orkin Dana Levasseur Thalia Papayannopoulou Kai-Hsin Chang Arthur Skoultchi Srikanta Gosh Christine Disteche Piper Treuting Yanli Wang Mitchell J Weiss Gerd A Blobel Xiaoyi Cao Sheng Zhong Ting Wang Peter J Good Rebecca F Lowdon Leslie B Adams Xiao-Qiao Zhou Michael J Pazin Elise A Feingold Barbara Wold James Taylor Ali Mortazavi Sherman M Weissman John A Stamatoyannopoulos Michael P Snyder Roderic Guigo Thomas R Gingeras David M Gilbert Ross C Hardison Michael A Beer Bing Ren

Nature 2014 Nov;515(7527):355-64

Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nature13992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266106PMC
November 2014

Function of GATA factors in the adult mouse liver.

PLoS One 2013 18;8(12):e83723. Epub 2013 Dec 18.

Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America ; Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0083723PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3867416PMC
October 2014

A comprehensive and high-resolution genome-wide response of p53 to stress.

Cell Rep 2014 Jul 17;8(2):514-27. Epub 2014 Jul 17.

Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.06.030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4113076PMC
July 2014

MRHMMs: multivariate regression hidden Markov models and the variantS.

Bioinformatics 2014 Jun 19;30(12):1755-6. Epub 2014 Feb 19.

Department of Statistics and Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16803, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058941PMC
June 2014

Discovering enhancers directly by activity.

Authors:
Ross C Hardison

Nat Methods 2014 May;11(5):491-2

Center for Comparative Genomics and Bioinformatics, Huck Institutes for Life Sciences and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA.

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http://dx.doi.org/10.1038/nmeth.2933DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4487868PMC
May 2014

Updates of the HbVar database of human hemoglobin variants and thalassemia mutations.

Nucleic Acids Res 2014 Jan 16;42(Database issue):D1063-9. Epub 2013 Oct 16.

The Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, University Park, PA, USA, Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta, MGC-Department of Cell Biology and Genetics, Erasmus MC, Faculty of Medicine and Health Sciences, Rotterdam, The Netherlands, Department of Computer Engineering and Informatics, University of Patras, Faculty of Engineering, Patras, Greece, Department of Pharmacy, University of Patras, School of Health Sciences, Patras, Greece, Department of Medical Genetics, Laboratory of Cytogenetics, Institute of Biology, Nantes, France, Hôpital Edouard Herriot, Unité de Pathologie Moléculaire du Globule Rouge, Lyon, France, Department of Computer and Informatics Engineering, Technological Educational Institute of Western Greece, Patras, Greece, INSERM U955, CHU Henri Mondor, Creteil, France and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.

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http://nar.oxfordjournals.org/content/early/2013/10/16/nar.g
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkt911
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http://dx.doi.org/10.1093/nar/gkt911DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964999PMC
January 2014

Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps.

Genome Res 2013 Dec 29;23(12):2136-48. Epub 2013 Oct 29.

Department of Developmental and Cell Biology, University of California, Irvine, California 92697, USA;

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http://dx.doi.org/10.1101/gr.158261.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3847782PMC
December 2013

Genetics. GWAS to therapy by genome edits?

Science 2013 Oct;342(6155):206-7

Department of Biochemistry and Molecular Biology, Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1126/science.1245813DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4500047PMC
October 2013

A cluster to remember.

Cell 2013 Aug;154(4):718-20

Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1016/j.cell.2013.07.041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3878159PMC
August 2013

Identification of biologically relevant enhancers in human erythroid cells.

J Biol Chem 2013 Mar 22;288(12):8433-44. Epub 2013 Jan 22.

Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut 06520, USA.

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http://dx.doi.org/10.1074/jbc.M112.413260DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3605659PMC
March 2013

Evolution of hemoglobin and its genes.

Authors:
Ross C Hardison

Cold Spring Harb Perspect Med 2012 Dec 1;2(12):a011627. Epub 2012 Dec 1.

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.

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http://dx.doi.org/10.1101/cshperspect.a011627DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3543078PMC
December 2012

Genome-wide epigenetic data facilitate understanding of disease susceptibility association studies.

Authors:
Ross C Hardison

J Biol Chem 2012 Sep 5;287(37):30932-40. Epub 2012 Sep 5.

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.

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http://www.jbc.org/lookup/doi/10.1074/jbc.R112.352427
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http://dx.doi.org/10.1074/jbc.R112.352427DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3438926PMC
September 2012

An encyclopedia of mouse DNA elements (Mouse ENCODE).

August 2012

Genomic approaches towards finding cis-regulatory modules in animals.

Nat Rev Genet 2012 Jun 18;13(7):469-83. Epub 2012 Jun 18.

Department of Biochemistry and Molecular Biology, Center for Comparative Genomics and Bioinformatics, 304 Wartik Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://www.nature.com/articles/nrg3242
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http://dx.doi.org/10.1038/nrg3242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3541939PMC
June 2012

What fraction of the human genome is functional?

Genome Res 2011 Nov 29;21(11):1769-76. Epub 2011 Aug 29.

MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.116814.110
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http://dx.doi.org/10.1101/gr.116814.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3205562PMC
November 2011

Conversion events in gene clusters.

BMC Evol Biol 2011 Jul 28;11:226. Epub 2011 Jul 28.

Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802 USA.

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http://dx.doi.org/10.1186/1471-2148-11-226DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3161012PMC
July 2011

MultiPipMaker: a comparative alignment server for multiple DNA sequences.

Curr Protoc Bioinformatics 2010 Jun;Chapter 10:Unit10.4

The Pennsylvania State University, University Park, Pennsylvania, USA.

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http://dx.doi.org/10.1002/0471250953.bi1004s30DOI Listing
June 2010

Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1.

Nucleic Acids Res 2009 Nov;37(21):7024-38

Center for Comparative Genomics and Bioinformatics, Huck Institutes of Life Sciences.

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http://dx.doi.org/10.1093/nar/gkp747DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2790884PMC
November 2009

It takes (LMO) 2 to tango.

Authors:
Ross C Hardison

Blood 2009 Jun;113(23):5693

Pennsylvania State University, USA.

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http://www.bloodjournal.org/cgi/doi/10.1182/blood-2009-03-20
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http://dx.doi.org/10.1182/blood-2009-03-207258DOI Listing
June 2009

Planning the human variome project: the Spain report.

Authors:
Jim Kaput Richard G H Cotton Lauren Hardman Michael Watson Aida I Al Aqeel Jumana Y Al-Aama Fahd Al-Mulla Santos Alonso Stefan Aretz Arleen D Auerbach Bharati Bapat Inge T Bernstein Jong Bhak Stacey L Bleoo Helmut Blöcker Steven E Brenner John Burn Mariona Bustamante Rita Calzone Anne Cambon-Thomsen Michele Cargill Paola Carrera Lawrence Cavedon Yoon Shin Cho Yeun-Jun Chung Mireille Claustres Garry Cutting Raymond Dalgleish Johan T den Dunnen Carlos Díaz Steven Dobrowolski M Rosário N dos Santos Rosemary Ekong Simon B Flanagan Paul Flicek Yoichi Furukawa Maurizio Genuardi Ho Ghang Maria V Golubenko Marc S Greenblatt Ada Hamosh John M Hancock Ross Hardison Terence M Harrison Robert Hoffmann Rania Horaitis Heather J Howard Carol Isaacson Barash Neskuts Izagirre Jongsun Jung Toshio Kojima Sandrine Laradi Yeon-Su Lee Jong-Young Lee Vera L Gil-da-Silva-Lopes Finlay A Macrae Donna Maglott Makia J Marafie Steven G E Marsh Yoichi Matsubara Ludwine M Messiaen Gabriela Möslein Mihai G Netea Melissa L Norton Peter J Oefner William S Oetting James C O'Leary Ana Maria Oller de Ramirez Mark H Paalman Jillian Parboosingh George P Patrinos Giuditta Perozzi Ian R Phillips Sue Povey Suyash Prasad Ming Qi David J Quin Rajkumar S Ramesar C Sue Richards Judith Savige Dagmar G Scheible Rodney J Scott Daniela Seminara Elizabeth A Shephard Rolf H Sijmons Timothy D Smith María-Jesús Sobrido Toshihiro Tanaka Sean V Tavtigian Graham R Taylor Jon Teague Thoralf Töpel Mollie Ullman-Cullere Joji Utsunomiya Henk J van Kranen Mauno Vihinen Elizabeth Webb Thomas K Weber Meredith Yeager Young I Yeom Seon-Hee Yim Hyang-Sook Yoo

Hum Mutat 2009 Apr;30(4):496-510

Division of Personalised Nutrition and Medicine, FDA/National Center for Toxicological Research, Jefferson, Arkansas 72079, USA.

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http://compbio.berkeley.edu/people/brenner/pubs/kaput-2009-h
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http://doi.wiley.com/10.1002/humu.20972
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http://dx.doi.org/10.1002/humu.20972DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5879779PMC
April 2009

Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif.

Genome Res 2008 Dec 25;18(12):1896-905. Epub 2008 Sep 25.

Center for Comparative Genomics and Bioinformatics of the Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.083089.108
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http://dx.doi.org/10.1101/gr.083089.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593580PMC
December 2008

Globin genes on the move.

Authors:
Ross C Hardison

J Biol 2008 Nov 20;7(9):35. Epub 2008 Nov 20.

Center for Comparative Genomics and Bioinformatics, Huck Institutes of Life Sciences, University Park, PA 16802, USA.

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http://jbiol.biomedcentral.com/articles/10.1186/jbiol92
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http://dx.doi.org/10.1186/jbiol92DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2776387PMC
November 2008

An iron responsive element-like stem-loop regulates alpha-hemoglobin-stabilizing protein mRNA.

J Biol Chem 2008 Oct 2;283(40):26956-64. Epub 2008 Aug 2.

Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.

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http://dx.doi.org/10.1074/jbc.M802421200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2555993PMC
October 2008

A T-to-G transversion at nucleotide -567 upstream of HBG2 in a GATA-1 binding motif is associated with elevated hemoglobin F.

Mol Cell Biol 2008 Jul 28;28(13):4386-93. Epub 2008 Apr 28.

Center of Excellence in Sickle Cell Disease, Division of Hematology/Oncology, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, USA.

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http://dx.doi.org/10.1128/MCB.00071-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447137PMC
July 2008

Genome analysis of the platypus reveals unique signatures of evolution.

Authors:
Wesley C Warren LaDeana W Hillier Jennifer A Marshall Graves Ewan Birney Chris P Ponting Frank Grützner Katherine Belov Webb Miller Laura Clarke Asif T Chinwalla Shiaw-Pyng Yang Andreas Heger Devin P Locke Pat Miethke Paul D Waters Frédéric Veyrunes Lucinda Fulton Bob Fulton Tina Graves John Wallis Xose S Puente Carlos López-Otín Gonzalo R Ordóñez Evan E Eichler Lin Chen Ze Cheng Janine E Deakin Amber Alsop Katherine Thompson Patrick Kirby Anthony T Papenfuss Matthew J Wakefield Tsviya Olender Doron Lancet Gavin A Huttley Arian F A Smit Andrew Pask Peter Temple-Smith Mark A Batzer Jerilyn A Walker Miriam K Konkel Robert S Harris Camilla M Whittington Emily S W Wong Neil J Gemmell Emmanuel Buschiazzo Iris M Vargas Jentzsch Angelika Merkel Juergen Schmitz Anja Zemann Gennady Churakov Jan Ole Kriegs Juergen Brosius Elizabeth P Murchison Ravi Sachidanandam Carly Smith Gregory J Hannon Enkhjargal Tsend-Ayush Daniel McMillan Rosalind Attenborough Willem Rens Malcolm Ferguson-Smith Christophe M Lefèvre Julie A Sharp Kevin R Nicholas David A Ray Michael Kube Richard Reinhardt Thomas H Pringle James Taylor Russell C Jones Brett Nixon Jean-Louis Dacheux Hitoshi Niwa Yoko Sekita Xiaoqiu Huang Alexander Stark Pouya Kheradpour Manolis Kellis Paul Flicek Yuan Chen Caleb Webber Ross Hardison Joanne Nelson Kym Hallsworth-Pepin Kim Delehaunty Chris Markovic Pat Minx Yucheng Feng Colin Kremitzki Makedonka Mitreva Jarret Glasscock Todd Wylie Patricia Wohldmann Prathapan Thiru Michael N Nhan Craig S Pohl Scott M Smith Shunfeng Hou Mikhail Nefedov Pieter J de Jong Marilyn B Renfree Elaine R Mardis Richard K Wilson

Nature 2008 May;453(7192):175-83

Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature06936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803040PMC
May 2008

Human-macaque comparisons illuminate variation in neutral substitution rates.

Genome Biol 2008 Apr 30;9(4):R76. Epub 2008 Apr 30.

Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2643947PMC
April 2008

A GATA-1-regulated microRNA locus essential for erythropoiesis.

Proc Natl Acad Sci U S A 2008 Mar 26;105(9):3333-8. Epub 2008 Feb 26.

Division of Hematology, Children's Hospital of Philadelphia and The University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1073/pnas.0712312105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2265118PMC
March 2008

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

Genome Res 2007 Jun;17(6):760-74

Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.6034307
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891336PMC
June 2007

Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data.

Genome Res 2007 Jun;17(6):775-86

Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891337PMC
June 2007

A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly.

Genome Res 2007 Jun;17(6):960-4

Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.5578007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891355PMC
June 2007

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

Evolutionary and biomedical insights from the rhesus macaque genome.

Authors:
Richard A Gibbs Jeffrey Rogers Michael G Katze Roger Bumgarner George M Weinstock Elaine R Mardis Karin A Remington Robert L Strausberg J Craig Venter Richard K Wilson Mark A Batzer Carlos D Bustamante Evan E Eichler Matthew W Hahn Ross C Hardison Kateryna D Makova Webb Miller Aleksandar Milosavljevic Robert E Palermo Adam Siepel James M Sikela Tony Attaway Stephanie Bell Kelly E Bernard Christian J Buhay Mimi N Chandrabose Marvin Dao Clay Davis Kimberly D Delehaunty Yan Ding Huyen H Dinh Shannon Dugan-Rocha Lucinda A Fulton Ramatu Ayiesha Gabisi Toni T Garner Jennifer Godfrey Alicia C Hawes Judith Hernandez Sandra Hines Michael Holder Jennifer Hume Shalini N Jhangiani Vandita Joshi Ziad Mohid Khan Ewen F Kirkness Andrew Cree R Gerald Fowler Sandra Lee Lora R Lewis Zhangwan Li Yih-Shin Liu Stephanie M Moore Donna Muzny Lynne V Nazareth Dinh Ngoc Ngo Geoffrey O Okwuonu Grace Pai David Parker Heidie A Paul Cynthia Pfannkoch Craig S Pohl Yu-Hui Rogers San Juana Ruiz Aniko Sabo Jireh Santibanez Brian W Schneider Scott M Smith Erica Sodergren Amanda F Svatek Teresa R Utterback Selina Vattathil Wesley Warren Courtney Sherell White Asif T Chinwalla Yucheng Feng Aaron L Halpern Ladeana W Hillier Xiaoqiu Huang Pat Minx Joanne O Nelson Kymberlie H Pepin Xiang Qin Granger G Sutton Eli Venter Brian P Walenz John W Wallis Kim C Worley Shiaw-Pyng Yang Steven M Jones Marco A Marra Mariano Rocchi Jacqueline E Schein Robert Baertsch Laura Clarke Miklós Csürös Jarret Glasscock R Alan Harris Paul Havlak Andrew R Jackson Huaiyang Jiang Yue Liu David N Messina Yufeng Shen Henry Xing-Zhi Song Todd Wylie Lan Zhang Ewan Birney Kyudong Han Miriam K Konkel Jungnam Lee Arian F A Smit Brygg Ullmer Hui Wang Jinchuan Xing Richard Burhans Ze Cheng John E Karro Jian Ma Brian Raney Xinwei She Michael J Cox Jeffery P Demuth Laura J Dumas Sang-Gook Han Janet Hopkins Anis Karimpour-Fard Young H Kim Jonathan R Pollack Tomas Vinar Charles Addo-Quaye Jeremiah Degenhardt Alexandra Denby Melissa J Hubisz Amit Indap Carolin Kosiol Bruce T Lahn Heather A Lawson Alison Marklein Rasmus Nielsen Eric J Vallender Andrew G Clark Betsy Ferguson Ryan D Hernandez Kashif Hirani Hildegard Kehrer-Sawatzki Jessica Kolb Shobha Patil Ling-Ling Pu Yanru Ren David Glenn Smith David A Wheeler Ian Schenck Edward V Ball Rui Chen David N Cooper Belinda Giardine Fan Hsu W James Kent Arthur Lesk David L Nelson William E O'brien Kay Prüfer Peter D Stenson James C Wallace Hui Ke Xiao-Ming Liu Peng Wang Andy Peng Xiang Fan Yang Galt P Barber David Haussler Donna Karolchik Andy D Kern Robert M Kuhn Kayla E Smith Ann S Zwieg

Science 2007 Apr;316(5822):222-34

Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.

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April 2007

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

Hum Mutat 2007 Feb;28(2):206

The Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, University Park, Pennsylvania, USA.

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February 2007

Experimental validation of predicted mammalian erythroid cis-regulatory modules.

Genome Res 2006 Dec 12;16(12):1480-92. Epub 2006 Oct 12.

Center for Comparative Genomics and Bioinformatics of the Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.5353806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1665632PMC
December 2006

ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements.

Genome Res 2006 Dec 19;16(12):1596-604. Epub 2006 Oct 19.

Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.4537706
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1665643PMC
December 2006

Computational prediction of cis-regulatory modules from multispecies alignments using Galaxy, Table Browser, and GALA.

Methods Mol Biol 2006 ;338:91-103

Genome Technology Branch, National Institutes of Health, Rockville, MD, USA.

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http://link.springer.com/10.1385/1-59745-097-9:91
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September 2006

Galaxy: a platform for interactive large-scale genome analysis.

Genome Res 2005 Oct 16;15(10):1451-5. Epub 2005 Sep 16.

Center for Comparative Genomics and Bioinformatics, Huck Institutes for Life Sciences, Penn State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.4086505DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240089PMC
October 2005

Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences.

Genome Res 2005 Aug 15;15(8):1051-60. Epub 2005 Jul 15.

Center for Comparative Genomics and Bioinformatics, Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.3642605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1182217PMC
August 2005

MultiPipMaker: comparative alignment server for multiple DNA sequences.

Curr Protoc Bioinformatics 2005 Apr;Chapter 10:Unit10.4

The Pennsylvania State University, University Park, Pennsylvania, USA.

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http://dx.doi.org/10.1002/0471250953.bi1004s9DOI Listing
April 2005

Mulan: multiple-sequence local alignment and visualization for studying function and evolution.

Genome Res 2005 Jan 8;15(1):184-94. Epub 2004 Dec 8.

Energy, Environment, Biology and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, California 94550, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.3007205
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC540288PMC
January 2005

Evolution and functional classification of vertebrate gene deserts.

Genome Res 2005 Jan 8;15(1):137-45. Epub 2004 Dec 8.

Energy, Environment, Biology, and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, California 94550, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC540279PMC
January 2005

PipMaker: a World Wide Web server for genomic sequence alignments.

Curr Protoc Bioinformatics 2003 Feb;Chapter 10:Unit 10.2

The Pennsylvania State University, University Park, Pennsylvania, USA.

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February 2003