Publications

  • Journal Papers

     

Publications

Total publications:49,  i10-index: 39; Total citations: 1700 (Google Scholar 2019-11)

  1. Steffens, Simon, Xiuling Fu, Fangfang He, Yuhao Li, Isaac A. Babarinde, and Andrew P. Hutchins. "DPre: computational identification of differentiation bias and genes underlying cell type conversions." Bioinformatics (2019).
  2. 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).
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. Zheng Y, Cai J, Hutchins AP, Jia L, Liu P, Chen S, Ge L, Pei D, Wei S (2016) Remission for loss of odontogenic potential in a new micromilieu in vitro. PLoS ONE. 11(4):e0152893
  22. Wang L, Li X, Huang W, Zhou T, Wang H, Lin A, Hutchins AP, Su Z, Chen Q, Pei D, Pan G. (2016) TGFβ signaling regulates the choice between pluripotent and neural fates during reprogramming of human urine derived cells. Scientific Reports. 6: 22484
  23. Ying Z, Chen K, Zheng L, Wu Y, Li L, Wang R, Long Q, Yang L, Guo J, Yao D, Li Y, Bao F, Xiang G, Liu J, Huang Q, Wu Z, Hutchins AP, Pei D, Liu X. (2016) Transient Activation of Mitoflashes Modulates Nanog at the Early Phase of Somatic Cell Reprogramming. Cell Metabolism. 23(1):220-6
  24. Hutchins AP#, Pei D#. (2015) Transposable elements at the center of the crossroads between embryogenesis, embryonic stem cells, reprogramming and long non-coding RNAs. Scientific Bulletin. 60(20):1722-1733. (Featured cover article) #Co-corresponding
  25. Hutchins AP#, Robson P#. (2015) Transcriptional Intricacies of Stem Cells. Cell Systems. 1(2); 100-101. #Co-corresponding authors.
  26. Liu J, Han Q, Peng T, Peng M, Wei B, Li D, Wang X, Yu S, Yang J, Cao S, Huang K, Hutchins AP, Liu H, Kuang J, Zhou Z, Chen J, Wu H, Lin G, Chen Y, Chen Y, Li X, Wu H, Liao B, He W, Song H, Yao H, Pan G, Chen J, Pei D. (2015) The oncogene c-Jun impedes somatic reprogramming. Nature Cell Biology. 17(7):856-67.
  27. Hatzihristidis T, Desai N, Hutchins AP, Meng T, Tremblay ML, Miranda-Saavedra D. (2015) A Drosophila-centric view of protein tyrosine phosphatases. FEBS Letters. 589(9):951-966.
  28. Hutchins AP#, Takahashi Y, Miranda-Saavedra D#. (2015) Genomic analysis of LPS-stimulated myeloid cells indicates a common pro-inflammatory response but divergent IL-10 anti-inflammatory responses. Scientific Reports. 5:9100. #Co-corresponding
  29. Bao X, Wu H, Zhu X, Guo X, Hutchins AP, Luo Z, Song H, Chen Y, Lai K, Yin M, Xu L, Zhou L, Chen J, Wang D, Qin B, Frampton J, Pei D, Wang H, Zhang B, Esteban MA. (2015) The p53-induced lincRNA-p21 derails somatic cell reprogramming by sustaining H3K9me3 and CpG methylation at pluripotency gene promoters. Cell Research. 25(1):80-92.
  30. Pike KA*, Hutchins AP*, Vinette V, Theberge J, Sabbagh L, Tremblay M, Miranda-Saavedra D. (2014) Protein tyrosine phosphatase-1B is a regulator of the IL-10 induced transcriptional program in macrophages. Science Signaling. 6;7(324)ra43. *Co-first authors
  31. Hutchins AP#, Dyla M, Jauch R, Miranda-Saavedra D. (2014) glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data. Cell Regeneration. 3(1):1. #Corresponding author
  32. Liu L, Xu Y, He M, Zhang M, Cui F, Lu L, Yao M, Tian W, Benda C, Zhuang Q, Huang Z, Li W, Li X, Zhao P, Fan W, Luo Z, Li Y, Wu Y, Hutchins AP, Wang D, Tse HF, Schambach A, Frampton J, Qin B, Bao X, Yao H, Zhang B, Sun H, Pei D, Wang H, Wang J, Esteban MA. (2014) Transcriptional Pause Release Is a Rate-Limiting Step for Somatic Cell Reprogramming. Cell Stem Cell. 15(5):574-88
  33. Zheng H, Hutchins AP, Pan G, Li Y, Pei D, Pei G. (2014) Where cell fate conversions meet Chinese philosophy. Cell Research. 24(10):1162-3
  34. Diez D, Hutchins AP, Miranda-Saavedra D. (2014) Systematic identification of transcriptional regulatory modules from protein-protein interaction networks. Nucleic Acids Research. 42(1); e6
  35. Bussières-Marmen S, Hutchins AP, Schirbel A, Rebert N, Tiganis T, Fiocchi C, Miranda-Saavedra D, Tremblay ML. (2014) Characterization of PTPN2 and its use as a biomarker. Methods. 65(2);239-46
  36. HatzihristidisT, Liu S, Pryszcz L, Hutchins AP, Gabaldon T, Tremblay ML, Miranda-Saavedra D. (2014)  PTP-central: A Comprehensive Resource of Protein Tyrosine Phosphatases in Eukaryotic Genomes. Methods. 65(2);156-64
  37. Hutchins AP#, Choo SW, Mistri TK, Rahmani M, Woon CT, Ng CKL, Jauch R, Robson P#. (2013) Co-motif discovery identifies an Esrrb-Sox2-DNA ternary complex as a mediator of transcriptional differences between mouse embryonic and epiblast stem cells. Stem Cells. 31(2):269-281. #Co-corresponding
  38. Aksoy I*, Jauch R*, Chen J, Dyla M, Divakar U, Bogu GK, Ng CKL, Herath W, Hutchins AP, Robson P, Kolatkar PR, Stanton LW. (2013) Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm. EMBO Journal. 32(7);938-953. *As co-first authors
  39. Clarke M, Lohan AJ, et al., … Hutchins AP, … Miranda-Saavedra D, … Loftus B. (40 authors in total) (2013) Genome of Acanthamoeba castellaniihighlights extensive lateral gene transfer and early evolution of pattern recognition and tyrosine kinase signalling. Genome Biology. 14(2):R11
  40. Hutchins AP, Diez D, Miranda-Saavedra D. (2013) The IL-10/STAT3-mediated anti-inflammatory response: recent developments and future challenges. Briefings in Functional Genomics. 12(6);489-98
  41. Hutchins AP, Diez D, Miranda-Saavedra D. (2013) Genomic and computational approaches to dissect the mechanisms of STAT3’s universal and cell-type-specific functions. JAK-STAT. 2(4);e25097
  42. Hutchins AP*, Liu S*, Diez D. Miranda-Saavedra D. (2013) The repertoires of ubiquitinating and deubiquitinating enzymes in eukaryotic genomes. Molecular Biology and Evolution. 30(5);1172-1187. *As co-first authors
  43. Hutchins AP, Diez D, Takahashi Y, Ahmad S, Jauch R, Tremblay M, Miranda-Saavedra D. (2013) Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions.Nucleic Acids Research. 41(4):2155-2170
  44. Hutchins AP, Poulain S, Fujii H, Miranda-Saavedra D. (2012) Discovery and characterization of new transcripts from RNA-seq data in mouse CD4+ T cells. Genomics. 100(5):303-313
  45. Hutchins AP, Poulain S, Miranda-Saavedra D. (2012) Genome-wide analysis of STAT3 binding in vivo predicts effectors of the anti-inflammatory response in macrophages. Blood. 119(13):e110-e119
  46. Jauch R*, Aksoy I*, Hutchins AP*, Ng CK, Tian XF, Chen J, Palasingam P, Robson P, Stanton LW, Kolatkar PR.(2011) Conversion of Sox17 into a Pluripotency Reprogramming Factor by Re-engineering its Association with Oct4 on DNA. Stem Cells. 29(6):940-951. *Co-first authors
  47. Hutchins AP, Robson P. (2009) Unraveling the Human Embryonic Stem Cell Phosphoproteome. Cell Stem Cell. 5(2):126-128
  48. Bush MS, Hutchins AP, Jones AME, Naldrett MJ, Jarmolowski A, Browning K, Lloyd CW, Doonan JH. (2009) Selective recruitment of proteins to 5' cap complexes during the growth cycle in ArabidopsisPlant Journal. 59(3):400-412
  49. Hutchins AP, Roberts GR, Lloyd CW, Doonan JH. (2004) In vivo interaction between CDKA and eIF4A: a possible mechanism linking translation and cell proliferation. FEBS Letters. 556(1-3):91-94

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