PUBLICATIONS

Preprint

[ † corresponding author | * co-first authors ]

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Quantitative single cell 5hmC sequencing reveals non-canonical gene regulation by non-CG hydroxymethylation

Fabyanic EB*, Hu P*, Qiu Q, Wang T, Berrios KN, Flournoy J, Connolly DR, Zhou Z, Kohli RM, Wu H (2021)

bioRxiv

Single-cell multi-omics reveals elevated plasticity and stem-cell-like blasts relevant to the poor prognosis of KMT2A-rearranged leukemia

Chen C, Yu W, Alikarami F, Qiu Q, Chen C, Flournoy J, Gao P, Uzun Y, Fang L, Yu Y, Zhu Q, Wang K, Libbrecht C, Felmeister A, Rozich I, Ding Y, Hunger SP, Wu H, Brown PA, Guest EM, Barrett DM, Bernt KM, Tan K (2020)

bioRxiv

Stress-induced epigenetic regulation of transcription in neocortical excitatory neurons drives depression-like behavior

Kwon DY, Hu P, Zhao Y, Beagan JA, Nofziger JH, Cui Y, Xu B, Zaitseva D, Phillips-Cremins JE, Blendy JA, Wu H, Zhou Z (2020)

bioRxiv

Peer-reviewed

2021

Predictive modeling of single-cell DNA methylome data enhances integration with transcriptome data

Uzun Y, Wu H, Tan K

Genome Research PMID: 33219054

Journal

 

2020

Massively parallel and time-resolved RNA sequencing in single cells with scNT-Seq

Qiu Q*, Hu P*, Qiu X, Govek KW, Camara PG, Wu H

Nature Methods PMID: 32868927

Journal | PDF Data | GitHub

Bisulfite-free sequencing of 5-hydroxymethylcytosine with APOBEC-coupled epigenetic sequencing (ACE-Seq)

Wang T, Luo M, Berrios KN, Schutsky EK, Wu H† Kohli RM†

Methods in Molecular Biology PMID: 32822044

Journal

Tet2-mediated epigenetic drive for astrocyte differentiation from embryonic neural stem cells

He F, Wu H, Zhou L, Lin Q, Cheng Y, Sun YE

Cell Death Discovery PMID: 32377393

Journal

The Human Tumor Atlas Network: Charting tumor transitions across space and time at single-cell resolution

Rozenblatt-Rosen et al, Human Tumor Atlas Network

Cell PMID: 32302568

Journal

Single-cell transcriptomic analysis of adult mouse pituitary reveals sexual dimorphism and physiologic demand-induced cellular plasticity

Ho Y*,, Hu P*, Peel MT, Chen, S, Camara PG, Epstein DJ, Wu H, Liebhaber SA

Protein & Cell PMID: 32193873

Journal | PDF | Data | GitHub

 

2018

Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase

Schutsky EK, DeNizio JE, Hu P, Liu MY, Nabel CS, Fabyanic EB, Hwang Y, Bushman FD, Wu H, Kohli RM†

Nature Biotechnology PMID: 30295673

Journal | PDF | Data  

Single-nucleus transcriptomic survey of cell diversity and functional maturation in the postnatal mammalian hearts

Hu P*, Liu J*, Zhao J*, Wilkins BJ, Lupino K, Wu H†, Pei L†

Genes & Development PMID: 30254108

Journal | PDF | Data | GitHub | Browser

2017

Dissecting cell-type composition and activity-dependent transcriptional state in mammalian brains by massively parallel single-nucleus RNA-seq

Hu P*, Fabyanic EB*, Kwon DY, Tang S, Zhou Z, Wu H

Molecular Cell PMID: 29220646

Journal | PDF | Data | GitHub | Browser Protocol.io

------------------ Starting the lab at UPenn in 2016 ------------------

2016

Base-resolution profiling of active DNA demethylation using MAB-seq and caMAB-seq

Wu H*, Wu X*, Zhang Y†

Nature Protocol PMID: 27172168

Journal | PDF

Negative allosteric modulation of mGluR5 partially corrects pathophysiology in a mouse model of Rett syndrome

Tao J, Wu H, Coronado AA, de Laittre E, Osterweil EK, Zhang Y, Bear MF†

The Journal of Neuroscience PMID: 27881780

Journal

Endothelin-1 supports clonal derivation and expansion of cardiovascular progenitors derived from human embryonic stem cells

Soh BS, Ng SY, Wu H, Buac K, Park JH, Lian X, Xu J, Foo KS, Felldin U, He X, Nichane M, Yang H, Bu L, Li RA, Lim B, Chien KR†

Nature Communications PMID: 26952167

Journal

2015

Charting oxidized methylcytosines at base resolution

Wu H, Zhang Y†

Nature Structural & Molecular Biology PMID: 26333715

Journal | PDF

2014

N-cadherin prevents the premature differentiation of anterior heart field progenitors inthe pharyngeal mesodermal microenvironment

Soh BS, Buac K, Xu H, Li E, Ng SY, Wu H, Chmielowiec J, Jiang X, Bu L, Li RA, Cowan C, Chien KR†

Cell Research PMID: 25367124

Journal

Single-base resolution analysis of active DNA demethylation using methylase-assisted bisulfite sequencing

Wu H*,†, Wu X*, Shen L, Zhang Y†

Nature Biotechnology PMID: 25362244

Journal | PDF | Data

Reversing DNA methylation: mechanisms, genomics, and biological functions

Wu H, Zhang Y†

Cell PMID: 24439369

Journal | PDF

2013

Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics

Shen L*, Wu H*,†, Diep D, Yamaguchi S, D'Alessio AC, Fung HL, Zhang K, Zhang Y†

Cell PMID: 23602152

Journal | PDF | Data

Kdm2b maintains murine embryonic stem cell status by recruiting PRC1 complex to CpG islands of developmental genes

He J, Shen L, Wan M, Taranova O, Wu H, Zhang Y†

Nature Cell Biology PMID: 23502314

Journal

Cardiac regenerative medicine 2.0

Soh BS, Wu H, Chien KR†

Nature Biotechnology PMID: 23471068

Journal

2012

Early embryos reprogram DNA methylation in two steps

Wu H, Zhang Y†

Cell Stem Cell PMID: 22560071

Journal | PDF

Regulation and function of mammalian DNA methylation patterns: a genomic perspective

Wu H†, Tao J, Sun YE†

Briefings in Functional Genomics PMID: 22402507

Journal | PDF

Highly efficient derivation of ventricular cardiomyocytes from induced pluripotent stem cells with a distinct epigenetic signature

Xu H*, Yi BA*, Wu H, Bock C, Gu H, Lui KO, Park JH, Shao Y, Riley AK, Domian IJ, Hu E, Willette R, Lepore J, Meissner A, Wang Z, Chien KR†

Cell Research PMID: 22064699

Journal

2011

Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation

Wu H, Zhang Y†

Genes & Development PMID: 22156206

Journal | PDF

Tet1 and 5-hydroxymethylation: a genome-wide view in mouse embryonic stem cells

Wu H†, Zhang Y†

Cell Cycle PMID: 21750410

Journal | PDF

Deletion of astroglial Dicer causes non-cell-autonomous neuronal dysfunction and degeneration

Tao J*, Wu H*, Lin Q, Wei W, Lu XH, Cantle JP, Ao Y, Olsen RW, Yang XW, Mody I, Sofroniew MV, Sun YE†

The Journal of Neuroscience PMID: 21632951

Journal | PDF | Data

Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells

Wu H*, D'Alessio AC*, Ito S, Xia K, Wang Z, Cui K, Zhao K, Sun YE, Zhang Y†

Nature PMID: 21451524

Journal | PDF | Data

Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse  embryonic stem cells

Wu H, D'Alessio AC, Ito S, Wang Z, Cui K, Zhao K, Sun YE, Zhang Y†

Genes & Development PMID: 21460036

Journal | PDF | Data

2010   

Dnmt3a-dependent nonpromoter DNA methylation facilitates transcription of neurogenic genes

Wu H*,†, Coskun V, Tao J, Xie W, Ge W, Yoshikawa K, Li E, Zhang Y, Sun YE†

Science PMID: 20651149

Journal | PDF | Data

Genome-wide analysis reveals methyl-CpG-binding protein 2-dependent regulation of microRNAs in a mouse model of Rett

syndrome

Wu H*,†, Tao J*, Chen PJ, Shahab A, Ge W, Hart RP, Ruan X, Ruan Y, Sun YE†

Proceedings of the National Academy of Sciences PMID: 20921386

Journal | PDF

2009

Ago2 immunoprecipitation identifies predicted microRNAs in human embryonic stem cells and neural precursors

Goff LA, Davila J, Swerdel MR, Moore JC, Cohen RI, Wu H, Sun YE, Hart RP†

PLoS One PMID: 1978436

Journal

Reversing DNA methylation: new insights from neuronal activity-induced Gadd45b in adult neurogenesis

Wu H, Sun YE†

Science Signaling PMID: 19336837

Journal

Phosphorylation of MeCP2 at Serine 80 regulates its chromatin association and neurological function

Tao J, Hu K, Chang Q, Wu H, Sherman NE, Martinowich K, Klose RJ, Schanen C, Jaenisch R, Wang W, Sun YE†

Proceedings of the National Academy of Sciences PMID: 19225110

Journal

Deciphering Rett syndrome with mouse genetics, epigenomics, and human neurons

Tao J, Wu H, Sun YE†

International Review of Neurobiology PMID: 19900619

Journal

2008

Copy number variant analysis of human embryonic stem cells

Wu H, Kim KJ, Mehta K, Paxia S, Sundstrom A, Anantharaman T, Kuraishy AI, Doan T, Ghosh J, Pyle AD, Clark A, Lowry W, Fan G, Baxter T, Mishra

B, Sun Y, Teitell MA†

Stem Cells PMID: 18369100

Journal

CD133+ neural stem cells in the ependyma of mammalian postnatal forebrain

Coskun V, Wu H, Blanchi B, Tsao S, Kim K, Zhao J, Biancotti JC, Hutnick L, Krueger RC Jr, Fan G, de Vellis J, Sun YE†

Proceedings of the National Academy of Science PMID: 18195354

Journal

2007

A phenotypic small-molecule screen identifies an orphan ligand-receptor pair that regulates neural stem cell differentiation

Saxe JP, Wu H, Kelly TK, Phelps ME, Sun YE†, Kornblum HI†, Huang J†

Chemistry & Biology PMID: 17884634

Journal

Integrative genomic and functional analyses reveal neuronal subtype differentiation bias in human embryonic stem cell lines

Wu H, Xu J, Pang ZP, Ge W, Kim KJ, Blanchi B, Chen C, Südhof TC, Sun YE†

Proceedings of the National Academy of Sciences PMID: 17693548

Journal| PDF

Histone modifications around individual BDNF gene promoters in prefrontal cortex are associated with extinction of conditioned fear

Bredy TW, Wu H, Crego C, Zellhoefer J, Sun YE, Barad M†

Learning & Memory PMID: 17522015

Journal

2006

Epigenetic regulation of stem cell differentiation

Wu H, Sun YE†

Pediatric Research PMID: 16549544

Journal

Neural progenitors populate the cerebrospinal fluid of preterm patients with hydrocephalus

Krueger RC Jr†, Wu H, Zandian M, Danielpour M, Kabos P, Yu JS, Sun YE†

The Journal of Pediatrics PMID: 16615963

Journal

The ups and downs of BDNF in Rett syndrome

Sun YE†, Wu H

Neuron PMID: 16446133

Journal

Coupling of cell migration with neurogenesis by proneural bHLH factors

Ge W, He F, Kim KJ, Blanchi B, Coskun V, Nguyen L, Wu X, Zhao J, Heng JI, Martinowich K, Tao J, Wu H, Castro D, Sobeih MM, Corfas G, Gleeson JG,

Greenberg ME, Guillemot F, Sun YE

Proceedings of the National Academy of Sciences PMID: 16432194

Journal

2005

DNA methylation controls the timing of astrogliogenesis through regulation of JAK-STAT signaling

Fan G, Martinowich K, Chin MH, He F, Fouse SD, Hutnick L, Hattori D, Ge W, Shen Y, Wu H, ten Hoeve J, Shuai K, Sun YE†

Development PMID: 16014513

Journal

A positive autoregulatory loop of Jak-STAT signaling controls the onset of astrogliogenesis

He F, Ge W, Martinowich K, Becker-Catania S, Coskun V, Zhu W, Wu H, Castro D, Guillemot F, Fan G, de Vellis J, Sun YE†

Nature Neuroscience PMID: 15852015

Journal

2004

Crystal structure of human coactosin-like protein at 1.9 A resolution

Li X, Liu X, Lou Z, Duan X, Wu H, Liu Y†, Rao Z†

Protein Science PMID: 15459340

Journal

2003

DNA methylation-related chromatin remodeling in activity-dependent BDNF gene regulation

Martinowich K, Hattori D#, Wu H#, Fouse S#, He F, Hu Y, Fan G, Sun YE† (#, co-2nd authors)

Science PMID: 14593184

Journal