Research Scientist

My research program sits at the interface of experimental and computational science.
We use computational models to understand experimental observations, with a particular focus on the use of next generation sequencing technologies and their utility to bring systematic understanding to aspects of cell biology, epigenetics and human disease.

Professional Experience:
2013-2015, Associate Investigator and Project Research Scientist, Guangzhou Institutes of Biomedicine and Health, China
2010-2013, Associate Investigator. Immunology Frontier Research Centre, Osaka University, Japan
2004-2010, Postdoctoral Fellow, Genome Institute of Singapore, Singapore
Educational Background:
2004, PhD, John Innes Centre, and University of East Anglia, Norwich, UK.
2000, BSc, University of Wolverhampton, UK.

Selected Publication:
1.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 (2015) Transient Activation of Mitoflashes Modulates Nanog at the Early Phase of Somatic Cell Reprogramming. Cell Metabolism. S1550-4131(15)00518-5
2.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. #Co-corresponding authors.
3.Hutchins AP#, Robson P# (2015) Transcriptional Intricacies of Stem Cells. Cell Systems. 1(2); 100-101. #Co-corresponding authors.
4.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.
5.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.
6.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 authors.
7.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.
8.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. *As co first authors.
9.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.
10.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.
11.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.
12.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.
13.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.
14.Hatzihristidis T, 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.
15.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 authors.
16.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.
17.Clarke M, Lohan AJ, et al., … Hutchins AP, … Miranda-Saavedra D, … Loftus B. (40 authors in total) (2013) Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of pattern recognition and tyrosine kinase signalling. Genome Biology. 14(2):R11.
18.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.
19.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
20.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.
21.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.
22.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.
23.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.
24.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. *As co-first authors.
25.Hutchins AP, Robson P. (2009) Unraveling the Human Embryonic Stem Cell Phosphoproteome. Cell Stem Cell. 5(2):126-128.
26.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 Arabidopsis. Plant Journal. 59(3):400-412.
27.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.