YAMDA: thousandfold speedup of EM-based motif discovery using deep learning libraries and GPU

por Quang, Daniel, Guan, Yuanfang, Parker, Stephen C J
Publicado 2018

Motif signatures in stretch enhancers are enriched for disease-associated genetic variants

por Quang, Daniel X, Erdos, Michael R, Parker, Stephen C J, Collins, Francis S
Publicado 2015

Super Enhancers in Cancers, Complex Disease, and Developmental Disorders

por Niederriter, Adrienne R., Varshney, Arushi, Parker, Stephen C. J., Martin, Donna M.
Publicado 2015

A Bioinformatics Approach for Determining Sample Identity from Different Lanes of High-Throughput Sequencing Data

por Goldfeder, Rachel L., Parker, Stephen C. J., Ajay, Subramanian S., Ozel Abaan, Hatice, Margulies, Elliott H.
Publicado 2011

Multi-omic profiling of pituitary thyrotropic cells and progenitors

por Daly, Alexandre Z., Dudley, Lindsey A., Peel, Michael T., Liebhaber, Stephen A., Parker, Stephen C. J., Camper, Sally A.
Publicado 2021

Three‐dimensional chromatin re‐organization during muscle stem cell aging

por Yang, Benjamin A., Larouche, Jacqueline A., Sabin, Kaitlyn M., Fraczek, Paula M., Parker, Stephen C. J., Aguilar, Carlos A.
Publicado 2023

Chromatin information content landscapes inform transcription factor and DNA interactions

por D’Oliveira Albanus, Ricardo, Kyono, Yasuhiro, Hensley, John, Varshney, Arushi, Orchard, Peter, Kitzman, Jacob O., Parker, Stephen C. J.
Publicado 2021

Global dynamics of stage-specific transcription factor binding during thymocyte development

por Hosoya, Tomonori, D’Oliveira Albanus, Ricardo, Hensley, John, Myers, Greggory, Kyono, Yasuhiro, Kitzman, Jacob, Parker, Stephen C. J., Engel, James Douglas
Publicado 2018

BoostMe accurately predicts DNA methylation values in whole-genome bisulfite sequencing of multiple human tissues

por Zou, Luli S., Erdos, Michael R., Taylor, D. Leland, Chines, Peter S., Varshney, Arushi, Parker, Stephen C. J., Collins, Francis S., Didion, John P.
Publicado 2018

GBshape: a genome browser database for DNA shape annotations

por Chiu, Tsu-Pei, Yang, Lin, Zhou, Tianyin, Main, Bradley J., Parker, Stephen C.J., Nuzhdin, Sergey V., Tullius, Thomas D., Rohs, Remo
Publicado 2014

BAF60a deficiency uncouples chromatin accessibility and cold sensitivity from white fat browning

por Liu, Tongyu, Mi, Lin, Xiong, Jing, Orchard, Peter, Yu, Qi, Yu, Lei, Zhao, Xu-Yun, Meng, Zhuo-Xian, Parker, Stephen C. J., Lin, Jiandie D., Li, Siming
Publicado 2020

Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits

por Orchard, Peter, Manickam, Nandini, Ventresca, Christa, Vadlamudi, Swarooparani, Varshney, Arushi, Rai, Vivek, Kaplan, Jeremy, Lalancette, Claudia, Mohlke, Karen L., Gallagher, Katherine, Burant, Charles F., Parker, Stephen C.J.
Publicado 2021

Single-cell ATAC-Seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures

por Rai, Vivek, Quang, Daniel X., Erdos, Michael R., Cusanovich, Darren A., Daza, Riza M., Narisu, Narisu, Zou, Luli S., Didion, John P., Guan, Yuanfang, Shendure, Jay, Parker, Stephen C.J., Collins, Francis S.
Publicado 2019

A Transcription Start Site Map in Human Pancreatic Islets Reveals Functional Regulatory Signatures

por Varshney, Arushi, Kyono, Yasuhiro, Elangovan, Venkateswaran Ramamoorthi, Wang, Collin, Erdos, Michael R., Narisu, Narisu, Albanus, Ricardo D’Oliveira, Orchard, Peter, Stitzel, Michael L., Collins, Francis S., Kitzman, Jacob O., Parker, Stephen C.J.
Publicado 2021

FixItFelix: improving genomic analysis by fixing reference errors

por Behera, Sairam, LeFaive, Jonathon, Orchard, Peter, Mahmoud, Medhat, Paulin, Luis F., Farek, Jesse, Soto, Daniela C., Parker, Stephen C. J., Smith, Albert V., Dennis, Megan Y., Zook, Justin M., Sedlazeck, Fritz J.
Publicado 2023

CHD7 promotes neural progenitor differentiation in embryonic stem cells via altered chromatin accessibility and nascent gene expression

por Yao, Hui, Hannum, Douglas F., Zhai, Yiwen, Hill, Sophie F., Albanus, Ricardo D.’Oliveira, Lou, Wenjia, Skidmore, Jennifer M., Sanchez, Gilson, Saiakhova, Alina, Bielas, Stephanie L., Scacheri, Peter, Ljungman, Mats, Parker, Stephen C. J., Martin, Donna M.
Publicado 2020

Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection

por 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.
Publicado 2012

Combinatorial transcription factor profiles predict mature and functional human islet α and β cells

por Shrestha, Shristi, Saunders, Diane C., Walker, John T., Camunas-Soler, Joan, Dai, Xiao-Qing, Haliyur, Rachana, Aramandla, Radhika, Poffenberger, Greg, Prasad, Nripesh, Bottino, Rita, Stein, Roland, Cartailler, Jean-Philippe, Parker, Stephen C.J., MacDonald, Patrick E., Levy, Shawn E., Powers, Alvin C., Brissova, Marcela
Publicado 2021

Somatic mutations in MAP3K5 attenuate its pro-apoptotic function in melanoma through increased binding to Thioredoxin

por Prickett, Todd D., Zerlanko, Brad, Gartner, Jared J., Parker, Stephen C. J., Dutton-Regester, Ken, Lin, Jimmy C., Teer, Jamie K., Wei, Xiaomu, Jiang, Jiji, Chen, Guo, Davies, Michael A., Gershenwald, Jeffrey E., Robinson, William, Robinson, Steven, Hayward, Nicholas K., Rosenberg, Steven, A., Margulies, Elliott H., Samuels, Yardena
Publicado 2013

Mutational Signatures of De-Differentiation in Functional Non-Coding Regions of Melanoma Genomes

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