Hidden Markov induced Dynamic Bayesian Network for recovering time evolving gene regulatory networks

por Zhu, Shijia, Wang, Yadong
Publicado 2015

Molecular heterogeneity in hepatocellular carcinoma

por Zhu, Shijia, Hoshida, Yujin
Publicado 2018

Modeling Exon Expression Using Histone Modifications

por Zhu, Shijia, Wang, Guohua, Liu, Bo, Wang, Yadong
Publicado 2013

Chromatin structure characteristics of pre-miRNA genomic sequences

por Zhu, Shijia, Jiang, Qinghua, Wang, Guohua, Liu, Bo, Teng, Mingxiang, Wang, Yadong
Publicado 2011

A Cytosine Methytransferase Modulates the Cell Envelope Stress Response in the Cholera Pathogen

por Chao, Michael C., Zhu, Shijia, Kimura, Satoshi, Davis, Brigid M., Schadt, Eric E., Fang, Gang, Waldor, Matthew K.
Publicado 2015

Correction: A Cytosine Methytransferase Modulates the Cell Envelope Stress Response in the Cholera Pathogen

por Chao, Michael C., Zhu, Shijia, Kimura, Satoshi, Davis, Brigid M., Schadt, Eric E., Fang, Gang, Waldor, Matthew K.
Publicado 2015

MPIC: Molecular Prognostic Indicators in Cirrhosis Database for Clinical Context-Specific in Silico Prognostic Biomarker Validation

por Yip, Shun H., Fujiwara, Naoto, Burke, Jason, Shetler, Anand, Peralta, Celina, Qian, Tongqi, Hoshida, Hiroki, Zhu, Shijia, Hoshida, Yujin
Publicado 2019

Restricted immunological and cellular pathways are shared by murine models of chronic alcohol consumption

por Vogle, Alyx, Qian, Tongqi, Zhu, Shijia, Burnett, Elizabeth, Fey, Holger, Zhu, Zhibin, Keshavarzian, Ali, Shaikh, Maliha, Hoshida, Yujin, Kim, Miran, Aloman, Costica
Publicado 2020

Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation

por Beaulaurier, John, Zhu, Shijia, Deikus, Gintaras, Mogno, Ilaria, Zhang, Xue-Song, Davis-Richardson, Austin, Canepa, Ronald, Triplett, Eric W., Faith, Jeremiah J., Sebra, Robert, Schadt, Eric E., Fang, Gang
Publicado 2017

Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes

por Beaulaurier, John, Zhang, Xue-Song, Zhu, Shijia, Sebra, Robert, Rosenbluh, Chaggai, Deikus, Gintaras, Shen, Nan, Munera, Diana, Waldor, Matthew K., Chess, Andrew, Blaser, Martin J., Schadt, Eric E., Fang, Gang
Publicado 2015

Mapping and characterizing N6-methyladenine in eukaryotic genomes using single-molecule real-time sequencing

por Zhu, Shijia, Beaulaurier, John, Deikus, Gintaras, Wu, Tao P., Strahl, Maya, Hao, Ziyang, Luo, Guanzheng, Gregory, James A., Chess, Andrew, He, Chuan, Xiao, Andrew, Sebra, Robert, Schadt, Eric E., Fang, Gang
Publicado 2018

A transcriptional landscape of 28 porcine tissues obtained by super deepSAGE sequencing

por Huang, Tinghua, Yang, Min, Dong, Kaihui, Xu, Mingjiang, Liu, Jinhui, Chen, Zhi, Zhu, Shijia, Chen, Wang, Yin, Jun, Jin, Kai, Deng, Yu, Guan, Zhou, Huang, Xiali, Yang, Jun, Han, Rongxun, Yao, Min
Publicado 2020

Neuronal impact of patient-specific aberrant NRXN1α splicing

por Flaherty, Erin, Zhu, Shijia, Barretto, Natalie, Cheng, Esther, Deans, Michael Peter, Fernando, Michael, Schrode, Nadine, Francoeur, Nancy, Antoine, Alesia, Alganem, Khaled, Halpern, Madeline, Deikus, Gintaras, Shah, Hardik, Fitzgerald, Megan, Ladran, Ian, Gochman, Peter, Rapoport, Judith, Tsankova, Nadejda, Mccullumsmith, Robert, Hoffman, Gabriel E., Sebra, Robert, Fang, Gang, Brennand, Kristen J.
Publicado 2019

Peroxidasin Deficiency Re-programs Macrophages Toward Pro-fibrolysis Function and Promotes Collagen Resolution in Liver

por Sojoodi, Mozhdeh, Erstad, Derek J., Barrett, Stephen C., Salloum, Shadi, Zhu, Shijia, Qian, Tongqi, Colon, Selene, Gale, Eric M., Jordan, Veronica Clavijo, Wang, Yongtao, Li, Shen, Ataeinia, Bahar, Jalilifiroozinezhad, Sasan, Lanuti, Michael, Zukerberg, Lawrence, Caravan, Peter, Hoshida, Yujin, Chung, Raymond T., Bhave, Gautam, Lauer, Georg M., Fuchs, Bryan C., Tanabe, Kenneth K.
Publicado 2022

Hepatocellular carcinoma chemoprevention by targeting the angiotensin-converting enzyme and EGFR transactivation

por Crouchet, Emilie, Li, Shen, Sojoodi, Mozhdeh, Bandiera, Simonetta, Fujiwara, Naoto, El Saghire, Hussein, Zhu, Shijia, Qian, Tongqi, Rasha, Fahmida Akter, Del Zompo, Fabio, Barrett, Stephen C., Schaeffer, Eugénie, Oudot, Marine A., Ponsolles, Clara, Durand, Sarah C., Ghoshal, Sarani, Arora, Gunisha, Giannone, Fabio, Chung, Raymond T., Slovic, Nevena, Van Renne, Nicolaas, Felli, Emanuele, Pessaux, Patrick, Lupberger, Joachim, Pochet, Nathalie, Schuster, Catherine, Tanabe, Kenneth K., Hoshida, Yujin, Fuchs, Bryan C., Baumert, Thomas F.
Publicado 2022

Epigenomic characterization of Clostridioides difficile finds a conserved DNA methyltransferase that mediates sporulation and pathogenesis

por Oliveira, Pedro H., Ribis, John W., Garrett, Elizabeth M., Trzilova, Dominika, Kim, Alex, Sekulovic, Ognjen, Mead, Edward A., Pak, Theodore, Zhu, Shijia, Deikus, Gintaras, Touchon, Marie, Lewis-Sandari, Martha, Beckford, Colleen, Zeitouni, Nathalie E., Altman, Deena R., Webster, Elizabeth, Oussenko, Irina, Bunyavanich, Supinda, Aggarwal, Aneel K., Bashir, Ali, Patel, Gopi, Wallach, Frances, Hamula, Camille, Huprikar, Shirish, Schadt, Eric E., Sebra, Robert, van Bakel, Harm, Kasarskis, Andrew, Tamayo, Rita, Shen, Aimee, Fang, Gang
Publicado 2019

A human liver cell-based system modeling a clinical prognostic liver signature for therapeutic discovery

por Crouchet, Emilie, Bandiera, Simonetta, Fujiwara, Naoto, Li, Shen, El Saghire, Hussein, Fernández-Vaquero, Mirian, Riedl, Tobias, Sun, Xiaochen, Hirschfield, Hadassa, Jühling, Frank, Zhu, Shijia, Roehlen, Natascha, Ponsolles, Clara, Heydmann, Laura, Saviano, Antonio, Qian, Tongqi, Venkatesh, Anu, Lupberger, Joachim, Verrier, Eloi R., Sojoodi, Mozhdeh, Oudot, Marine A., Duong, François H. T., Masia, Ricard, Wei, Lan, Thumann, Christine, Durand, Sarah C., González-Motos, Victor, Heide, Danijela, Hetzer, Jenny, Nakagawa, Shigeki, Ono, Atsushi, Song, Won-Min, Higashi, Takaaki, Sanchez, Roberto, Kim, Rosa S., Bian, C. Billie, Kiani, Karun, Croonenborghs, Tom, Subramanian, Aravind, Chung, Raymond T., Straub, Beate K., Schuppan, Detlef, Ankavay, Maliki, Cocquerel, Laurence, Schaeffer, Evelyne, Goossens, Nicolas, Koh, Anna P., Mahajan, Milind, Nair, Venugopalan D., Gunasekaran, Ganesh, Schwartz, Myron E., Bardeesy, Nabeel, Shalek, Alex K., Rozenblatt-Rosen, Orit, Regev, Aviv, Felli, Emanuele, Pessaux, Patrick, Tanabe, Kenneth K., Heikenwälder, Mathias, Schuster, Catherine, Pochet, Nathalie, Zeisel, Mirjam B., Fuchs, Bryan C., Hoshida, Yujin, Baumert, Thomas F.
Publicado 2021