A semi-parametric statistical model for integrating gene expression profiles across different platforms

por Lyu, Yafei, Li, Qunhua
Publicado 2016

powerTCR: A model-based approach to comparative analysis of the clone size distribution of the T cell receptor repertoire

por Koch, Hillary, Starenki, Dmytro, Cooper, Sara J., Myers, Richard M., Li, Qunhua
Publicado 2018

RCFGL: Rapid Condition adaptive Fused Graphical Lasso and application to modeling brain region co-expression networks

por Seal, Souvik, Li, Qunhua, Basner, Elle Butler, Saba, Laura M., Kechris, Katerina
Publicado 2023

RETROFIT: Reference-free deconvolution of cell-type mixtures in spatial transcriptomics

por Singh, Roopali, He, Xi, Park, Adam Keebum, Hardison, Ross Cameron, Zhu, Xiang, Li, Qunhua
Publicado 2023

Condition-adaptive fused graphical lasso (CFGL): An adaptive procedure for inferring condition-specific gene co-expression network

por Lyu, Yafei, Xue, Lingzhou, Zhang, Feipeng, Koch, Hillary, Saba, Laura, Kechris, Katerina, Li, Qunhua
Publicado 2018

S3norm: simultaneous normalization of sequencing depth and signal-to-noise ratio in epigenomic data

por Xiang, Guanjue, Keller, Cheryl A, Giardine, Belinda, An, Lin, Li, Qunhua, Zhang, Yu, Hardison, Ross C
Publicado 2020

OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries

por An, Lin, Yang, Tao, Yang, Jiahao, Nuebler, Johannes, Xiang, Guanjue, Hardison, Ross C., Li, Qunhua, Zhang, Yu
Publicado 2019

Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data

por Bailey, Timothy, Krajewski, Pawel, Ladunga, Istvan, Lefebvre, Celine, Li, Qunhua, Liu, Tao, Madrigal, Pedro, Taslim, Cenny, Zhang, Jie
Publicado 2013

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

por Koch, Hillary, Keller, Cheryl A., Xiang, Guanjue, Giardine, Belinda, Zhang, Feipeng, Wang, Yicheng, Hardison, Ross C., Li, Qunhua
Publicado 2022

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

por Yang, Tao, Zhang, Feipeng, Yardımcı, Galip Gürkan, Song, Fan, Hardison, Ross C., Noble, William Stafford, Yue, Feng, Li, Qunhua
Publicado 2017

Transcriptional Profiling of the Small Intestine and the Colon Reveals Modulation of Gut Infection with Citrobacter rodentium According to the Vitamin A Status

por Chai, Zhi, Lyu, Yafei, Chen, Qiuyan, Wei, Cheng-Hsin, Snyder, Lindsay M., Weaver, Veronika, Sebastian, Aswathy, Albert, István, Li, Qunhua, Cantorna, Margherita T., Ross, Catharine
Publicado 2022

RNAseq studies reveal distinct transcriptional response to vitamin A deficiency in small intestine versus colon, uncovering novel vitamin A-regulated genes

por Chai, Zhi, Lyu, Yafei, Chen, Qiuyan, Wei, Cheng-Hsin, Snyder, Lindsay M., Weaver, Veronika, Sebastian, Aswathy, Albert, István, Li, Qunhua, Cantorna, Margherita T., Ross, A. Catharine
Publicado 2021

Model-based assessment of replicability for genome-wide association meta-analysis

por McGuire, Daniel, Jiang, Yu, Liu, Mengzhen, Weissenkampen, J. Dylan, Eckert, Scott, Yang, Lina, Chen, Fang, Berg, Arthur, Vrieze, Scott, Jiang, Bibo, Li, Qunhua, Liu, Dajiang J.
Publicado 2021

Galaxy tools to study genome diversity

por Bedoya-Reina, Oscar C, Ratan, Aakrosh, Burhans, Richard, Kim, Hie Lim, Giardine, Belinda, Riemer, Cathy, Li, Qunhua, Olson, Thomas L, Loughran, Thomas P, vonHoldt, Bridgett M, Perry, George H, Schuster, Stephan C, Miller, Webb
Publicado 2013

Systematic evaluation of factors influencing ChIP-seq fidelity

por Chen, Yiwen, Negre, Nicolas, Li, Qunhua, Mieczkowska, Joanna O., Slattery, Matthew, Liu, Tao, Zhang, Yong, Kim, Tae-Kyung, He, Housheng Hansen, Zieba, Jennifer, Ruan, Yijun, Bickel, Peter J., Myers, Richard M., Wold, Barbara J., White, Kevin P., Lieb, Jason D., Liu, X. Shirley
Publicado 2012

Measuring the reproducibility and quality of Hi-C data

por Yardımcı, Galip Gürkan, Ozadam, Hakan, Sauria, Michael E. G., Ursu, Oana, Yan, Koon-Kiu, Yang, Tao, Chakraborty, Abhijit, Kaul, Arya, Lajoie, Bryan R., Song, Fan, Zhan, Ye, Ay, Ferhat, Gerstein, Mark, Kundaje, Anshul, Li, Qunhua, Taylor, James, Yue, Feng, Dekker, Job, Noble, William S.
Publicado 2019

Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells

por Hardison, Ross C., Zhang, Yu, Keller, Cheryl A., Xiang, Guanjue, Heuston, Elisabeth F., An, Lin, Lichtenberg, Jens, Giardine, Belinda M., Bodine, David, Mahony, Shaun, Li, Qunhua, Yue, Feng, Weiss, Mitchell J., Blobel, Gerd A., Taylor, James, Hughes, Jim, Higgs, Douglas R., Göttgens, Berthold
Publicado 2019

An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis

por 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, Göttgens, Berthold, Li, Qunhua, Bodine, David, Mahony, Shaun, Taylor, James, Blobel, Gerd A., Weiss, Mitchell J., Cheng, Yong, Yue, Feng, Hughes, Jim, Higgs, Douglas R., Zhang, Yu, Hardison, Ross C.
Publicado 2020

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

por Landt, Stephen G., Marinov, Georgi K., Kundaje, Anshul, Kheradpour, Pouya, Pauli, Florencia, Batzoglou, Serafim, Bernstein, Bradley E., Bickel, Peter, Brown, James B., Cayting, Philip, Chen, Yiwen, DeSalvo, Gilberto, Epstein, Charles, Fisher-Aylor, Katherine I., Euskirchen, Ghia, Gerstein, Mark, Gertz, Jason, Hartemink, Alexander J., Hoffman, Michael M., Iyer, Vishwanath R., Jung, Youngsook L., Karmakar, Subhradip, Kellis, Manolis, Kharchenko, Peter V., Li, Qunhua, Liu, Tao, Liu, X. Shirley, Ma, Lijia, Milosavljevic, Aleksandar, Myers, Richard M., Park, Peter J., Pazin, Michael J., Perry, Marc D., Raha, Debasish, Reddy, Timothy E., Rozowsky, Joel, Shoresh, Noam, Sidow, Arend, Slattery, Matthew, Stamatoyannopoulos, John A., Tolstorukov, Michael Y., White, Kevin P., Xi, Simon, Farnham, Peggy J., Lieb, Jason D., Wold, Barbara J., Snyder, Michael
Publicado 2012