Published and Accepted Research Articles (*, equal contribution; # corresponding author; Yao Lab mentees are underlined). Selected publications are highlighted in green. Total citations can be found in Dr. Yao's Google Scholar page)
Wang, F.*, Li, Y.*, Shen, H., Martinez-Feduchi, P., Ji X., Krishnakumar S., Teng, P., Hu, J., Chen, L., Feng, Y. #, and Yao, B. # (Corresponding author, Lead Contact) （2024） Identification of pathological pathways centered on circRNA dysregulation in association with irreversible progression of Alzheimer’s disease. Genome Med, 16, Article number: 129
Zhao, F.*, Li, Y.*, Chen, L.# and Yao, B. # (Corresponding author, Lead Contact) (2024) Identification of brain region-specific landscape and functions of clustered circRNAs in Alzheimer’s disease using circMeta2. Commun Biol. 7, Article number: 1353.
Ma, X., Thela, S.R., Zhao, F., Yao, B., Wen, Z., Jin, P., Zhao, J. and Chen, L. # (2024) Deep5hmC: Predicting genome-wide 5-Hydroxymethylcytosine landscape via a multimodal deep learning model. Bioinformatics. 2024 Aug 28:btae528
Zhao, F., Ma, X., Yao, B., Lu, Q. and Chen, L. # (2024) scaDA: A novel statistical method for differential analysis of single-cell chromatin accessibility sequencing data. PLoS Comput Biol, 20, e1011854.
Zakutansky, P. M., Ku, L., Zhang, G., Shi, L., Li, Y., Yao, B., Bassell, G.J., Read, R. D. and Feng, Y. #. (2024). Isoform balance of the long non-coding RNA NEAT1 is regulated by the RNA-binding protein QKI, governs the glioma transcriptome, and impacts glioma cell migration. J Biol Chem. 107595.
Hou, Y.*, Li, Y.*, Xiang, J.F., Tilahun, K., Jiang, J., Corces, V.G. and Yao, B. # (Corresponding author, Lead Contact) (2024) TDP-43 chronic deficiency leads to dysregulation of transposable elements and gene expression by affecting R-loop and 5hmC crosstalk. Cell Rep, 43, 113662. Featured by Emory News; ScienceFeatured
de Amorim, J.L., Leung, S.W., Haji-Seyed-Javadi, R., Hou, Y., Yu, D.S., Ghalei, H., Khoshnevis, S., Yao, B. and Corbett, A.H.# (2024) The putative RNA helicase DDX1 associates with the nuclear RNA exosome and modulates RNA/DNA hybrids (R-loops). J Biol Chem, 300, 105646.
Ma, L.*, Wang F.*, Li Y.*, Wang J.*, Chang Q., Du Y., Sadan J., Zhao Z., Fan G. #, Yao B. # (Corresponding author) and Chen J.F. # (2023) Brain methylome remodeling selectively regulates neuronal activity genes linking to emotional behaviors in mice exposed to maternal immune activation. Nat Commun. 14, Article number: 7829.
Teng, P.*, Li, Y.*, Ku, L., Wang, F., Goldsmith, D.R., Wen, Z., Yao, B. # (Corresponding author) and Feng, Y#. (2023) The human lncRNA GOMAFU suppresses neuronal interferon response pathways affected in neuropsychiatric diseases. Brain Behav Immun, 112, 175-187.
Kuehner, J. Walia, N.R., Seong R, Li, Y., Martinez-Feduchi, P. and Yao, B. # (Corresponding author, Lead Contact). (2023) Social defeat stress induces genome-wide 5mC and 5hmC alterations in the mouse brain. G3 Genes|Genomes|Genetics. jkad114, https://doi.org/10.1093/g3journal/jkad114
Liu, Q., Zhang, K., Kang, Y., Li, Y., Deng, P., Li, Y., Tian, Y., Sun, Q., Tang, Y., Xu, K., Zhou, Y., Wang, J.L., Guo, J., Li, J.D., Xia, K., Meng, Q., Allen, E.G., Wen, Z., Li, Z., Jiang, H., Shen, L., Duan, R., Yao, B., Tang, B., # Jin, P. # and Pan, Y. # (2022) Expression of expanded GGC repeats within NOTCH2NLC causes behavioral deficits and neurodegeneration in a mouse model of neuronal intranuclear inclusion disease. Sci Adv, 8, eadd6391.
Chen, L. #, Saykin, A.J., Yao, B., Zhao F. Alzheimer’s Disease Neuroimaging Initiative (ADNI) (2022) Multi-task deep autoencoder to predict Alzheimer’s disease progression using temporal DNA methylation data in peripheral blood. Comput Struct Biotechnol J. 20, 5761-5774.
Li, Y.*, Wang, F.*, Teng, P.*, Ku, L., Chen, L., Feng, Y. # and Yao, B. # (Corresponding author, Lead Contact) (2022) Accurate identification of circRNA landscape and complexity reveals their pivotal roles in human oligodendroglia differentiation. Genome Biol, 23, 48.
Ma, L., Wang, J., Ge, J., Wang, Y., Zhang, W., Du, Y., Luo, J., Li, Y., Wang, F., Fan, G., Chen, R., Yao, B., Zhao, Z., Guo, M.L., Kim, W.K., Chai, Y. and Chen, J.F. # (2021) Reversing neural circuit and behavior deficit in mice exposed to maternal inflammation by Zika virus. EMBO Rep, 22.
Wang, Y., Jiang, Y., Yao, B., Huang, K., Liu, Y., Wang, Y., Qin, X., Saykin, A.J. and Chen, L. # (2021) WEVar: a novel statistical learning framework for predicting noncoding regulatory variants. Brief Bioinform, 22.
Kuehner, J.N.*, Chen, J.*, Bruggeman, E.C., Wang, F., Li, Y., Xu, C., McEachin, Z.T., Li, Z., Chen, L., Hales, C.M., Wen, Z.#, Yang, J.# and Yao, B. # (Corresponding author, Lead Contact) (2021) 5-hydroxymethylcytosine is dynamically regulated during forebrain organoid development and aberrantly altered in Alzheimer's disease. Cell Rep, 35, 109042. Featured by Epigenie
Shafik, A.M., Zhang, F., Guo, Z., Dai, Q., Pajdzik, K., Li, Y., Kang, Y., Yao, B., Wu, H., He, C., Allen, E.G., Duan, R. and Jin, P. # (2021) N6-methyladenosine dynamics in neurodevelopment and aging, and its potential role in Alzheimer's disease. Genome Biol, 22.
Wingo, T.S., Yang, J., Fan, W., Min Canon, S., Gerasimov, E.S., Lori, A., Logsdon, B., Yao, B., Seyfried, N.T., Lah, J.J., Levey, A.I., Boyle, P.A., Schneider, J.A., De Jager, P.L., Bennett, D.A. and Wingo, A.P. # (2020) Brain microRNAs associated with late-life depressive symptoms are also associated with cognitive trajectory and dementia. npj Genomic Medicine, 5.
Chen, L.#, Wang, F., Bruggeman, E.C., Li, C. and Yao, B. # (Corresponding author) (2020) circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs. Bioinformatics, 36, 539-545.
Cisternas, C.D., Cortes, L.R., Bruggeman, E.C., Yao, B. and Forger, N.G. # (2019) Developmental changes and sex differences in DNA methylation and demethylation in hypothalamic regions of the mouse brain. Epigenetics, 1-13.
Byun, P.K., Zhang, C., Yao, B., Wardwell-Ozgo, J., Terry, D., Jin, P. and Moberg, K. # (2019) The Taiman Transcriptional Coactivator Engages Toll Signals to Promote Apoptosis and Intertissue Invasion in Drosophila. Current Biology, 29, 2790-2800.e2794.
Chen, L. #, Wang, Y., Yao, B., Mitra, A., Wang, X. and Qin, X. (2019) TIVAN: tissue-specific cis-eQTL single nucleotide variant annotation and prediction. Bioinformatics, 35, 1573-1575.
Aoued, H.S., Sannigrahi, S., Doshi, N., Morrison, F.G., Linsenbaum, H., Hunter, S.C., Walum, H., Baman, J., Yao, B., Jin, P., Ressler, K.J. and Dias, B.G. # (2019) Reversing Behavioral, Neuroanatomical, and Germline Influences of Intergenerational Stress. Biol Psychiatry, 85, 248-256.
Cheng, Y., Sun, M., Chen, L., Li, Y., Lin, L., Yao, B., Li, Z., Wang, Z., Chen, J., Miao, Z., Xin, N., Huang, L., Allen, E.G., Wu, H., Xu, X. # and Jin, P. # (2018) Ten-Eleven Translocation Proteins Modulate the Response to Environmental Stress in Mice. Cell Rep, 25, 3194-3203 e3194.
Yao, B. *# (co-first author, co-corresponding author), Li, Y.*, Wang, Z., Chen, L., Poidevin, M., Zhang, C., Lin, L., Wang, F., Bao, H., Jiao, B., Lim, J., Cheng, Y., Huang, L., Phillips, B.L., Xu, T., Duan, R., Moberg, K.H., Wu, H. and Jin, P. # (2018) Active N(6)-Methyladenine Demethylation by DMAD Regulates Gene Expression by Coordinating with Polycomb Protein in Neurons. Mol Cell, 71, 848-857 e846.
Yao, B. * (co-first author), Cheng, Y.*, Wang, Z., Li, Y., Chen, L., Huang, L., Zhang, W., Chen, D., Wu, H., Tang, B., and Jin, P. # (2017) DNA N6-methyladenine is dynamically regulated in the mouse brain following environmental stress. Nat Commun, 8, 1122.
Li, X.*#, Yao, B.* (co-first author), Chen, L., Kang, Y., Li, Y., Cheng, Y., Li, L., Lin, L., Wang, Z., Wang, M., Pan, F., Dai, Q., Zhang, W., Wu, H., Shu, Q., Qin, Z., He, C., Xu, M. and Jin, P. # (2017) Ten-eleven translocation 2 interacts with forkhead box O3 and regulates adult neurogenesis. Nat Commun, 8, 15903.
Pan, F., Wingo, T.S., Zhao, Z., Gao, R., Makishima, H., Qu, G., Lin, L., Yu, M., Ortega, J.R., Wang, J., Nazha, A., Chen, L., Yao, B., Liu, C., Chen, S., Weeks, O., Ni, H., Phillips, B.L., Huang, S., Wang, J., He, C., Li, G.M., Radivoyevitch, T., Aifantis, I., Maciejewski, J.P., Yang, F.C., Jin, P #. and Xu, M. # (2017) Tet2 loss leads to hypermutagenicity in haematopoietic stem/progenitor cells. Nat Commun, 8, 15102.
Zhang, F., Hammack, C., Ogden, S.C., Cheng, Y., Lee, E.M., Wen, Z., Qian, X., Nguyen, H.N., Li, Y., Yao, B., Xu, M., Xu, T., Chen, L., Wang, Z., Feng, H., Huang, W.K., Yoon, K.J., Shan, C., Huang, L., Qin, Z., Christian, K.M., Shi, P.Y., Xu, M., Xia, M., Zheng, W., Wu, H., Song, H., Tang, H., Ming, G.L. and Jin, P. # (2016) Molecular signatures associated with ZIKV exposure in human cortical neural progenitors. Nucleic Acids Res, 44, 8610-8620.
Qian, X., Nguyen, H.N., Song, M.M., Hadiono, C., Ogden, S.C., Hammack, C., Yao, B., Hamersky, G.R., Jacob, F., Zhong, C., Yoon, K.J., Jeang, W., Lin, L., Li, Y., Thakor, J., Berg, D.A., Zhang, C., Kang, E., Chickering, M., Nauen, D., Ho, C.Y., Wen, Z., Christian, K.M., Shi, P.Y., Maher, B.J., Wu, H., Jin, P., Tang, H., Song, H. # and Ming, G.L. # (2016) Brain-Region-Specific Organoids Using Mini-bioreactors for Modeling ZIKV Exposure. Cell, 165, 1238-1254.
Sun, M., Song, M.M., Wei, B., Gao, Q., Li, L., Yao, B., Chen, L., Lin, L., Dai, Q., Zhou, X., Tao, J., Chen, J., He, C., Jin, P #. and Xu, Z. # (2016) 5-Hydroxymethylcytosine-mediated alteration of transposon activity associated with the exposure to adverse in utero environments in human. Hum Mol Genet, 25, 2208-2219.
Tang, H., Hammack, C., Ogden, S.C., Wen, Z., Qian, X., Li, Y., Yao, B., Shin, J., Zhang, F., Lee, E.M., Christian, K.M., Didier, R.A., Jin, P. #, Song, H. # and Ming, G.L. # (2016) Zika Virus Infects Human Cortical Neural Progenitors and Attenuates Their Growth. Cell Stem Cell, 18, 587-590.
Zeng, Y.*, Yao, B.* (co-first author), Shin, J., Lin, L., Kim, N., Song, Q., Liu, S., Su, Y., Guo, J.U., Huang, L., Wan, J., Wu, H., Qian, J., Cheng, X., Zhu, H., Ming, G.L., Jin, P. # and Song, H. # (2016) Lin28A Binds Active Promoters and Recruits Tet1 to Regulate Gene Expression. Mol Cell, 61, 153-160. (Cover feature)
Wu, H. #, Xu, T., Feng, H., Chen, L., Li, B., Yao, B., Qin, Z., Jin, P. and Conneely, K.N. (2015) Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates. Nucleic Acids Res, 43, e141.
Zhang, C., Robinson, B.S., Xu, W., Yang, L., Yao, B., Zhao, H., Byun, P.K., Jin, P., Veraksa, A. and Moberg, K.H. # (2015) The ecdysone receptor coactivator Taiman links Yorkie to transcriptional control of germline stem cell factors in somatic tissue. Dev Cell, 34, 168-180.
Zeng, J., Mi, R., Wang, Y., Li, Y., Lin, L., Yao, B., Song, L., van Die, I., Chapman, A.B., Cummings, R.D., Jin, P. and Ju, T. # (2015) Promoters of Human Cosmc and T-synthase Genes Are Similar. in Structure, Yet Different in Epigenetic Regulation. J Biol Chem, 290, 19018-19033.
Xu, T., Li, B., Zhao, M., Szulwach, K.E., Street, R.C., Lin, L., Yao, B., Zhang, F., Jin, P. #, Wu, H. # and Qin, Z.S. # (2015) Base-resolution methylation patterns accurately predict transcription factor bindings in vivo. Nucleic Acids Res, 43, 2757-2766.
Irier, H., Street, R.C., Dave, R., Lin, L., Cai, C., Davis, T.H., Yao, B., Cheng, Y., and Jin, P. # (2014) Environmental enrichment modulates 5-hydroxymethylcytosine dynamics in hippocampus. Genomics, 104, 376-382.
Yao, B., Lin, L., Street, R.C., Zalewski, Z.A., Galloway, J.N., Wu, H., Nelson, D.L. and Jin, P. # (2014) Genome-wide alteration of 5-hydroxymethylcytosine in a mouse model of fragile X-associated tremor/ataxia syndrome. Hum Mol Genet, 23, 1095-1107.
Guo, J.U., Szulwach, K.E., Su, Y., Li, Y., Yao, B., Xu, Z., Shin, J.H., Xie, B., Gao, Y., Ming, G.L., Jin, P. # and Song, H. # (2014) Genome-wide antagonism between 5-hydroxymethylcytosine and DNA methylation in the adult mouse brain. Front Biol, 9, 66-74.
Nahid, M.A., Yao, B., Dominguez-Gutierrez, P.R., Kesavalu, L., Satoh, M. and Chan, E.K. # (2013) Regulation of TLR2-mediated tolerance and cross-tolerance through IRAK4 modulation by miR-132 and miR-212. J Immunol, 190, 1250-1263.
Yao, B., La, L.B., Chen, Y.C., Chang, L.J. and Chan, E.K. # (2012) Defining a new role of GW182 in maintaining miRNA stability. EMBO Rep, 13, 1102-1108.
Patel, R.S., Jakymiw, A., Yao, B., Pauley, B.A., Carcamo, W.C., Katz, J., Cheng, J.Q. and Chan, E.K. # (2011) High resolution of microRNA signatures in whole human saliva. Arch Oral Biol, 56, 1506-1513.
Yao, B. * (co-first author), Li, S.*, Jung, H.M., Lian, S.L., Abadal, G.X., Han, F., Fritzler, M.J., and Chan, E.K. # (2011) Divergent GW182 functional domains in the regulation of translational silencing. Nucleic Acids Res, 39, 2534-2547.
Yao, B., Li, S., Lian, S.L., Fritzler, M.J. and Chan, E.K. # (2011) Mapping of Ago2-GW182 functional interactions. Methods Mol Biol, 725, 45-62.
Carcamo, W.C., Satoh, M., Kasahara, H., Terada, N., Hamazaki, T., Chan, J.Y., Yao, B., Tamayo, S., Covini, G., von Muhlen, C.A. and Chan, E.K. # (2011) Induction of cytoplasmic rods and rings structures by inhibition of the CTP and GTP synthetic pathway in mammalian cells. PLoS One, 6, e29690.
Jin, B., Yao, B., Li, J.L., Fields, C.R., Delmas, A.L., Liu, C., and Robertson, K.D. # (2009) DNMT1 and DNMT3B modulate distinct polycomb-mediated histone modifications in colon cancer. Cancer Res, 69, 7412-7421.
Qiu, J., Ai, L., Ramachandran, C., Yao, B., Gopalakrishnan, S., Fields, C.R., Delmas, A.L., Dyer, L.M., Melnick, S.J., Yachnis, A.T., Schwartz, P.H., Fine, H.A., Brown, K.D. and Robertson, K.D. # (2008) Invasion suppressor cystatin E/M (CST6): high-level cell type-specific expression in normal brain and epigenetic silencing in gliomas. Lab Invest, 88, 910-925.
Zhang, Y., Lin, N., Carroll, P.M., Chan, G., Guan, B., Xiao, H., Yao, B., Wu, S.S. and Zhou, L. # (2008) Epigenetic Blocking of an Enhancer Region Controls Irradiation-Induced Proapoptotic Gene Expression in Drosophila Embryos. Dev Cell, 14, 481-493.
Selected Review and Book Chapters
Martinez-Feduchi, P., Jin, P. and Yao, B. # (Corresponding author, Lead Contact) (2024) Epigenetic modifications of DNA and RNA in Alzheimer's disease. Front Mol Neurosci, 17, 1398026.
Westover, K.R., Jin, P. # and Yao, B. # (Corresponding author, Lead Contact) (2024) Bridging the gap: R-loop mediated genomic instability and its implications in neurological diseases. Epigenomics, 16, 589-608.
Kuehner, J.N., Bruggeman, E.C., Wen, Z. and Yao, B # (Corresponding author, Lead Contact). (2019) Epigenetic Regulations in Neuropsychiatric Disorders. Front Genet, 10, 268.
Kuehner, J.N. and Yao, B. # (corresponding author) (2019) The Dynamic Partnership of Polycomb and Trithorax in Brain Development and Diseases. Epigenomes, 3, 17.
Bruggeman, E.C. and Yao, B. # (2019) DNA Methylation in Neuronal Development and Disease. RNA Technologies. Springer International Publishing, pp. 103-140.
Yao, B., Christian, K.M., He, C., Jin, P., Ming, G.L. and Song, H. (2016) Epigenetic mechanisms in neurogenesis. Nat Rev Neurosci, 17, 537-549.
Yao, B. and Jin, P. (2014) Unlocking epigenetic codes in neurogenesis. Genes Dev, 28, 1253-1271.
Yao, B., Li, S. and Chan, E.K. (2013) Function of GW182 and GW bodies in siRNA and miRNA pathways. Adv Exp Med Biol, 768, 71-96.
Yao, B., Li, S., Lian, S.L., Fritzler, M.J. and Chan, E.K. (2011) Mapping of Ago2-GW182 functional interactions. Methods Mol Biol, 725, 45-62.
Please check my full publications from Google Scholar here.
Wang, F.*, Li, Y.*, Shen, H., Martinez-Feduchi, P., Ji X., Krishnakumar S., Teng, P., Hu, J., Chen, L., Feng, Y. #, and Yao, B. # (Corresponding author, Lead Contact) （2024） Identification of pathological pathways centered on circRNA dysregulation in association with irreversible progression of Alzheimer’s disease. Genome Med, 16, Article number: 129
Zhao, F.*, Li, Y.*, Chen, L.# and Yao, B. # (Corresponding author, Lead Contact) (2024) Identification of brain region-specific landscape and functions of clustered circRNAs in Alzheimer’s disease using circMeta2. Commun Biol. 7, Article number: 1353.
Ma, X., Thela, S.R., Zhao, F., Yao, B., Wen, Z., Jin, P., Zhao, J. and Chen, L. # (2024) Deep5hmC: Predicting genome-wide 5-Hydroxymethylcytosine landscape via a multimodal deep learning model. Bioinformatics. 2024 Aug 28:btae528
Zhao, F., Ma, X., Yao, B., Lu, Q. and Chen, L. # (2024) scaDA: A novel statistical method for differential analysis of single-cell chromatin accessibility sequencing data. PLoS Comput Biol, 20, e1011854.
Zakutansky, P. M., Ku, L., Zhang, G., Shi, L., Li, Y., Yao, B., Bassell, G.J., Read, R. D. and Feng, Y. #. (2024). Isoform balance of the long non-coding RNA NEAT1 is regulated by the RNA-binding protein QKI, governs the glioma transcriptome, and impacts glioma cell migration. J Biol Chem. 107595.
Hou, Y.*, Li, Y.*, Xiang, J.F., Tilahun, K., Jiang, J., Corces, V.G. and Yao, B. # (Corresponding author, Lead Contact) (2024) TDP-43 chronic deficiency leads to dysregulation of transposable elements and gene expression by affecting R-loop and 5hmC crosstalk. Cell Rep, 43, 113662. Featured by Emory News; ScienceFeatured
de Amorim, J.L., Leung, S.W., Haji-Seyed-Javadi, R., Hou, Y., Yu, D.S., Ghalei, H., Khoshnevis, S., Yao, B. and Corbett, A.H.# (2024) The putative RNA helicase DDX1 associates with the nuclear RNA exosome and modulates RNA/DNA hybrids (R-loops). J Biol Chem, 300, 105646.
Ma, L.*, Wang F.*, Li Y.*, Wang J.*, Chang Q., Du Y., Sadan J., Zhao Z., Fan G. #, Yao B. # (Corresponding author) and Chen J.F. # (2023) Brain methylome remodeling selectively regulates neuronal activity genes linking to emotional behaviors in mice exposed to maternal immune activation. Nat Commun. 14, Article number: 7829.
Teng, P.*, Li, Y.*, Ku, L., Wang, F., Goldsmith, D.R., Wen, Z., Yao, B. # (Corresponding author) and Feng, Y#. (2023) The human lncRNA GOMAFU suppresses neuronal interferon response pathways affected in neuropsychiatric diseases. Brain Behav Immun, 112, 175-187.
Kuehner, J. Walia, N.R., Seong R, Li, Y., Martinez-Feduchi, P. and Yao, B. # (Corresponding author, Lead Contact). (2023) Social defeat stress induces genome-wide 5mC and 5hmC alterations in the mouse brain. G3 Genes|Genomes|Genetics. jkad114, https://doi.org/10.1093/g3journal/jkad114
Liu, Q., Zhang, K., Kang, Y., Li, Y., Deng, P., Li, Y., Tian, Y., Sun, Q., Tang, Y., Xu, K., Zhou, Y., Wang, J.L., Guo, J., Li, J.D., Xia, K., Meng, Q., Allen, E.G., Wen, Z., Li, Z., Jiang, H., Shen, L., Duan, R., Yao, B., Tang, B., # Jin, P. # and Pan, Y. # (2022) Expression of expanded GGC repeats within NOTCH2NLC causes behavioral deficits and neurodegeneration in a mouse model of neuronal intranuclear inclusion disease. Sci Adv, 8, eadd6391.
Chen, L. #, Saykin, A.J., Yao, B., Zhao F. Alzheimer’s Disease Neuroimaging Initiative (ADNI) (2022) Multi-task deep autoencoder to predict Alzheimer’s disease progression using temporal DNA methylation data in peripheral blood. Comput Struct Biotechnol J. 20, 5761-5774.
Li, Y.*, Wang, F.*, Teng, P.*, Ku, L., Chen, L., Feng, Y. # and Yao, B. # (Corresponding author, Lead Contact) (2022) Accurate identification of circRNA landscape and complexity reveals their pivotal roles in human oligodendroglia differentiation. Genome Biol, 23, 48.
Ma, L., Wang, J., Ge, J., Wang, Y., Zhang, W., Du, Y., Luo, J., Li, Y., Wang, F., Fan, G., Chen, R., Yao, B., Zhao, Z., Guo, M.L., Kim, W.K., Chai, Y. and Chen, J.F. # (2021) Reversing neural circuit and behavior deficit in mice exposed to maternal inflammation by Zika virus. EMBO Rep, 22.
Wang, Y., Jiang, Y., Yao, B., Huang, K., Liu, Y., Wang, Y., Qin, X., Saykin, A.J. and Chen, L. # (2021) WEVar: a novel statistical learning framework for predicting noncoding regulatory variants. Brief Bioinform, 22.
Kuehner, J.N.*, Chen, J.*, Bruggeman, E.C., Wang, F., Li, Y., Xu, C., McEachin, Z.T., Li, Z., Chen, L., Hales, C.M., Wen, Z.#, Yang, J.# and Yao, B. # (Corresponding author, Lead Contact) (2021) 5-hydroxymethylcytosine is dynamically regulated during forebrain organoid development and aberrantly altered in Alzheimer's disease. Cell Rep, 35, 109042. Featured by Epigenie
Shafik, A.M., Zhang, F., Guo, Z., Dai, Q., Pajdzik, K., Li, Y., Kang, Y., Yao, B., Wu, H., He, C., Allen, E.G., Duan, R. and Jin, P. # (2021) N6-methyladenosine dynamics in neurodevelopment and aging, and its potential role in Alzheimer's disease. Genome Biol, 22.
Wingo, T.S., Yang, J., Fan, W., Min Canon, S., Gerasimov, E.S., Lori, A., Logsdon, B., Yao, B., Seyfried, N.T., Lah, J.J., Levey, A.I., Boyle, P.A., Schneider, J.A., De Jager, P.L., Bennett, D.A. and Wingo, A.P. # (2020) Brain microRNAs associated with late-life depressive symptoms are also associated with cognitive trajectory and dementia. npj Genomic Medicine, 5.
Chen, L.#, Wang, F., Bruggeman, E.C., Li, C. and Yao, B. # (Corresponding author) (2020) circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs. Bioinformatics, 36, 539-545.
Cisternas, C.D., Cortes, L.R., Bruggeman, E.C., Yao, B. and Forger, N.G. # (2019) Developmental changes and sex differences in DNA methylation and demethylation in hypothalamic regions of the mouse brain. Epigenetics, 1-13.
Byun, P.K., Zhang, C., Yao, B., Wardwell-Ozgo, J., Terry, D., Jin, P. and Moberg, K. # (2019) The Taiman Transcriptional Coactivator Engages Toll Signals to Promote Apoptosis and Intertissue Invasion in Drosophila. Current Biology, 29, 2790-2800.e2794.
Chen, L. #, Wang, Y., Yao, B., Mitra, A., Wang, X. and Qin, X. (2019) TIVAN: tissue-specific cis-eQTL single nucleotide variant annotation and prediction. Bioinformatics, 35, 1573-1575.
Aoued, H.S., Sannigrahi, S., Doshi, N., Morrison, F.G., Linsenbaum, H., Hunter, S.C., Walum, H., Baman, J., Yao, B., Jin, P., Ressler, K.J. and Dias, B.G. # (2019) Reversing Behavioral, Neuroanatomical, and Germline Influences of Intergenerational Stress. Biol Psychiatry, 85, 248-256.
Cheng, Y., Sun, M., Chen, L., Li, Y., Lin, L., Yao, B., Li, Z., Wang, Z., Chen, J., Miao, Z., Xin, N., Huang, L., Allen, E.G., Wu, H., Xu, X. # and Jin, P. # (2018) Ten-Eleven Translocation Proteins Modulate the Response to Environmental Stress in Mice. Cell Rep, 25, 3194-3203 e3194.
Yao, B. *# (co-first author, co-corresponding author), Li, Y.*, Wang, Z., Chen, L., Poidevin, M., Zhang, C., Lin, L., Wang, F., Bao, H., Jiao, B., Lim, J., Cheng, Y., Huang, L., Phillips, B.L., Xu, T., Duan, R., Moberg, K.H., Wu, H. and Jin, P. # (2018) Active N(6)-Methyladenine Demethylation by DMAD Regulates Gene Expression by Coordinating with Polycomb Protein in Neurons. Mol Cell, 71, 848-857 e846.
Yao, B. * (co-first author), Cheng, Y.*, Wang, Z., Li, Y., Chen, L., Huang, L., Zhang, W., Chen, D., Wu, H., Tang, B., and Jin, P. # (2017) DNA N6-methyladenine is dynamically regulated in the mouse brain following environmental stress. Nat Commun, 8, 1122.
Li, X.*#, Yao, B.* (co-first author), Chen, L., Kang, Y., Li, Y., Cheng, Y., Li, L., Lin, L., Wang, Z., Wang, M., Pan, F., Dai, Q., Zhang, W., Wu, H., Shu, Q., Qin, Z., He, C., Xu, M. and Jin, P. # (2017) Ten-eleven translocation 2 interacts with forkhead box O3 and regulates adult neurogenesis. Nat Commun, 8, 15903.
Pan, F., Wingo, T.S., Zhao, Z., Gao, R., Makishima, H., Qu, G., Lin, L., Yu, M., Ortega, J.R., Wang, J., Nazha, A., Chen, L., Yao, B., Liu, C., Chen, S., Weeks, O., Ni, H., Phillips, B.L., Huang, S., Wang, J., He, C., Li, G.M., Radivoyevitch, T., Aifantis, I., Maciejewski, J.P., Yang, F.C., Jin, P #. and Xu, M. # (2017) Tet2 loss leads to hypermutagenicity in haematopoietic stem/progenitor cells. Nat Commun, 8, 15102.
Zhang, F., Hammack, C., Ogden, S.C., Cheng, Y., Lee, E.M., Wen, Z., Qian, X., Nguyen, H.N., Li, Y., Yao, B., Xu, M., Xu, T., Chen, L., Wang, Z., Feng, H., Huang, W.K., Yoon, K.J., Shan, C., Huang, L., Qin, Z., Christian, K.M., Shi, P.Y., Xu, M., Xia, M., Zheng, W., Wu, H., Song, H., Tang, H., Ming, G.L. and Jin, P. # (2016) Molecular signatures associated with ZIKV exposure in human cortical neural progenitors. Nucleic Acids Res, 44, 8610-8620.
Qian, X., Nguyen, H.N., Song, M.M., Hadiono, C., Ogden, S.C., Hammack, C., Yao, B., Hamersky, G.R., Jacob, F., Zhong, C., Yoon, K.J., Jeang, W., Lin, L., Li, Y., Thakor, J., Berg, D.A., Zhang, C., Kang, E., Chickering, M., Nauen, D., Ho, C.Y., Wen, Z., Christian, K.M., Shi, P.Y., Maher, B.J., Wu, H., Jin, P., Tang, H., Song, H. # and Ming, G.L. # (2016) Brain-Region-Specific Organoids Using Mini-bioreactors for Modeling ZIKV Exposure. Cell, 165, 1238-1254.
Sun, M., Song, M.M., Wei, B., Gao, Q., Li, L., Yao, B., Chen, L., Lin, L., Dai, Q., Zhou, X., Tao, J., Chen, J., He, C., Jin, P #. and Xu, Z. # (2016) 5-Hydroxymethylcytosine-mediated alteration of transposon activity associated with the exposure to adverse in utero environments in human. Hum Mol Genet, 25, 2208-2219.
Tang, H., Hammack, C., Ogden, S.C., Wen, Z., Qian, X., Li, Y., Yao, B., Shin, J., Zhang, F., Lee, E.M., Christian, K.M., Didier, R.A., Jin, P. #, Song, H. # and Ming, G.L. # (2016) Zika Virus Infects Human Cortical Neural Progenitors and Attenuates Their Growth. Cell Stem Cell, 18, 587-590.
Zeng, Y.*, Yao, B.* (co-first author), Shin, J., Lin, L., Kim, N., Song, Q., Liu, S., Su, Y., Guo, J.U., Huang, L., Wan, J., Wu, H., Qian, J., Cheng, X., Zhu, H., Ming, G.L., Jin, P. # and Song, H. # (2016) Lin28A Binds Active Promoters and Recruits Tet1 to Regulate Gene Expression. Mol Cell, 61, 153-160. (Cover feature)
Wu, H. #, Xu, T., Feng, H., Chen, L., Li, B., Yao, B., Qin, Z., Jin, P. and Conneely, K.N. (2015) Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates. Nucleic Acids Res, 43, e141.
Zhang, C., Robinson, B.S., Xu, W., Yang, L., Yao, B., Zhao, H., Byun, P.K., Jin, P., Veraksa, A. and Moberg, K.H. # (2015) The ecdysone receptor coactivator Taiman links Yorkie to transcriptional control of germline stem cell factors in somatic tissue. Dev Cell, 34, 168-180.
Zeng, J., Mi, R., Wang, Y., Li, Y., Lin, L., Yao, B., Song, L., van Die, I., Chapman, A.B., Cummings, R.D., Jin, P. and Ju, T. # (2015) Promoters of Human Cosmc and T-synthase Genes Are Similar. in Structure, Yet Different in Epigenetic Regulation. J Biol Chem, 290, 19018-19033.
Xu, T., Li, B., Zhao, M., Szulwach, K.E., Street, R.C., Lin, L., Yao, B., Zhang, F., Jin, P. #, Wu, H. # and Qin, Z.S. # (2015) Base-resolution methylation patterns accurately predict transcription factor bindings in vivo. Nucleic Acids Res, 43, 2757-2766.
Irier, H., Street, R.C., Dave, R., Lin, L., Cai, C., Davis, T.H., Yao, B., Cheng, Y., and Jin, P. # (2014) Environmental enrichment modulates 5-hydroxymethylcytosine dynamics in hippocampus. Genomics, 104, 376-382.
Yao, B., Lin, L., Street, R.C., Zalewski, Z.A., Galloway, J.N., Wu, H., Nelson, D.L. and Jin, P. # (2014) Genome-wide alteration of 5-hydroxymethylcytosine in a mouse model of fragile X-associated tremor/ataxia syndrome. Hum Mol Genet, 23, 1095-1107.
Guo, J.U., Szulwach, K.E., Su, Y., Li, Y., Yao, B., Xu, Z., Shin, J.H., Xie, B., Gao, Y., Ming, G.L., Jin, P. # and Song, H. # (2014) Genome-wide antagonism between 5-hydroxymethylcytosine and DNA methylation in the adult mouse brain. Front Biol, 9, 66-74.
Nahid, M.A., Yao, B., Dominguez-Gutierrez, P.R., Kesavalu, L., Satoh, M. and Chan, E.K. # (2013) Regulation of TLR2-mediated tolerance and cross-tolerance through IRAK4 modulation by miR-132 and miR-212. J Immunol, 190, 1250-1263.
Yao, B., La, L.B., Chen, Y.C., Chang, L.J. and Chan, E.K. # (2012) Defining a new role of GW182 in maintaining miRNA stability. EMBO Rep, 13, 1102-1108.
Patel, R.S., Jakymiw, A., Yao, B., Pauley, B.A., Carcamo, W.C., Katz, J., Cheng, J.Q. and Chan, E.K. # (2011) High resolution of microRNA signatures in whole human saliva. Arch Oral Biol, 56, 1506-1513.
Yao, B. * (co-first author), Li, S.*, Jung, H.M., Lian, S.L., Abadal, G.X., Han, F., Fritzler, M.J., and Chan, E.K. # (2011) Divergent GW182 functional domains in the regulation of translational silencing. Nucleic Acids Res, 39, 2534-2547.
Yao, B., Li, S., Lian, S.L., Fritzler, M.J. and Chan, E.K. # (2011) Mapping of Ago2-GW182 functional interactions. Methods Mol Biol, 725, 45-62.
Carcamo, W.C., Satoh, M., Kasahara, H., Terada, N., Hamazaki, T., Chan, J.Y., Yao, B., Tamayo, S., Covini, G., von Muhlen, C.A. and Chan, E.K. # (2011) Induction of cytoplasmic rods and rings structures by inhibition of the CTP and GTP synthetic pathway in mammalian cells. PLoS One, 6, e29690.
Jin, B., Yao, B., Li, J.L., Fields, C.R., Delmas, A.L., Liu, C., and Robertson, K.D. # (2009) DNMT1 and DNMT3B modulate distinct polycomb-mediated histone modifications in colon cancer. Cancer Res, 69, 7412-7421.
Qiu, J., Ai, L., Ramachandran, C., Yao, B., Gopalakrishnan, S., Fields, C.R., Delmas, A.L., Dyer, L.M., Melnick, S.J., Yachnis, A.T., Schwartz, P.H., Fine, H.A., Brown, K.D. and Robertson, K.D. # (2008) Invasion suppressor cystatin E/M (CST6): high-level cell type-specific expression in normal brain and epigenetic silencing in gliomas. Lab Invest, 88, 910-925.
Zhang, Y., Lin, N., Carroll, P.M., Chan, G., Guan, B., Xiao, H., Yao, B., Wu, S.S. and Zhou, L. # (2008) Epigenetic Blocking of an Enhancer Region Controls Irradiation-Induced Proapoptotic Gene Expression in Drosophila Embryos. Dev Cell, 14, 481-493.
Selected Review and Book Chapters
Martinez-Feduchi, P., Jin, P. and Yao, B. # (Corresponding author, Lead Contact) (2024) Epigenetic modifications of DNA and RNA in Alzheimer's disease. Front Mol Neurosci, 17, 1398026.
Westover, K.R., Jin, P. # and Yao, B. # (Corresponding author, Lead Contact) (2024) Bridging the gap: R-loop mediated genomic instability and its implications in neurological diseases. Epigenomics, 16, 589-608.
Kuehner, J.N., Bruggeman, E.C., Wen, Z. and Yao, B # (Corresponding author, Lead Contact). (2019) Epigenetic Regulations in Neuropsychiatric Disorders. Front Genet, 10, 268.
Kuehner, J.N. and Yao, B. # (corresponding author) (2019) The Dynamic Partnership of Polycomb and Trithorax in Brain Development and Diseases. Epigenomes, 3, 17.
Bruggeman, E.C. and Yao, B. # (2019) DNA Methylation in Neuronal Development and Disease. RNA Technologies. Springer International Publishing, pp. 103-140.
Yao, B., Christian, K.M., He, C., Jin, P., Ming, G.L. and Song, H. (2016) Epigenetic mechanisms in neurogenesis. Nat Rev Neurosci, 17, 537-549.
Yao, B. and Jin, P. (2014) Unlocking epigenetic codes in neurogenesis. Genes Dev, 28, 1253-1271.
Yao, B., Li, S. and Chan, E.K. (2013) Function of GW182 and GW bodies in siRNA and miRNA pathways. Adv Exp Med Biol, 768, 71-96.
Yao, B., Li, S., Lian, S.L., Fritzler, M.J. and Chan, E.K. (2011) Mapping of Ago2-GW182 functional interactions. Methods Mol Biol, 725, 45-62.
Please check my full publications from Google Scholar here.