Ross Hardison

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Ross C. Hardison (born March 29, 1951) is an American biochemist and molecular biologist, currently the T. Ming Chu Professor of Biochemistry and Molecular Biology at the Eberly College of Science,[1] of the Pennsylvania State University.

Education and career[edit]

Hardison received a B.A. in chemistry from Vanderbilt University in 1973, where he did undergraduate research on steroid hormone analogs[2] with Prof. Howard Smith. He did his thesis research on histone interaction patterns in chromatin[3][4] in the laboratory of Prof. Roger Chalkley at the University of Iowa, receiving a Ph.D. in biochemistry in 1977. He then trained as a Jane Coffin Childs postdoctoral fellow with Prof. Tom Maniatis at the California Institute of Technology. He joined the faculty at the Pennsylvania State University in 1980 and was promoted to professor in 1991.

Research[edit]

Hardison's research lab studies the molecular basis of gene regulation using genomic and epigenetic approaches, with a special emphasis on the erythroid and myeloid hematopoietic lineages of mouse and human. His research over five decades has investigated the genomics of gene regulation at many levels, from isolation of gene clusters from representative clone libraries of mammalian DNA[5][6] to genome-wide determination[7][8] and integrative analysis of epigenetic features and their association with regulated transcriptomes.[9] One enduring theme of his research is the application of genomic and epigenomic analyses to the prediction of gene regulatory elements, including distal enhancers, followed by rigorous testing of those predictions experimentally.[10][11][12] He and his collaborators have shown that strong signatures of evolutionary conservation, derived from whole-genome alignments,[13] are good predictors of a subset of regulatory elements.[14][15][16] Further, they have utilized systematic integration of epigenomic data to predict a broader set of regulatory elements, which were then evaluated and annotated for potential roles in different cell lineages.[17][9][18][19] More information about his research and teaching is available from his website. Resources produced from his collaborative research are available from the VISION (ValIdated Systematic IntegratiON of hematopoietic epigenomic data) project website and the ENCODE data portal.

Hardison has published many papers (listed in PubMed at this link), which have been widely cited by his peers (documented in Google Scholar at this link).

Some of Hardison's research presentations are available as videos online, including a keynote address at the Rat Genomics and Models meeting at Cold Spring Harbor Laboratory (Dec. 11, 2013) and a talk on "A VISION for integration & application of ENCODE data in differentiating blood cells" for an ENCODE User's meeting (Oct. 08, 2020).

References[edit]

  1. ^ "Holders of Endowed Chairs". science.psu.edu. Retrieved August 22, 2016.
  2. ^ Smith, Howard E.; Neergaard, Jon R.; Burrows, Elizabeth P.; Hardison, Ross G.; Smith, Roy G. (1975), [34] Synthesis of affinity labels for steroid-receptor proteins, Methods in Enzymology, vol. 36, Elsevier, pp. 411–426, doi:10.1016/s0076-6879(75)36037-0, ISBN 978-0-12-181936-1, PMID 162995, retrieved 2022-01-04
  3. ^ Hardison, R; Zeitler, DP; Murphy, JM; Chalkley, R (1977). "Histone neighbors in nuclei and extended chromatin". Cell. 12 (2): 417–427. doi:10.1016/0092-8674(77)90118-0. PMID 912751. S2CID 623347.
  4. ^ Hardison, Ross C.; Eichner, Mary Ellen; Chalkley, Roger (1975). "An approach to histone nearest neighbours in extended chromatin". Nucleic Acids Research. 2 (10): 1751–1770. doi:10.1093/nar/2.10.1751. ISSN 0305-1048. PMC 343543. PMID 1187345.
  5. ^ Maniatis, T.; Hardison, R. C.; Lacy, E.; Lauer, J.; O'Connell, C.; Quon, D.; Sim, G. K.; Efstratiadis, A. (1978). "The isolation of structural genes from libraries of eucaryotic DNA". Cell. 15 (2): 687–701. doi:10.1016/0092-8674(78)90036-3. ISSN 0092-8674. PMID 719759. S2CID 21402986.
  6. ^ Hardison, R. C.; Butler, E. T.; Lacy, E.; Maniatis, T.; Rosenthal, N.; Efstratiadis, A. (1979). "The structure and transcription of four linked rabbit beta-like globin genes". Cell. 18 (4): 1285–1297. doi:10.1016/0092-8674(79)90239-3. ISSN 0092-8674. PMID 519769. S2CID 54331923.
  7. ^ Cheng, Yong; Wu, Weisheng; Kumar, Swathi Ashok; Yu, Duonan; Deng, Wulan; Tripic, Tamara; King, David C.; Chen, Kuan-Bei; Zhang, Ying; Drautz, Daniela; Giardine, Belinda (2009). "Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression". Genome Research. 19 (12): 2172–2184. doi:10.1101/gr.098921.109. ISSN 1549-5469. PMC 2792182. PMID 19887574.
  8. ^ Wu, Weisheng; Cheng, Yong; Keller, Cheryl A.; Ernst, Jason; Kumar, Swathi Ashok; Mishra, Tejaswini; Morrissey, Christapher; Dorman, Christine M.; Chen, Kuan-Bei; Drautz, Daniela; Giardine, Belinda (2011). "Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration". Genome Research. 21 (10): 1659–1671. doi:10.1101/gr.125088.111. ISSN 1549-5469. PMC 3202283. PMID 21795386.
  9. ^ a b Xiang, Guanjue; Keller, Cheryl A.; Heuston, Elisabeth; Giardine, Belinda M.; An, Lin; Wixom, Alexander Q.; Miller, Amber; Cockburn, April; Sauria, Michael E. G.; Weaver, Kathryn; Lichtenberg, Jens (2020). "An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis". Genome Research. 30 (3): 472–484. doi:10.1101/gr.255760.119. ISSN 1549-5469. PMC 7111515. PMID 32132109.
  10. ^ Hardison, Ross C.; Taylor, James (2012-06-18). "Genomic approaches towards finding cis-regulatory modules in animals". Nature Reviews. Genetics. 13 (7): 469–483. doi:10.1038/nrg3242. ISSN 1471-0064. PMC 3541939. PMID 22705667.
  11. ^ Taylor, James; Tyekucheva, Svitlana; King, David C.; Hardison, Ross C.; Miller, Webb; Chiaromonte, Francesca (2006). "ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements". Genome Research. 16 (12): 1596–1604. doi:10.1101/gr.4537706. ISSN 1088-9051. PMC 1665643. PMID 17053093.
  12. ^ Wang, Hao; Zhang, Ying; Cheng, Yong; Zhou, Yuepin; King, David C.; Taylor, James; Chiaromonte, Francesca; Kasturi, Jyotsna; Petrykowska, Hanna; Gibb, Brian; Dorman, Christine (2006). "Experimental validation of predicted mammalian erythroid cis-regulatory modules". Genome Research. 16 (12): 1480–1492. doi:10.1101/gr.5353806. ISSN 1088-9051. PMC 1665632. PMID 17038566.
  13. ^ Schwartz, Scott; Kent, W. James; Smit, Arian; Zhang, Zheng; Baertsch, Robert; Hardison, Ross C.; Haussler, David; Miller, Webb (2003). "Human-mouse alignments with BLASTZ". Genome Research. 13 (1): 103–107. doi:10.1101/gr.809403. ISSN 1088-9051. PMC 430961. PMID 12529312.
  14. ^ Hardison, R. C. (2000). "Conserved noncoding sequences are reliable guides to regulatory elements". Trends in Genetics. 16 (9): 369–372. doi:10.1016/s0168-9525(00)02081-3. ISSN 0168-9525. PMID 10973062.
  15. ^ Miller, Webb; Makova, Kateryna D.; Nekrutenko, Anton; Hardison, Ross C. (2004). "Comparative genomics". Annual Review of Genomics and Human Genetics. 5: 15–56. doi:10.1146/annurev.genom.5.061903.180057. ISSN 1527-8204. PMID 15485342.
  16. ^ King, David C.; Taylor, James; Zhang, Ying; Cheng, Yong; Lawson, Heather A.; Martin, Joel; ENCODE groups for Transcriptional Regulation and Multispecies Sequence Analysis; Chiaromonte, Francesca; Miller, Webb; Hardison, Ross C. (2007). "Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data". Genome Research. 17 (6): 775–786. doi:10.1101/gr.5592107. ISSN 1088-9051. PMC 1891337. PMID 17567996.
  17. ^ Zhang, Yu; An, Lin; Yue, Feng; Hardison, Ross C. (2016-08-19). "Jointly characterizing epigenetic dynamics across multiple human cell types". Nucleic Acids Research. 44 (14): 6721–6731. doi:10.1093/nar/gkw278. ISSN 1362-4962. PMC 5772166. PMID 27095202.
  18. ^ Cheng, Yong; Ma, Zhihai; Kim, Bong-Hyun; Wu, Weisheng; Cayting, Philip; Boyle, Alan P.; Sundaram, Vasavi; Xing, Xiaoyun; Dogan, Nergiz; Li, Jingjing; Euskirchen, Ghia (2014-11-20). "Principles of regulatory information conservation between mouse and human". Nature. 515 (7527): 371–375. Bibcode:2014Natur.515..371C. doi:10.1038/nature13985. ISSN 1476-4687. PMC 4343047. PMID 25409826.
  19. ^ ENCODE Project Consortium; Moore, Jill E.; Purcaro, Michael J.; Pratt, Henry E.; Epstein, Charles B.; Shoresh, Noam; Adrian, Jessika; Kawli, Trupti; Davis, Carrie A.; Dobin, Alexander; Kaul, Rajinder (2020). "Expanded encyclopaedias of DNA elements in the human and mouse genomes". Nature. 583 (7818): 699–710. Bibcode:2020Natur.583..699E. doi:10.1038/s41586-020-2493-4. ISSN 1476-4687. PMC 7410828. PMID 32728249.

External links[edit]

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