Yang Shen

ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 23

Top Venues

Proteins

Human mutation

eLife

Nature computational science

Boston University (PHD)

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

Education History

Boston University Sep 01 2002

United States

PHD

Publications

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)
Yang Shen
Predicting protein structure from single sequences. Nature computational science 2 (12) (2024)
Yang Shen
Predicting protein structure from single sequences. Nature computational science 2 (12) (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)
Marc F Lensink, Guillaume Brysbaert, Nessim Raouraoua, Paul A Bates, Marco Giulini, Rodrigo V Honorato, Charlotte van Noort, Joao M C Teixeira, Alexandre M J J Bonvin, Ren Kong, Hang Shi, Xufeng Lu, Shan Chang, Jian Liu, Zhiye Guo, Xiao Chen, Alex Morehead, Raj S Roy, Tianqi Wu, Nabin Giri, Farhan Quadir, Chen Chen, Jianlin Cheng, Carlos A Del Carpio, Eichiro Ichiishi, Luis A Rodriguez-Lumbreras, Juan Fernandez-Recio, Ameya Harmalkar, Lee-Shin Chu, Sam Canner, Rituparna Smanta, Jeffrey J Gray, Hao Li, Peicong Lin, Jiahua He, Huanyu Tao, Sheng-You Huang, Jorge Roel-Touris, Brian Jimenez-Garcia, Charles W Christoffer, Anika J Jain, Yuki Kagaya, Harini Kannan, Tsukasa Nakamura, Genki Terashi, Jacob C Verburgt, Yuanyuan Zhang, Zicong Zhang, Hayato Fujuta, Masakazu Sekijima, Daisuke Kihara, Omeir Khan, Sergei Kotelnikov, Usman Ghani, Dzmitry Padhorny, Dmitri Beglov, Sandor Vajda, Dima Kozakov, Surendra S Negi, Tiziana Ricciardelli, Didier Barradas-Bautista, Zhen Cao, Mohit Chawla, Luigi Cavallo, Romina Oliva, Rui Yin, Melyssa Cheung, Johnathan D Guest, Jessica Lee, Brian G Pierce, Ben Shor, Tomer Cohen, Matan Halfon, Dina Schneidman-Duhovny, Shaowen Zhu, Rujie Yin, Yuanfei Sun, Yang Shen, Martyna Maszota-Zieleniak, Krzysztof K Bojarski, Emilia A Lubecka, Mateusz Marcisz, Annemarie Danielsson, Lukasz Dziadek, Margrethe Gaardlos, Artur Gieldon, Adam Liwo, Sergey A Samsonov, Rafal Slusarz, Karolina Zieba, Adam K Sieradzan, Cezary Czaplewski, Shinpei Kobayashi, Yuta Miyakawa, Yasuomi Kiyota, Mayuko Takeda-Shitaka, Kliment Olechnovič, Lukas Valancauskas, Justas Dapkunas, Ceslovas Venclovas, Björn Wallner, Lin Yang, Chengyu Hou, Xiaodong He, Shuai Guo, Shenda Jiang, Xiaoliang Ma, Rui Duan, Liming Qui, Xianjin Xu, Xiaoqin Zou, Sameer Velankar, Shoshana J Wodak
Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment. Proteins (2023)
Sarah L Stenton, Melanie O'Leary, Gabrielle T Lemire, Grace E VanNoy, Stephanie DiTroia, Vijay S Ganesh, Emily Groopman, Emily O'Heir, Brian Mangilog, Ikeoluwa Osei-Owusu, Lynn S Pais, Jillian G Serrano, Moriel H Singer-Berk, Ben Weisburd, Michael Wilson, Christina Austin-Tse, Marwa Abdelhakim, Azza Thamer Althagafi, Giulia Babbi, Riccardo Bellazzi, Samuele Bovo, Maria Giulia Carta, Rita Casadio, Pieter-Jan Coenen, Federica De Paoli, Matteo Floris, Manavalan Gajapathy, Hoehndorf Robert, Julius O B Jacobsen, Thomas Joseph, Akash Kamandula, Panagiostis Katsonis, Cyrielle Kint, Olivier Lichtarge, Ivan Limongelli, Yulan Lu, Paolo Magni, Tarun Karthik Kumar Mamidi, Pier Luigi Martelli, Marta Mulargia, Giovanna Nicora, Keith Nykamp, Vikas Pejaver, Yisu Peng, Thi Hong Cam Pham, Maurizio S Podda, Aditya Rao, Ettore Rizzo, Vangala G Saipradeep, Castrense Savojardo, Peter Schols, Yang Shen, Naveen Sivadasan, Damian Smedley, Dorian Soru, Rajgopal Srinivasan, Yuanfei Sun, Uma Sunderam, Wuwei Tan, Naina Tiwari, Xiao Wang, Yaqiong Wang, Amanda Williams, Elizabeth A Worthey, Rujie Yin, Yuning You, Daniel Zeiberg, Susanna Zucca, Constantina Bakolitsa, Steven E Brenner, Stephanie Malia Fullerton, Predrag Radivojac, Michael J Bamshad, Anne H O'Donnell-Luria
Critical assessment of variant prioritization methods for rare disease diagnosis within the Rare Genomes Project. medRxiv : the preprint server for health sciences (2023)
Lamiaa El-Shennawy, Andrew D Hoffmann, Nurmaa Khund Dashzeveg, Kathleen M McAndrews, Paul J Mehl, Daphne Cornish, Zihao Yu, Valerie L Tokars, Vlad Nicolaescu, Anastasia Tomatsidou, Chengsheng Mao, Christopher J Felicelli, Chia-Feng Tsai, Carolina Ostiguin, Yuzhi Jia, Lin Li, Kevin Furlong, Jan Wysocki, Xin Luo, Carolina F Ruivo, Daniel Batlle, Thomas J Hope, Yang Shen, Young Kwang Chae, Hui Zhang, Valerie S LeBleu, Tujin Shi, Suchitra Swaminathan, Yuan Luo, Dominique Missiakas, Glenn C Randall, Alexis R Demonbreun, Michael G Ison, Raghu Kalluri, Deyu Fang, Huiping Liu
Circulating ACE2-expressing extracellular vesicles block broad strains of SARS-CoV-2. Nature communications 13 (1) (2022)
Yuning You, Yang Shen
Cross-modality and self-supervised protein embedding for compound-protein affinity and contact prediction. Bioinformatics (Oxford, England) 38 (Supplement_2) (2022)
Erika K Ramos, Chia-Feng Tsai, Yuzhi Jia, Yue Cao, Megan Manu, Rokana Taftaf, Andrew D Hoffmann, Lamiaa El-Shennawy, Marina A Gritsenko, Valery Adorno-Cruz, Emma J Schuster, David Scholten, Dhwani Patel, Xia Liu, Priyam A Patel, Brian Wray, Youbin Zhang, Shanshan Zhang, Ronald J Moore, Jeremy V Mathews, Matthew John Schipma, Tao Liu, Valerie L Tokars, Massimo Cristofanilli, Tujin Shi, Yang Shen, Nurmaa K Dashzeveg, Huiping Liu
Machine learning-assisted elucidation of CD81-CD44 interactions in promoting cancer stemness and extracellular vesicle integrity. eLife 11 (2022)
Rokana Taftaf, Xia Liu, Salendra Singh, Yuzhi Jia, Nurmaa K Dashzeveg, Andrew D Hoffmann, Lamiaa El-Shennawy, Erika K Ramos, Valery Adorno-Cruz, Emma J Schuster, David Scholten, Dhwani Patel, Youbin Zhang, Andrew A Davis, Giancarlo Feliciello, Yue Cao, Paolo D'Amico, Yang Shen, Massimo Cristofanilli, William A Muller, Vinay Varadan, Huiping Liu
ICAM1 initiates CTC cluster formation and trans-endothelial migration in lung metastasis of breast cancer. Nature communications 12 (1) (2021)
Marc F Lensink, Guillaume Brysbaert, Théo Mauri, Nurul Nadzirin, Sameer Velankar, Raphael A G Chaleil, Tereza Clarence, Paul A Bates, Ren Kong, Bin Liu, Guangbo Yang, Ming Liu, Hang Shi, Xufeng Lu, Shan Chang, Raj S Roy, Farhan Quadir, Jian Liu, Jianlin Cheng, Anna Antoniak, Cezary Czaplewski, Artur Giełdoń, Mateusz Kogut, Agnieszka G Lipska, Adam Liwo, Emilia A Lubecka, Martyna Maszota-Zieleniak, Adam K Sieradzan, Rafał Ślusarz, Patryk A Wesołowski, Karolina Zięba, Carlos A Del Carpio Muñoz, Eiichiro Ichiishi, Ameya Harmalkar, Jeffrey J Gray, Alexandre M J J Bonvin, Francesco Ambrosetti, Rodrigo Vargas Honorato, Zuzana Jandova, Brian Jiménez-García, Panagiotis I Koukos, Siri Van Keulen, Charlotte W Van Noort, Manon Réau, Jorge Roel-Touris, Sergei Kotelnikov, Dzmitry Padhorny, Kathryn A Porter, Andrey Alekseenko, Mikhail Ignatov, Israel Desta, Ryota Ashizawa, Zhuyezi Sun, Usman Ghani, Nasser Hashemi, Sandor Vajda, Dima Kozakov, Mireia Rosell, Luis A Rodríguez-Lumbreras, Juan Fernández-Recio, Agnieszka Karczynska, Sergei Grudinin, Yumeng Yan, Hao Li, Peicong Lin, Sheng-You Huang, Charles W Christoffer, Genki Terashi, Jacob Verburgt, Daipayan Sarkar, Tunde Aderinwale, Xiao Wang, Daisuke Kihara, Tsukasa Nakamura, Yuya Hanazono, Ragul Gowthaman, Johnathan D Guest, Rui Yin, Ghazaleh Taherzadeh, Brian G Pierce, Didier Barradas-Bautista, Zhen Cao, Luigi Cavallo, Romina Oliva, Yuanfei Sun, Shaowen Zhu, Yang Shen, Taeyong Park, Hyeonuk Woo, Jinsol Yang, Sohee Kwon, Jonghun Won, Chaok Seok, Yasuomi Kiyota, Shinpei Kobayashi, Yoshiki Harada, Mayuko Takeda-Shitaka, Petras J Kundrotas, Amar Singh, Ilya A Vakser, Justas Dapkunas, Kliment Olechnovič, Česlovas Venclovas, Rui Duan, Liming Qiu, Xianjin Xu, Shuang Zhang, Xiaoqin Zou, Shoshana J Wodak
Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment. Proteins 89 (12) (2021)
Yue Cao, Yang Shen
Bayesian Active Learning for Optimization and Uncertainty Quantification in Protein Docking. Journal of chemical theory and computation 16 (8) (2020)
Mostafa Karimi, Di Wu, Zhangyang Wang, Yang Shen
Explainable Deep Relational Networks for Predicting Compound-Protein Affinities and Contacts. Journal of chemical information and modeling 61 (1) (2020)
Mostafa Karimi, Shaowen Zhu, Yue Cao, Yang Shen
De Novo Protein Design for Novel Folds Using Guided Conditional Wasserstein Generative Adversarial Networks. Journal of chemical information and modeling 60 (12) (2020)
Yue Cao, Yuanfei Sun, Mostafa Karimi, Haoran Chen, Oluwaseyi Moronfoye, Yang Shen
Predicting pathogenicity of missense variants with weakly supervised regression. Human mutation 40 (9) (2019)
Melissa S Cline, Giulia Babbi, Sandra Bonache, Yue Cao, Rita Casadio, Xavier de la Cruz, Orland Díez, Sara Gutiérrez-Enríquez, Panagiostis Katsonis, Carmen Lai, Olivier Lichtarge, Pier Luigi Martelli, Gilad Mishne, Alejandro Moles-Fernández, Gemma Montalban, Sean D Mooney, Robert O'Conner, Lars Ootes, Selen Özkan, Natalia Padilla, Kymberleigh A Pagel, Vikas Pejaver, Predrag Radivojac, Casandra Riera, Castrense Savojardo, Yang Shen, Yuanfei Sun, Scott Topper, Michael T Parsons, Amanda B Spurdle, David E Goldgar, null null
Assessment of blind predictions of the clinical significance of BRCA1 and BRCA2 variants. Human mutation 40 (9) (2019)
Jeffrey C Kang, Wei Sun, Priyanka Khare, Mostafa Karimi, Xiaoli Wang, Yang Shen, Raimund J Ober, E Sally Ward
Engineering a HER2-specific antibody-drug conjugate to increase lysosomal delivery and therapeutic efficacy. Nature biotechnology 37 (5) (2019)
Alin Voskanian-Kordi, Panagiostis Katsonis, Olivier Lichtarge, Vikas Pejaver, Predrag Radivojac, Sean D Mooney, Emidio Capriotti, Yana Bromberg, Yanran Wang, Maximilian Miller, Pier Luigi Martelli, Castrense Savojardo, Giulia Babbi, Rita Casadio, Yue Cao, Yuanfei Sun, Yang Shen, Aditi Garg, Debnath Pal, Yao Yu, Chad D Huff, Sean V Tavtigian, Erin Young, Susan L Neuhausen, Elad Ziv, Lipika R Pal, Gaia Andreoletti, Steven E Brenner, Maricel G Kann
Assessing the performance of in silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer. Human mutation 40 (9) (2019)
Castrense Savojardo, Maria Petrosino, Giulia Babbi, Samuele Bovo, Carles Corbi-Verge, Rita Casadio, Piero Fariselli, Lukas Folkman, Aditi Garg, Mostafa Karimi, Panagiostis Katsonis, Philip M Kim, Olivier Lichtarge, Pier Luigi Martelli, Alessandra Pasquo, Debnath Pal, Yang Shen, Alexey V Strokach, Paola Turina, Yaoqi Zhou, Gaia Andreoletti, Steven E Brenner, Roberta Chiaraluce, Valerio Consalvi, Emidio Capriotti
Evaluating the predictions of the protein stability change upon single amino acid substitutions for the FXN CAGI5 challenge. Human mutation 40 (9) (2019)
Marc F Lensink, Guillaume Brysbaert, Nurul Nadzirin, Sameer Velankar, Raphael A G Chaleil, Tereza Gerguri, Paul A Bates, Elodie Laine, Alessandra Carbone, Sergei Grudinin, Ren Kong, Ran-Ran Liu, Xi-Ming Xu, Hang Shi, Shan Chang, Miriam Eisenstein, Agnieszka Karczynska, Cezary Czaplewski, Emilia Lubecka, Agnieszka Lipska, Paweł Krupa, Magdalena Mozolewska, Łukasz Golon, Sergey Samsonov, Adam Liwo, Silvia Crivelli, Guillaume Pagès, Mikhail Karasikov, Maria Kadukova, Yumeng Yan, Sheng-You Huang, Mireia Rosell, Luis A Rodríguez-Lumbreras, Miguel Romero-Durana, Lucía Díaz-Bueno, Juan Fernández-Recio, Charles W Christoffer, Genki Terashi, Woong-Hee Shin, Tunde Aderinwale, Sai Raghavendra Maddhuri Venkata Subraman, Daisuke Kihara, Dima Kozakov, Sandor Vajda, Kathryn Porter, Dzmitry Padhorny, Israel Desta, Dmitri Beglov, Mikhail Ignatov, Sergey Kotelnikov, Iain H Moal, David W Ritchie, Isaure Chauvot de Beauchene, Bernard Maigret, Marie-Dominique Devignes, Maria E Ruiz Echartea, Didier Barradas-Bautista, Zhen Cao, Luigi Cavallo, Romina Oliva, Yue Cao, Yang Shen, Minkyung Baek, Taeyong Park, Hyeonuk Woo, Chaok Seok, Merav Braitbard, Lirane Bitton, Dina Scheidman-Duhovny, Justas Dapkunas, Kliment Olechnovič, Česlovas Venclovas, Petras J Kundrotas, Saveliy Belkin, Devlina Chakravarty, Varsha D Badal, Ilya A Vakser, Thom Vreven, Sweta Vangaveti, Tyler Borrman, Nishigandha Phalke, Johnathan D Guest, Ragul Gowthaman, Brian G Pierce, Xianjin Xu, Rui Duan, Liming Qiu, Jie Hou, Benjamin Ryan Merideth, Zhiwei Ma, Jianlin Cheng, Xiaoqin Zou, Panagiotis I Koukos, Jorge Roel-Touris, Francesco Ambrosetti, Cunliang Geng, Jörg Schaarschmidt, Mikael E Trellet, Adrien S J Melquiond, Li Xue, Brian Jiménez-García, Charlotte W van Noort, Rodrigo V Honorato, Alexandre M J J Bonvin, Shoshana J Wodak
Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment. Proteins 87 (12) (2019)
Sean W Fanning, Rinath Jeselsohn, Venkatasubramanian Dharmarajan, Christopher G Mayne, Mostafa Karimi, Gilles Buchwalter, René Houtman, Weiyi Toy, Colin E Fowler, Ross Han, Muriel Lainé, Kathryn E Carlson, Teresa A Martin, Jason Nowak, Jerome C Nwachukwu, David J Hosfield, Sarat Chandarlapaty, Emad Tajkhorshid, Kendall W Nettles, Patrick R Griffin, Yang Shen, John A Katzenellenbogen, Myles A Brown, Geoffrey L Greene
The SERM/SERD bazedoxifene disrupts ESR1 helix 12 to overcome acquired hormone resistance in breast cancer cells. eLife 7 (2018)
Xia Liu, Rokana Taftaf, Madoka Kawaguchi, Ya-Fang Chang, Wenjing Chen, David Entenberg, Youbin Zhang, Lorenzo Gerratana, Simo Huang, Dhwani B Patel, Elizabeth Tsui, Valery Adorno-Cruz, Steven M Chirieleison, Yue Cao, Allison S Harney, Shivani Patel, Antonia Patsialou, Yang Shen, Stefanie Avril, Hannah L Gilmore, Justin D Lathia, Derek W Abbott, Massimo Cristofanilli, John S Condeelis, Huiping Liu
Homophilic CD44 Interactions Mediate Tumor Cell Aggregation and Polyclonal Metastasis in Patient-Derived Breast Cancer Models. Cancer discovery 9 (1) (2018)
Haoran Chen, Yuanfei Sun, Yang Shen
Predicting protein conformational changes for unbound and homology docking: learning from intrinsic and induced flexibility. Proteins 85 (3) (2016)

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Publication Activity (10 Years)

Top Topics

Top Venues

Yang Shen