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Steffens, Simon, Xiuling Fu, Fangfang He, Yuhao Li, Isaac A. Babarinde, andAndrew P. Hutchins. "DPre: computational identification of differentiation bias and genes underlying cell type conversions." Bioinformatics (2019).
Babarinde, Isaac A., Yuhao Li, and Andrew P. Hutchins. "Computational methods for mapping, assembly and quantification for coding and non-coding transcripts." Computational and structural biotechnology journal(2019).
Vikas Malik, Laura V. Glaser, Dennis Zimmer, Sergiy Velychko, Mingxi Weng, Markus Holzner, Marius Arend, Yanpu Chen, Yogesh Srivastava, Veeramohan Veerapandian, Zahir Shah, Miguel A. Esteban, Huating Wang, Jiekai Chen, Hans R. Schöler, Andrew P. Hutchins, Sebastiaan H. Meijsing, Sebastian Pott & Ralf Jauch. "Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2." Nature communications10, no. 1 (2019): 1-16.
He J, Fu X, Zhang M, He F, Li W, Abdul M, Zhou J, Sun L, Chang C, Li Y, Liu H, Wu K, Babarinde IA, Zhuang Q, Loh YH, Chen J, Esteban MA, Hutchins AP. (2019). Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells. Nature Communications. 10(1);34.
Guo L, Lin L, Wang X, Gao M, Cao S, Mai Y, Wu F, Kuang J, Liu H, Yang J, Chu S, Song H, Li D, Liu Y, Wu K, Liu J, Wang J, Pang G,Hutchins AP, Liu J, Pei D, Chen J. (2019) Resolving Cell Fate Decisions during Somatic Cell Reprogramming by Single-Cell RNA-Seq. Mol Cell, 73(4)815-829.
Li J, Huang K, Hu G, Babarinde IA, Li Y, Dong X, Chen Y, Shang L, Guo W, Wang J, Chen Z, Hutchins AP, Yang Y, Yao H. (2019) An alternative CTCF isoform antagonizes canonical CTCF occupancy and changes chromatin architecture to promote cell apoptosis. Nature Communications. Accepted.
Zhuang Q*, Li W*, Benda C*, Huang Z, Ahmed T, Liu P, Guo X, Ibañez D, Luo Z, Zhang M, Abdul M, Yang Z, Yang J, Huang Y, Zhang H, Huang D, Zhou J, Zhong X, Zhu X, Fu X, Fan W, Liu Y, Xu Y, Ward C, Khan M, Kanwal S, Mirza B, Tortorella M, Tse HF, Chen J, Qin B, Bao X, Gao S, Hutchins AP#, Esteban MA#. (2018) NCoR/SMRT co-repressors cooperate with c-MYC to create an epigenetic barrier to somatic cell reprogramming. Nature Cell Biology. 20(4):400-412. *Co-first, #Co-corresponding
Yao M. Zhou X. Zhou J. Gong S. Hu G. Li J. Huang K. Lai P. Shi G. Hutchins AP. Sun H. Wang H. Yao H. (2018) PCGF5 is required for neural differentiation ofembryonic stem cells. Nature Communications. 9(1);1463
Bao X*, Guo X*, Yin M, Tariq M, Lai Y, Kanwal S, Zhou J, Li N, Lv Y, Pulido-Quetglas C, Wang X, Ji L, Khan M, Zhu X, Luo Z, Shao C, Lim D, Liu X, Li N, Wang W, He M, Liu Y, Ward C, Wang T, Zhang G, Wang D, Yang J, Chen Y, Zhang C, Jauch R, Yang Y, Wang Y, Qin B, Anko M, Hutchins AP, Sun H, Wang H, Fu X, Zhang B#. Esteban MA#. (2018) Capturing the Interactome of Newly Transcribed RNA. Nature Methods. 15(3)213-220. *Co-first, #Co-corresponding
Li D*, Liu J*, Yang X*, Zhou C, Guo J, Wu C, Qin L, He J, Yu S, Liu H, Wang X, Wu F, Kuang J, Hutchins AP#, Chen J#, Pei D# (2017) Chromatin accessibility dynamics during iPSC reprogramming. Cell Stem Cell.21(6):819-833. *Co-first, #Co-corresponding
Zhou Z, Yang Y, He J, Liu J, Wu F, Yu S, Liu Y, Lin R, Liu H, Cui Y, Wang X, Cao S, Guo L, Lin L, Wang T, Peng X, Hutchins AP, Pei D#, Chen J#. (2017) Kdm2b regulates somatic reprogramming through variant PRC1 complex dependent function. Cell Reports. 21(8):2160-2170. #Co-corresponding
Fu X, He F, Li Y, Shahveranov A, Hutchins AP# (2017) Genomic and molecular control of cell type and cell type conversions. Cell Regeneration. 6:1. #Corresponding
Hutchins AP#, Yang Z, Li Y, He F, Fu X, Wang X, Li D, Liu K, He J, Wang Y, Chen J, Esteban MA, Pei D#. (2017) Models of global gene expression define major domains of cell type and tissue identity. Nucleic Acids Research. 45(5):2354. #Co-corresponding
Andrabi M, Hutchins AP, Miranda-Saavedra D, Kono H, Nussinov R, Mizugichi K, Ahmad S. (2017) Predicting conformational ensembles and genome-wide transcription factor binding from DNA sequences. Scientific Reports. 7(1):4071
Li Q*, Hutchins AP*, Chen Y, Li S, Shan Y, Liao B, Zheng D, Shi X, Li Y, Chan W, Pan G, Wei S, Shu X#, Pei D#. (2017) A sequential EMT-MET mechanism drives the differentiation of human embryonic stem cells towards hepatocytes. Nature Communications. 8:15166. *Co-first, #Co-corresponding
Yang J*, Wang Y*, Zhou T, Wong L, Tian X, Hong X, Lai W, Au K, Wei R, Liu Y, Cheng L, Liang G, Huang Z, Fan W, Zhao P, Wang X, Ibanez DP, Luo Z, Li Y, Chen S, Wang D, Li L, Lai L, Qin B, Hutchins AP, Siu C, Huang Y, Esteban MA#, Tse H#. (2017) Generation of Human Liver Chimeric Mice with Hepatocytes from Familial Hypercholesterolemia Induced Pluripotent Stem Cells. Stem Cell Reports. 8(3):605-618. *Co-first, #Co-corresponding
Li H*, Lai P*, Jia J*, Song Y, Xia Q, Huang K, He N, Ping W, Chen J, Yang Z, Li J, Yao M, Gong X, Zhao J, Hou C, Esteban MA, Gao S, Pei D, Hutchins AP, Yao H. (2017) RNA Helicase DDX5 Inhibits Reprogramming to pluripotency by miRNA-based repression of RYBP and its PRC1-dependent and -independent Functions. Cell Stem Cell. 20(4):462 *Co-first authors
Huang K*, Gao J*, Du J*, Ma N, Zhu Y, Wu P, Zhang T, Wang W, Li Y, Chen Q, Hutchins AP, Yang Z, Zheng Y, Shan Y, Li X, Liao B, Liu J, Wang J, Liu D, Pan G (2016) Generation and analysis of GATA2w/eGFP human ESCs reveal ITGB3/CD61 as a reliable marker for defining hemogenic endothelial cells during hematopoiesis. Stem Cell Reports. 7(5):854-868. *Co-first authors
Pugacheva E, Teplyakov E, Wu Q, Li J, Chen C, Meng C, Liu J, Robinson S, Loukinov D, Hutchins AP, Boukaba A, Lobanenkov V, Strunnikov AV. (2016) The cancer-associated CTCFL/BORIS protein targets multiple classes of genomic repeats, with a distinct binding and functional preference for humanoid-specific SVA transposable elements. Epigenetics & Chromatin. 9(1):35
Xu Y, Zhang M, Li W, Zhu X, Bao X, Hutchins AP#, Esteban MA#. (2016) Transcriptional control of somatic cell reprogramming. Trends in Cell Biology. 26(4):272-88 #Co-corresponding
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