Ross Hardison

Associate Director of the Genome Sciences Institute; T. Ming Chu Professor of Biochemistry and Molecular Biology

Ross Hardison

Research Summary

Regulation of gene expression during development.

Huck Affiliations

Links

Publication Tags

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Genome Chromatin Genes Dna Mutation Globins Fetal Hemoglobin Transcription Factors Human Genome Hemoglobins Erythroid Cells Encyclopedias Gene Editing Thalassemia Hemoglobinopathies Sickle Cell Anemia Gamma Globins Beta Globins Hemoglobin Subunits Rna Hemoglobin Population Datasets Composite Material T Cell Antigen Receptor

Most Recent Publications

Gene silencing dynamics are modulated by transiently active regulatory elements

Marit W. Vermunt, Jing Luan, Zhe Zhang, A. Josephine Thrasher, Anran Huang, Megan S. Saari, Eugene Khandros, Robert A. Beagrie, Shiping Zhang, Pranay Vemulamada, Matilda Brilleman, Kiwon Lee, Jennifer A. Yano, Belinda M. Giardine, Cheryl A. Keller, Ross C. Hardison, Gerd A. Blobel, 2023, Molecular Cell on p. 715-730.e6

Identification and characterization of RBM12 as a novel regulator of fetal hemoglobin expression

A Wakabayashi, M Kihiu, M Sharma, A Thrasher, M Saari, M Quesnel-Vallières, O Abdulmalik, S Peslak, E Khandros, Cheryl A. Keller Capone, C Keller, B Giardine, Y Barash, Ross C. Hardison, J Shi, G Blobel, 2022, Blood advances on p. 5956-5968

CLIMB: High-dimensional association detection in large scale genomic data

H Koch, Cheryl Keller, G Xiang, B Giardine, F Zhang, Y Wang, Ross Hardison, Qunhua Li, 2022, Nature Communications on p. 6874

CTCF blocks antisense transcription initiation at divergent promoters

J Luan, M Vermunt, C Syrett, A Coté, J Tome, H Zhang, A Huang, J Luppino, Cheryl Keller, B Giardine, S Zhang, M Dunagin, Z Zhang, E Joyce, J Lis, A Raj, Ross C. Hardison, G Blobel, 2022, Nature Structural Biology on p. 1136-1144

Subtype-specific 3D genome alteration in acute myeloid leukaemia

J Xu, Fan Song, Huijue Lyu, Mikoto Kobayashi, Baozhen Zhang, Ziyu Zhao, Ye Hou, Xiaotao Wang, Yu Luan, Bei Jia, Lena Stasiak, Josiah Wong, Qixuan Wang, Qi Jin, Qiushi Jin, Yihao Fu, Hongbo Yang, Ross C. Hardison, Sinisa Dovat, Leonidas Platanias, Yarui Diao, Yue Yang, Tomoko Yamada, Aaron Viny, Ross Levine, David Claxton, James R. Broach, Hong Zheng, Feng Yue, 2022, Nature on p. 387-398

HIC2 controls developmental hemoglobin switching by repressing BCL11A transcription

P Huang, S Peslak, R Ren, E Khandros, K Qin, Cheryl A. Keller, B Giardine, H Bell, X Lan, M Sharma, J Horton, O Abdulmalik, S Chou, J Shi, M Crossley, Ross C. Hardison, X Cheng, G Blobel, 2022, Nature Genetics on p. 1417-1426

Dual function NFI factors control fetal hemoglobin silencing in adult erythroid cells

K Qin, P Huang, R Feng, Cheryl A. Keller, S Peslak, E Khandros, M Saari, X Lan, T Mayuranathan, P Doerfler, O Abdulmalik, B Giardine, S Chou, J Shi, Ross C. Hardison, M Weiss, G Blobel, 2022, Nature Genetics on p. 874-884

Publisher Correction: Dual function NFI factors control fetal hemoglobin silencing in adult erythroid cells (Nature Genetics, (2022), 54, 6, (874-884), 10.1038/s41588-022-01076-1)

Kunhua Qin, Peng Huang, Ruopeng Feng, Cheryl A. Keller, Scott A. Peslak, Eugene Khandros, Megan S. Saari, Xianjiang Lan, Thiyagaraj Mayuranathan, Phillip A. Doerfler, Osheiza Abdulmalik, Belinda Giardine, Stella T. Chou, Junwei Shi, Ross C. Hardison, Mitchell J. Weiss, Gerd A. Blobel, 2022, Nature Genetics on p. 906

Genomic landscape of TCRαβ and TCRγδ T-large granular lymphocyte leukemia

H Cheon, J Xing, K Moosic, J Ung, V Chan, D Chung, M Toro, O Elghawy, J Wang, C Hamele, Ross C. Hardison, T Olson, S Tan, D Feith, A Ratan, T Loughran, 2022, Blood on p. 3058-3072

Author Correction: Perspectives on ENCODE (Nature, (2020), 583, 7818, (693-698), 10.1038/s41586-020-2449-8)

Michael P. Snyder, Federi Bronwen co Abascal, Thomas R. Gingeras, Reyes Acosta, Jill E. Moore, Nicholas J. Addleman, Jessika Adrian, Zhiping Weng, Mark B. Gerstein, Veena Afzal, Bing Ren, Bronwen Aken, Rizi Ai, Jennifer A. Akiyama, John A. Stamatoyannopoulos, Omar Al Jammal, Brenton R. Graveley, Henry Amrhein, Elise A. Feingold, Michael J. Pazin, Stacie M. Anderson, Michael Pagan, Gregory R. Andrews, Daniel A. Gilchrist, Igor Antoshechkin, Kristin G. Ardlie, Benjamin C. Hitz, J. Michael Cherry, Joel Armstrong, Matthew Astley, Bradley E. Bernstein, Eric M. Mendenhall, Budhaditya Banerjee, Amira A. Barkal, Daniel R. Zerbino, If H.A. Barnes, Adam Frankish, Paul Flicek, Iros Barozzi, Richard M. Myers, Daniel Barrell, Gemma Barson, Daniel Bates, Ulugbek K. Baymuradov, Cassandra Bazile, Michael A. Beer, Samantha Beik, M. A. Bender, Ruth Bennett, Louis Philip Benoit Bouvrette, Bradley E. Bernstein, Andrew Berry, Anand Bhaskar, Alexandra Bignell, Steven M. Blue, David M. Bodine, Carles Boix, Nathan Boley, Tyler Borrman, Beatrice Borsari, Alan P. Boyle, Laurel A. Brandsmeier, Alessandra Breschi, Emery H. Bresnick, Jason A. Brooks, Michael Buckley, Ross C. Hardison, Cheryl A. Keller, Hongbo Yang, Feng Yue, 2022, Nature on p. E4

Most-Cited Papers

A comparative encyclopedia of DNA elements in the mouse genome

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, 2014, Nature on p. 355-64

Topologically associating domains are stable units of replication-timing regulation

Benjamin D. Pope, Tyrone Ryba, Vishnu Dileep, Feng Yue, Weisheng Wu, Olgert Denas, Daniel L. Vera, Yanli Wang, R. Scott Hansen, Theresa K. Canfield, Robert E. Thurman, Yong Cheng, Günhan Gülsoy, Jonathan H. Dennis, Michael P. Snyder, John A. Stamatoyannopoulos, James Taylor, Ross C. Hardison, Tamer Kahveci, Bing Ren, David M. Gilbert, 2014, Nature on p. 402-405

Expanded encyclopaedias of DNA elements in the human and mouse genomes

Federico Abascal, Reyes Acosta, Nicholas J. Addleman, Jessika Adrian, Veena Afzal, Bronwen Aken, Jennifer A. Akiyama, Omar Al Jammal, Henry Amrhein, Stacie M. Anderson, Gregory R. Andrews, Igor Antoshechkin, Kristin G. Ardlie, Joel Armstrong, Matthew Astley, Budhaditya Banerjee, Amira A. Barkal, If H.A. Barnes, Iros Barozzi, Daniel Barrell, Gemma Barson, Daniel Bates, Ulugbek K. Baymuradov, Cassandra Bazile, Michael A. Beer, Samantha Beik, M. A. Bender, Ruth Bennett, Louis Philip Benoit Bouvrette, Bradley E. Bernstein, Andrew Berry, Anand Bhaskar, Alexandra Bignell, Steven M. Blue, David M. Bodine, Carles Boix, Nathan Boley, Tyler Borrman, Beatrice Borsari, Alan P. Boyle, Laurel A. Brandsmeier, Alessandra Breschi, Emery H. Bresnick, Jason A. Brooks, Michael Buckley, Ross C. Hardison, Cheryl A. Keller, Hongbo Yang, Feng Yue, Lijun Zhang, 2020, Nature on p. 699-710

Defining functional DNA elements in the human genome

Manolis Kellis, Barbara Wold, Michael P. Snyder, Bradley E. Bernstein, Anshul Kundaje, Georgi K. Marinov, Lucas D. Ward, Ewan Birney, Gregory E. Crawford, Job Dekker, Ian Dunham, Laura L. Elnitski, Peggy J. Farnham, Elise A. Feingold, Mark Gerstein, Morgan C. Giddings, David M. Gilbert, Thomas R. Gingeras, Eric D. Green, Roderic Guigo, Tim Hubbard, Jim Kent, Jason D. Lieb, Richard M. Myers, Michael J. Pazin, Bing Ren, John A. Stamatoyannopoulos, Zhiping Weng, Kevin P. White, Ross C. Hardison, 2014, Proceedings of the National Academy of Sciences of the United States of America on p. 6131-6138

Integrative annotation of chromatin elements from ENCODE data

Michael M. Hoffman, Jason Ernst, Steven P. Wilder, Anshul Kundaje, Robert S. Harris, Max Libbrecht, Belinda Giardine, Paul M. Ellenbogen, Jeffrey A. Bilmes, Ewan Birney, Ross C. Hardison, Ian Dunham, Manolis Kellis, William Stafford Noble, 2013, Nucleic Acids Research on p. 827-841

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

Belinda Giardine, Joseph Borg, Emmanouil Viennas, Cristiana Pavlidis, Kamran Moradkhani, Philippe Joly, Marina Bartsakoulia, Cathy Riemer, Webb Miller, Giannis Tzimas, Henri Wajcman, Ross C. Hardison, George P. Patrinos, 2014, Nucleic Acids Research on p. D1063-D1069

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

Yanli Wang, Fan Song, Bo Zhang, Lijun Zhang, Jie Xu, Da Kuang, Daofeng Li, Mayank N.K. Choudhary, Yun Li, Ming Hu, Ross Hardison, Ting Wang, Feng Yue, 2018, Genome Biology

A genome-editing strategy to treat β-hemoglobinopathies that recapitulates a mutation associated with a benign genetic condition

Elizabeth A. Traxler, Yu Yao, Yong Dong Wang, Kaitly J. Woodard, Ryo Kurita, Yukio Nakamura, Jim R. Hughes, Ross C. Hardison, Gerd A. Blobel, Chunliang Li, Mitchell J. Weiss, 2016, Nature Medicine on p. 987-990

Principles of regulatory information conservation between mouse and human

Yong Cheng, Zhihai Ma, Bong Hyun Kim, Weisheng Wu, Philip Cayting, Alan P. Boyle, Vasavi Sundaram, Xiaoyun Xing, Nergiz Dogan, Jingjing Li, Ghia Euskirchen, Shin Lin, Yiing Lin, Axel Visel, Trupti Kawli, Xinqiong Yang, Dorrelyn Patacsil, Cheryl A. Keller, Belinda Giardine, Anshul Kundaje, Ting Wang, Len A. Pennacchio, Zhiping Weng, Ross C. Hardison, Michael P. Snyder, 2014, Nature on p. 371-375

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

Tao Yang, Feipeng Zhang, Galip Gürkan Yardımci, Fan Song, Ross C. Hardison, William Stafford Noble, Feng Yue, Qunhua Li, 2017, Genome Research on p. 1939-1949

News Articles Featuring Ross Hardison

Nov 14, 2022

New statistical method improves genomic analyses

A new statistical method provides a more efficient way to uncover biologically meaningful changes in genomic data that span multiple conditions — such as cell types or tissues.

Full Article

Dec 17, 2019

New tool reveals DNA structures that influence disease

Disruption of certain DNA structures — called topologically associating domains, or TADs — is linked with the development of disease, including some cancers. With its newly created algorithm that quickly locates and helps elucidate the complex functions of TADs, an international team of researchers is making it easier to study these important structures and help prevent disease.

Full Article

May 06, 2019

Icefish Study Adds Another Color to the Story of Blood

The rainbow of pigments that animals use for blood illustrates a central truth about evolution

Full Article

Apr 22, 2019

Icefish Study Adds Another Color to the Story of Blood

The Antarctic blackfin icefish is the only known vertebrate animal that lacks red blood cells containing hemoglobin. But the use of hemoglobin to transport oxygen through the body is actually a rarity among invertebrates, which rely on a variety of other pigments in their versions of blood.

Full Article

Mar 26, 2019

CBIOS Trainee Hillary Koch Awarded NIH Fellowship

Koch's dissertation proposal, "Statistical Methods for Differential Peak Detection in Hi-C Data," was funded upon its first submission to the National Human Genome Research Institute.

Full Article