Publications

• Brain 5-hydroxymethylcytosine alterations are associated with Alzheimer's disease neuropathology.
  Nat Commun Volume: 16 Page(s): 2842
  03/22/2025 Authors: Zhao J; Gu T; Gao C; Miao G; Palma-Gudiel H; Yu L; Yang J; Wang Y; Li Y; Lim J
• Mapping the developmental trajectory of human astrocytes reveals divergence in glioblastoma.
  Nat Cell Biol Volume: 27 Page(s): 347 - 359
  02/01/2025 Authors: Sojka C; Wang H-LV; Bhatia TN; Li Y; Chopra P; Sing A; Voss A; King A; Wang F; Joseph K
• Basic Science and Pathogenesis.
  Alzheimers Dement Volume: 20 Suppl 1 Page(s): e089983
  12/01/2024 Authors: Wang F; Li Y; Shen H; Feng Y; Yao B
• Identification of pathological pathways centered on circRNA dysregulation in association with irreversible progression of Alzheimer's disease.
  Genome Med Volume: 16 Page(s): 129
  11/11/2024 Authors: Wang F; Li Y; Shen H; Martinez-Feduchi P; Ji X; Teng P; Krishnakumar S; Hu J; Chen L; Feng Y
• Identification of brain region-specific landscape and functions of clustered circRNAs in Alzheimer's disease using circMeta2.
  Commun Biol Volume: 7 Page(s): 1353
  10/19/2024 Authors: Zhao F; Li Y; Chen L; Yao B
• Deep5hmC: predicting genome-wide 5-hydroxymethylcytosine landscape via a multimodal deep learning model.
  Bioinformatics Volume: 40
  09/02/2024 Authors: Ma X; Thela SR; Zhao F; Yao B; Wen Z; Jin P; Zhao J; Chen L
• New ZNHIT3 Variants Disrupting snoRNP Assembly Cause Prenatal PEHO Syndrome with Isolated Hydrops.
  medRxiv
  08/26/2024 Authors: Rahman ML; Bonnard AA; Wang F; Ruaud L; Guimiot F; Li Y; Defer I; Wang Y; Marchand V; Motorin Y
• scaDA: A novel statistical method for differential analysis of single-cell chromatin accessibility sequencing data.
  PLoS Comput Biol Volume: 20 Page(s): e1011854
  08/01/2024 Authors: Zhao F; Ma X; Yao B; Lu Q; Chen L
• Isoform balance of the long noncoding RNA NEAT1 is regulated by the RNA-binding protein QKI, governs the glioma transcriptome, and impacts cell migration.
  J Biol Chem Volume: 300 Page(s): 107595
  08/01/2024 Authors: Zakutansky PM; Ku L; Zhang G; Shi L; Li Y; Yao B; Bassell GJ; Read RD; Feng Y
• Bridging the gap: R-loop mediated genomic instability and its implications in neurological diseases.
  Epigenomics Volume: 16 Page(s): 589 - 608
  03/26/2024 Authors: Westover KR; Jin P; Yao B
• The putative RNA helicase DDX1 associates with the nuclear RNA exosome and modulates RNA/DNA hybrids (R-loops).
  J Biol Chem Volume: 300 Page(s): 105646
  02/01/2024 Authors: de Amorim JL; Leung SW; Haji-Seyed-Javadi R; Hou Y; Yu DS; Ghalei H; Khoshnevis S; Yao B; Corbett AH
• TDP-43 chronic deficiency leads to dysregulation of transposable elements and gene expression by affecting R-loop and 5hmC crosstalk.
  Cell Rep Volume: 43 Page(s): 113662
  01/23/2024 Authors: Hou Y; Li Y; Xiang J-F; Tilahun K; Jiang J; Corces VG; Yao B
• Epigenetic modifications of DNA and RNA in Alzheimer's disease.
  Front Mol Neurosci Volume: 17 Page(s): 1398026
  01/01/2024 Authors: Martinez-Feduchi P; Jin P; Yao B
• HELZ promotes R loop resolution to facilitate DNA double-strand break repair by homologous recombination.
  bioRxiv
  12/15/2023 Authors: Haji-Seyed-Javadi R; Koyen AE; Rath SK; Madden MZ; Hou Y; Song BS; Kenney AM; Lan L; Yao B; Yu DS
• Brain methylome remodeling selectively regulates neuronal activity genes linking to emotional behaviors in mice exposed to maternal immune activation.
  Nat Commun Volume: 14 Page(s): 7829
  11/29/2023 Authors: Ma L; Wang F; Li Y; Wang J; Chang Q; Du Y; Sadan J; Zhao Z; Fan G; Yao B
• Social defeat stress induces genome-wide 5mC and 5hmC alterations in the mouse brain.
  G3 (Bethesda) Volume: 13
  08/09/2023 Authors: Kuehner JN; Walia NR; Seong R; Li Y; Martinez-Feduchi P; Yao B
• The human lncRNA GOMAFU suppresses neuronal interferon response pathways affected in neuropsychiatric diseases.
  Brain Behav Immun Volume: 112 Page(s): 175 - 187
  08/01/2023 Authors: Teng P; Li Y; Ku L; Wang F; Goldsmith DR; Wen Z; Yao B; Feng Y
• Expression of expanded GGC repeats within NOTCH2NLC causes behavioral deficits and neurodegeneration in a mouse model of neuronal intranuclear inclusion disease.
  Sci Adv Volume: 8 Page(s): eadd6391
  11/25/2022 Authors: Liu Q; Zhang K; Kang Y; Li Y; Deng P; Li Y; Tian Y; Sun Q; Tang Y; Xu K
• Accurate identification of circRNA landscape and complexity reveals their pivotal roles in human oligodendroglia differentiation.
  Genome Biol Volume: 23 Page(s): 48
  02/07/2022 Authors: Li Y; Wang F; Teng P; Ku L; Chen L; Feng Y; Yao B
• Multi-task deep autoencoder to predict Alzheimer's disease progression using temporal DNA methylation data in peripheral blood.
  Comput Struct Biotechnol J Volume: 20 Page(s): 5761 - 5774
  01/01/2022 Authors: Chen L; Saykin AJ; Yao B; Zhao F; Alzheimers Disease Neuroimaging Initiative (ADNI)
• WEVar: a novel statistical learning framework for predicting noncoding regulatory variants.
  Brief Bioinform Volume: 22
  11/05/2021 Authors: Wang Y; Jiang Y; Yao B; Huang K; Liu Y; Wang Y; Qin X; Saykin AJ; Chen L
• Reversing neural circuit and behavior deficit in mice exposed to maternal inflammation by Zikavirus.
  EMBO Rep Volume: 22 Page(s): e51978
  08/04/2021 Authors: Ma L; Wang J; Ge J; Wang Y; Zhang W; Du Y; Luo J; Li Y; Wang F; Fan G
• 5-hydroxymethylcytosine is dynamically regulated during forebrain organoid development and aberrantly altered in Alzheimer's disease.
  Cell Rep Volume: 35 Page(s): 109042
  04/27/2021 Authors: Kuehner JN; Chen J; Bruggeman EC; Wang F; Li Y; Xu C; McEachin ZT; Li Z; Chen L; Hales CM
• N6-methyladenosine dynamics in neurodevelopment and aging, and its potential role in Alzheimer's disease.
  Genome Biol Volume: 22 Page(s): 17
  01/05/2021 Authors: Shafik AM; Zhang F; Guo Z; Dai Q; Pajdzik K; Li Y; Kang Y; Yao B; Wu H; He C
• circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs.
  Bioinformatics Volume: 36 Page(s): 539 - 545
  01/15/2020 Authors: Chen L; Wang F; Bruggeman EC; Li C; Yao B
• Brain microRNAs associated with late-life depressive symptoms are also associated with cognitive trajectory and dementia.
  NPJ Genom Med Volume: 5 Page(s): 6
  01/01/2020 Authors: Wingo TS; Yang J; Fan W; Min Canon S; Gerasimov ES; Lori A; Logsdon B; Yao B; Seyfried NT; Lah JJ
• Developmental changes and sex differences in DNA methylation and demethylation in hypothalamic regions of the mouse brain.
  Epigenetics Volume: 15 Page(s): 72 - 84
  01/01/2020 Authors: Cisternas CD; Cortes LR; Bruggeman EC; Yao B; Forger NG
• The Taiman Transcriptional Coactivator Engages Toll Signals to Promote Apoptosis and Intertissue Invasion in Drosophila.
  Curr Biol Volume: 29 Page(s): 2790 - 2800.e4
  09/09/2019 Authors: Byun PK; Zhang C; Yao B; Wardwell-Ozgo J; Terry D; Jin P; Moberg K
• TIVAN: tissue-specific cis-eQTL single nucleotide variant annotation and prediction.
  Bioinformatics Volume: 35 Page(s): 1573 - 1575
  05/01/2019 Authors: Chen L; Wang Y; Yao B; Mitra A; Wang X; Qin X
• Reversing Behavioral, Neuroanatomical, and Germline Influences of Intergenerational Stress.
  Biol Psychiatry Volume: 85 Page(s): 248 - 256
  02/01/2019 Authors: Aoued HS; Sannigrahi S; Doshi N; Morrison FG; Linsenbaum H; Hunter SC; Walum H; Baman J; Yao B; Jin P
• The Dynamic Partnership of Polycomb and Trithorax in Brain Development and Diseases.
  Epigenomes Volume: 3 Page(s): 17 - 24
  01/01/2019 Authors: Kuehner JN; Yao B
• Epigenetic Regulations in Neuropsychiatric Disorders.
  Front Genet Volume: 10 Page(s): 268
  01/01/2019 Authors: Kuehner JN; Bruggeman EC; Wen Z; Yao B
• Ten-Eleven Translocation Proteins Modulate the Response to Environmental Stress in Mice.
  Cell Rep Volume: 25 Page(s): 3194 - 3203.e4
  12/11/2018 Authors: Cheng Y; Sun M; Chen L; Li Y; Lin L; Yao B; Li Z; Wang Z; Chen J; Miao Z
• Active N6-Methyladenine Demethylation by DMAD Regulates Gene Expression by Coordinating with Polycomb Protein in Neurons.
  Mol Cell Volume: 71 Page(s): 848 - 857.e6
  09/06/2018 Authors: Yao B; Li Y; Wang Z; Chen L; Poidevin M; Zhang C; Lin L; Wang F; Bao H; Jiao B
• A unique epigenomic landscape defines the characteristics and differentiation potentials of glioma stem cells.
  Genome Biol Volume: 19 Page(s): 51
  04/10/2018 Authors: Yao B; Jin P
• DNA N6-methyladenine is dynamically regulated in the mouse brain following environmental stress.
  Nat Commun Volume: 8 Page(s): 1122
  10/24/2017 Authors: Yao B; Cheng Y; Wang Z; Li Y; Chen L; Huang L; Zhang W; Chen D; Wu H; Tang B
• Ten-eleven translocation 2 interacts with forkhead box O3 and regulates adult neurogenesis.
  Nat Commun Volume: 8 Page(s): 15903
  06/29/2017 Authors: Li X; Yao B; Chen L; Kang Y; Li Y; Cheng Y; Li L; Lin L; Wang Z; Wang M
• Tet2 loss leads to hypermutagenicity in haematopoietic stem/progenitor cells.
  Nat Commun Volume: 8 Page(s): 15102
  04/25/2017 Authors: Pan F; Wingo TS; Zhao Z; Gao R; Makishima H; Qu G; Lin L; Yu M; Ortega JR; Wang J
• Molecular signatures associated with ZIKV exposure in human cortical neural progenitors.
  Nucleic Acids Res Volume: 44 Page(s): 8610 - 8620
  10/14/2016 Authors: Zhang F; Hammack C; Ogden SC; Cheng Y; Lee EM; Wen Z; Qian X; Nguyen HN; Li Y; Yao B
• Epigenetic mechanisms in neurogenesis.
  Nat Rev Neurosci Volume: 17 Page(s): 537 - 549
  09/01/2016 Authors: Yao B; Christian KM; He C; Jin P; Ming G-L; Song H
• 5-Hydroxymethylcytosine-mediated alteration of transposon activity associated with the exposure to adverse in utero environments in human.
  Hum Mol Genet Volume: 25 Page(s): 2208 - 2219
  06/01/2016 Authors: Sun M; Song MM; Wei B; Gao Q; Li L; Yao B; Chen L; Lin L; Dai Q; Zhou X
• Brain-Region-Specific Organoids Using Mini-bioreactors for Modeling ZIKV Exposure.
  Cell Volume: 165 Page(s): 1238 - 1254
  05/19/2016 Authors: Qian X; Nguyen HN; Song MM; Hadiono C; Ogden SC; Hammack C; Yao B; Hamersky GR; Jacob F; Zhong C
• Zika Virus Infects Human Cortical Neural Progenitors and Attenuates Their Growth.
  Cell Stem Cell Volume: 18 Page(s): 587 - 590
  05/05/2016 Authors: Tang H; Hammack C; Ogden SC; Wen Z; Qian X; Li Y; Yao B; Shin J; Zhang F; Lee EM
• Lin28A Binds Active Promoters and Recruits Tet1 to Regulate Gene Expression.
  Mol Cell Volume: 61 Page(s): 153 - 160
  01/07/2016 Authors: Zeng Y; Yao B; Shin J; Lin L; Kim N; Song Q; Liu S; Su Y; Guo JU; Huang L
• Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates.
  Nucleic Acids Res Volume: 43 Page(s): e141
  12/02/2015 Authors: Wu H; Xu T; Feng H; Chen L; Li B; Yao B; Qin Z; Jin P; Conneely KN
• Promoters of Human Cosmc and T-synthase Genes Are Similar in Structure, Yet Different in Epigenetic Regulation.
  J Biol Chem Volume: 290 Page(s): 19018 - 19033
  07/31/2015 Authors: Zeng J; Mi R; Wang Y; Li Y; Lin L; Yao B; Song L; van Die I; Chapman AB; Cummings RD
• The ecdysone receptor coactivator Taiman links Yorkie to transcriptional control of germline stem cell factors in somatic tissue.
  Dev Cell Volume: 34 Page(s): 168 - 180
  07/27/2015 Authors: Zhang C; Robinson BS; Xu W; Yang L; Yao B; Zhao H; Byun PK; Jin P; Veraksa A; Moberg KH
• Base-resolution methylation patterns accurately predict transcription factor bindings in vivo.
  Nucleic Acids Res Volume: 43 Page(s): 2757 - 2766
  03/11/2015 Authors: Xu T; Li B; Zhao M; Szulwach KE; Street RC; Lin L; Yao B; Zhang F; Jin P; Wu H
• Environmental enrichment modulates 5-hydroxymethylcytosine dynamics in hippocampus.
  Genomics Volume: 104 Page(s): 376 - 382
  11/01/2014 Authors: Irier H; Street RC; Dave R; Lin L; Cai C; Davis TH; Yao B; Cheng Y; Jin P
• Unlocking epigenetic codes in neurogenesis.
  Genes Dev Volume: 28 Page(s): 1253 - 1271
  06/15/2014 Authors: Yao B; Jin P
• Genome-wide alteration of 5-hydroxymethylcytosine in a mouse model of fragile X-associated tremor/ataxia syndrome.
  Hum Mol Genet Volume: 23 Page(s): 1095 - 1107
  02/15/2014 Authors: Yao B; Lin L; Street RC; Zalewski ZA; Galloway JN; Wu H; Nelson DL; Jin P
• Genome-wide antagonism between 5-hydroxymethylcytosine and DNA methylation in the adult mouse brain.
  Front Biol (Beijing) Volume: 9 Page(s): 66 - 74
  02/01/2014 Authors: Guo JU; Szulwach KE; Su Y; Li Y; Yao B; Xu Z; Shin JH; Xie B; Gao Y; Ming G-L
• Cytosine modifications in neurodevelopment and diseases.
  Cell Mol Life Sci Volume: 71 Page(s): 405 - 418
  02/01/2014 Authors: Yao B; Jin P
• Regulation of TLR2-mediated tolerance and cross-tolerance through IRAK4 modulation by miR-132 and miR-212.
  J Immunol Volume: 190 Page(s): 1250 - 1263
  02/01/2013 Authors: Nahid MA; Yao B; Dominguez-Gutierrez PR; Kesavalu L; Satoh M; Chan EKL
• Reflections on ten years of history of, and future prospects for, GW182 and GW/P body research.
  Adv Exp Med Biol Volume: 768 Page(s): 261 - 270
  01/01/2013 Authors: Chan EKL; Yao B; Fritzler MJ
• Function of GW182 and GW bodies in siRNA and miRNA pathways.
  Adv Exp Med Biol Volume: 768 Page(s): 71 - 96
  01/01/2013 Authors: Yao B; Li S; Chan EKL
• Defining a new role of GW182 in maintaining miRNA stability.
  EMBO Rep Volume: 13 Page(s): 1102 - 1108
  12/01/2012 Authors: Yao B; La LB; Chen Y-C; Chang L-J; Chan EKL
• High resolution of microRNA signatures in human whole saliva.
  Arch Oral Biol Volume: 56 Page(s): 1506 - 1513
  12/01/2011 Authors: Patel RS; Jakymiw A; Yao B; Pauley BA; Carcamo WC; Katz J; Cheng JQ; Chan EKL
• MicroRNAs in systemic rheumatic diseases.
  Arthritis Res Ther Volume: 13 Page(s): 229
  07/13/2011 Authors: Ceribelli A; Yao B; Dominguez-Gutierrez PR; Nahid MA; Satoh M; Chan EKL
• Lupus T cells switched on by DNA hypomethylation via microRNA?
  Arthritis Rheum Volume: 63 Page(s): 1177 - 1181
  05/01/2011 Authors: Ceribelli A; Yao B; Dominguez-Gutierrez PR; Chan EKL
• Divergent GW182 functional domains in the regulation of translational silencing.
  Nucleic Acids Res Volume: 39 Page(s): 2534 - 2547
  04/01/2011 Authors: Yao B; Li S; Jung HM; Lian SL; Abadal GX; Han F; Fritzler MJ; Chan EKL
• Mapping of Ago2-GW182 functional interactions.
  Methods Mol Biol Volume: 725 Page(s): 45 - 62
  01/01/2011 Authors: Yao B; Li S; Lian SL; Fritzler MJ; Chan EKL
• Induction of cytoplasmic rods and rings structures by inhibition of the CTP and GTP synthetic pathway in mammalian cells.
  PLoS One Volume: 6 Page(s): e29690
  01/01/2011 Authors: Carcamo WC; Satoh M; Kasahara H; Terada N; Hamazaki T; Chan JYF; Yao B; Tamayo S; Covini G; von Mhlen CA
• DNMT1 and DNMT3B modulate distinct polycomb-mediated histone modifications in colon cancer.
  Cancer Res Volume: 69 Page(s): 7412 - 7421
  09/15/2009 Authors: Jin B; Yao B; Li J-L; Fields CR; Delmas AL; Liu C; Robertson KD
• Invasion suppressor cystatin E/M (CST6): high-level cell type-specific expression in normal brain and epigenetic silencing in gliomas.
  Lab Invest Volume: 88 Page(s): 910 - 925
  09/01/2008 Authors: Qiu J; Ai L; Ramachandran C; Yao B; Gopalakrishnan S; Fields CR; Delmas AL; Dyer LM; Melnick SJ; Yachnis AT
• Epigenetic blocking of an enhancer region controls irradiation-induced proapoptotic gene expression in Drosophila embryos.
  Dev Cell Volume: 14 Page(s): 481 - 493
  04/01/2008 Authors: Zhang Y; Lin N; Carroll PM; Chan G; Guan B; Xiao H; Yao B; Wu SS; Zhou L
• Nucleotide sequence of a cDNA encoding head domain of Zhikong scallop Chlamys farreri myosin VI
  FISHERIES SCIENCE Volume: 73 Page(s): 217 - 219
  02/01/2007 Authors: Hu X; Bao Z; Zhang L; Pan J; Yao B; Guo W
• Polymorphic microsatellite markers in the Zhikong scallop Chlamys farreri
  MOLECULAR ECOLOGY NOTES Volume: 6 Page(s): 127 - 129
  03/01/2006 Authors: Zhan AB; Bao ZM; Yao B; Wang XL; Hui M; Hu JJ