ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions von Furey, Terrence S.

Volltext

Redefining the IBDs using genome-scale molecular phenotyping von Furey, Terrence S., Sethupathy, Praveen, Sheikh, Shehzad Z.

Volltext

Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells von Lickwar, Colin R, Camp, J Gray, Weiser, Matthew, Cocchiaro, Jordan L, Kingsley, David M, Furey, Terrence S, Sheikh, Shehzad Z, Rawls, John F

Volltext

CoVar: A generalizable machine learning approach to identify the coordinated regulators driving variational gene expression von Roy, Satyaki, Sheikh, Shehzad Z, Furey, Terrence S

Volltext

Genetics Driving Epigenetics von Furey, Terrence S., Sethupathy, Praveen

Volltext

High-Resolution Mapping and Characterization of Open Chromatin across the Genome von Boyle, Alan P., Davis, Sean, Shulha, Hennady P., Meltzer, Paul, Margulies, Elliott H., Weng, Zhiping, Furey, Terrence S., Crawford, Gregory E.

Volltext

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells von Boyle, Alan P, Song, Lingyun, Lee, Bum-Kyu, London, Darin, Keefe, Damian, Birney, Ewan, Iyer, Vishwanath R, Crawford, Gregory E, Furey, Terrence S

Volltext

F-Seq: a feature density estimator for high-throughput sequence tags von Boyle, Alan P., Guinney, Justin, Crawford, Gregory E., Furey, Terrence S.

Volltext

A machine learning approach identifies 5-ASA and ulcerative colitis as being linked with higher COVID-19 mortality in patients with IBD von Roy, Satyaki, Sheikh, Shehzad Z., Furey, Terrence S.

Volltext

Nuclear actin structure regulates chromatin accessibility von Sen, Buer, Xie, Zhihui, Thomas, Michelle D., Pattenden, Samantha G., Howard, Sean, McGrath, Cody, Styner, Maya, Uzer, Gunes, Furey, Terrence S., Rubin, Janet

Volltext

Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation von Keele, Gregory R., Quach, Bryan C., Israel, Jennifer W., Chappell, Grace A., Lewis, Lauren, Safi, Alexias, Simon, Jeremy M., Cotney, Paul, Crawford, Gregory E., Valdar, William, Rusyn, Ivan, Furey, Terrence S.

Volltext

Correcting nucleotide-specific biases in high-throughput sequencing data von Wang, Jeremy R, Quach, Bryan, Furey, Terrence S

Volltext

Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans von McDaniell, Ryan, Lee, Bum-Kyu, Song, Lingyun, Liu, Zheng, Boyle, Alan P., Erdos, Michael R., Scott, Laura J., Morken, Mario A., Kucera, Katerina S., Battenhouse, Anna, Keefe, Damian, Collins, Francis S., Willard, Huntington F., Lieb, Jason D., Furey, Terrence S., Crawford, Gregory E., lyer, Vishwanath R., Birney, Ewan

Volltext

The human genome browser at UCSC von Kent, W James, Sugnet, Charles W, Furey, Terrence S, Roskin, Krishna M, Pringle, Tom H, Zahler, Alan M, Haussler, David

Volltext

Linking gene expression to clinical outcomes in pediatric Crohn’s disease using machine learning von Chen, Kevin A., Nishiyama, Nina C., Kennedy Ng, Meaghan M., Shumway, Alexandria, Joisa, Chinmaya U., Schaner, Matthew R., Lian, Grace, Beasley, Caroline, Zhu, Lee-Ching, Bantumilli, Surekha, Kapadia, Muneera R., Gomez, Shawn M., Furey, Terrence S., Sheikh, Shehzad Z.

Volltext

Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells von Lee, Bum-Kyu, Bhinge, Akshay A, Battenhouse, Anna, McDaniell, Ryan M, Liu, Zheng, Song, Lingyun, Ni, Yunyun, Birney, Ewan, Lieb, Jason D, Furey, Terrence S, Crawford, Gregory E, Iyer, Vishwanath R

Volltext

MicroRNAs Classify Different Disease Behavior Phenotypes of Crohn's Disease and May Have Prognostic Utility von Peck, Bailey C E, Weiser, Matthew, Lee, Saangyoung E, Gipson, Gregory R, Iyer, Vishal B, Sartor, Ryan B, Herfarth, Hans H, Long, Millie D, Hansen, Jonathan J, Isaacs, Kim L, Trembath, Dimitri G, Rahbar, Reza, Sadiq, Timothy S, Furey, Terrence S, Sethupathy, Praveen, Sheikh, Shehzad Z

Volltext

Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection von Shibata, Yoichiro, Sheffield, Nathan C, Fedrigo, Olivier, Babbitt, Courtney C, Wortham, Matthew, Tewari, Alok K, London, Darin, Song, Lingyun, Lee, Bum-Kyu, Iyer, Vishwanath R, Parker, Stephen C J, Margulies, Elliott H, Wray, Gregory A, Furey, Terrence S, Crawford, Gregory E

Volltext

Increased colonic expression of ACE2 associates with poor prognosis in Crohn’s disease von Toyonaga, Takahiko, Araba, Kenza C., Kennedy, Meaghan M., Keith, Benjamin P., Wolber, Elisabeth A., Beasley, Caroline, Steinbach, Erin C., Schaner, Matthew R., Jain, Animesh, Long, Millie D., Barnes, Edward L., Herfarth, Hans H., Isaacs, Kim L., Hansen, Jonathan J., Kapadia, Muneera R., Guillem, José Gaston, Gulati, Ajay S., Sethupathy, Praveen, Furey, Terrence S., Ehre, Camille, Sheikh, Shehzad Z.

Volltext

Comparative recombination rates in the rat, mouse, and human genomes von Jensen-Seaman, Michael I, Furey, Terrence S, Payseur, Bret A, Lu, Yontao, Roskin, Krishna M, Chen, Chin-Fu, Thomas, Michael A, Haussler, David, Jacob, Howard J

Volltext