Interactions of chromatin context, binding site sequence content, and sequence evolution in stress-induced p53 occupancy and transactivation.

by Dan Su, Xuting Wang, Michelle R Campbell, Lingyun Song, Alexias Safi, Gregory E Crawford, Douglas A Bell
Published 2015-01-01

Epstein-Barr virus induces germinal center light zone chromatin architecture and promotes survival through enhancer looping at the BCL2A1 locus

by Joanne Dai, Elliott D. SoRelle, Emma Heckenberg, Lingyun Song, Jana M. Cable, Gregory E. Crawford, Micah A. Luftig
Published 2024-01-01

Characterization of enhancer activity in early human neurodevelopment using Massively Parallel Reporter Assay (MPRA) and forebrain organoids

by Davide Capauto, Yifan Wang, Feinan Wu, Scott Norton, Jessica Mariani, Fumitaka Inoue, Gregory E. Crawford, Nadav Ahituv, Alexej Abyzov, Flora M. Vaccarino
Published 2024-02-01

Chromatin accessibility mapping identifies mediators of basal transcription and retinoid-induced repression of OTX2 in medulloblastoma.

by Matthew Wortham, Changcun Guo, Monica Zhang, Lingyun Song, Bum-Kyu Lee, Vishwanath R Iyer, Terrence S Furey, Gregory E Crawford, Hai Yan, Yiping He
Published 2014-01-01

Deletion of a conserved cis-element in the Ifng locus highlights the role of acute histone acetylation in modulating inducible gene transcription.

by Anand Balasubramani, Colleen J Winstead, Henrietta Turner, Karen M Janowski, Stacey N Harbour, Yoichiro Shibata, Gregory E Crawford, Robin D Hatton, Casey T Weaver
Published 2014-01-01

Integrative single-nucleus multi-omics analysis prioritizes candidate cis and trans regulatory networks and their target genes in Alzheimer’s disease brains

by Julia Gamache, Daniel Gingerich, E. Keats Shwab, Julio Barrera, Melanie E. Garrett, Cordelia Hume, Gregory E. Crawford, Allison E. Ashley-Koch, Ornit Chiba-Falek
Published 2023-10-01

Integrated chromatin and transcriptomic profiling of patient-derived colon cancer organoids identifies personalized drug targets to overcome oxaliplatin resistance

by Kuei-Ling Tung, Kai-Yuan Chen, Marcos Negrete, Tianyi Chen, Alexias Safi, Abed Alhalim Aljamal, Lingyun Song, Gregory E. Crawford, Shengli Ding, David S. Hsu, Xiling Shen
Published 2021-03-01

Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis.

by Peter C Scacheri, Sean Davis, Duncan T Odom, Gregory E Crawford, Stacie Perkins, Mohamad J Halawi, Sunita K Agarwal, Stephen J Marx, Allen M Spiegel, Paul S Meltzer, Francis S Collins
Published 2006-04-01

Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation.

by Gregory R Keele, Bryan C Quach, Jennifer W Israel, Grace A Chappell, Lauren Lewis, Alexias Safi, Jeremy M Simon, Paul Cotney, Gregory E Crawford, William Valdar, Ivan Rusyn, Terrence S Furey
Published 2020-01-01

Open Chromatin Profiling in Adipose Tissue Marks Genomic Regions with Functional Roles in Cardiometabolic Traits

by Maren E. Cannon, Kevin W. Currin, Kristin L. Young, Hannah J. Perrin, Swarooparani Vadlamudi, Alexias Safi, Lingyun Song, Ying Wu, Martin Wabitsch, Markku Laakso, Gregory E. Crawford, Karen L. Mohlke
Published 2019-08-01

Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.

by Zhihao Ding, Yunyun Ni, Sander W Timmer, Bum-Kyu Lee, Anna Battenhouse, Sandra Louzada, Fengtang Yang, Ian Dunham, Gregory E Crawford, Jason D Lieb, Richard Durbin, Vishwanath R Iyer, Ewan Birney
Published 2014-11-01

Correction: Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.

by Zhihao Ding, Yunyun Ni, Sander W Timmer, Bum-Kyu Lee, Anna Battenhouse, Sandra Louzada, Fengtang Yang, Ian Dunham, Gregory E Crawford, Jason D Lieb, Richard Durbin, Vishwanath R Iyer, Ewan Birney
Published 2015-04-01

CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression.

by Michael P Schnetz, Lusy Handoko, Batool Akhtar-Zaidi, Cynthia F Bartels, C Filipe Pereira, Amanda G Fisher, David J Adams, Paul Flicek, Gregory E Crawford, Thomas Laframboise, Paul Tesar, Chia-Lin Wei, Peter C Scacheri
Published 2010-07-01

Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome.

by Hualin Xi, Hennady P Shulha, Jane M Lin, Teresa R Vales, Yutao Fu, David M Bodine, Ronald D G McKay, Josh G Chenoweth, Paul J Tesar, Terrence S Furey, Bing Ren, Zhiping Weng, Gregory E Crawford
Published 2007-08-01

Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer’s disease brains

by Julio Barrera, Lingyun Song, Julia E. Gamache, Melanie E. Garrett, Alexias Safi, Young Yun, Ivana Premasinghe, Daniel Sprague, Danielle Chipman, Jeffrey Li, Hélène Fradin, Karen Soldano, Raluca Gordân, Allison E. Ashley-Koch, Gregory E. Crawford, Ornit Chiba-Falek
Published 2021-08-01

Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection.

by Yoichiro Shibata, Nathan C Sheffield, Olivier Fedrigo, Courtney C Babbitt, Matthew Wortham, Alok K Tewari, Darin London, Lingyun Song, Bum-Kyu Lee, Vishwanath R Iyer, Stephen C J Parker, Elliott H Margulies, Gregory A Wray, Terrence S Furey, Gregory E Crawford
Published 2012-06-01

Ascl1 Coordinately Regulates Gene Expression and the Chromatin Landscape during Neurogenesis

by Alexandre A.S.F. Raposo, Francisca F. Vasconcelos, Daniela Drechsel, Corentine Marie, Caroline Johnston, Dirk Dolle, Angela Bithell, Sébastien Gillotin, Debbie L.C. van den Berg, Laurence Ettwiller, Paul Flicek, Gregory E. Crawford, Carlos M. Parras, Benedikt Berninger, Noel J. Buckley, François Guillemot, Diogo S. Castro
Published 2015-03-01

Single cell profiling at the maternal–fetal interface reveals a deficiency of PD-L1+ non-immune cells in human spontaneous preterm labor

by Xiao Liu, Ivy Aneas, Noboru Sakabe, Rebecca L. Anderson, Christine Billstrand, Cristina Paz, Harjot Kaur, Brian Furner, Seong Choi, Adriana Y. Prichina, Elizabeth Ann L. Enninga, Haidong Dong, Amy Murtha, Gregory E. Crawford, John A. Kessler, William Grobman, Marcelo A. Nobrega, Sarosh Rana, Carole Ober
Published 2023-05-01

Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes.

by Stephen C J Parker, Jared Gartner, Isabel Cardenas-Navia, Xiaomu Wei, Hatice Ozel Abaan, Subramanian S Ajay, Nancy F Hansen, Lingyun Song, Umesh K Bhanot, J Keith Killian, Yevgeniy Gindin, Robert L Walker, Paul S Meltzer, James C Mullikin, Terrence S Furey, Gregory E Crawford, Steven A Rosenberg, Yardena Samuels, Elliott H Margulies
Published 2012-01-01

Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia

by Julien Bryois, Melanie E. Garrett, Lingyun Song, Alexias Safi, Paola Giusti-Rodriguez, Graham D. Johnson, Annie W. Shieh, Alfonso Buil, John F. Fullard, Panos Roussos, Pamela Sklar, Schahram Akbarian, Vahram Haroutunian, Craig A. Stockmeier, Gregory A. Wray, Kevin P. White, Chunyu Liu, Timothy E. Reddy, Allison Ashley-Koch, Patrick F. Sullivan, Gregory E. Crawford
Published 2018-08-01