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

od Zhao, Chengchen, Hu, Sheng’en, Huo, Xiao, Zhang, Yong
izdano v PLoS One (2017)

CAM: A quality control pipeline for MNase-seq data

od Hu, Sheng’en, Chen, Xiaolan, Liao, Ji, Chen, Yiqing, Zhao, Chengchen, Zhang, Yong
izdano v PLoS One (2017)

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

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

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

od 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
Izdano 2013

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

od 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
Izdano 2012

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

od 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
izdano v Nat Commun (2016)

Comparative analysis of metazoan chromatin organization

od 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.
izdano v Nature (2014)