Mark B Gerstein (Mark Gerstein)

ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 122

Top Venues

Science (New York, N.Y.)

Bioinformatics (Oxford, England)

Nature communications

Nature

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

Publications

Jinrui Xu, Jiahao Gao, Pengyu Ni, Mark B Gerstein
Less-is-more: selecting transcription factor binding regions informative for motif inference. Nucleic acids research 52 (4) (2024)
Jonathan Warrell, Leonidas Salichos, Michael Gancz, Mark B Gerstein
Latent evolutionary signatures: a general framework for analysing music and cultural evolution. Journal of the Royal Society, Interface 21 (212) (2024)
Cindy Wen, Michael Margolis, Rujia Dai, Pan Zhang, Pawel F Przytycki, Daniel D Vo, Arjun Bhattacharya, Nana Matoba, Miao Tang, Chuan Jiao, Minsoo Kim, Ellen Tsai, Celine Hoh, Nil Aygün, Rebecca L Walker, Christos Chatzinakos, Declan Clarke, Henry E Pratt, null null, Mette A Peters, Mark B Gerstein, Nikolaos P Daskalakis, Nishigandha Phalke, Andrew E Jaffe, Joel E Kleinman, Thomas M Hyde, Daniel R Weinberger, Nicholas J Bray, Nenad Sestan, Daniel H Geschwind, Kathryn Roeder, Alexander Gusev, Bogdan Pasaniuc, Jason L Stein, Michael I Love, Katherine S Pollard, Yanling Liu, Michael J Gandal, null null
Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain. Science (New York, N.Y.) 384 (6698) (2024)
Jinrui Xu, Jiahao Gao, Pengyu Ni, Mark B Gerstein
Less-is-more: selecting transcription factor binding regions informative for motif inference. Nucleic acids research (2024)
Mor Frank, Zhengchang Su, Matthew Jensen, Mark B Gerstein
Leveraging a large language model to predict protein phase transition: A physical, multiscale, and interpretable approach. Proceedings of the National Academy of Sciences of the United States of America 121 (33) (2024)
Thazin Nwe Aung, Jonathan Warrell, Sandra Martinez-Morilla, Niki Gavrielatou, Ioannis A Vathiotis, Vesal Yaghoobi, Harriet M Kluger, Mark B Gerstein, David L Rimm
Spatially informed gene signatures for response to immunotherapy in melanoma. Clinical cancer research : an official journal of the American Association for Cancer Research (2024)
Xiangru Tang, Andrew Tran, Jeffrey Tan, Mark B Gerstein
MolLM: a unified language model for integrating biomedical text with 2D and 3D molecular representations. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Jia-Hao Gao, Mark B Gerstein
Representing core gene expression activity relationships using the latent structure implicit in Bayesian networks. Bioinformatics (Oxford, England) 40 (8) (2024)
Xiangru Tang, Howard Dai, Elizabeth Knight, Fang Wu, Yunyang Li, Tianxiao Li, Mark B Gerstein
A survey of generative AI for de novo drug design: new frontiers in molecule and protein generation. Briefings in bioinformatics 25 (4) (2024)
Jonathan Warrell, Leonidas Salichos, Michael Gancz, Mark B Gerstein
Latent evolutionary signatures: a general framework for analysing music and cultural evolution. Journal of the Royal Society, Interface 21 (212) (2024)
Cindy Wen, Michael Margolis, Rujia Dai, Pan Zhang, Pawel F Przytycki, Daniel D Vo, Arjun Bhattacharya, Nana Matoba, Miao Tang, Chuan Jiao, Minsoo Kim, Ellen Tsai, Celine Hoh, Nil Aygün, Rebecca L Walker, Christos Chatzinakos, Declan Clarke, Henry E Pratt, null null, Mette A Peters, Mark B Gerstein, Nikolaos P Daskalakis, Nishigandha Phalke, Andrew E Jaffe, Joel E Kleinman, Thomas M Hyde, Daniel R Weinberger, Nicholas J Bray, Nenad Sestan, Daniel H Geschwind, Kathryn Roeder, Alexander Gusev, Bogdan Pasaniuc, Jason L Stein, Michael I Love, Katherine S Pollard, Yanling Liu, Michael J Gandal, null null
Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain. Science (New York, N.Y.) 384 (6698) (2024)
Xiangru Tang, Bill Qian, Rick Gao, Jiakang Chen, Xinyun Chen, Mark B Gerstein
BioCoder: a benchmark for bioinformatics code generation with large language models. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Jonathan Warrell, Leonidas Salichos, Michael Gancz, Mark B Gerstein
Latent evolutionary signatures: a general framework for analysing music and cultural evolution. Journal of the Royal Society, Interface 21 (212) (2024)
Thazin Nwe Aung, Jonathan Warrell, Sandra Martinez-Morilla, Niki Gavrielatou, Ioannis A Vathiotis, Vesal Yaghoobi, Harriet M Kluger, Mark B Gerstein, David L Rimm
Spatially Informed Gene Signatures for Response to Immunotherapy in Melanoma. Clinical cancer research : an official journal of the American Association for Cancer Research 30 (16) (2024)
Prashant S Emani, Jason J Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che Yu Lee, Siwei Xu, Cagatay Dursun, Shaoke Lou, Yuhang Chen, Zhiyuan Chu, Timur Galeev, Ahyeon Hwang, Yunyang Li, Zhengchang Su, Xiao Zhou, null null, Trygve E Bakken, Jaroslav Bendl, Lucy K Bicks, Tanima Chatterjee, Lijun Cheng, Yuyan Cheng, Yi Dai, Ziheng Duan, Mary Flaherty, John F Fullard, Michael Gancz, Diego Garrido-Martín, Sophia C Gaynor-Gillett, Jennifer Grundman, Natalie Hawken, Ella Henry, Gabriel E Hoffman, Ao Huang, Yunzhe Jiang, Ting Jin, Nikolas L Jorstad, Riki Kawaguchi, Saniya Khullar, Jianyin Liu, Junhao Liu, Shuang Liu, Shaojie Ma, Michael Margolis, Samantha Mazariegos, Jill E Moore, Jennifer R Moran, Eric Nguyen, Nishigandha Phalke, Milos Pjanic, Henry E Pratt, Diana Quintero, Ananya S Rajagopalan, Tiernon R Riesenmy, Nicole Shedd, Manman Shi, Megan Spector, Rosemarie Terwilliger, Kyle J Travaglini, Brie Wamsley, Gaoyuan Wang, Yan Xia, Shaohua Xiao, Andrew C Yang, Suchen Zheng, Michael J Gandal, Donghoon Lee, Ed S Lein, Panagiotis Roussos, Nenad Sestan, Nishigandha Phalke, Kevin P White, Hyejung Won, Matthew J Girgenti, Jing Zhang, Daifeng Wang, Daniel H Geschwind, Mark B Gerstein, null null
Single-cell genomics and regulatory networks for 388 human brains. Science (New York, N.Y.) 384 (6698) (2024)
Jia-Hao Gao, Mark B Gerstein
Representing core gene expression activity relationships using the latent structure implicit in Bayesian networks. Bioinformatics (Oxford, England) 40 (8) (2024)
Thazin Nwe Aung, Jonathan Warrell, Sandra Martinez-Morilla, Niki Gavrielatou, Ioannis A Vathiotis, Vesal Yaghoobi, Harriet M Kluger, Mark B Gerstein, David L Rimm
Spatially informed gene signatures for response to immunotherapy in melanoma. Clinical cancer research : an official journal of the American Association for Cancer Research (2024)
Cindy Wen, Michael Margolis, Rujia Dai, Pan Zhang, Pawel F Przytycki, Daniel D Vo, Arjun Bhattacharya, Nana Matoba, Miao Tang, Chuan Jiao, Minsoo Kim, Ellen Tsai, Celine Hoh, Nil Aygün, Rebecca L Walker, Christos Chatzinakos, Declan Clarke, Henry E Pratt, null null, Mette A Peters, Mark B Gerstein, Nikolaos P Daskalakis, Nishigandha Phalke, Andrew E Jaffe, Joel E Kleinman, Thomas M Hyde, Daniel R Weinberger, Nicholas J Bray, Nenad Sestan, Daniel H Geschwind, Kathryn Roeder, Alexander Gusev, Bogdan Pasaniuc, Jason L Stein, Michael I Love, Katherine S Pollard, Yanling Liu, Michael J Gandal, null null
Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain. Science (New York, N.Y.) 384 (6698) (2024)
Xiangru Tang, Bill Qian, Rick Gao, Jiakang Chen, Xinyun Chen, Mark B Gerstein
BioCoder: a benchmark for bioinformatics code generation with large language models. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Seth A Ament, Rianne R Campbell, Mary Kay Lobo, Joseph Paul Receveur, Kriti Agrawal, Alejandra Borjabad, Siddappa N Byrareddy, Linda Chang, Declan Clarke, Prashant S Emani, Dana Gabuzda, Kyle J Gaulton, Michelle G Giglio, Federico M Giorgi, Busra Gok, Chittibabu Guda, Eran Hadas, Brian R Herb, Wen Hu, Anita Huttner, Mohammad R Ishmam, Michelle M Jacobs, Jennifer Kelschenbach, Dong-Wook Kim, Cheyu Lee, Shuhui Liu, Xiaokun Liu, Bertha K Madras, Anup A Mahurkar, Deborah C Mash, Eran A Mukamel, Meng Niu, Richard M O'Connor, Chelsea M Pagan, Alina P S Pang, Piya Pillai, Vez Repunte-Canonigo, W Brad Ruzicka, Jay Stanley, Timothy L Tickle, Shang-Yi A Tsai, Allen Wang, Lauren Wills, Alyssa M Wilson, Susan N Wright, Siwei Xu, Junchen Yang, Maryam Zand, Le Zhang, Jing Zhang, Schahram Akbarian, Shilpa Buch, Christine S Cheng, Michael J Corley, Howard S Fox, Mark B Gerstein, Suryaram Gummuluru, Myriam Heiman, Ya-Chi Ho, Manolis Kellis, Paul J Kenny, Yuval Kluger, Teresa A Milner, David J Moore, Susan Morgello, Lishomwa C Ndhlovu, Tariq M Rana, Pietro Paolo Sanna, John S Satterlee, Nenad Sestan, Stephen A Spector, Serena Spudich, Hagen U Tilgner, David J Volsky, Owen R White, Dionna W Williams, Hongkui Zeng
The single-cell opioid responses in the context of HIV (SCORCH) consortium. Molecular psychiatry (2024)
Cindy Wen, Michael Margolis, Rujia Dai, Pan Zhang, Pawel F Przytycki, Daniel D Vo, Arjun Bhattacharya, Nana Matoba, Miao Tang, Chuan Jiao, Minsoo Kim, Ellen Tsai, Celine Hoh, Nil Aygün, Rebecca L Walker, Christos Chatzinakos, Declan Clarke, Henry E Pratt, null null, Mette A Peters, Mark B Gerstein, Nikolaos P Daskalakis, Nishigandha Phalke, Andrew E Jaffe, Joel E Kleinman, Thomas M Hyde, Daniel R Weinberger, Nicholas J Bray, Nenad Sestan, Daniel H Geschwind, Kathryn Roeder, Alexander Gusev, Bogdan Pasaniuc, Jason L Stein, Michael I Love, Katherine S Pollard, Yanling Liu, Michael J Gandal, null null
Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain. Science (New York, N.Y.) 384 (6698) (2024)
Henry E Pratt, Gregory Andrews, Nicole Shedd, Nishigandha Phalke, Tongxin Li, Anusri Pampari, Matthew Jensen, Cindy Wen, PsychENCODE Consortium, Michael J Gandal, Daniel H Geschwind, Mark B Gerstein, Jill E Moore, Anshul Kundaje, Andres Colubri, Nishigandha Phalke
Using a comprehensive atlas and predictive models to reveal the complexity and evolution of brain-active regulatory elements. Science advances 10 (21) (2024)
Thazin Nwe Aung, Jonathan Warrell, Sandra Martinez-Morilla, Niki Gavrielatou, Ioannis A Vathiotis, Vesal Yaghoobi, Harriet M Kluger, Mark B Gerstein, David L Rimm
Spatially Informed Gene Signatures for Response to Immunotherapy in Melanoma. Clinical cancer research : an official journal of the American Association for Cancer Research 30 (16) (2024)
Thazin Nwe Aung, Jonathan Warrell, Sandra Martinez-Morilla, Niki Gavrielatou, Ioannis A Vathiotis, Vesal Yaghoobi, Harriet M Kluger, Mark B Gerstein, David L Rimm
Spatially Informed Gene Signatures for Response to Immunotherapy in Melanoma. Clinical cancer research : an official journal of the American Association for Cancer Research 30 (16) (2024)
Jia-Hao Gao, Mark B Gerstein
Representing core gene expression activity relationships using the latent structure implicit in Bayesian networks. Bioinformatics (Oxford, England) 40 (8) (2024)
Seth A Ament, Rianne R Campbell, Mary Kay Lobo, Joseph Paul Receveur, Kriti Agrawal, Alejandra Borjabad, Siddappa N Byrareddy, Linda Chang, Declan Clarke, Prashant S Emani, Dana Gabuzda, Kyle J Gaulton, Michelle G Giglio, Federico M Giorgi, Busra Gok, Chittibabu Guda, Eran Hadas, Brian R Herb, Wen Hu, Anita Huttner, Mohammad R Ishmam, Michelle M Jacobs, Jennifer Kelschenbach, Dong-Wook Kim, Cheyu Lee, Shuhui Liu, Xiaokun Liu, Bertha K Madras, Anup A Mahurkar, Deborah C Mash, Eran A Mukamel, Meng Niu, Richard M O'Connor, Chelsea M Pagan, Alina P S Pang, Piya Pillai, Vez Repunte-Canonigo, W Brad Ruzicka, Jay Stanley, Timothy L Tickle, Shang-Yi A Tsai, Allen Wang, Lauren Wills, Alyssa M Wilson, Susan N Wright, Siwei Xu, Junchen Yang, Maryam Zand, Le Zhang, Jing Zhang, Schahram Akbarian, Shilpa Buch, Christine S Cheng, Michael J Corley, Howard S Fox, Mark B Gerstein, Suryaram Gummuluru, Myriam Heiman, Ya-Chi Ho, Manolis Kellis, Paul J Kenny, Yuval Kluger, Teresa A Milner, David J Moore, Susan Morgello, Lishomwa C Ndhlovu, Tariq M Rana, Pietro Paolo Sanna, John S Satterlee, Nenad Sestan, Stephen A Spector, Serena Spudich, Hagen U Tilgner, David J Volsky, Owen R White, Dionna W Williams, Hongkui Zeng
The single-cell opioid responses in the context of HIV (SCORCH) consortium. Molecular psychiatry (2024)
Sophia C Gaynor-Gillett, Lijun Cheng, Manman Shi, Jason J Liu, Gaoyuan Wang, Megan Spector, Mary Flaherty, Martha Wall, Ahyeon Hwang, Mengting Gu, Zhanlin Chen, Yuhang Chen, PsychENCODE Consortium, Jennifer R Moran, Jing Zhang, Donghoon Lee, Mark B Gerstein, Daniel H Geschwind, Kevin P White
Validation of Enhancer Regions in Primary Human Neural Progenitor Cells using Capture STARR-seq. bioRxiv : the preprint server for biology (2024)
Mor Frank, Zhengchang Su, Matthew Jensen, Mark B Gerstein
Leveraging a large language model to predict protein phase transition: A physical, multiscale, and interpretable approach. Proceedings of the National Academy of Sciences of the United States of America 121 (33) (2024)
Jinrui Xu, Jiahao Gao, Pengyu Ni, Mark B Gerstein
Less-is-more: selecting transcription factor binding regions informative for motif inference. Nucleic acids research 52 (4) (2024)
Jonathan Warrell, Leonidas Salichos, Michael Gancz, Mark B Gerstein
Latent evolutionary signatures: a general framework for analysing music and cultural evolution. Journal of the Royal Society, Interface 21 (212) (2024)
Jia-Hao Gao, Mark B Gerstein
Representing core gene expression activity relationships using the latent structure implicit in Bayesian networks. Bioinformatics (Oxford, England) 40 (8) (2024)
Jonathan Warrell, Leonidas Salichos, Michael Gancz, Mark B Gerstein
Latent evolutionary signatures: a general framework for analysing music and cultural evolution. Journal of the Royal Society, Interface 21 (212) (2024)
Sophia C Gaynor-Gillett, Lijun Cheng, Manman Shi, Jason J Liu, Gaoyuan Wang, Megan Spector, Mary Flaherty, Martha Wall, Ahyeon Hwang, Mengting Gu, Zhanlin Chen, Yuhang Chen, null null, Jennifer R Moran, Jing Zhang, Donghoon Lee, Mark B Gerstein, Daniel H Geschwind, Kevin P White
Validation of Enhancer Regions in Primary Human Neural Progenitor Cells using Capture STARR-seq. bioRxiv : the preprint server for biology (2024)
Xiangru Tang, Howard Dai, Elizabeth Knight, Fang Wu, Yunyang Li, Tianxiao Li, Mark B Gerstein
A survey of generative AI for de novo drug design: new frontiers in molecule and protein generation. Briefings in bioinformatics 25 (4) (2024)
Seth A Ament, Rianne R Campbell, Mary Kay Lobo, Joseph Paul Receveur, Kriti Agrawal, Alejandra Borjabad, Siddappa N Byrareddy, Linda Chang, Declan Clarke, Prashant S Emani, Dana Gabuzda, Kyle J Gaulton, Michelle G Giglio, Federico M Giorgi, Busra Gok, Chittibabu Guda, Eran Hadas, Brian R Herb, Wen Hu, Anita Huttner, Mohammad R Ishmam, Michelle M Jacobs, Jennifer Kelschenbach, Dong-Wook Kim, Cheyu Lee, Shuhui Liu, Xiaokun Liu, Bertha K Madras, Anup A Mahurkar, Deborah C Mash, Eran A Mukamel, Meng Niu, Richard M O'Connor, Chelsea M Pagan, Alina P S Pang, Piya Pillai, Vez Repunte-Canonigo, W Brad Ruzicka, Jay Stanley, Timothy L Tickle, Shang-Yi A Tsai, Allen Wang, Lauren Wills, Alyssa M Wilson, Susan N Wright, Siwei Xu, Junchen Yang, Maryam Zand, Le Zhang, Jing Zhang, Schahram Akbarian, Shilpa Buch, Christine S Cheng, Michael J Corley, Howard S Fox, Mark B Gerstein, Suryaram Gummuluru, Myriam Heiman, Ya-Chi Ho, Manolis Kellis, Paul J Kenny, Yuval Kluger, Teresa A Milner, David J Moore, Susan Morgello, Lishomwa C Ndhlovu, Tariq M Rana, Pietro Paolo Sanna, John S Satterlee, Nenad Sestan, Stephen A Spector, Serena Spudich, Hagen U Tilgner, David J Volsky, Owen R White, Dionna W Williams, Hongkui Zeng
The single-cell opioid responses in the context of HIV (SCORCH) consortium. Molecular psychiatry (2024)
Prashant S Emani, Jason J Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che Yu Lee, Siwei Xu, Cagatay Dursun, Shaoke Lou, Yuhang Chen, Zhiyuan Chu, Timur Galeev, Ahyeon Hwang, Yunyang Li, Zhengchang Su, Xiao Zhou, null null, Trygve E Bakken, Jaroslav Bendl, Lucy K Bicks, Tanima Chatterjee, Lijun Cheng, Yuyan Cheng, Yi Dai, Ziheng Duan, Mary Flaherty, John F Fullard, Michael Gancz, Diego Garrido-Martín, Sophia C Gaynor-Gillett, Jennifer Grundman, Natalie Hawken, Ella Henry, Gabriel E Hoffman, Ao Huang, Yunzhe Jiang, Ting Jin, Nikolas L Jorstad, Riki Kawaguchi, Saniya Khullar, Jianyin Liu, Junhao Liu, Shuang Liu, Shaojie Ma, Michael Margolis, Samantha Mazariegos, Jill E Moore, Jennifer R Moran, Eric Nguyen, Nishigandha Phalke, Milos Pjanic, Henry E Pratt, Diana Quintero, Ananya S Rajagopalan, Tiernon R Riesenmy, Nicole Shedd, Manman Shi, Megan Spector, Rosemarie Terwilliger, Kyle J Travaglini, Brie Wamsley, Gaoyuan Wang, Yan Xia, Shaohua Xiao, Andrew C Yang, Suchen Zheng, Michael J Gandal, Donghoon Lee, Ed S Lein, Panagiotis Roussos, Nenad Sestan, Nishigandha Phalke, Kevin P White, Hyejung Won, Matthew J Girgenti, Jing Zhang, Daifeng Wang, Daniel H Geschwind, Mark B Gerstein, null null
Single-cell genomics and regulatory networks for 388 human brains. Science (New York, N.Y.) 384 (6698) (2024)
Xiangru Tang, Andrew Tran, Jeffrey Tan, Mark B Gerstein
MolLM: a unified language model for integrating biomedical text with 2D and 3D molecular representations. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Prashant S Emani, Jason J Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che Yu Lee, Siwei Xu, Cagatay Dursun, Shaoke Lou, Yuhang Chen, Zhiyuan Chu, Timur Galeev, Ahyeon Hwang, Yunyang Li, Zhengchang Su, Xiao Zhou, null null, Trygve E Bakken, Jaroslav Bendl, Lucy K Bicks, Tanima Chatterjee, Lijun Cheng, Yuyan Cheng, Yi Dai, Ziheng Duan, Mary Flaherty, John F Fullard, Michael Gancz, Diego Garrido-Martín, Sophia C Gaynor-Gillett, Jennifer Grundman, Natalie Hawken, Ella Henry, Gabriel E Hoffman, Ao Huang, Yunzhe Jiang, Ting Jin, Nikolas L Jorstad, Riki Kawaguchi, Saniya Khullar, Jianyin Liu, Junhao Liu, Shuang Liu, Shaojie Ma, Michael Margolis, Samantha Mazariegos, Jill E Moore, Jennifer R Moran, Eric Nguyen, Nishigandha Phalke, Milos Pjanic, Henry E Pratt, Diana Quintero, Ananya S Rajagopalan, Tiernon R Riesenmy, Nicole Shedd, Manman Shi, Megan Spector, Rosemarie Terwilliger, Kyle J Travaglini, Brie Wamsley, Gaoyuan Wang, Yan Xia, Shaohua Xiao, Andrew C Yang, Suchen Zheng, Michael J Gandal, Donghoon Lee, Ed S Lein, Panagiotis Roussos, Nenad Sestan, Nishigandha Phalke, Kevin P White, Hyejung Won, Matthew J Girgenti, Jing Zhang, Daifeng Wang, Daniel H Geschwind, Mark B Gerstein, null null
Single-cell genomics and regulatory networks for 388 human brains. Science (New York, N.Y.) 384 (6698) (2024)
Prashant S Emani, Jason J Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che Yu Lee, Siwei Xu, Cagatay Dursun, Shaoke Lou, Yuhang Chen, Zhiyuan Chu, Timur Galeev, Ahyeon Hwang, Yunyang Li, Zhengchang Su, Xiao Zhou, null null, Trygve E Bakken, Jaroslav Bendl, Lucy K Bicks, Tanima Chatterjee, Lijun Cheng, Yuyan Cheng, Yi Dai, Ziheng Duan, Mary Flaherty, John F Fullard, Michael Gancz, Diego Garrido-Martín, Sophia C Gaynor-Gillett, Jennifer Grundman, Natalie Hawken, Ella Henry, Gabriel E Hoffman, Ao Huang, Yunzhe Jiang, Ting Jin, Nikolas L Jorstad, Riki Kawaguchi, Saniya Khullar, Jianyin Liu, Junhao Liu, Shuang Liu, Shaojie Ma, Michael Margolis, Samantha Mazariegos, Jill E Moore, Jennifer R Moran, Eric Nguyen, Nishigandha Phalke, Milos Pjanic, Henry E Pratt, Diana Quintero, Ananya S Rajagopalan, Tiernon R Riesenmy, Nicole Shedd, Manman Shi, Megan Spector, Rosemarie Terwilliger, Kyle J Travaglini, Brie Wamsley, Gaoyuan Wang, Yan Xia, Shaohua Xiao, Andrew C Yang, Suchen Zheng, Michael J Gandal, Donghoon Lee, Ed S Lein, Panagiotis Roussos, Nenad Sestan, Nishigandha Phalke, Kevin P White, Hyejung Won, Matthew J Girgenti, Jing Zhang, Daifeng Wang, Daniel H Geschwind, Mark B Gerstein, null null
Single-cell genomics and regulatory networks for 388 human brains. Science (New York, N.Y.) 384 (6698) (2024)
Jinrui Xu, Jiahao Gao, Pengyu Ni, Mark B Gerstein
Less-is-more: selecting transcription factor binding regions informative for motif inference. Nucleic acids research 52 (4) (2024)
Prashant S Emani, Jason J Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che Yu Lee, Siwei Xu, Cagatay Dursun, Shaoke Lou, Yuhang Chen, Zhiyuan Chu, Timur Galeev, Ahyeon Hwang, Yunyang Li, Zhengchang Su, Xiao Zhou, null null, Trygve E Bakken, Jaroslav Bendl, Lucy K Bicks, Tanima Chatterjee, Lijun Cheng, Yuyan Cheng, Yi Dai, Ziheng Duan, Mary Flaherty, John F Fullard, Michael Gancz, Diego Garrido-Martín, Sophia C Gaynor-Gillett, Jennifer Grundman, Natalie Hawken, Ella Henry, Gabriel E Hoffman, Ao Huang, Yunzhe Jiang, Ting Jin, Nikolas L Jorstad, Riki Kawaguchi, Saniya Khullar, Jianyin Liu, Junhao Liu, Shuang Liu, Shaojie Ma, Michael Margolis, Samantha Mazariegos, Jill E Moore, Jennifer R Moran, Eric Nguyen, Nishigandha Phalke, Milos Pjanic, Henry E Pratt, Diana Quintero, Ananya S Rajagopalan, Tiernon R Riesenmy, Nicole Shedd, Manman Shi, Megan Spector, Rosemarie Terwilliger, Kyle J Travaglini, Brie Wamsley, Gaoyuan Wang, Yan Xia, Shaohua Xiao, Andrew C Yang, Suchen Zheng, Michael J Gandal, Donghoon Lee, Ed S Lein, Panagiotis Roussos, Nenad Sestan, Nishigandha Phalke, Kevin P White, Hyejung Won, Matthew J Girgenti, Jing Zhang, Daifeng Wang, Daniel H Geschwind, Mark B Gerstein, null null
Single-cell genomics and regulatory networks for 388 human brains. Science (New York, N.Y.) 384 (6698) (2024)
Jinrui Xu, Jiahao Gao, Pengyu Ni, Mark B Gerstein
Less-is-more: selecting transcription factor binding regions informative for motif inference. Nucleic acids research (2024)
Henry E Pratt, Gregory Andrews, Nicole Shedd, Nishigandha Phalke, Tongxin Li, Anusri Pampari, Matthew Jensen, Cindy Wen, PsychENCODE Consortium, Michael J Gandal, Daniel H Geschwind, Mark B Gerstein, Jill E Moore, Anshul Kundaje, Andres Colubri, Nishigandha Phalke
Using a comprehensive atlas and predictive models to reveal the complexity and evolution of brain-active regulatory elements. Science advances 10 (21) (2024)
Prashant S Emani, Jason J Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che Yu Lee, Siwei Xu, Cagatay Dursun, Shaoke Lou, Yuhang Chen, Zhiyuan Chu, Timur Galeev, Ahyeon Hwang, Yunyang Li, Zhengchang Su, Xiao Zhou, null null, Trygve E Bakken, Jaroslav Bendl, Lucy K Bicks, Tanima Chatterjee, Lijun Cheng, Yuyan Cheng, Yi Dai, Ziheng Duan, Mary Flaherty, John F Fullard, Michael Gancz, Diego Garrido-Martín, Sophia C Gaynor-Gillett, Jennifer Grundman, Natalie Hawken, Ella Henry, Gabriel E Hoffman, Ao Huang, Yunzhe Jiang, Ting Jin, Nikolas L Jorstad, Riki Kawaguchi, Saniya Khullar, Jianyin Liu, Junhao Liu, Shuang Liu, Shaojie Ma, Michael Margolis, Samantha Mazariegos, Jill E Moore, Jennifer R Moran, Eric Nguyen, Nishigandha Phalke, Milos Pjanic, Henry E Pratt, Diana Quintero, Ananya S Rajagopalan, Tiernon R Riesenmy, Nicole Shedd, Manman Shi, Megan Spector, Rosemarie Terwilliger, Kyle J Travaglini, Brie Wamsley, Gaoyuan Wang, Yan Xia, Shaohua Xiao, Andrew C Yang, Suchen Zheng, Michael J Gandal, Donghoon Lee, Ed S Lein, Panagiotis Roussos, Nenad Sestan, Nishigandha Phalke, Kevin P White, Hyejung Won, Matthew J Girgenti, Jing Zhang, Daifeng Wang, Daniel H Geschwind, Mark B Gerstein, null null
Single-cell genomics and regulatory networks for 388 human brains. Science (New York, N.Y.) 384 (6698) (2024)
Xiangru Tang, Andrew Tran, Jeffrey Tan, Mark B Gerstein
MolLM: a unified language model for integrating biomedical text with 2D and 3D molecular representations. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Xiangru Tang, Bill Qian, Rick Gao, Jiakang Chen, Xinyun Chen, Mark B Gerstein
BioCoder: a benchmark for bioinformatics code generation with large language models. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Thazin Nwe Aung, Jonathan Warrell, Sandra Martinez-Morilla, Niki Gavrielatou, Ioannis A Vathiotis, Vesal Yaghoobi, Harriet M Kluger, Mark B Gerstein, David L Rimm
Spatially Informed Gene Signatures for Response to Immunotherapy in Melanoma. Clinical cancer research : an official journal of the American Association for Cancer Research 30 (16) (2024)
Prashant S Emani, Jason J Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che Yu Lee, Siwei Xu, Cagatay Dursun, Shaoke Lou, Yuhang Chen, Zhiyuan Chu, Timur Galeev, Ahyeon Hwang, Yunyang Li, Zhengchang Su, Xiao Zhou, null null, Trygve E Bakken, Jaroslav Bendl, Lucy K Bicks, Tanima Chatterjee, Lijun Cheng, Yuyan Cheng, Yi Dai, Ziheng Duan, Mary Flaherty, John F Fullard, Michael Gancz, Diego Garrido-Martín, Sophia C Gaynor-Gillett, Jennifer Grundman, Natalie Hawken, Ella Henry, Gabriel E Hoffman, Ao Huang, Yunzhe Jiang, Ting Jin, Nikolas L Jorstad, Riki Kawaguchi, Saniya Khullar, Jianyin Liu, Junhao Liu, Shuang Liu, Shaojie Ma, Michael Margolis, Samantha Mazariegos, Jill E Moore, Jennifer R Moran, Eric Nguyen, Nishigandha Phalke, Milos Pjanic, Henry E Pratt, Diana Quintero, Ananya S Rajagopalan, Tiernon R Riesenmy, Nicole Shedd, Manman Shi, Megan Spector, Rosemarie Terwilliger, Kyle J Travaglini, Brie Wamsley, Gaoyuan Wang, Yan Xia, Shaohua Xiao, Andrew C Yang, Suchen Zheng, Michael J Gandal, Donghoon Lee, Ed S Lein, Panagiotis Roussos, Nenad Sestan, Nishigandha Phalke, Kevin P White, Hyejung Won, Matthew J Girgenti, Jing Zhang, Daifeng Wang, Daniel H Geschwind, Mark B Gerstein, null null
Single-cell genomics and regulatory networks for 388 human brains. Science (New York, N.Y.) 384 (6698) (2024)
Mor Frank, Zhengchang Su, Matthew Jensen, Mark B Gerstein
Leveraging a large language model to predict protein phase transition: A physical, multiscale, and interpretable approach. Proceedings of the National Academy of Sciences of the United States of America 121 (33) (2024)
Shaoke Lou, Mingjun Yang, Tianxiao Li, Weihao Zhao, Hannah Cevasco, Yucheng T Yang, Mark B Gerstein
Constructing a full, multiple-layer interactome for SARS-CoV-2 in the context of lung disease: Linking the virus with human genes and microbes. PLoS computational biology 19 (7) (2023)
Guangda Shi, Claire Song, Jaylissa Torres Robles, Leonidas Salichos, Hua Jane Lou, Tukiet T Lam, Mark B Gerstein, Benjamin E Turk
Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors. Science signaling 16 (767) (2023)
Christopher J Minteer, Kyra Thrush-Evensen, John T González, Peter Niimi, Mariya Rozenblit, Joel Rozowsky, Jason J Liu, Mor Frank, Thomas McCabe, Albert T Higgins-Chen, Erin Hofstatter, Lajos Pusztai, Kenneth B Beckman, Mark B Gerstein, Morgan E Levine
More than bad luck: Cancer and aging are linked to replication-driven changes to the epigenome. Science advances 9 (29) (2023)
William U Meyerson, Sarah K Fineberg, Ye Kyung Song, Adam Faber, Garrett I Ash, Fernanda C Andrade, Philip Robert Corlett, Mark B Gerstein, Rick H Hoyle
Estimation of Bedtimes of Reddit Users: Integrated Analysis of Time Stamps and Surveys. JMIR formative research 7 (2023)
Guangda Shi, Claire Song, Jaylissa Torres Robles, Leonidas Salichos, Hua Jane Lou, Tukiet T Lam, Mark B Gerstein, Benjamin E Turk
Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors. Science signaling 16 (767) (2023)
William U Meyerson, Sarah K Fineberg, Ye Kyung Song, Adam Faber, Garrett I Ash, Fernanda C Andrade, Philip Robert Corlett, Mark B Gerstein, Rick H Hoyle
Estimation of Bedtimes of Reddit Users: Integrated Analysis of Time Stamps and Surveys. JMIR formative research 7 (2023)
William U Meyerson, Sarah K Fineberg, Ye Kyung Song, Adam Faber, Garrett I Ash, Fernanda C Andrade, Philip Robert Corlett, Mark B Gerstein, Rick H Hoyle
Estimation of Bedtimes of Reddit Users: Integrated Analysis of Time Stamps and Surveys. JMIR formative research 7 (2023)
Guangda Shi, Claire Song, Jaylissa Torres Robles, Leonidas Salichos, Hua Jane Lou, Tukiet T Lam, Mark B Gerstein, Benjamin E Turk
Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors. Science signaling 16 (767) (2023)
Prashant S Emani, Maya N Geradi, Gamze Gürsoy, Monica R Grasty, Andrew D Miranker, Mark B Gerstein
Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases. Genome research 33 (12) (2023)
William U Meyerson, Sarah K Fineberg, Ye Kyung Song, Adam Faber, Garrett I Ash, Fernanda C Andrade, Philip Robert Corlett, Mark B Gerstein, Rick H Hoyle
Estimation of Bedtimes of Reddit Users: Integrated Analysis of Time Stamps and Surveys. JMIR formative research 7 (2023)
Guangda Shi, Claire Song, Jaylissa Torres Robles, Leonidas Salichos, Hua Jane Lou, Tukiet T Lam, Mark B Gerstein, Benjamin E Turk
Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors. Science signaling 16 (767) (2023)
Prashant S Emani, Maya N Geradi, Gamze Gürsoy, Monica R Grasty, Andrew D Miranker, Mark B Gerstein
Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases. Genome research (2023)
Prashant S Emani, Maya N Geradi, Gamze Gürsoy, Monica R Grasty, Andrew D Miranker, Mark B Gerstein
Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases. Genome research (2023)
Fairlie Reese, Brian A Williams, Gabriela Balderrama-Gutierrez, Dana Wyman, Muhammed Hasan Çelik, Elisabeth Rebboah, Narges Rezaie, Diane Trout, Milad Razavi-Mohseni, Yunzhe Jiang, Beatrice Borsari, Samuel J Morabito, Heidi Yahan Liang, Cassandra J McGill, Sorena Rahmanian, Jasmine Sakr, Shan Jiang, Weihua Zeng, Klebea Carvalho, Annika K Weimer, Louise A Dionne, Ariel McShane, Karan Bedi, Shaimae I Elhajjajy, Sean Upchurch, Jennifer Jou, Ingrid Youngworth, Aditi K Narayanan, Paul Sud, Otto Jolanki, Benjamin C Hitz, Meenakshi S Kagda, Michael Paul Snyder, Benjamin C Hitz, Jill E Moore, Nishigandha Phalke, David A Bennett, Laura G Reinholdt, Mats Ljungman, Michael A Beer, Mark B Gerstein, Lior Pachter, Roderic Guigo, Barbara J Wold, Ali Mortazavi
The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity. bioRxiv : the preprint server for biology (2023)
William U Meyerson, Sarah K Fineberg, Ye Kyung Song, Adam Faber, Garrett I Ash, Fernanda C Andrade, Philip Robert Corlett, Mark B Gerstein, Rick H Hoyle
Estimation of Bedtimes of Reddit Users: Integrated Analysis of Time Stamps and Surveys. JMIR formative research 7 (2023)
Prashant S Emani, Maya N Geradi, Gamze Gürsoy, Monica R Grasty, Andrew D Miranker, Mark B Gerstein
Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases. Genome research (2023)
Zhanlin Chen, Jeremy Goldwasser, Philip Tuckman, Jason Liu, Jing Zhang, Mark B Gerstein
Forest Fire Clustering for single-cell sequencing combines iterative label propagation with parallelized Monte Carlo simulations. Nature communications 13 (1) (2022)
Graham S Erwin, Gamze Gürsoy, Rashid Al-Abri, Ashwini Suriyaprakash, Egor Dolzhenko, Kevin Zhu, Christian R Hoerner, Shannon M White, Lucia Ramirez, Ananya Vadlakonda, Alekhya Vadlakonda, Konor von Kraut, Julia Park, Charlotte M Brannon, Daniel A Sumano, Raushun A Kirtikar, Alicia A Erwin, Thomas J Metzner, Ryan K C Yuen, Alice C Fan, John T Leppert, Michael A Eberle, Mark B Gerstein, Michael Paul Snyder
Recurrent repeat expansions in human cancer genomes. Nature 613 (7942) (2022)
Graham S Erwin, Gamze Gürsoy, Rashid Al-Abri, Ashwini Suriyaprakash, Egor Dolzhenko, Kevin Zhu, Christian R Hoerner, Shannon M White, Lucia Ramirez, Ananya Vadlakonda, Alekhya Vadlakonda, Konor von Kraut, Julia Park, Charlotte M Brannon, Daniel A Sumano, Raushun A Kirtikar, Alicia A Erwin, Thomas J Metzner, Ryan K C Yuen, Alice C Fan, John T Leppert, Michael A Eberle, Mark B Gerstein, Michael Paul Snyder
Recurrent repeat expansions in human cancer genomes. Nature 613 (7942) (2022)
Graham S Erwin, Gamze Gürsoy, Rashid Al-Abri, Ashwini Suriyaprakash, Egor Dolzhenko, Kevin Zhu, Christian R Hoerner, Shannon M White, Lucia Ramirez, Ananya Vadlakonda, Alekhya Vadlakonda, Konor von Kraut, Julia Park, Charlotte M Brannon, Daniel A Sumano, Raushun A Kirtikar, Alicia A Erwin, Thomas J Metzner, Ryan K C Yuen, Alice C Fan, John T Leppert, Michael A Eberle, Mark B Gerstein, Michael Paul Snyder
Recurrent repeat expansions in human cancer genomes. Nature 613 (7942) (2022)
Graham S Erwin, Gamze Gürsoy, Rashid Al-Abri, Ashwini Suriyaprakash, Egor Dolzhenko, Kevin Zhu, Christian R Hoerner, Shannon M White, Lucia Ramirez, Ananya Vadlakonda, Alekhya Vadlakonda, Konor von Kraut, Julia Park, Charlotte M Brannon, Daniel A Sumano, Raushun A Kirtikar, Alicia A Erwin, Thomas J Metzner, Ryan K C Yuen, Alice C Fan, John T Leppert, Michael A Eberle, Mark B Gerstein, Michael Paul Snyder
Recurrent repeat expansions in human cancer genomes. Nature (2022)
Shuang Liu, Hyejung Won, Declan Clarke, Nana Matoba, Saniya Khullar, Yudi Mu, Daifeng Wang, Mark B Gerstein
Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex. Genome medicine 14 (1) (2022)
Ioannis A Vathiotis, Leonidas Salichos, Sandra Martinez-Morilla, Niki Gavrielatou, Thazin Nwe Aung, Saba Shafi, Pok Fai Wong, Shlomit Jessel, Harriet M Kluger, Konstantinos N Syrigos, Sarah Warren, Mark B Gerstein, David L Rimm
Baseline gene expression profiling determines long-term benefit to programmed cell death protein 1 axis blockade. NPJ precision oncology 6 (1) (2022)
Kun Xiong, Mark B Gerstein, Joanna Masel
Differences in evolutionary accessibility determine which equally effective regulatory motif evolves to generate pulses. Genetics 219 (3) (2022)
Graham S Erwin, Gamze Gürsoy, Rashid Al-Abri, Ashwini Suriyaprakash, Egor Dolzhenko, Kevin Zhu, Christian R Hoerner, Shannon M White, Lucia Ramirez, Ananya Vadlakonda, Alekhya Vadlakonda, Konor von Kraut, Julia Park, Charlotte M Brannon, Daniel A Sumano, Raushun A Kirtikar, Alicia A Erwin, Thomas J Metzner, Ryan K C Yuen, Alice C Fan, John T Leppert, Michael A Eberle, Mark B Gerstein, Michael Paul Snyder
Recurrent repeat expansions in human cancer genomes. Nature (2022)
Ioannis A Vathiotis, Leonidas Salichos, Sandra Martinez-Morilla, Niki Gavrielatou, Thazin Nwe Aung, Saba Shafi, Pok Fai Wong, Shlomit Jessel, Harriet M Kluger, Konstantinos N Syrigos, Sarah Warren, Mark B Gerstein, David L Rimm
Baseline gene expression profiling determines long-term benefit to programmed cell death protein 1 axis blockade. NPJ precision oncology 6 (1) (2022)
Graham S Erwin, Gamze Gürsoy, Rashid Al-Abri, Ashwini Suriyaprakash, Egor Dolzhenko, Kevin Zhu, Christian R Hoerner, Shannon M White, Lucia Ramirez, Ananya Vadlakonda, Alekhya Vadlakonda, Konor von Kraut, Julia Park, Charlotte M Brannon, Daniel A Sumano, Raushun A Kirtikar, Alicia A Erwin, Thomas J Metzner, Ryan K C Yuen, Alice C Fan, John T Leppert, Michael A Eberle, Mark B Gerstein, Michael Paul Snyder
Recurrent repeat expansions in human cancer genomes. Nature 613 (7942) (2022)
Ioannis A Vathiotis, Leonidas Salichos, Sandra Martinez-Morilla, Niki Gavrielatou, Thazin Nwe Aung, Saba Shafi, Pok Fai Wong, Shlomit Jessel, Harriet M Kluger, Konstantinos N Syrigos, Sarah Warren, Mark B Gerstein, David L Rimm
Baseline gene expression profiling determines long-term benefit to programmed cell death protein 1 axis blockade. NPJ precision oncology 6 (1) (2022)
Gamze Gürsoy, Charlotte M Brannon, Eric Ni, Sarah Wagner, Amol Khanna, Mark B Gerstein
Storing and analyzing a genome on a blockchain. Genome biology 23 (1) (2022)
Ioannis A Vathiotis, Leonidas Salichos, Sandra Martinez-Morilla, Niki Gavrielatou, Thazin Nwe Aung, Saba Shafi, Pok Fai Wong, Shlomit Jessel, Harriet M Kluger, Konstantinos N Syrigos, Sarah Warren, Mark B Gerstein, David L Rimm
Baseline gene expression profiling determines long-term benefit to programmed cell death protein 1 axis blockade. NPJ precision oncology 6 (1) (2022)
Zhanlin Chen, William C King, Ahyeon Hwang, Mark B Gerstein, Jing Zhang
DeepVelo : Single-cell transcriptomic deep velocity field learning with neural ordinary differential equations. Science advances 8 (48) (2022)
Graham S Erwin, Gamze Gürsoy, Rashid Al-Abri, Ashwini Suriyaprakash, Egor Dolzhenko, Kevin Zhu, Christian R Hoerner, Shannon M White, Lucia Ramirez, Ananya Vadlakonda, Alekhya Vadlakonda, Konor von Kraut, Julia Park, Charlotte M Brannon, Daniel A Sumano, Raushun A Kirtikar, Alicia A Erwin, Thomas J Metzner, Ryan K C Yuen, Alice C Fan, John T Leppert, Michael A Eberle, Mark B Gerstein, Michael Paul Snyder
Recurrent repeat expansions in human cancer genomes. Nature 613 (7942) (2022)
Dov Greenbaum, Mark B Gerstein
GATTACA is still pertinent 25 years later. Nature genetics 54 (12) (2022)
Graham S Erwin, Gamze Gürsoy, Rashid Al-Abri, Ashwini Suriyaprakash, Egor Dolzhenko, Kevin Zhu, Christian R Hoerner, Shannon M White, Lucia Ramirez, Ananya Vadlakonda, Alekhya Vadlakonda, Konor von Kraut, Julia Park, Charlotte M Brannon, Daniel A Sumano, Raushun A Kirtikar, Alicia A Erwin, Thomas J Metzner, Ryan K C Yuen, Alice C Fan, John T Leppert, Michael A Eberle, Mark B Gerstein, Michael Paul Snyder
Recurrent repeat expansions in human cancer genomes. Nature 613 (7942) (2022)
Dov Greenbaum, Mark B Gerstein
GATTACA is still pertinent 25 years later. Nature genetics 54 (12) (2022)
Gamze Gürsoy, Nancy Lu, Sarah Wagner, Mark B Gerstein
Recovering genotypes and phenotypes using allele-specific genes. Genome biology 22 (1) (2021)
Peter Ebert, Peter A Audano, Qihui Zhu, Bernardo Rodriguez-Martin, David Porubsky, Marc Jan Bonder, Arvis Sulovari, Jana Ebler, Weichen Zhou, Rebecca Serra Mari, Feyza Yilmaz, Xuefang Zhao, PingHsun Hsieh, Joyce Lee, Sushant Kumar, Jiadong Lin, Tobias Rausch, Yu Chen, Jingwen Ren, Martin Santamarina, Wolfram Höps, Hufsah Ashraf, Nelson T Chuang, Xiaofei Yang, Katherine M Munson, Alexandra P Lewis, Susan Fairley, Luke J Tallon, Wayne E Clarke, Anna O Basile, Marta Byrska-Bishop, André Corvelo, Uday S Evani, Tsung-Yu Lu, Mark J P Chaisson, Junjie Chen, Chong Li, Harrison Brand, Aaron M Wenger, Maryam Ghareghani, William T Harvey, Benjamin Raeder, Patrick Hasenfeld, Allison A Regier, Haley J Abel, Ira M Hall, Paul Flicek, Oliver Stegle, Mark B Gerstein, Jose M C Tubio, Zepeng Mu, Yang I Li, Xinghua Shi, Alex R Hastie, Kai Ye, Zechen Chong, Ashley D Sanders, Michael C Zody, Michael E Talkowski, Ryan E Mills, Scott E Devine, Charles Lee, Jan O Korbel, Tobias Marschall, Evan E Eichler
Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science (New York, N.Y.) 372 (6537) (2021)
Xiaotong Li, Sushant Kumar, Arif Harmanci, Shantao Li, Robert R Kitchen, Yan Zhang, Vikram B Wali, Sangeetha M Reddy, Wendy A Woodward, James M Reuben, Joel Rozowsky, Christos Hatzis, Naoto T Ueno, Savitri Krishnamurthy, Lajos Pusztai, Mark B Gerstein
Whole-genome sequencing of phenotypically distinct inflammatory breast cancers reveals similar genomic alterations to non-inflammatory breast cancers. Genome medicine 13 (1) (2021)
Prashant S Emani, Jonathan Warrell, Alan Anticevic, Stefan Bekiranov, Michael J Gandal, Michael J McConnell, Guillermo Sapiro, Alán Aspuru-Guzik, Justin T Baker, Matteo Bastiani, John D Murray, Stamatios N Sotiropoulos, Jacob Taylor, Geetha Senthil, Thomas Lehner, Mark B Gerstein, Aram W Harrow
Quantum computing at the frontiers of biological sciences. Nature methods 18 (7) (2021)
Andrew J Armstrong, Xiaotong Li, Matthew Tucker, Shantao Li, Xinmeng Jasmine Mu, Kenneth Wha Eng, Andrea Sboner, Mark A Rubin, Mark B Gerstein
Molecular medicine tumor board: whole-genome sequencing to inform on personalized medicine for a man with advanced prostate cancer. Prostate cancer and prostatic diseases 24 (3) (2021)
Gamze Gürsoy, Tianxiao Li, Susanna Liu, Eric Ni, Charlotte M Brannon, Mark B Gerstein
Functional genomics data: privacy risk assessment and technological mitigation. Nature reviews. Genetics (2021)
Jason J Liu, Daniel J Spakowicz, Garrett I Ash, Rebecca Hoyd, Rohan Ahluwalia, Andrew Zhang, Shaoke Lou, Donghoon Lee, Jing Zhang, Carolyn J Presley, Ann Greene, Matthew A Stults-Kolehmainen, Laura M Nally, Julien Steven Baker, Lisa M Fucito, Stuart A Weinzimer, Andrew V Papachristos, Mark B Gerstein
Bayesian structural time series for biomedical sensor data: A flexible modeling framework for evaluating interventions. PLoS computational biology 17 (8) (2021)
Gamze Gürsoy, Tianxiao Li, Susanna Liu, Eric Ni, Charlotte M Brannon, Mark B Gerstein
Author Correction: Functional genomics data: privacy risk assessment and technological mitigation. Nature reviews. Genetics (2021)
Esha Sarkar, Eduardo Chielle, Gamze Gürsoy, Oleg Mazonka, Mark B Gerstein, Michail Maniatakos
Fast and Scalable Private Genotype Imputation Using Machine Learning and Partially Homomorphic Encryption. IEEE access : practical innovations, open solutions 9 (2021)
Donghoon Lee, Jing Zhang, Jason J Liu, Mark B Gerstein
Epigenome-based splicing prediction using a recurrent neural network. PLoS computational biology 16 (6) (2020)
Cristina Sisu, Paul Muir, Adam Frankish, Ian Fiddes, Mark E Diekhans, David Thybert, Duncan T Odom, Paul Flicek, Thomas M Keane, Tim Hubbard, Jennifer Harrow, Mark B Gerstein
Transcriptional activity and strain-specific history of mouse pseudogenes. Nature communications 11 (1) (2020)
Matthew H Bailey, William U Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, Shantao Li, Yize Li, Sean Kelso, null null, null null, Gordon Saksena, Kyle Ellrott, Michael C Wendl, David A Wheeler, Gad A Getz, Jared T Simpson, Mark B Gerstein, Li Ding, null null
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature communications 11 (1) (2020)
Tao Chen, Ye Chen, Mengxue Yuan, Mark B Gerstein, Ting-Yu Li, Huiying Liang, Tanya E Froehlich, Long Lu
The Development of a Practical Artificial Intelligence Tool for Diagnosing and Evaluating Autism Spectrum Disorder: Multicenter Study. JMIR medical informatics 8 (5) (2020)
Shantao Li, Forrest W Crawford, Mark B Gerstein
Using sigLASSO to optimize cancer mutation signatures jointly with sampling likelihood. Nature communications 11 (1) (2020)
Anurag Sethi, Mengting Gu, Emrah Gumusgoz, Landon Chan, Koon-Kiu Yan, Joel Rozowsky, Iros Barozzi, Veena Afzal, Jennifer A Akiyama, Ingrid Plajzer-Frick, Chengfei Yan, Catherine S Novak, Momoe Kato, Tyler H Garvin, Quan Pham, Anne Harrington, Brandon J Mannion, Elizabeth A Lee, Yoko Fukuda-Yuzawa, Axel Visel, Diane E Dickel, Kevin Y Yip, Richard Sutton, Len A Pennacchio, Mark B Gerstein
Supervised enhancer prediction with epigenetic pattern recognition and targeted validation. Nature methods 17 (8) (2020)
Jing Zhang, Donghoon Lee, Vineet Dhiman, Peng Jiang, Jie Xu, Patrick McGillivray, Hongbo Yang, Jason Liu, William Meyerson, Declan Clarke, Mengting Gu, Shantao Li, Shaoke Lou, Jinrui Xu, Lucas Lochovsky, Matthew Ung, Lijia Ma, Shan Yu, Qin Cao, Arif O Harmanci, Koon-Kiu Yan, Anurag Sethi, Gamze Gürsoy, Michael Rutenberg Schoenberg, Joel Rozowsky, Jonathan Warrell, Prashant Emani, Yucheng T Yang, Timur Galeev, Xiangmeng Kong, Shuang Liu, Xiaotong Li, Jayanth Krishnan, Yanlin Feng, Juan Carlos Rivera-Mulia, Jessica Adrian, James R Broach, Michael Bolt, Jennifer Moran, Dominic Fitzgerald, Vishnu Dileep, Tingting Liu, Shenglin Mei, Takayo Sasaki, Claudia Trevilla-Garcia, Su Wang, Yanli Wang, Chongzhi Zang, Daifeng Wang, Robert J Klein, Michael Paul Snyder, David M Gilbert, Kevin Y Yip, Chao Cheng, Feng Yue, X Shirley Liu, Kevin P White, Mark B Gerstein
An integrative ENCODE resource for cancer genomics. Nature communications 11 (1) (2020)

Mark B Gerstein.css-eqlu8i{font-size:small;padding-left:4px;} (Mark Gerstein)

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Mark B Gerstein (Mark Gerstein)