Laboratory of Ross Hardison

Current Directory Entry

March 2011, 3rd floor Wartik Lab. Pictured are (front row, sitting) Swathi Ashok Kumar, Marta Byrska-Bishop, Tejaswini Mishra, (second row, standing) Kuan-Bei Chen, Deepti Jain, Chris Morrissey, Belinda Giardine, Ross, Cheryl Keller Capone, Christine Dorman, Weisheng Wu, Nergiz Dogan (L to R).

Photos of lab folks in earlier years

Lab reunion article in Genome Technology, June 2009, about training in the Hardison lab, entitled "Data is Truth" (by Matthew Dublin).

Ross Hardison is the T. Ming Chu Professor of Biochemistry and Molecular Biology at the Penn State University. Ross and his co-workers (who are part of the Center for Comparative Genomics and Bioinformatics) use comparative genomics to predict gene regulatory modules, test them for function in the laboratory, and work to pull all this together into a more thorough understanding of global regulation of erythroid genes. The techniques developed and utilized in this and associated labs should be applicable to a wide variety of regulated systems and organismal groups.

Research

• Description of Research
• Publications, including full text for many recent articles
• Supplements to papers and useful datasets, including predicted erythroid cis-regulatory modules
• Genome browser with erythroid transcription factor occupancy and other features of gene regulation, genome-wide in mouse
• Datasets of features relating to regulation of transcription, human genome

An example of data integration, Hardison lab-style! March 29, 2011.

Teaching

• Textbook, full text and free Working with Molecular Genetics
• Course on Functional Genomics: Illuminating the dark matter of the genome, offered Spring semesters
• Course material, comprised of lecture presentations (ppt), for a molecular genetics course, 2002.

Connections and collaborations at PSU

• Almost all our work is done in a long-standing collaboration with Dr. Webb Miller.
• Center for Comparative Genomics and Bioinformatics (CCGB). This site has:
  • Algorithms and servers for genome sequence alignments
  • Methods to analyze of those alignments for functional prediction and greater understanding of genome evolution
  • Databases, servers and metaservers to facilitate that analysis.
• Globin Gene Server
• Department of Biochemistry and Molecular Biology
• The Huck Institutes of the Life Sciences
• The Pennsylvania State University.

Folks from many labs in the CCGB, March 29, 2011.

Collaborations with researchers at other institutions

• Whole-genome alignments and analysis with Dr. David Haussler in the Center for Biomolecular Science and Engineering at the University of California at Santa Cruz and Howard Hughes Medical Institute
• Sequence alignments, analysis and database development with Dr. Jim Kent at UCSC.
• Application of genomics and bioinformatics to understand erythroid gene regulation with Dr. Mitch Weiss, and co-workers at The Children's Hospital of Philadelphia.
• Assist Dr. Ivan Ovcharenko at the Lawrence Livermore National Laboratory in his development of a suite of tools at dcode.org for genome sequence alignments, discovery of candidate cis-regulatory elements and conserved matches to transcription factor binding sites.

Hardison family material

• You can get a copy of a remembrance of our Aunt Anne ("Big Anne") and our grandparents (Hardison side) by their children and grandchildren here. This is a collective work by the family, edited and illustrated by Doug Shields, Jr. Copyrights are held by the family. This is the new, improved 2007 edition.
• You can get a picture of four generations of descendants of Hershel and Jane McKay Hardison, taken by Jane Jones at a reunion on June 29, 2008, here.
• The first edition (from about 2005) about the grandparents can be obtained here.
• You can get a copy of historical material, remembrances and photos from several generations of the Shields/Srygley/Scobey branches of the extended "Hardison" family, entitled "One Day at a Time", here. This came from Doug Shields, Jr.
• A movie of the Penn State BlueBand marching in the Homecoming Parade, Oct 08, 2010.

Page created: Wednesday, 12-Jan-2005, last modified 10-January-2012