Marinka Zitnik

Publication Activity (10 Years)

Years Active: 2021-2024
Publications (10 Years): 48

Top Topics

Artificial Intelligence

Autism Spectrum Disorder

Top Venues

bioRxiv : the preprint server for biology

Scientific data

medRxiv : the preprint server for health sciences

This page only lists publications with an associated author ORCID identifier.

Publications

Guadalupe Gonzalez, Isuru Herath, Kirill Veselkov, Michael Bronstein, Marinka Zitnik
Combinatorial prediction of therapeutic perturbations using causally-inspired neural networks. bioRxiv : the preprint server for biology (2024)
Michelle M Li, Yepeng Huang, Marissa Sumathipala, Man Qing Liang, Alberto Valdeolivas, Ashwin N Ananthakrishnan, Katherine Liao, Daniel Marbach, Marinka Zitnik
Contextual AI models for single-cell protein biology. Nature methods (2024)
Michelle M Li, Yepeng Huang, Marissa Sumathipala, Man Qing Liang, Alberto Valdeolivas, Ashwin N Ananthakrishnan, Katherine Liao, Daniel Marbach, Marinka Zitnik
Contextual AI models for single-cell protein biology. Nature methods 21 (8) (2024)
Alejandro Velez-Arce, Kexin Huang, Michelle M Li, Xiang Lin, Wenhao Gao, Tianfan Fu, Manolis Kellis, Bradley L Pentelute, Marinka Zitnik
TDC-2: Multimodal Foundation for Therapeutic Science. bioRxiv : the preprint server for biology (2024)
Michelle M Li, Yepeng Huang, Marissa Sumathipala, Man Qing Liang, Alberto Valdeolivas, Ashwin N Ananthakrishnan, Katherine Liao, Daniel Marbach, Marinka Zitnik
Contextual AI models for single-cell protein biology. Nature methods (2024)
Guadalupe Gonzalez, Isuru Herath, Kirill Veselkov, Michael Bronstein, Marinka Zitnik
Combinatorial prediction of therapeutic perturbations using causally-inspired neural networks. bioRxiv : the preprint server for biology (2024)
Alejandro Velez-Arce, Kexin Huang, Michelle M Li, Xiang Lin, Wenhao Gao, Tianfan Fu, Manolis Kellis, Bradley L Pentelute, Marinka Zitnik
TDC-2: Multimodal Foundation for Therapeutic Science. bioRxiv : the preprint server for biology (2024)
Yasha Ektefaie, Andrew Shen, Daria Bykova, Maximillian Marin, Marinka Zitnik, Maha Farhat
Evaluating generalizability of artificial intelligence models for molecular datasets. bioRxiv : the preprint server for biology (2024)
Marinka Zitnik, Michelle M Li, Aydin Wells, Kimberly Glass, Deisy Morselli Gysi, Arjun Krishnan, T M Murali, Predrag Radivojac, Sushmita Roy, Anaïs Baudot, Serdar Bozdag, Danny Z Chen, Lenore J Cowen, Kapil Devkota, Anthony Gitter, Sara J C Gosline, Pengfei Gu, Pietro Hiram Guzzi, Heng Huang, Meng Jiang, Ziynet Nesibe Kesimoglu, Mehmet Koyuturk, Jian Ma, Alexander R Pico, Nataša Pržulj, Teresa M Przytycka, Benjamin J Raphael, Tunç Başar Köse, Roded Sharan, Yang Shen, Mona Singh, Donna K Slonim, Hanghang Tong, Xinan Holly Yang, Byung-Jun Yoon, Haiyuan Yu, Tijana Milenković
Current and future directions in network biology. Bioinformatics advances 4 (1) (2024)
Yasha Ektefaie, Andrew Shen, Daria Bykova, Maximillian Marin, Marinka Zitnik, Maha Farhat
Evaluating generalizability of artificial intelligence models for molecular datasets. bioRxiv : the preprint server for biology (2024)
Zaixi Zhang, Wanxiang Shen, Qi Liu, Marinka Zitnik
Efficient Generation of Protein Pockets with PocketGen. bioRxiv : the preprint server for biology (2024)
Alejandro Velez-Arce, Kexin Huang, Michelle M Li, Xiang Lin, Wenhao Gao, Tianfan Fu, Manolis Kellis, Bradley L Pentelute, Marinka Zitnik
TDC-2: Multimodal Foundation for Therapeutic Science. bioRxiv : the preprint server for biology (2024)
Kexin Huang, Payal Chandak, Qianwen Wang, Shreyas Havaldar, Akhil Vaid, Jure Leskovec, Girish Nitin Nadkarni, Benjamin Scott Glicksberg, Nils Gehlenborg, Marinka Zitnik
A foundation model for clinician-centered drug repurposing. medRxiv : the preprint server for health sciences (2024)
Michelle M Li, Yepeng Huang, Marissa Sumathipala, Man Qing Liang, Alberto Valdeolivas, Ashwin N Ananthakrishnan, Katherine Liao, Daniel Marbach, Marinka Zitnik
Contextual AI models for single-cell protein biology. Nature methods 21 (8) (2024)
Zaixi Zhang, Wanxiang Shen, Qi Liu, Marinka Zitnik
PocketGen: Generating Full-Atom Ligand-Binding Protein Pockets. bioRxiv : the preprint server for biology (2024)
Kexin Huang, Payal Chandak, Qianwen Wang, Shreyas Havaldar, Akhil Vaid, Jure Leskovec, Girish Nitin Nadkarni, Benjamin Scott Glicksberg, Nils Gehlenborg, Marinka Zitnik
A foundation model for clinician-centered drug repurposing. medRxiv : the preprint server for health sciences (2024)
Alejandro Velez-Arce, Kexin Huang, Michelle M Li, Xiang Lin, Wenhao Gao, Tianfan Fu, Manolis Kellis, Bradley L Pentelute, Marinka Zitnik
TDC-2: Multimodal Foundation for Therapeutic Science. bioRxiv : the preprint server for biology (2024)
Michelle M Li, Yepeng Huang, Marissa Sumathipala, Man Qing Liang, Alberto Valdeolivas, Ashwin N Ananthakrishnan, Katherine Liao, Daniel Marbach, Marinka Zitnik
Contextual AI models for single-cell protein biology. Nature methods 21 (8) (2024)
Guadalupe Gonzalez, Isuru Herath, Kirill Veselkov, Michael Bronstein, Marinka Zitnik
Combinatorial prediction of therapeutic perturbations using causally-inspired neural networks. bioRxiv : the preprint server for biology (2024)
Yasha Ektefaie, Andrew Shen, Daria Bykova, Maximillian Marin, Marinka Zitnik, Maha Farhat
Evaluating generalizability of artificial intelligence models for molecular datasets. bioRxiv : the preprint server for biology (2024)
Michelle M Li, Yepeng Huang, Marissa Sumathipala, Man Qing Liang, Alberto Valdeolivas, Ashwin N Ananthakrishnan, Katherine Liao, Daniel Marbach, Marinka Zitnik
Contextual AI models for single-cell protein biology. Nature methods 21 (8) (2024)
Yasha Ektefaie, Andrew Shen, Daria Bykova, Maximillian Marin, Marinka Zitnik, Maha Farhat
Evaluating generalizability of artificial intelligence models for molecular datasets. bioRxiv : the preprint server for biology (2024)
Marinka Zitnik, Michelle M Li, Aydin Wells, Kimberly Glass, Deisy Morselli Gysi, Arjun Krishnan, T M Murali, Predrag Radivojac, Sushmita Roy, Anaïs Baudot, Serdar Bozdag, Danny Z Chen, Lenore J Cowen, Kapil Devkota, Anthony Gitter, Sara J C Gosline, Pengfei Gu, Pietro Hiram Guzzi, Heng Huang, Meng Jiang, Ziynet Nesibe Kesimoglu, Mehmet Koyuturk, Jian Ma, Alexander R Pico, Nataša Pržulj, Teresa M Przytycka, Benjamin J Raphael, Tunç Başar Köse, Roded Sharan, Yang Shen, Mona Singh, Donna K Slonim, Hanghang Tong, Xinan Holly Yang, Byung-Jun Yoon, Haiyuan Yu, Tijana Milenković
Current and future directions in network biology. Bioinformatics advances 4 (1) (2024)
Alejandro Velez-Arce, Kexin Huang, Michelle M Li, Xiang Lin, Wenhao Gao, Tianfan Fu, Manolis Kellis, Bradley L Pentelute, Marinka Zitnik
TDC-2: Multimodal Foundation for Therapeutic Science. bioRxiv : the preprint server for biology (2024)
Zaixi Zhang, Wanxiang Shen, Qi Liu, Marinka Zitnik
PocketGen: Generating Full-Atom Ligand-Binding Protein Pockets. bioRxiv : the preprint server for biology (2024)
Zaixi Zhang, Wanxiang Shen, Qi Liu, Marinka Zitnik
Efficient Generation of Protein Pockets with PocketGen. bioRxiv : the preprint server for biology (2024)
Kexin Huang, Payal Chandak, Qianwen Wang, Shreyas Havaldar, Akhil Vaid, Jure Leskovec, Girish Nitin Nadkarni, Benjamin Scott Glicksberg, Nils Gehlenborg, Marinka Zitnik
A foundation model for clinician-centered drug repurposing. medRxiv : the preprint server for health sciences (2024)
Payal Chandak, Kexin Huang, Marinka Zitnik
Building a knowledge graph to enable precision medicine. Scientific data 10 (1) (2023)
Payal Chandak, Kexin Huang, Marinka Zitnik
Building a knowledge graph to enable precision medicine. Scientific data 10 (1) (2023)
Jun Wen, Xiang Zhang, Everett Rush, Vidul A Panickan, Xingyu Li, Tianrun Cai, Doudou Zhou, Yuk-Lam Ho, Lauren Costa, Edmon Begoli, Chuan Hong, J Michael Gaziano, Kelly Cho, Junwei Lu, Katherine P Liao, Marinka Zitnik, Tianxi Cai
Multimodal representation learning for predicting molecule-disease relations. Bioinformatics (Oxford, England) 39 (2) (2023)
Payal Chandak, Kexin Huang, Marinka Zitnik
Building a knowledge graph to enable precision medicine. Scientific data 10 (1) (2023)
Hanchen Wang, Tianfan Fu, Yuanqi Du, Wenhao Gao, Kexin Huang, Ziming Liu, Payal Chandak, Shengchao Liu, Peter Van Katwyk, Andreea Deac, Anima Anandkumar, Karianne Bergen, Carla P Gomes, Shirley Ho, Pushmeet Kohli, Joan Lasenby, Jure Leskovec, Tie-Yan Liu, Arjun Manrai, Debora S Marks, Bharath Ramsundar, Le Song, Jimeng Sun, Jian Tang, Petar Veličković, Max Welling, Linfeng Zhang, Connor W Coley, Yoshua Bengio, Marinka Zitnik
Scientific discovery in the age of artificial intelligence. Nature 620 (7972) (2023)
Chirag Agarwal, Owen Queen, Himabindu Lakkaraju, Marinka Zitnik
Evaluating explainability for graph neural networks. Scientific data 10 (1) (2023)
Michelle M Li, Yepeng Huang, Marissa Sumathipala, Man Qing Liang, Alberto Valdeolivas, Ashwin N Ananthakrishnan, Katherine P Liao, Daniel Marbach, Marinka Zitnik
Contextualizing protein representations using deep learning on protein networks and single-cell data. bioRxiv : the preprint server for biology (2023)
Payal Chandak, Kexin Huang, Marinka Zitnik
Building a knowledge graph to enable precision medicine. Scientific data 10 (1) (2023)
Chirag Agarwal, Owen Queen, Himabindu Lakkaraju, Marinka Zitnik
Evaluating explainability for graph neural networks. Scientific data 10 (1) (2023)
Jun Wen, Xiang Zhang, Everett Rush, Vidul A Panickan, Xingyu Li, Tianrun Cai, Doudou Zhou, Yuk-Lam Ho, Lauren Costa, Edmon Begoli, Chuan Hong, J Michael Gaziano, Kelly Cho, Junwei Lu, Katherine P Liao, Marinka Zitnik, Tianxi Cai
Multimodal representation learning for predicting molecule-disease relations. Bioinformatics (Oxford, England) 39 (2) (2023)
Jun Wen, Xiang Zhang, Everett Rush, Vidul A Panickan, Xingyu Li, Tianrun Cai, Doudou Zhou, Yuk-Lam Ho, Lauren Costa, Edmon Begoli, Chuan Hong, J Michael Gaziano, Kelly Cho, Junwei Lu, Katherine P Liao, Marinka Zitnik, Tianxi Cai
Multimodal representation learning for predicting molecule-disease relations. Bioinformatics (Oxford, England) 39 (2) (2023)
Hanchen Wang, Tianfan Fu, Yuanqi Du, Wenhao Gao, Kexin Huang, Ziming Liu, Payal Chandak, Shengchao Liu, Peter Van Katwyk, Andreea Deac, Anima Anandkumar, Karianne Bergen, Carla P Gomes, Shirley Ho, Pushmeet Kohli, Joan Lasenby, Jure Leskovec, Tie-Yan Liu, Arjun Manrai, Debora S Marks, Bharath Ramsundar, Le Song, Jimeng Sun, Jian Tang, Petar Veličković, Max Welling, Linfeng Zhang, Connor W Coley, Yoshua Bengio, Marinka Zitnik
Publisher Correction: Scientific discovery in the age of artificial intelligence. Nature (2023)
Chirag Agarwal, Owen Queen, Himabindu Lakkaraju, Marinka Zitnik
Evaluating explainability for graph neural networks. Scientific data 10 (1) (2023)
Payal Chandak, Kexin Huang, Marinka Zitnik
Building a knowledge graph to enable precision medicine. Scientific data 10 (1) (2023)
Payal Chandak, Kexin Huang, Marinka Zitnik
Building a knowledge graph to enable precision medicine. Scientific data 10 (1) (2023)
Chirag Agarwal, Owen Queen, Himabindu Lakkaraju, Marinka Zitnik
Evaluating explainability for graph neural networks. Scientific data 10 (1) (2023)
Kexin Huang, Tianfan Fu, Wenhao Gao, Yue Zhao, Yusuf Roohani, Jure Leskovec, Connor W Coley, Cao Xiao, Jimeng Sun, Marinka Zitnik
Artificial intelligence foundation for therapeutic science. Nature chemical biology 18 (10) (2022)
Michelle M Li, Kexin Huang, Marinka Zitnik
Graph representation learning in biomedicine and healthcare. Nature biomedical engineering (2022)
Doron Stupp, Elad Sharon, Idit Bloch, Marinka Zitnik, Or Zuk, Yuval Tabach
Co-evolution based machine-learning for predicting functional interactions between human genes. Nature communications 12 (1) (2021)
Xiang Zhang, Marissa Sumathipala, Marinka Zitnik
Population-scale identification of differential adverse events before and during a pandemic. Nature computational science 1 (10) (2021)
Xiang Zhang, Marissa Sumathipala, Marinka Zitnik
Population-scale identification of differential adverse events before and during a pandemic. Nature computational science 1 (10) (2021)