Yucheng T. Yang, Ph.D.  

Institute of Science and Technology for Brain-inspired Intelligence

MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence

Fudan University

Email: yangyy [at] fudan.edu.cn

Office: Room 2320, East Main Building, Guanghua Building, Handan Campus, Fudan University



About

I received my Ph.D. degree in Bioinformatics from Tsinghua University in 2016 (Advisor: Prof. Zhi John Lu), and M.S. degree in statistics from University of California, Los Angeles in 2017 (Advisor: Prof. Jingyi Jessica Li). Then I did my postdoc training at Yale University (Advisor: Prof. Mark B. Gerstein). Currently, I'm an Assistant Professor at the Institute of Science and Technology for Brain-inspired Intelligence (ISTBI), Fudan University.



Research

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.



Publication

Full publication list: Google Scholar ; ResearchGate

author*: co-first author, equal contribution

author: corresponding author


-- 2024 --

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.
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Database

-- 2023 --

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.
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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.
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Supplementary website

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.
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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.
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Supplementary website

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.
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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.
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Database

-- 2022 --

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.
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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.
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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.
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Database

-- 2021 --

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.
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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.
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Supplementary website

GENCODE 2021
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.
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-- 2020 --

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.
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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.
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-- 2019 --

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.
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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.
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-- 2018 --

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 Gümüş, 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.
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Supplementary website

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.
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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.
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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.
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Database

-- 2017 --

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.
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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.
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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.
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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.
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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.
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-- 2016 --

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.
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-- 2015 --

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.
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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.
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-- 2014 --

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.
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-- 2013 --

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.
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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.
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Teaching

Introduction to Computational Genomics (STBI737010)
2021 Fall

Introduction to Bioinformatics (STBI820002, As Co-Instructor)
2023 Spring, 2022 Spring, 2021 Spring