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Efficient Generation of Protein Pockets with PocketGen.
Zhang Z, Shen WX, Liu Q, Zitnik M. Zhang Z, et al. Among authors: zitnik m. bioRxiv [Preprint]. 2024 Sep 23:2024.02.25.581968. doi: 10.1101/2024.02.25.581968. bioRxiv. 2024. PMID: 38464121 Free PMC article. Preprint.
Identification of druggable host targets needed for SARS-CoV-2 infection by combined pharmacological evaluation and cellular network directed prioritization both in vitro and in vivo.
Patten JJ, Keiser PT, Gysi D, Menichetti G, Mori H, Donahue CJ, Gan X, do Valle I, Geoghegan-Barek K, Anantpadma M, Boytz R, Berrigan JL, Hulsey-Stubbs S, Ayazika T, O'Leary C, Jalloh S, Wagner F, Ayehunie S, Elledge SJ, Anderson D, Loscalzo J, Zitnik M, Gummuluru S, Namchuk MN, Barabási AL, Davey RA. Patten JJ, et al. Among authors: zitnik m. bioRxiv [Preprint]. 2022 Feb 1:2021.04.20.440626. doi: 10.1101/2021.04.20.440626. bioRxiv. 2022. Update in: iScience. 2022 Sep 16;25(9):104925. doi: 10.1016/j.isci.2022.104925. PMID: 33907750 Free PMC article. Updated. Preprint.
How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities.
Bunne C, Roohani Y, Rosen Y, Gupta A, Zhang X, Roed M, Alexandrov T, AlQuraishi M, Brennan P, Burkhardt DB, Califano A, Cool J, Dernburg AF, Ewing K, Fox EB, Haury M, Herr AE, Horvitz E, Hsu PD, Jain V, Johnson GR, Kalil T, Kelley DR, Kelley SO, Kreshuk A, Mitchison T, Otte S, Shendure J, Sofroniew NJ, Theis F, Theodoris CV, Upadhyayula S, Valer M, Wang B, Xing E, Yeung-Levy S, Zitnik M, Karaletsos T, Regev A, Lundberg E, Leskovec J, Quake SR. Bunne C, et al. Among authors: zitnik m. ArXiv [Preprint]. 2024 Sep 18:arXiv:2409.11654v1. ArXiv. 2024. PMID: 39398201 Free PMC article. Preprint.
A foundation model for clinician-centered drug repurposing.
Huang K, Chandak P, Wang Q, Havaldar S, Vaid A, Leskovec J, Nadkarni GN, Glicksberg BS, Gehlenborg N, Zitnik M. Huang K, et al. Among authors: zitnik m. Nat Med. 2024 Sep 25. doi: 10.1038/s41591-024-03233-x. Online ahead of print. Nat Med. 2024. PMID: 39322717
Current and future directions in network biology.
Zitnik M, Li MM, Wells A, Glass K, Morselli Gysi D, Krishnan A, Murali TM, Radivojac P, Roy S, Baudot A, Bozdag S, Chen DZ, Cowen L, Devkota K, Gitter A, Gosline SJC, Gu P, Guzzi PH, Huang H, Jiang M, Kesimoglu ZN, Koyuturk M, Ma J, Pico AR, Pržulj N, Przytycka TM, Raphael BJ, Ritz A, Sharan R, Shen Y, Singh M, Slonim DK, Tong H, Yang XH, Yoon BJ, Yu H, Milenković T. Zitnik M, et al. Bioinform Adv. 2024 Aug 14;4(1):vbae099. doi: 10.1093/bioadv/vbae099. eCollection 2024. Bioinform Adv. 2024. PMID: 39143982 Free PMC article.
Contextual AI models for single-cell protein biology.
Li MM, Huang Y, Sumathipala M, Liang MQ, Valdeolivas A, Ananthakrishnan AN, Liao K, Marbach D, Zitnik M. Li MM, et al. Among authors: zitnik m. Nat Methods. 2024 Aug;21(8):1546-1557. doi: 10.1038/s41592-024-02341-3. Epub 2024 Jul 22. Nat Methods. 2024. PMID: 39039335 Free PMC article.
TDC-2: Multimodal Foundation for Therapeutic Science.
Velez-Arce A, Huang K, Li MM, Lin X, Gao W, Fu T, Kellis M, Pentelute BL, Zitnik M. Velez-Arce A, et al. Among authors: zitnik m. bioRxiv [Preprint]. 2024 Jun 21:2024.06.12.598655. doi: 10.1101/2024.06.12.598655. bioRxiv. 2024. PMID: 38948789 Free PMC article. Preprint.
113 results