[1] Bin Huang, Tingwen Fan, Kaiyue Wang, 张海仓, Chungong Yu, Shuyu Nie, Yangshuo Qi, Wei-Mou Zheng, Jian Han, Zheng Fan, Shiwei Sun, Sheng Ye, Huaiyi Yang, Dongbo Bu. Accurate and efficient protein sequence design through learning concise local environment of residues. Bioinformatics[J]. 2023, [2] 张海仓, Michelle S. Xu, CHUNG Wendy Kay, SHEN, YUFENG. Predicting functional effect of missense variants using graph attention neural networks. Nature Machine Intelligence[J]. 2022, https://doi.org/10.1038/s42256-022-00561-w.
[3] Xueya Zhou, Pamela Feliciano, Chang Shu, Tianyun Wang, Irina Astrovskaya, Jacob B Hall, Joseph U Obiajulu, Jessica R Wright, Shwetha C Murali, Simon Xuming Xu, Leo Brueggeman, Taylor R Thomas, Olena Marchenko, Christopher Fleisch, Sarah D Barns, LeeAnne Green Snyder, Bing Han, Timothy S Chang, Tychele N Turner, William T Harvey, Andrew Nishida, Brian J ORoak, Daniel H Geschwind, Jacob J Michaelson, Natalia Volfovsky, Evan E Eichler, Yufeng Shen, Wendy K Chung. Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes. NATURE GENETICS[J]. 2022, 54(9): 1305-1319, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9470534/.
[4] Bi, Bei, Wang, Yaojun, Zhang, Haicang, Gao, Yang. Microblog-HAN: A micro-blog rumor detection model based on heterogeneous graph attention network. PLOS ONE[J]. 2022, 17(4): http://dx.doi.org/10.1371/journal.pone.0266598.
[5] Hongjian Qi, Haicang Zhang, Yige Zhao, Chen Chen, John J Long, Wendy K Chung, Yongtao Guan, Yufeng Shen. MVP predicts the pathogenicity of missense variants by deep learning. NATURE COMMUNICATIONS[J]. 2021, 12(1): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7820281/.
[6] Kong, Lupeng, Ju, Fusong, Zhang, Haicang, Sun, Shiwei, Bu, Dongbo. FALCON2: a web server for high-quality prediction of protein tertiary structures. BMC BIOINFORMATICS[J]. 2021, 22(1): http://dx.doi.org/10.1186/s12859-021-04353-8.
[7] Zhang, Haicang, Shen, Yufeng. Template-based prediction of protein structure with deep learning. BMC GENOMICS[J]. 2020, 21(Suppl 11): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7771081/.
[8] Siying Chen, xueya zhou, Eve Byington, Samuel L. Bruce, 张海仓, SHEN, YUFENG. Dissecting Autism Genetic Risk Using Single-cell RNA-seq Data. biorxivnull. 2020, https://doi.org/10.1101/2020.06.15.153031.
[9] Feliciano, Pamela, Zhou, Xueya, Astrovskaya, Irina, Turner, Tychele N, Wang, Tianyun, Brueggeman, Leo, Barnard, Rebecca, Hsieh, Alexander, Snyder, LeeAnne Green, Muzny, Donna M, Sabo, Aniko, Gibbs, Richard A, Eichler, Evan E, ORoak, Brian J, Michaelson, Jacob J, Volfovsky, Natalia, Shen, Yufeng, Chung, Wendy K, Abbeduto, Leonard, Acampado, John, Ace, Andrea J, Albright, Charles, Alessandri, Michael, Amaral, David G, Amatya, Alpha, Annett, Robert D, Arriaga, Ivette, Bahl, Ethan, Balasubramanian, Adithya, Bardett, Nicole, Bashar, Asif, Beaudet, Arthur, Beeson, Landon, Bernier, Raphael A, BerryKravis, Elizabeth, Booker, Stephanie, Brewster, Stephanie J, Brooks, Elizabeth, Butler, Martin E, Butter, Eric M, Callahan, Kristen, Camba, Alexies, Carpenter, Sarah, Carriero, Nicholas, Cartner, Lindsey A, Chatha, Ahmad S, Chin, Wubin, Clark, Renee D, Cohen, Cheryl, Courchesne, Eric, Cubells, Joseph F, Currin, Mary Hannah, Daniels, Amy M, DeMarco, Lindsey, Dennis, Megan Y, Dichter, Gabriel S, Ding, Yan, Huyen Dinh, Doan, Ryan, Doddapaneni, HarshaVardhan, Eldred, Sara, Eng, Christine, Erickson, Craig A, Esler, Amy, Fatemi, Ali, Fischer, Gregory J, Fisk, Ian, Fombonne, Eric J, Fox, Emily A, Francis, Sunday, Friedman, Sandra L, Ganesan, Swami, Garrett, Michael, Gazestani, Vahid, Geisheker, Madeleine R, Gerdts, Jennifer A, Geschwind, Daniel H, GoinKochel, Robin P, Griswold, Anthony J, Grosvenor, Luke P, Gruber, Angela J, Gulsrud, Amanda C, Gunderson, Jaclyn, Gutierrez, Anibal, Hale, Melissa N, Haley, Monica, Hall, Jacob B, Hamer, Kira E, Han, Bing, Hanna, Nathan, Harkins, Christina, Harris, Nina, Hauf, Brenda, Hayes, Caitlin, Hepburn, Susan L, Herbert, Lynette M, Heyman, Michelle, Phillips, Brittani A, Horner, Susannah, Hu, Jianhong, HuangStorms, Lark Y, Hutter, Hanna, Istephanous, Dalia, Jacob, Suma, Jensen, William, Jones, Mark, Jordy, Michelle, Juarez, A Pablo, Kanne, Stephen, Kaplan, Hannah E, Kent, Matt, Kitaygorodsky, Alex, Koomar, Tanner, Korchina, Viktoriya, Krentz, Anthony D, Schneider, Hoa Lam, Lamarche, Elena, Landa, Rebecca J, Lash, Alex E, Law, J Kiely, Lawson, Noah, Layman, Kevin, Lechniak, Holly, Lee, Sandra, Lee, Soo J, Coury, Daniel Lee, Martin, Christa Lese, Li, Deana, Li, Hai, Lillie, Natasha, Liu, Xiuping, Lord, Catherine, Mallardi, Malcolm D, Manning, Patricia, Manoharan, Julie, Marini, Richard, Marzano, Gabriela, Mason, Andrew, Matthews, Emily T, McCracken, James T, McKenzie, Alexander P, Momin, Zeineen, Morrier, Michael J, Murali, Shwetha, Myers, Vincent J, Neely, Jason, Nessner, Caitlin, Nicholson, Amy, OBrien, Kaela, OConnor, Eirene, OchoaLubinoff, Cesar, Orobio, Jessica, Ousley, Opal Y, Pacheco, Lillian D, Pandey, Juhi, Paolicelli, Anna Marie, Pawlowski, Katherine G, Pierce, Karen L, Piven, Joseph, Plate, Samantha, Popp, Marc, Pramparo, Tiziano, Prock, Lisa M, Qi, Hongjian, Qiu, Shanping, Rachubinski, Angela L, Rajbhandari, Kshitij, Rana, Rishiraj, Remington, Rick, Rice, Catherine E, Rigby, Chris, Robertson, Beverly E, Roeder, Katherine, Rosenberg, Cordelia R, RussoPonsaran, Nicole, Ruzzo, Elizabeth, Sahin, Mustafa, Salomatov, Andrei, Sandhu, Sophia, Santangelo, Susan, Sarver, Dustin E, Scherr, Jessica, Schultz, Robert T, Schweers, Kathryn A, Shah, Swapnil, Shaikh, Tamim, Shocklee, Amanda D, Simon, Laura, Simon, Andrea R, Singh, Vini, Skinner, Steve, Smith, Kaitlin, Smith, Christopher J, Soorya, Latha, V, Soucy, Aubrie, Stephens, Alexandra N, Stock, Colleen M, Sutcliffe, James S, Swanson, Amy, Tafolla, Maira, Takahashi, Nicole, Thomas, Taylor, Thomas, Carrie, Thompson, Samantha, Tjernagel, Jennifer, Van Metre, Bonnie, VeenstraVanderweele, Jeremy, Vernoia, Brianna M, Wallace, Jermel, Walston, Corrie H, Wang, Jiayao, Warren, Zachary, Wasserburg, Lucy, White, Loran Casey, White, Sabrina, Wodka, Ericka L, Xu, Simon, Yang, Wha S, Yinger, Meredith, Yu, Timothy, Zang, Lan, Zaydens, Hana, Zhang, Haicang, Zhao, Haoquan, SPARK Consortium. Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes. NPJ GENOMIC MEDICINE[J]. 2019, 4(1): http://dx.doi.org/10.1038/s41525-019-0093-8.
[10] Zhang, Haicang, Zhang, Qi, Ju, Fusong, Zhu, Jianwei, Gao, Yujuan, Xie, Ziwei, Deng, Minghua, Sun, Shiwei, Zheng, WeiMou, Bu, Dongbo. Predicting protein inter-residue contacts using composite likelihood maximization and deep learning. BMC BIOINFORMATICS[J]. 2019, 20(1): http://dx.doi.org/10.1186/s12859-019-3051-7.
[11] Chao Wang, Yi Wei, Haicang Zhang, Lupeng Kong, Shiwei Sun, WeiMou Zheng, Dongbo Bu. Constructing effective energy functions for protein structure prediction through broadening attraction-basin and reverse Monte Carlo sampling. BMC BIOINFORMATICS[J]. 2019, 20(S3): 99-108, https://doaj.org/article/6ed28e082ad847f19e2703f86cd71abd.
[12] Zhu, Jianwei, Zhang, Haicang, Li, Shuai Cheng, Wang, Chao, Kong, Lupeng, Sun, Shiwei, Zheng, WeiMou, Bu, Dongbo. Improving protein fold recognition by extracting fold-specific features from predicted residue-residue contacts. BIOINFORMATICS[J]. 2017, 33(23): 3749-3757, http://dx.doi.org/10.1093/bioinformatics/btx514.
[13] Gong, Haie, Zhang, Haicang, Zhu, Jianwei, Wang, Chao, Sun, Shiwei, Zheng, WeiMou, Bu, Dongbo. Improving prediction of burial state of residues by exploiting correlation among residues. BMC BIOINFORMATICS[J]. 2017, 18(Suppl 3): http://dx.doi.org/10.1186/s12859-017-1475-5.
[14] Zhang, Haicang, Gao, Yujuan, Deng, Minghua, Wang, Chao, Zhu, Jianwei, Li, Shuai Cheng, Zheng, WeiMou, Bu, Dongbo. Improving residue-residue contact prediction via low-rank and sparse decomposition of residue correlation matrix. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS[J]. 2016, 472(1): 217-222, http://ir.itp.ac.cn/handle/311006/23180.
[15] Huang, Chunlin, Liu, Xingwu, Sun, Shiwei, Li, Shuai Cheng, Deng, Minghua, He, Guangxue, Zhang, Haicang, Wang, Chao, Zhou, Yang, Zhao, Yanlin, Bu, Dongbo. Insights into the transmission of respiratory infectious diseases through empirical human contact networks. SCIENTIFIC REPORTS[J]. 2016, 6: http://ir.itp.ac.cn/handle/311006/23184.
[16] Wang, Chao, Zhang, Haicang, Zheng, WeiMou, Xu, Dong, Zhu, Jianwei, Wang, Bing, Ning, Kang, Sun, Shiwei, Li, Shuai Cheng, Bu, Dongbo. FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition. BIOINFORMATICS[J]. 2016, 32(3): 462-464, http://ir.itp.ac.cn/handle/311006/23139.
[17] Nie, Lei, Liu, Jingjie, Zhang, Haicang, Xu, Zhiwei. On the inapproximability of minimizing cascading failures under the deterministic threshold model. INFORMATION PROCESSING LETTERS[J]. 2014, 114(1-2): 1-4, http://dx.doi.org/10.1016/j.ipl.2013.10.007.