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[ † 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 




Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects

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

Nature Biotechnology PMID: 37640946

Journal | PDF Data | GitHub | bioRxiv

TET1 facilitates specification of early human lineages including germ cells

Hsu F, Wu Q, Fabyanic EB, Wei AWu H, Clark AT

iScience PMCID: PMC10345126


Direct enzymatic sequencing of 5-methylcytosine at single-base resolution

Wang T, Fowler JM, Liu L, Loo CE, Luo M, Schutsky EK, Berríos KN, DeNizio JE, Dvorak A, Downey N, Montermoso S, Pingul BY, Nasrallah M, Gosal WS, Wu H, Kohli RM

Nat Chem Biol PMID: 37322153


Integrating Single-Cell Methylome and Transcriptome Data with MAPLE

Uzun Y, Wu H, Tan K

Methods Mol Biol PMID: 36723808



Mammalian DNA methylome dynamics: mechanisms, functions and new frontiers

Wei A, Wu H

Development PMID: 36519514


Molecular landscapes of human hippocampal immature neurons across lifespan

Zhou Y, Su Y, Li S, Kennedy BC, Zhang DY, Bond AM, Sun Y, Jacob F, Lu L, Hu P, Viaene AN, Helbig I, Kessler SK, Lucas T, Salinas RD, Gu X, Chen HI, Wu H, Kleinman JE, Hyde TM, Nauen DW, Weinberger DR, Ming GL, Song H

Nature PMID: 35794479


Single-cell multiomics reveals increased plasticity, resistant populations and stem-cell-like blasts in KMT2A-rearranged leukemia

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

Blood PMID: 34864916


Neuronal Yin Yang1 in the prefrontal cortex regulates transcriptional and behavioral responses to chronic stress in mice

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

Nature Communications 

Journal PMID: 35013139   


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

Uzun Y, Wu H, Tan K

Genome Research PMID: 33219054




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


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


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


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



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


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

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


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



Charting oxidized methylcytosines at base resolution

Wu H, Zhang Y†

Nature Structural & Molecular Biology PMID: 26333715

Journal | PDF


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


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


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


Cardiac regenerative medicine 2.0

Soh BS, Wu H, Chien KR†

Nature Biotechnology PMID: 23471068



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



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


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


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


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


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

Wu H, Sun YE†

Science Signaling PMID: 19336837


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


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

Tao J, Wu H, Sun YE†

International Review of Neurobiology PMID: 19900619



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


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



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


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



Epigenetic regulation of stem cell differentiation

Wu H, Sun YE†

Pediatric Research PMID: 16549544


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


The ups and downs of BDNF in Rett syndrome

Sun YE†, Wu H

Neuron PMID: 16446133


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



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


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



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



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


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