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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.
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