A map of cis-regulatory modules and constituent transcription factor binding sites in 80% of the mouse genome von Ni, Pengyu, Wilson, David, Su, Zhengchang

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Accurate prediction of functional states of cis-regulatory modules reveals common epigenetic rules in humans and mice von Ni, Pengyu, Moe, Joshua, Su, Zhengchang

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Deciphering epigenomic code for cell differentiation using deep learning von Ni, Pengyu, Su, Zhengchang

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Validated Negative Regions (VNRs) in the VISTA Database might be Truncated Forms of Bona Fide Enhancers von Ni, Pengyu, Wu, Siwen, Su, Zhengchang

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Transcriptional determinism and stochasticity contribute to the complexity of autism-associated SHANK family genes von Lu, Xiaona, Ni, Pengyu, Suarez-Meade, Paola, Ma, Yu, Forrest, Emily Niemitz, Wang, Guilin, Wang, Yi, Quiñones-Hinojosa, Alfredo, Gerstein, Mark, Jiang, Yong-hui

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Prevalent use and evolution of exonic regulatory sequences in the human genome von Chen, Jing, Ni, Pengyu, Wu, Siwen, Niu, Meng, Guo, Jun‐tao, Su, Zhengsheng

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PCRMS: a database of predicted cis-regulatory modules and constituent transcription factor binding sites in genomes von Ni, Pengyu, Su, Zhengchang

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Accurate prediction of cis-regulatory modules reveals a prevalent regulatory genome of humans von Ni, Pengyu, Su, Zhengchang

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Less-is-more: selecting transcription factor binding regions informative for motif inference von Xu, Jinrui, Gao, Jiahao, Ni, Pengyu, Gerstein, Mark

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ProSampler: an ultrafast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery von Li, Yang, Ni, Pengyu, Zhang, Shaoqiang, Li, Guojun, Su, Zhengchang

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Leveraging a large language model to predict protein phase transition: A physical, multiscale, and interpretable approach von Frank, Mor, Ni, Pengyu, Jensen, Matthew, Gerstein, Mark B

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Towards a map of cis-regulatory sequences in the human genome von Niu, Meng, Tabari, Ehsan, Ni, Pengyu, Su, Zhengchang

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Underlying causes for prevalent false positives and false negatives in STARR-seq data von Ni, Pengyu, Wu, Siwen, Su, Zhengchang

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GENCODE: reference annotation for the human and mouse genomes in 2023 von Frankish, Adam, Carbonell-Sala, Sílvia, Diekhans, Mark, Jungreis, Irwin, Loveland, Jane E, Mudge, Jonathan M, Sisu, Cristina, Wright, James C, Arnan, Carme, Barnes, If, Banerjee, Abhimanyu, Bennett, Ruth, Berry, Andrew, Bignell, Alexandra, Boix, Carles, Calvet, Ferriol, Cerdán-Vélez, Daniel, Cunningham, Fiona, Davidson, Claire, Donaldson, Sarah, Dursun, Cagatay, Fatima, Reham, Giorgetti, Stefano, Giron, Carlos Garcıa, Gonzalez, Jose Manuel, Hardy, Matthew, Harrison, Peter W, Hourlier, Thibaut, Hollis, Zoe, Hunt, Toby, James, Benjamin, Jiang, Yunzhe, Johnson, Rory, Kay, Mike, Lagarde, Julien, Martin, Fergal J, Gómez, Laura Martínez, Nair, Surag, Ni, Pengyu, Pozo, Fernando, Ramalingam, Vivek, Ruffier, Magali, Schmitt, Bianca M, Schreiber, Jacob M, Steed, Emily, Suner, Marie-Marthe, Sumathipala, Dulika, Sycheva, Irina, Uszczynska-Ratajczak, Barbara, Wass, Elizabeth, Yang, Yucheng T, Yates, Andrew, Zafrulla, Zahoor, Choudhary, Jyoti S, Gerstein, Mark, Guigo, Roderic, Hubbard, Tim J P, Kellis, Manolis, Kundaje, Anshul, Paten, Benedict, Tress, Michael L, Flicek, Paul

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Single-cell genomics and regulatory networks for 388 human brains von Emani, Prashant S, Liu, Jason J, Clarke, Declan, Jensen, Matthew, Warrell, Jonathan, Gupta, Chirag, Meng, Ran, Lee, Che Yu, Xu, Siwei, Dursun, Cagatay, Lou, Shaoke, Chen, Yuhang, Chu, Zhiyuan, Galeev, Timur, Hwang, Ahyeon, Li, Yunyang, Ni, Pengyu, Zhou, Xiao, Bakken, Trygve E, Bendl, Jaroslav, Bicks, Lucy, Chatterjee, Tanima, Cheng, Lijun, Cheng, Yuyan, Dai, Yi, Duan, Ziheng, Flaherty, Mary, Fullard, John F, Gancz, Michael, Garrido-Martín, Diego, Gaynor-Gillett, Sophia, Grundman, Jennifer, Hawken, Natalie, Henry, Ella, Hoffman, Gabriel E, Huang, Ao, Jiang, Yunzhe, Jin, Ting, Jorstad, Nikolas L, Kawaguchi, Riki, Khullar, Saniya, Liu, Jianyin, Liu, Junhao, Liu, Shuang, Ma, Shaojie, Margolis, Michael, Mazariegos, Samantha, Moore, Jill, Moran, Jennifer R, Nguyen, Eric, Phalke, Nishigandha, Pjanic, Milos, Pratt, Henry, Quintero, Diana, Rajagopalan, Ananya S, Riesenmy, Tiernon R, Shedd, Nicole, Shi, Manman, Spector, Megan, Terwilliger, Rosemarie, Travaglini, Kyle J, Wamsley, Brie, Wang, Gaoyuan, Xia, Yan, Xiao, Shaohua, Yang, Andrew C, Zheng, Suchen, Gandal, Michael J, Lee, Donghoon, Lein, Ed S, Roussos, Panos, Sestan, Nenad, Weng, Zhiping, White, Kevin P, Won, Hyejung, Girgenti, Matthew J, Zhang, Jing, Wang, Daifeng, Geschwind, Daniel, Gerstein, Mark

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GENCODE 2025: reference gene annotation for human and mouse von Mudge, Jonathan M, Carbonell-Sala, Sílvia, Diekhans, Mark, Martinez, Jose Gonzalez, Hunt, Toby, Jungreis, Irwin, Loveland, Jane E, Arnan, Carme, Barnes, If, Bennett, Ruth, Berry, Andrew, Bignell, Alexandra, Cerdán-Vélez, Daniel, Cochran, Kelly, Cortés, Lucas T, Davidson, Claire, Donaldson, Sarah, Dursun, Cagatay, Fatima, Reham, Hardy, Matthew, Hebbar, Prajna, Hollis, Zoe, James, Benjamin T, Jiang, Yunzhe, Johnson, Rory, Kaur, Gazaldeep, Kay, Mike, Mangan, Riley J, Maquedano, Miguel, Gómez, Laura Martínez, Mathlouthi, Nourhen, Merritt, Ryan, Ni, Pengyu, Palumbo, Emilio, Perteghella, Tamara, Pozo, Fernando, Raj, Shriya, Sisu, Cristina, Steed, Emily, Sumathipala, Dulika, Suner, Marie-Marthe, Uszczynska-Ratajczak, Barbara, Wass, Elizabeth, Yang, Yucheng T, Zhang, Dingyao, Finn, Robert D, Gerstein, Mark, Guigó, Roderic, Hubbard, Tim J P, Kellis, Manolis, Kundaje, Anshul, Paten, Benedict, Tress, Michael L, Birney, Ewan, Martin, Fergal J, Frankish, Adam

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The human and non-human primate developmental GTEx projects von Coorens, Tim H. H., Guillaumet-Adkins, Amy, Kovner, Rothem, Linn, Rebecca L., Roberts, Victoria H. J., Sule, Amrita, Van Hoose, Patrick M.

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Influence of Resting Venous Blood Volume Fraction on Dynamic Causal Modeling and System Identifiability von Hu, Zhenghui, Ni, Pengyu, Wan, Qun, Zhang, Yan, Shi, Pengcheng, Lin, Qiang

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ProSampler: an ultra-fast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery von Li, Yang, Ni, Pengyu, Zhang, Shaoqiang, Li, Guojun, Su, Zhengchang

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Quantitative Evaluation of Activation State in Functional Brain Imaging von Hu, Zhenghui, Ni, Pengyu, Liu, Cong, Zhao, Xiaohu, Liu, Huafeng, Shi, Pengcheng

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