杨禹丞 - 复旦大学 - 类脑智能科学与技术研究院

个人简介

杨禹丞于清华大学获得生物信息学博士学位，在耶鲁大学进行博士后研究。主要从事利用高通量功能基因组学测序数据的计算基因组学研究，致力于通过大数据整合挖掘以及数据库构建等手段研究基因表达调控机制，及其在大脑发育与疾病过程中的作用。近年来以第一作者和通讯作者（含共同）在Cell、Cell Research、Nucleic Acids Research、Genome Medicine、Briefings in Bioinformatics等期刊发表多篇论文。发表研究论文曾入选2021年度“中国生物信息学十大进展”。主持或参与上海市自然科学面上项目、上海市重大科技专项、科技部重点研发计划等项目。

研究领域

I work in the area of bioinformatics and computational genomics. My research focuses on applying computational and statistical methods to uncover the underlying principles of gene regulatory networks, and improve our understanding on the genotype-phenotype relationship in complex biological systems and/or disease context. I am particularly interested in interpreting the functions of non-coding genome, and how the genetic variation in the non-coding regions can result in brain disorders and other human diseases.

近期论文

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STAB2: an updated spatio-temporal cell atlas of the human and mouse brain YT Yang*, Z Gan*, J Zhang*, X Zhao, Y Yang, S Han, W Wu, X-M Zhao. (2024) Nucleic Acids Research 52(D1), D1033-D1041. An augmented Mendelian randomization approach provides causality of brain imaging features on complex traits in a single biobank-scale dataset A Yang*, YT Yang, X-M Zhao. (2023) PLoS Genetics 19(12), e1011112. Prioritizing genes associated with brain disorders by leveraging enhancer-promoter interactions in diverse neural cells and tissues X Zhao*, L Song*, A Yang, Z Zhang, J Zhang, YT Yang, X-M Zhao. (2023) Genome Medicine 15(1), 56. Constructing a full, multiple-layer interactome for SARS-CoV-2 in the context of lung disease: Linking the virus with human genes and microbes S Lou*, M Yang*, T Li, W Zhao, H Cevasco, YT Yang, M Gerstein. (2023) PLoS Computational Biology 19(7), e1011222. The EN-TEx resource of multi-tissue personal epigenomes and variant-impact models J Rozowsky*, J Gao*, B Borsari*, YT Yang*, T Galeev*, G Gursoy*, CB Epstein*, K Xiong*, J Xu*, T Li*, J Liu*, K Yu, A Berthel, Z Chen, F Navarro, MS Sun, J Wright, J Chang, CJF Cameron, N Shoresh, E Gaskell, J Drenkow, J Adrian, S Aganezov, F Aguet, G Balderrama-Gutierrez, S Banskota, GB Corona, S Chee, SB Chhetri, G Conte C Martins, C Danyko, CA Davis, D Farid, NP Farrell, I Gabdank, Y Gofin, DU Gorkin, M Gu, V Hecht, BC Hitz, R Issner, Y Jiang, M Kirsche, X Kong, BR Lam, S Li, B Li, X Li, KZ Lin, R Luo, M Mackiewicz, R Meng, JE Moore, J Mudge, N Nelson, C Nusbaum, I Popov, HE Pratt, Y Qiu, S Ramakrishnan, J Raymond, L Salichos, A Scavelli, JM Schreiber, FJ Sedlazeck, LH See, RM Sherman, X Shi, M Shi, CA Sloan, JS Strattan, Z Tan, FY Tanaka, A Vlasova, J Wang, J Werner, B Williams, M Xu, C Yan, L Yu, C Zaleski, J Zhang, K Ardlie, JM Cherry, EM Mendenhall, WS Noble, Z Weng, ME Levine, A Dobin, B Wold, A Mortazavi, B Ren, J Gillis, RM Myers, MP Snyder, J Choudhary, A Milosavljevic, MC Schatz, BE Bernstein, R Guigó, TR Gingeras, M Gerstein. (2023) Cell 186(7), 1493-1511. Deciphering the genetic architecture of human brain structure and function: a brief survey on recent advances of neuroimaging genomics X Zhao*, A Yang*, Z-C Zhang, YT Yang, X-M Zhao. (2023) Briefings in Bioinformatics 24(2), bbad060. GENCODE: reference annotation for the human and mouse genomes in 2023 A Frankish, S Carbonell-Sala, M Diekhans, I Jungreis, JE Loveland, JM Mudge, C Sisu, JC Wright, C Arnan, I Barnes, A Banerjee, R Bennett, A Berry, A Bignell, C Boix, F Calvet, D Cerdán-Vélez, F Cunningham, C Davidson, S Donaldson, C Dursun, R Fatima, S Giorgetti, CG Giron, JM Gonzalez, M Hardy, P W Harrison, T Hourlier, Z Hollis, T Hunt, B James, Y Jiang, R Johnson, M Kay, J Lagarde, FJ Martin, LM Gómez, S Nair, P Ni, F Pozo, V Ramalingam, M Ruffier, BM Schmitt, JM Schreiber, E Steed, M-M Suner, D Sumathipala, I Sycheva, B Uszczynska-Ratajczak, E Wass, YT Yang, A Yates, Z Zafrulla, JS Choudhary, M Gerstein, R Guigo, TJP Hubbard, M Kellis, A Kundaje, B Paten, ML Tress, P Flicek. (2023) Nucleic Acids Research 51(D1), D942-D949. Cellular transcriptional alterations of peripheral blood in Alzheimer’s disease L Song, YT Yang, Q Guo, ZIB Consortium, X-M Zhao. (2022) BMC Medicine 20(1), 266. Standardized annotation of translated open reading frames JM Mudge*, J Ruiz-Orera*, JR Prensner*, MA Brunet, F Calvet, I Jungreis, JM Gonzalez, M Magrane, TF Martinez, JF Schulz, YT Yang, MM Albà, JL Aspden, PV Baranov, AA Bazzini, E Bruford, MJ Martin, L Calviello, A-R Carvunis, J Chen, JP Couso, EW Deutsch, P Flicek, A Frankish, M Gerstein, N Hubner, NT Ingolia, M Kellis, G Menschaert, RL Moritz, U Ohler, X Roucou, A Saghatelian, JS Weissman, S van Heesch. (2022) Nature Biotechnology 40(7), 994-1000. POSTAR3: an updated platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins W Zhao*, S Zhang*, Y Zhu, X Xi, P Bao, Z Ma, TH Kapral, S Chen, B Zagrovic, YT Yang, ZJ Lu. (2022) Nucleic Acids Research 50(D1), D287-D294. Do Students With Different Majors Have Different Personality Traits? Evidence From Two Chinese Agricultural Universities X Wen*, Y Zhao*, YT Yang, S Wang, X Cao. (2021) Frontiers in Psychology 12, 641333. Predicting dynamic cellular protein-RNA interactions by deep learning using in vivo RNA structure L Sun*, K Xu*, W Huang*, YT Yang*, P Li, L Tang, T Xiong, QC Zhang. (2021) Cell Research 31(5), 495-516. A Frankish, M Diekhans, I Jungreis, J Lagarde, JE Loveland, JM Mudge, C Sisu, JC Wright, J Armstrong, I Barnes, A Berry, A Bignell, C Boix, SC Sala, F Cunningham, TD Domenico, S Donaldson, IT Fiddes, CG Girón, JM Gonzalez, T Grego, M Hardy, T Hourlier, KL Howe, T Hunt, OG Izuogu, R Johnson, FJ Martin, L Martínez, S Mohanan, P Muir, FCP Navarro, A Parker, B Pei, F Pozo, FC Riera, M Ruffier, BM Schmitt, E Stapleton, MM Suner, I Sycheva, B Uszczynska-Ratajczak, MY Wolf, J Xu, YT Yang, A Yates, D Zerbino, Y Zhang, JS Choudhary, M Gerstein, R Guigó, TJP Hubbard, M Kellis, B Paten, ML Tress, P Flicek. (2021) Nucleic Acids Research 49(D1), D916-D923. Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks B Li, YT Yang, JA Capra, MB Gerstein. (2020) PLoS Computational Biology 16(11), e1008291. An integrative ENCODE resource for cancer genomics J Zhang*, D Lee*, V Dhiman*, P Jiang*, J Xu*, P McGillivray*, H Yang*, J Liu, W Meyerson, D Clarke, M Gu, S Li, S Lou, J Xu, L Lochovsky, M Ung, L Ma, S Yu, Q Cao, A Harmanci, KK Yan, A Sethi, G Gursoy, MR Schoenberg, J Rozowsky, J Warrell, P Emani, YT Yang, T Galeev, X Kong, S Liu, X Li, J Krishnan, Y Feng, JC Rivera-Mulia, J Adrian, JR Broach, M Bolt, J Moran, D Fitzgerald, V Dileep, T Liu, S Mei, T Sasaki, C Trevilla-Garcia, S Wang, Y Wang, C Zang, D Wang, R Klein, M Snyder, DM Gilbert, K Yip, C Cheng, F Yue, XS Liu, K White, M Gerstein. (2020) Nature Communications 11(1), 3696. Building a Hybrid Physical-Statistical Classifier for Predicting the Effect of Variants Related to Protein-Drug Interactions B Wang*, C Yan*, S Lou, P Emani, B Li, M Xu, X Kong, W Meyerson, YT Yang, D Lee, M Gerstein. (2019) Structure 27(9), 1469-1481. POSTAR2: deciphering the post-transcriptional regulatory logics Y Zhu*, G Xu*, YT Yang*, Z Xu, X Chen, B Shi, D Xie, ZJ Lu, P Wang. (2019) Nucleic Acids Research 47(D1), D203-D211. Comprehensive functional genomic resource and integrative model for the human brain D Wang*, S Liu*, J Warrell*, H Won*, X Shi*, FCP Navarro*, D Clarke*, M Gu*, P Emani*, YT Yang, M Xu, MJ Gandal, S Lou, J Zhang, JJ Park, C Yan, SK Rhie, K Manakongtreecheep, H Zhou, A Nathan, M Peters, E Mattei, D Fitzgerald, T Brunetti, J Moore, Y Jiang, K Girdhar, GE Hoffman, S Kalayci, ZH Gu?mu??, GE Crawford, PsychENCODE Consortium, P Roussos, S Akbarian, AE Jaffe, KP White, Z Weng, N Sestan, DH Geschwind, JA Knowles, MB Gerstein. (2018) Science 362(6420), eaat8464. Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder MJ Gandal, P Zhang, E Hadjimichael, RL Walker, C Chen, S Liu, H Won, H van Bakel, M Varghese, Y Wang, AW Shieh, J Haney, S Parhami, J Belmont, M Kim, PM Losada, Z Khan, J Mleczko, Y Xia, R Dai, D Wang, YT Yang, M Xu, K Fish, PR Hof, J Warrell, D Fitzgerald, K White, AE Jaffe, PsychENCODE Consortium, MA Peters, M Gerstein, C Liu, LM Iakoucheva, D Pinto, DH Geschwind. (2018) Science 362(6420), eaat8127. Investigation of RNA-RNA interactions using the RISE database Y Ju*, J Gong*, YT Yang, QC Zhang. (2018) Current Protocols in Bioinformatics 64(1), e58. RISE: a database of RNA Interactome from Sequencing Experiments J Gong*, D Shao*, K Xu, Z Lu, ZJ Lu, YT Yang, QC Zhang. (2018) Nucleic Acids Research 46(D1), D194-D201. Identification of high-confidence RNA regulatory elements by combinatorial classification of RNA-protein binding sites YE Li*, M Xiao*, B Shi*, YT Yang, D Wang, F Wang, M Marcia, ZJ Lu. (2017) Genome Biology 18(1), 169. Recurrently deregulated lncRNAs in hepatocellular carcinoma Y Yang*, L Chen*, J Gu*, H Zhang*, J Yuan, Q Lian, G Lv, S Wang, Y Wu, YT Yang, D Wang, Y Liu, J Tang, G Luo, Y Li, L Hu, X Sun, D Wang, M Guo, Q Xi, J Xi, H Wang, MQ Zhang, ZJ Lu. (2017) Nature Communications 8, 14421. Large-scale mapping of mammalian transcriptomes identifies conserved genes associated with different cell differentiation states Y Yang*, YT Yang*, J Yuan, ZJ Lu, JJ Li. (2017) Nucleic Acids Research 45(4), 1657-1672. Comprehensive analysis of long non-coding RNAs highlights their spatio-temporal expression patterns and evolutional conservation in Sus scrofa Z Tang*, Y Wu*, Y Yang*, YT Yang, Z Wang, J Yuan, Y Yang, C Hua, X Fan, G Niu, Y Zhang, ZJ Lu, K Li. (2017) Scientific Reports 7, 43166. POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins B Hu*, YT Yang*, Y Huang, Y Zhu, ZJ Lu. (2017) Nucleic Acids Research 45(D1), D104-D114. CCG: an integrative resource of cancer protein-coding and long noncoding RNA genes M Liu*, YT Yang*, G Xu, C Tan, ZJ Lu. (2016) Discovery Medicine 22(123), 351-359. A common set of distinct features that characterize noncoding RNAs across multiple species L Hu, C Di, M Kai, YT Yang, Y Li, Y Qiu, X Hu, KY Yip, MQ Zhang, ZJ Lu. (2015) Nucleic Acids Research 43(1), 104-114. CLIPdb: a CLIP-seq database for protein-RNA interactions YT Yang*, C Di*, B Hu*, M Zhou, Y Liu, N Song, Y Li, J Umetsu, ZJ Lu. (2015) BMC Genomics 16(1), 51-58. Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae Y-C Yang, J Umetsu, ZJ Lu. (2014) Science China Life Sciences 57(1), 22-35. Genomic study of polyhydroxyalkanoates producing Aeromonas hydrophila 4AK4 X Gao, J Jian, W-J Li, Y-C Yang, X-W Shen, Z-R Sun, Q Wu, G-Q Chen. (2013) Applied Microbiology and Biotechnology 97(20), 9099-9109. Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae MA Freeberg*, T Han*, JJ Moresco, A Kong, Y-C Yang, ZJ Lu, JR Yates, JK Kim. (2013) Genome Biology 14(2), R13.