PUBLICATIONS

2019

DPre: Computational identification of differentiation bias and genes underlying cell type conversions

Steffens S, Fu X, He F, Li Y, Babarinde IA, Hutchins AP

Bioinformatics

Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2

Malik V, Glaser LV, Zimmer D, Velychko S, Weng M, Holzner M, Arend M, Chen Y, Srivastava Y, Veerapandian V, Shah Z, Esteban MA, Wang H, Chen J, Scholer H, Hutchins AP, Meijsing SH, Pott S, Jauch R.

Nature Communications

Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts

Babarinde IA, Li Y, Hutchins AP

Computational Structural Biotechnology Journal 

An alternative CTCF isoform antagonizes canonical CTCF occupancy and changes chromatin architecture to promote apoptosis

Li J, Huang K, Hu G, Babarinde IA, Li Y, Dong X, Chen YS, Shang L, Guo W, Wang J, Chen Z, Hutchins AP, Yang YG, Yao H

Nature Communications

Resolving Cell Fate Decisions during Somatic Cell Reprogramming by Single-Cell RNA-Seq.
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, Pan G, Hutchins AP, Liu J, Pei D, Chen J

Molecular Cell

Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells

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

Nature Communications

2018

PCGF5 is required for neural differentiation of embryonic stem cells.

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

Nature Communications. 

 

Capturing the Interactome of Newly Transcribed RNA

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# *Co-first, #Co-corresponding

Nature Methods

 

NCoR/SMRT co-repressors cooperate with c-MYC to create an epigenetic barrier to somatic cell reprogramming

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# *Co-first, #Co-corresponding

Nature Cell Biology

2017

Chromatin accessibility dynamics during iPSC reprogramming

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# 

Cell Stem Cell. *Co-first, #Co-corresponding

Kdm2b regulates somatic reprogramming through variant PRC1 complex dependent function.

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#.

Cell Reports. #Co-corresponding

Genomic and molecular control of cell type and cell type conversions

Fu X, He F, Li Y, Shahveranov A, Hutchins AP#

Cell Regeneration. #Corresponding

Models of global gene expression define major domains of cell type and tissue identity

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#.

Nucleic Acids Research. #Co-corresponding

Predicting conformational ensembles and genome-wide transcription factor binding from DNA sequences

Andrabi M, Hutchins AP, Miranda-Saavedra D, Kono H, Nussinov R, Mizugichi K, Ahmad S.

Scientific Reports. 

A sequential EMT-MET mechanism drives the differentiation of human embryonic stem cells towards hepatocytes

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#.

Nature Communications. *Co-first, #Co-corresponding

 

Generation of Human Liver Chimeric Mice with Hepatocytes from Familial Hypercholesterolemia Induced Pluripotent Stem Cells

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#.

Stem Cell Reports. *Co-first, #Co-corresponding

 

RNA Helicase DDX5 Inhibits Reprogramming to pluripotency by miRNA-based repression of RYBP and its PRC1-dependent and -independent Functions

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.

Cell Stem Cell *Co-first authors

2016

Generation and analysis of GATA2w/eGFP human ESCs reveal ITGB3/CD61 as a reliable marker for defining hemogenic endothelial cells during hematopoiesis

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

Stem Cell Reports. *Co-first authors

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

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.

Epigenetics & Chromatin.

 

Transcriptional control of somatic cell reprogramming

Xu Y, Zhang M, Li W, Zhu X, Bao X, Hutchins AP#, Esteban MA#.

Trends in Cell Biology. #Co-corresponding

 

Remission for loss of odontogenic potential in a new micromilieu in vitro

Zheng Y, Cai J, Hutchins AP, Jia L, Liu P, Chen S, Ge L, Pei D, Wei S

PLoS ONE. 

 

TGFβ signaling regulates the choice between pluripotent and neural fates during reprogramming of human urine derived cells.

Wang L, Li X, Huang W, Zhou T, Wang H, Lin A, Hutchins AP, Su Z, Chen Q, Pei D, Pan G.

Scientific Reports. 

 

Transient Activation of Mitoflashes Modulates Nanog at the Early Phase of Somatic Cell Reprogramming.

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)

Cell Metabolism. 

2015

Transposable elements at the center of the crossroads between embryogenesis, embryonic stem cells, reprogramming and long non-coding RNAs

Hutchins AP#, Pei D#.

Scientific Bulletin. (Featured cover article) #Co-corresponding

 

Transcriptional Intricacies of Stem Cells

Hutchins AP#, Robson P#

Cell Systems. #Co-corresponding authors.

 

The oncogene c-Jun impedes somatic reprogramming.

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.

Nature Cell Biology. 

 

A Drosophila-centric view of protein tyrosine phosphatases

Hatzihristidis T, Desai N, Hutchins AP, Meng T, Tremblay ML, Miranda-Saavedra D.

FEBS Letters. 

 

Genomic analysis of LPS-stimulated myeloid cells indicates a common pro-inflammatory response but divergent IL-10 anti-inflammatory responses

Hutchins AP#, Takahashi Y, Miranda-Saavedra D#.

Scientific Reports. 5:9100. #Co-corresponding

The p53-induced lincRNA-p21 derails somatic cell reprogramming by sustaining H3K9me3 and CpG methylation at pluripotency gene promoters

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. 

Cell Research

2014

Protein tyrosine phosphatase-1B is a regulator of the IL-10 induced transcriptional program in macrophages

​Pike KA*, Hutchins AP*, Vinette V, Theberge J, Sabbagh L, Tremblay M, Miranda-Saavedra D.

Science Signaling. *Co-first authors

glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data

Hutchins AP#, Dyla M, Jauch R, Miranda-Saavedra D.

Cell Regeneration. #Corresponding author

 

Transcriptional Pause Release Is a Rate-Limiting Step for Somatic Cell Reprogramming

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.

Cell Stem Cell

 

Where cell fate conversions meet Chinese philosophy

Zheng H, Hutchins AP, Pan G, Li Y, Pei D, Pei G. (2014)

Cell Research. 

 

Systematic identification of transcriptional regulatory modules from protein-protein interaction networks

Diez D, Hutchins AP, Miranda-Saavedra D. 

Nucleic Acids Research. 

 

Characterization of PTPN2 and its use as a biomarker

Bussières-Marmen S, Hutchins AP, Schirbel A, Rebert N, Tiganis T, Fiocchi C, Miranda-Saavedra D, Tremblay ML. Methods. 

PTP-central: A Comprehensive Resource of Protein Tyrosine Phosphatases in Eukaryotic Genomes

Hatzihristidis T, Liu S, Pryszcz L, Hutchins AP, Gabaldon T, Tremblay ML, Miranda-Saavedra D.

Methods

2013

Co-motif discovery identifies an Esrrb-Sox2-DNA ternary complex as a mediator of transcriptional differences between mouse embryonic and epiblast stem cells

Hutchins AP#, Choo SW, Mistri TK, Rahmani M, Woon CT, Ng CKL, Jauch R, Robson P#. #Co-corresponding

Stem Cells 

 

Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm

Aksoy I*, Jauch R*, Chen J, Dyla M, Divakar U, Bogu GK, Ng CKL, Herath W, Hutchins AP, Robson P, Kolatkar PR, Stanton LW.

EMBO Journal *As co-first authors

 

Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of pattern recognition and tyrosine kinase signalling

Clarke M, Lohan AJ, et al., … Hutchins AP, … Miranda-Saavedra D, … Loftus B. (40 authors in total)

Genome Biology

 

The IL-10/STAT3-mediated anti-inflammatory response: recent developments and future challenges

Hutchins AP, Diez D, Miranda-Saavedra D. 

Briefings in Functional Genomics

 

Genomic and computational approaches to dissect the mechanisms of STAT3’s universal and cell-type-specific functions

Hutchins AP, Diez D, Miranda-Saavedra D.

JAK-STAT

 

The repertoires of ubiquitinating and deubiquitinating enzymes in eukaryotic genomes

Hutchins AP*, Liu S*, Diez D. Miranda-Saavedra D. (2013)

Molecular Biology and Evolution. *As co-first authors

 

Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions

Hutchins AP, Diez D, Takahashi Y, Ahmad S, Jauch R, Tremblay M, Miranda-Saavedra D.

Nucleic Acids Research

2012

Discovery and characterization of new transcripts from RNA-seq data in mouse CD4+ T cells

Hutchins AP, Poulain S, Fujii H, Miranda-Saavedra D. 

Genomics

 

Genome-wide analysis of STAT3 binding in vivo predicts effectors of the anti-inflammatory response in macrophages.

Hutchins AP, Poulain S, Miranda-Saavedra D. 

Blood

2011--

Conversion of Sox17 into a Pluripotency Reprogramming Factor by Re-engineering its Association with Oct4 on DNA

Jauch R*, Aksoy I*, Hutchins AP*, Ng CK, Tian XF, Chen J, Palasingam P, Robson P, Stanton LW, Kolatkar PR. (2011)

Stem Cells. *Co-first authors

 

Unraveling the Human Embryonic Stem Cell Phosphoproteome

Hutchins AP, Robson P. (2009) .

Cell Stem Cell

 

Selective recruitment of proteins to 5' cap complexes during the growth cycle in Arabidopsis.

Bush MS, Hutchins AP, Jones AME, Naldrett MJ, Jarmolowski A, Browning K, Lloyd CW, Doonan JH. (2009)

Plant Journal

In vivo interaction between CDKA and eIF4A: a possible mechanism linking translation and cell proliferation.

Hutchins AP, Roberts GR, Lloyd CW, Doonan JH. (2004)

FEBS Letters

Southern University of Science and Technology, Shenzhen, China

© 2017-19