Dr.seq2: A quality control and analysis pipeline for parallel single cell transcriptome and epigenome data

per Zhao, Chengchen, Hu, Sheng’en, Huo, Xiao, Zhang, Yong
Publicat a PLoS One (2017)

CAM: A quality control pipeline for MNase-seq data

per Hu, Sheng’en, Chen, Xiaolan, Liao, Ji, Chen, Yiqing, Zhao, Chengchen, Zhang, Yong
Publicat a PLoS One (2017)

Ectopic Tcf1 expression instills a stem-like program in exhausted CD8(+) T cells to enhance viral and tumor immunity

per Shan, Qiang, Hu, Sheng’en, Chen, Xia, Danahy, Derek B., Badovinac, Vladimir P., Zang, Chongzhi, Xue, Hai-Hui
Publicat a Cell Mol Immunol (2020)

Analysis of optimized DNase-seq reveals intrinsic bias in transcription factor footprint identification

per He, Housheng Hansen, Meyer, Clifford A., Hu, Sheng'en Shawn, Chen, Mei-Wei, Zang, Chongzhi, Liu, Yin, Rao, Prakash K., Fei, Teng, Xu, Han, Long, Henry, Liu, X. Shirley, Brown, Myles
Publicat 2013

CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human

per Qin, Bo, Zhou, Meng, Ge, Ying, Taing, Len, Liu, Tao, Wang, Qian, Wang, Su, Chen, Junsheng, Shen, Lingling, Duan, Xikun, Hu, Sheng'en, Li, Wei, Long, Henry, Zhang, Yong, Liu, X. Shirley
Publicat 2012

High-dimensional genomic data bias correction and data integration using MANCIE

per Zang, Chongzhi, Wang, Tao, Deng, Ke, Li, Bo, Hu, Sheng'en, Qin, Qian, Xiao, Tengfei, Zhang, Shihua, Meyer, Clifford A., He, Housheng Hansen, Brown, Myles, Liu, Jun S., Xie, Yang, Liu, X. Shirley
Publicat a Nat Commun (2016)

Comparative analysis of metazoan chromatin organization

per Ho, Joshua W. K., Jung, Youngsook L., Liu, Tao, Alver, Burak H., Lee, Soohyun, Ikegami, Kohta, Sohn, Kyung-Ah, Minoda, Aki, Tolstorukov, Michael Y., Appert, Alex, Parker, Stephen C. J., Gu, Tingting, Kundaje, Anshul, Riddle, Nicole C., Bishop, Eric, Egelhofer, Thea A., Hu, Sheng’en Shawn, Alekseyenko, Artyom A., Rechtsteiner, Andreas, Asker, Dalal, Belsky, Jason A., Bowman, Sarah K., Chen, Q. Brent, Chen, Ron A-J, Day, Daniel S., Dong, Yan, Dose, Andrea C., Duan, Xikun, Epstein, Charles B., Ercan, Sevinc, Feingold, Elise A., Ferrari, Francesco, Garrigues, Jacob M., Gehlenborg, Nils, Good, Peter J., Haseley, Psalm, He, Daniel, Herrmann, Moritz, Hoffman, Michael M., Jeffers, Tess E., Kharchenko, Peter V., Kolasinska-Zwierz, Paulina, Kotwaliwale, Chitra V., Kumar, Nischay, Langley, Sasha A., Larschan, Erica N., Latorre, Isabel, Libbrecht, Maxwell W., Lin, Xueqiu, Park, Richard, Pazin, Michael J., Pham, Hoang N., Plachetka, Annette, Qin, Bo, Schwartz, Yuri B., Shoresh, Noam, Stempor, Przemyslaw, Vielle, Anne, Wang, Chengyang, Whittle, Christina M., Xue, Huiling, Kingston, Robert E., Kim, Ju Han, Bernstein, Bradley E., Dernburg, Abby F., Pirrotta, Vincenzo, Kuroda, Mitzi I., Noble, William S., Tullius, Thomas D., Kellis, Manolis, MacAlpine, David M., Strome, Susan, Elgin, Sarah C. R., Liu, Xiaole Shirley, Lieb, Jason D., Ahringer, Julie, Karpen, Gary H., Park, Peter J.
Publicat a Nature (2014)