Mark Gerstein - RankMe

149 papers A* 5A 3B 1C 2Misc 2Journal 118Unranked 17

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	ASTRO: Automated Spatial-Transcriptome whole RNA Output. Bioinform. Dingyao Zhang, Zhiyuan Chu, Yiran Huo, Yunzhe Jiang, Yuhang Chen, Zhiliang Bai, Rong Fan, Jun Lu, Mark Gerstein
2026	J	`jnl`	Dispersion Loss Counteracts Embedding Condensation and Improves Generalization in Small Language Models. CoRR Chen Liu, Xingzhi Sun, Xi Xiao, Alexandre Van Tassel, Ke Xu, Kristof Reimann, Danqi Liao, Mark Gerstein, Tianyang Wang, Xiao Wang, Smita Krishnaswamy
2026	J	`jnl`	Elign: Equivariant Diffusion Model Alignment from Foundational Machine Learning Force Fields. CoRR Yunyang Li, Lin Huang, Luojia Xia, Wenhe Zhang, Mark Gerstein
2026	J	`jnl`	MIOFlow 2.0: A unified framework for inferring cellular stochastic dynamics from single cell and spatial transcriptomics data. CoRR Xingzhi Sun, João F. Rocha, Brett Phelan, Dhananjay Bhaskar, Guillaume Huguet, Yanlei Zhang, Daniel Sumner Magruder, Alexander Tong, Ke Xu, Oluwadamilola Fasina, Mark Gerstein, Guy Wolf, Natalia Ivanova, Christine L. Chaffer, Smita Krishnaswamy
2025	J	`jnl`	CellForge: Agentic Design of Virtual Cell Models. CoRR Xiangru Tang, Zhuoyun Yu, Jiapeng Chen, Yan Cui, Daniel Shao, Weixu Wang, Fang Wu, Yuchen Zhuang, Wenqi Shi, Zhi Huang, Arman Cohan, Xihong Lin, Fabian J. Theis, Smita Krishnaswamy, Mark Gerstein
2025	J	`jnl`	ChemAgent: Self-updating Library in Large Language Models Improves Chemical Reasoning. CoRR Xiangru Tang, Tianyu Hu, Muyang Ye, Yanjun Shao, Xunjian Yin, Siru Ouyang, Wangchunshu Zhou, Pan Lu, Zhuosheng Zhang, Yilun Zhao, Arman Cohan, Mark Gerstein
2025	A*	`conf`	ChemAgent: Self-updating Memories in Large Language Models Improves Chemical Reasoning. ICLR Xiangru Tang, Tianyu Hu, Muyang Ye, Yanjun Shao, Xunjian Yin, Siru Ouyang, Wangchunshu Zhou, Pan Lu, Zhuosheng Zhang, Yilun Zhao, Arman Cohan, Mark Gerstein
2025	J	`jnl`	E2Former: A Linear-time Efficient and Equivariant Transformer for Scalable Molecular Modeling. CoRR Yunyang Li, Lin Huang, Zhihao Ding, Chu Wang, Xinran Wei, Han Yang, Zun Wang, Chang Liu, Yu Shi, Peiran Jin, Jia Zhang, Mark Gerstein, Tao Qin
2025	A*	`conf`	Enhancing the Scalability and Applicability of Kohn-Sham Hamiltonians for Molecular Systems. ICLR Yunyang Li, Zaishuo Xia, Lin Huang, Xinran Wei, Samuel Harshe, Han Yang, Erpai Luo, Zun Wang, Jia Zhang, Chang Liu, Bin Shao, Mark Gerstein
2025	J	`jnl`	Igniting Language Intelligence: The Hitchhiker's Guide from Chain-of-Thought Reasoning to Language Agents. ACM Comput. Surv. Zhuosheng Zhang, Yao Yao, Aston Zhang, Xiangru Tang, Xinbei Ma, Zhiwei He, Yiming Wang, Mark Gerstein, Rui Wang, Gongshen Liu, Hai Zhao
2025	A*	`conf`	Med-PRM: Medical Reasoning Models with Stepwise, Guideline-verified Process Rewards. EMNLP Jaehoon Yun, Jiwoong Sohn, Jungwoo Park, Hyunjae Kim, Xiangru Tang, Daniel Shao, Yonghoe Koo, Minhyeok Ko, Qingyu Chen, Mark Gerstein, Michael Moor, Jaewoo Kang
2025	J	`jnl`	Med-PRM: Medical Reasoning Models with Stepwise, Guideline-verified Process Rewards. CoRR Jaehoon Yun, Jiwoong Sohn, Jungwoo Park, Hyunjae Kim, Xiangru Tang, Yanjun Shao, Yonghoe Koo, Minhyeok Ko, Qingyu Chen, Mark Gerstein, Michael Moor, Jaewoo Kang
2025	J	`jnl`	MedAgentsBench: Benchmarking Thinking Models and Agent Frameworks for Complex Medical Reasoning. CoRR Xiangru Tang, Daniel Shao, Jiwoong Sohn, Jiapeng Chen, Jiayi Zhang, Jinyu Xiang, Fang Wu, Yilun Zhao, Chenglin Wu, Wenqi Shi, Arman Cohan, Mark Gerstein
2025	—	`conf`	STAGED: A Multi-Agent Neural Network for Learning Cellular Interaction Dynamics. MLCB João F. Rocha, Ke Xu, Xingzhi Sun, Ananya Krishna, Dhananjay Bhaskar, Blanche Mongeon, Morgan Craig, Mark Gerstein, Smita Krishnaswamy
2025	J	`jnl`	STAGED: A Multi-Agent Neural Network for Learning Cellular Interaction Dynamics. CoRR João F. Rocha, Ke Xu, Xingzhi Sun, Ananya Krishna, Dhananjay Bhaskar, Blanche Mongeon, Morgan Craig, Mark Gerstein, Smita Krishnaswamy
2025	J	`jnl`	Scalable and efficient on-chain data management in blockchain for large biomedical data. J. Biomed. Informatics Eric Ni, Elizabeth Knight, Mark Gerstein
2025	J	`jnl`	Towards Artificial Intelligence Research Assistant for Expert-Involved Learning. CoRR Tianyu Liu, Simeng Han, Xiao Luo, Hanchen Wang, Pan Lu, Biqing Zhu, Yuge Wang, Keyi Li, Jiapeng Chen, Rihao Qu, Yufeng Liu, Xinyue Cui, Aviv Yaish, Yuhang Chen, Minsheng Hao, Chuhan Li, Kexing Li, Arman Cohan, Hua Xu, Mark Gerstein, James Zou, Hongyu Zhao
2024	J	`jnl`	A Survey of Generative AI for De Novo Drug Design: New Frontiers in Molecule and Protein Generation. CoRR Xiangru Tang, Howard Dai, Elizabeth Knight, Fang Wu, Yunyang Li, Tianxiao Li, Mark Gerstein
2024	J	`jnl`	A survey of generative AI for Briefings Bioinform. Xiangru Tang, Howard Dai, Elizabeth Knight, Fang Wu, Yunyang Li, Tianxiao Li, Mark Gerstein
2024	J	`jnl`	ChemSafetyBench: Benchmarking LLM Safety on Chemistry Domain. CoRR Haochen Zhao, Xiangru Tang, Ziran Yang, Xiao Han, Xuanzhi Feng, Yueqing Fan, Senhao Cheng, Di Jin, Yilun Zhao, Arman Cohan, Mark Gerstein
2024	J	`jnl`	Epitope-anchored contrastive transfer learning for paired CD8+ T cell receptor-antigen recognition. Nat. Mac. Intell. Yumeng Zhang, Zhikang Wang, Yunzhe Jiang, Dene R. Littler, Mark Gerstein, Anthony W. Purcell, Jamie Rossjohn, Hong-Yu Ou, Jiangning Song
2024	—	`conf`	Investigating Data Contamination in Modern Benchmarks for Large Language Models. NAACL-HLT Chunyuan Deng, Yilun Zhao, Xiangru Tang, Mark Gerstein, Arman Cohan
2024	—	`conf`	MIMIR: A Customizable Agent Tuning Platform for Enhanced Scientific Applications. EMNLP (System Demonstrations) Xiangru Tang, Chunyuan Deng, Hanming Wang, Haoran Wang, Yilun Zhao, Wenqi Shi, May Fung, Wangchunshu Zhou, Jiannan Cao, Heng Ji, Arman Cohan, Mark Gerstein
2024	J	`jnl`	MIMIR: A Streamlined Platform for Personalized Agent Tuning in Domain Expertise. CoRR Chunyuan Deng, Xiangru Tang, Yilun Zhao, Hanming Wang, Haoran Wang, Wangchunshu Zhou, Arman Cohan, Mark Gerstein
2024	—	`conf`	MedAgents: Large Language Models as Collaborators for Zero-shot Medical Reasoning. ACL (Findings) Xiangru Tang, Anni Zou, Zhuosheng Zhang, Ziming Li, Yilun Zhao, Xingyao Zhang, Arman Cohan, Mark Gerstein
2024	J	`jnl`	Predicting spatially resolved gene expression via tissue morphology using adaptive spatial GNNs. Bioinform. Tianci Song, Eric Cosatto, Gaoyuan Wang, Rui Kuang, Mark Gerstein, Martin Renqiang Min, Jonathan Warrell
2024	J	`jnl`	Prioritizing Safeguarding Over Autonomy: Risks of LLM Agents for Science. CoRR Xiangru Tang, Qiao Jin, Kunlun Zhu, Tongxin Yuan, Yichi Zhang, Wangchunshu Zhou, Meng Qu, Yilun Zhao, Jian Tang, Zhuosheng Zhang, Arman Cohan, Zhiyong Lu, Mark Gerstein
2024	J	`jnl`	Representing core gene expression activity relationships using the latent structure implicit in Bayesian networks. Bioinform. Jiahao Gao, Mark Gerstein
2024	J	`jnl`	Step-Back Profiling: Distilling User History for Personalized Scientific Writing. CoRR Xiangru Tang, Xingyao Zhang, Yanjun Shao, Jie Wu, Yilun Zhao, Arman Cohan, Ming Gong, Dongmei Zhang, Mark Gerstein
2024	—	`conf`	Struc-Bench: Are Large Language Models Good at Generating Complex Structured Tabular Data? NAACL (Short Papers) Xiangru Tang, Yiming Zong, Jason Phang, Yilun Zhao, Wangchunshu Zhou, Arman Cohan, Mark Gerstein
2024	A*	`conf`	ToolLLM: Facilitating Large Language Models to Master 16000+ Real-world APIs. ICLR Yujia Qin, Shihao Liang, Yining Ye, Kunlun Zhu, Lan Yan, Yaxi Lu, Yankai Lin, Xin Cong, Xiangru Tang, Bill Qian, Sihan Zhao, Lauren Hong, Runchu Tian, Ruobing Xie, Jie Zhou, Mark Gerstein, Dahai Li, Zhiyuan Liu, Maosong Sun
2024	J	`jnl`	scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding. Briefings Bioinform. Ziheng Duan, Siwei Xu, Shushrruth Sai Srinivasan, Ahyeon Hwang, Cheyu Lee, Feng Yue, Mark Gerstein, Yu Luan, Matthew J. Girgenti, Jing Zhang
2023	—	`conf`	Aligning Factual Consistency for Clinical Studies Summarization through Reinforcement Learning. ClinicalNLP@ACL Xiangru Tang, Arman Cohan, Mark Gerstein
2023	J	`jnl`	Binding peptide generation for MHC Class I proteins with deep reinforcement learning. Bioinform. Ziqi Chen, Baoyi Zhang, Hongyu Guo, Prashant S. Emani, Trevor Clancy, Chongming Jiang, Mark Gerstein, Xia Ning, Chao Cheng, Martin Renqiang Min
2023	J	`jnl`	BioCoder: A Benchmark for Bioinformatics Code Generation with Contextual Pragmatic Knowledge. CoRR Xiangru Tang, Bill Qian, Rick Gao, Jiakang Chen, Xinyun Chen, Mark Gerstein
2023	J	`jnl`	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 Comput. Biol. Shaoke Lou, Mingjun Yang, Tianxiao Li, Weihao Zhao, Hannah Cevasco, Yucheng T. Yang, Mark Gerstein
2023	A*	`conf`	Disentangled Wasserstein Autoencoder for T-Cell Receptor Engineering. NeurIPS Tianxiao Li, Hongyu Guo, Filippo Grazioli, Mark Gerstein, Martin Renqiang Min
2023	J	`jnl`	FAVOR: functional annotation of variants online resource and annotator for variation across the human genome. Nucleic Acids Res. Hufeng Zhou, Theodore Arapoglou, Xihao Li, Zilin Li, Xiuwen Zheng, Jill Moore, Abhijith Asok, Sushant Kumar, Elizabeth E. Blue, Steven Buyske, Nancy J. Cox, Adam Felsenfeld, Mark Gerstein, Eimear Kenny, Bingshan Li, Tara Cox Matise, Anthony Philippakis, Heidi L. Rehm, Heidi J. Sofia, Grace Snyder, Zhiping Weng, Benjamin M. Neale, Shamil R. Sunyaev, Xihong Lin
2023	J	`jnl`	GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Res. Adam Frankish, Silvia Carbonell Sala, Mark Diekhans, Irwin Jungreis, Jane E. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Carme Arnan, If Barnes, Abhimanyu Banerjee, Ruth Bennett, Andrew E. Berry, Alexandra Bignell, Carles Boix, Ferriol Calvet Riera, Daniel Cerdán-Vélez, Fiona Cunningham, Claire Davidson, Sarah M. Donaldson, Cagatay Dursun, Reham Fatima, Stefano Giorgetti, Carlos García-Girón, Jose M. Gonzalez, Matthew Hardy, Peter W. Harrison, Thibaut Hourlier, Zoe Hollis, Toby Hunt, Benjamin James, Yunzhe Jiang, Rory Johnson, Mike P. Kay, Julien Lagarde, Fergal J. Martin, Laura Martínez Gómez, Surag Nair, Pengyu Ni, Fernando Pozo, Vivek Ramalingam, Magali Ruffier, Bianca M. Schmitt, Jacob M. Schreiber, Emily Steed, Marie-Marthe Suner, Dulika Sumathipala, Irina Sycheva, Barbara Uszczynska-Ratajczak, Elizabeth Wass, Yucheng T. Yang, Andrew D. Yates, Zahoor Zafrulla, Jyoti Choudhary, Mark Gerstein, Roderic Guigó, Tim J. P. Hubbard, Manolis Kellis, Anshul Kundaje, Benedict Paten, Michael L. Tress, Paul Flicek
2023	—	`conf`	GersteinLab at MEDIQA-Chat 2023: Clinical Note Summarization from Doctor-Patient Conversations through Fine-tuning and In-context Learning. ClinicalNLP@ACL Xiangru Tang, Andrew Tran, Jeffrey Tan, Mark Gerstein
2023	J	`jnl`	GersteinLab at MEDIQA-Chat 2023: Clinical Note Summarization from Doctor-Patient Conversations through Fine-tuning and In-context Learning. CoRR Xiangru Tang, Andrew Tran, Jeffrey Tan, Mark Gerstein
2023	J	`jnl`	Igniting Language Intelligence: The Hitchhiker's Guide From Chain-of-Thought Reasoning to Language Agents. CoRR Zhuosheng Zhang, Yao Yao, Aston Zhang, Xiangru Tang, Xinbei Ma, Zhiwei He, Yiming Wang, Mark Gerstein, Rui Wang, Gongshen Liu, Hai Zhao
2023	J	`jnl`	Investigating Data Contamination in Modern Benchmarks for Large Language Models. CoRR Chunyuan Deng, Yilun Zhao, Xiangru Tang, Mark Gerstein, Arman Cohan
2023	J	`jnl`	ML-Bench: Large Language Models Leverage Open-source Libraries for Machine Learning Tasks. CoRR Yuliang Liu, Xiangru Tang, Zefan Cai, Junjie Lu, Yichi Zhang, Yanjun Shao, Zexuan Deng, Helan Hu, Zengxian Yang, Kaikai An, Ruijun Huang, Shuzheng Si, Sheng Chen, Haozhe Zhao, Zhengliang Li, Liang Chen, Yiming Zong, Yan Wang, Tianyu Liu, Zhiwei Jiang, Baobao Chang, Yujia Qin, Wangchunshu Zhou, Yilun Zhao, Arman Cohan, Mark Gerstein
2023	J	`jnl`	MedAgents: Large Language Models as Collaborators for Zero-shot Medical Reasoning. CoRR Xiangru Tang, Anni Zou, Zhuosheng Zhang, Yilun Zhao, Xingyao Zhang, Arman Cohan, Mark Gerstein
2023	J	`jnl`	Struc-Bench: Are Large Language Models Really Good at Generating Complex Structured Data? CoRR Xiangru Tang, Yiming Zong, Jason Phang, Yilun Zhao, Wangchunshu Zhou, Arman Cohan, Mark Gerstein
2023	J	`jnl`	ToolLLM: Facilitating Large Language Models to Master 16000+ Real-world APIs. CoRR Yujia Qin, Shihao Liang, Yining Ye, Kunlun Zhu, Lan Yan, Yaxi Lu, Yankai Lin, Xin Cong, Xiangru Tang, Bill Qian, Sihan Zhao, Runchu Tian, Ruobing Xie, Jie Zhou, Mark Gerstein, Dahai Li, Zhiyuan Liu, Maosong Sun
2022	J	`jnl`	Higher-Order Generalization Bounds: Learning Deep Probabilistic Programs via PAC-Bayes Objectives. CoRR Jonathan Warrell, Mark Gerstein
2022	—	`conf`	Privacy-preserving Model Training for Disease Prediction Using Federated Learning with Differential Privacy. EMBC Amol Khanna, Vincent Schaffer, Gamze Gürsoy, Mark Gerstein
2022	J	`jnl`	Scalable privacy-preserving cancer type prediction with homomorphic encryption. CoRR Esha Sarkar, Eduardo Chielle, Gamze Gürsoy, Leo Chen, Mark Gerstein, Michail Maniatakos
2022	J	`jnl`	Venus: An efficient virus infection detection and fusion site discovery method using single-cell and bulk RNA-seq data. PLoS Comput. Biol. Cheyu Lee, Yuhang Chen, Ziheng Duan, Min Xu, Matthew J. Girgenti, Ke Xu, Mark Gerstein, Jing Zhang
2021	J	`jnl`	Bayesian structural time series for biomedical sensor data: A flexible modeling framework for evaluating interventions. PLoS Comput. Biol. Jason Liu, Daniel J. Spakowicz, Garrett I. Ash, Rebecca Hoyd, Rohan Ahluwalia, Andrew Zhang, Shaoke Lou, Donghoon Lee, Jing Zhang, Carolyn Presley, Ann Greene, Matthew Stults-Kolehmainen, Laura M. Nally, Julien S. Baker, Lisa M. Fucito, Stuart A. Weinzimer, Andrew V. Papachristos, Mark Gerstein
2021	J	`jnl`	DECODE: a Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays. Bioinform. Zhanlin Chen, Jing Zhang, Jason Liu, Yi Dai, Donghoon Lee, Martin Renqiang Min, Min Xu, Mark Gerstein
2021	J	`jnl`	FANCY: fast estimation of privacy risk in functional genomics data. Bioinform. Gamze Gürsoy, Charlotte M. Brannon, Fabio C. P. Navarro, Mark Gerstein
2021	J	`jnl`	Fast and Scalable Private Genotype Imputation Using Machine Learning and Partially Homomorphic Encryption. IEEE Access Esha Sarkar, Eduardo Chielle, Gamze Gürsoy, Oleg Mazonka, Mark Gerstein, Michail Maniatakos
2021	J	`jnl`	Forest Fire Clustering: Cluster-oriented Label Propagation Clustering and Monte Carlo Verification Inspired by Forest Fire Dynamics. CoRR Zhanlin Chen, Philip Tuckman, Jeremy Goldwasser, Jing Zhang, Mark Gerstein
2021	J	`jnl`	GENCODE 2021. Nucleic Acids Res. Adam Frankish, Mark Diekhans, Irwin Jungreis, Julien Lagarde, Jane E. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Joel Armstrong, If Barnes, Andrew E. Berry, Alexandra Bignell, Carles Boix, Silvia Carbonell Sala, Fiona Cunningham, Tomás Di Domenico, Sarah M. Donaldson, Ian T. Fiddes, Carlos García-Girón, Jose M. Gonzalez, Tiago Grego, Matthew Hardy, Thibaut Hourlier, Kevin L. Howe, Toby Hunt, Osagie G. Izuogu, Rory Johnson, Fergal J. Martin, Laura Martínez, Shamika Mohanan, Paul Muir, Fabio C. P. Navarro, Anne Parker, Baikang Pei, Fernando Pozo, Ferriol Calvet Riera, Magali Ruffier, Bianca M. Schmitt, Eloise Stapleton, Marie-Marthe Suner, Irina Sycheva, Barbara Uszczynska-Ratajczak, Maxim Y. Wolf, Jinrui Xu, Yucheng T. Yang, Andrew D. Yates, Daniel R. Zerbino, Yan Zhang, Jyoti Choudhary, Mark Gerstein, Roderic Guigó, Tim J. P. Hubbard, Manolis Kellis, Benedict Paten, Michael L. Tress, Paul Flicek
2021	J	`jnl`	Gene Tracer: a smart, interactive, voice-controlled Alexa skill For gene information retrieval and browsing, mutation annotation and network visualization. Bioinform. Shaoke Lou, Tianxiao Li, Jason Liu, Mark Gerstein
2021	J	`jnl`	SCAN-ATAC-Sim: a scalable and efficient method for simulating single-cell ATAC-seq data from bulk-tissue experiments. Bioinform. Zhanlin Chen, Jing Zhang, Jason Liu, Zixuan Zhang, Jiangqi Zhu, Donghoon Lee, Min Xu, Mark Gerstein
2020	J	`jnl`	Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah Wala, Ofer Shapira, Grace Tiao, Henrik Hornshøj, Julian M. Hess, Randi Istrup Juul, Ziao Lin, Lars Feuerbach, Radhakrishnan Sabarinathan, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andrés Lanzós, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin Wing Yiu Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A. Fonseca, Abel González-Pérez, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, André Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nasa Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose M. C. Tubio, Husen M. Umer, Liis Uusküla-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, Cheng-Zhong Zhang, Jing Zhang, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Benjamin J. Raphael, Mark A. Rubin, Chris Sander, Lincoln D. Stein, Joshua M. Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Jüri Reimand, Mark Gerstein, Ekta Khurana, Peter J. Campbell, Núria López-Bigas, Gary D. Bader, Jonathan Barenboim, Rameen Beroukhim, Søren Brunak, Ken Chen, Jung Kyoon Choi, Jordi Deu-Pons, J. Lynn Fink, Joan Frigola, Carlo Gambacorti Passerini, Dale W. Garsed, Gad Getz, Ivo Glynne Gut, David Haan, Arif Ozgun Harmanci, Mohamed Helmy, Ermin Hodzic, José M. G. Izarzugaza, Jong K. Kim, Jan O. Korbel, Erik Larsson, Shantao Li, Xiaotong Li, Shaoke Lou, Kathleen Marchal, Iñigo Martincorena, Alexander Martínez-Fundichely, Patrick D. McGillivray, William Meyerson, Ferran Muiños, Marta Paczkowska, Kiejung Park, Jakob Skou Pedersen, Tirso Pons, Sergio Pulido-Tamayo, Iker Reyes-Salazar, Matthew A. Reyna, Carlota Rubio-Perez, Süleyman Cenk Sahinalp, Leonidas Salichos, Mark Shackleton, Raunak Shrestha, Alfonso Valencia, Miguel Vazquez, Lieven P. C. Verbeke, Jiayin Wang, Jonathan Warrell, Sebastian M. Waszak, Joachim Weischenfeldt, Guanming Wu, Jun Yu, Xuanping Zhang, Yan Zhang, Zhongming Zhao, Lihua Zou, Kadir C. Akdemir, Eva G. Alvarez, Adrian Baez-Ortega, Paul C. Boutros, David D. L. Bowtell, Benedikt Brors, Kathleen H. Burns, Kin Chan, Isidro Cortés-Ciriano, Ana Dueso-Barroso, Andrew J. Dunford, Paul A. Edwards, Xavier Estivill, Dariush Etemadmoghadam, Milana Frenkel-Morgenstern, Dmitry A. Gordenin, Barbara Hutter, David T. W. Jones, Young Seok Ju, Marat D. Kazanov, Leszek J. Klimczak, Youngil Koh, Eunjung Alice Lee, Jake June-Koo Lee, Andy G. Lynch, Geoff MacIntyre, Florian Markowetz, Matthew Meyerson, Satoru Miyano, Fabio C. P. Navarro, Stephan Ossowski, Peter J. Park, John V. Pearson, Montserrat Puiggròs, Karsten Rippe, Steven A. Roberts, Bernardo Rodriguez-Martin, Ralph Scully, David Torrents, Izar Villasante, Nicola Waddell, Jeremiah A. Wala, Lixing Yang, Sung-Soo Yoon, Jorge Zamora
2020	J	`jnl`	DiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring. BMC Bioinform. Jing Zhang, Jason Liu, Donghoon Lee, Shaoke Lou, Zhanlin Chen, Gamze Gürsoy, Mark Gerstein
2020	J	`jnl`	Epigenome-based splicing prediction using a recurrent neural network. PLoS Comput. Biol. Donghoon Lee, Jing Zhang, Jason Liu, Mark Gerstein
2020	J	`jnl`	Latent-space embedding of expression data identifies gene signatures from sputum samples of asthmatic patients. BMC Bioinform. Shaoke Lou, Tianxiao Li, Daniel Spakowicz, Xiting Yan, Geoffrey Lowell Chupp, Mark Gerstein
2020	J	`jnl`	NIMBus: a negative binomial regression based Integrative Method for mutation Burden Analysis. BMC Bioinform. Jing Zhang, Jason Liu, Patrick D. McGillivray, Caroline Yi, Lucas Lochovsky, Donghoon Lee, Mark Gerstein
2020	J	`jnl`	Origins and characterization of variants shared between databases of somatic and germline human mutations. BMC Bioinform. William Meyerson, John Leisman, Fabio C. P. Navarro, Mark Gerstein
2020	J	`jnl`	Shaping the nebulous enhancer in the era of high-throughput assays and genome editing. Briefings Bioinform. Edwin Yu-Kiu Ho, Qin Cao, Mengting Gu, Ricky Wai-Lun Chan, Qiong Wu, Mark Gerstein, Kevin Y. Yip
2020	J	`jnl`	The corrected gene proximity map for analyzing the 3D genome organization using Hi-C data. BMC Bioinform. Cheng Ye, Alberto Paccanaro, Mark Gerstein, Koon-Kiu Yan
2020	J	`jnl`	TopicNet: a framework for measuring transcriptional regulatory network change. Bioinform. Shaoke Lou, Tianxiao Li, Xiangmeng Kong, Jing Zhang, Jason Liu, Donghoon Lee, Mark Gerstein
2019	J	`jnl`	GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res. Adam Frankish, Mark Diekhans, Anne-Maud Ferreira, Rory Johnson, Irwin Jungreis, Jane E. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Joel Armstrong, If Barnes, Andrew E. Berry, Alexandra Bignell, Silvia Carbonell Sala, Jacqueline Chrast, Fiona Cunningham, Tomás Di Domenico, Sarah M. Donaldson, Ian T. Fiddes, Carlos García-Girón, Jose M. Gonzalez, Tiago Grego, Matthew Hardy, Thibaut Hourlier, Toby Hunt, Osagie G. Izuogu, Julien Lagarde, Fergal J. Martin, Laura Martínez, Shamika Mohanan, Paul Muir, Fabio C. P. Navarro, Anne Parker, Baikang Pei, Fernando Pozo, Magali Ruffier, Bianca M. Schmitt, Eloise Stapleton, Marie-Marthe Suner, Irina Sycheva, Barbara Uszczynska-Ratajczak, Jinrui Xu, Andrew D. Yates, Daniel R. Zerbino, Yan Zhang, Bronwen L. Aken, Jyoti Choudhary, Mark Gerstein, Roderic Guigó, Tim J. P. Hubbard, Manolis Kellis, Benedict Paten, Alexandre Reymond, Michael L. Tress, Paul Flicek
2018	J	`jnl`	MOAT: efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool. Bioinform. Lucas Lochovsky, Jing Zhang, Mark Gerstein
2018	J	`jnl`	Multiple-Swarm Ensembles: Improving the Predictive Power and Robustness of Predictive Models and Its Use in Computational Biology. IEEE ACM Trans. Comput. Biol. Bioinform. Pedro Alves, Shuang Liu, Daifeng Wang, Mark Gerstein
2018	J	`jnl`	Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development. Bioinform. Karolina Elzbieta Kaczor-Urbanowicz, Yong Kim, Feng Li, Timur Galeev, Robert R. Kitchen, Mark Gerstein, Kikuye Koyano, Sung-Hee Jeong, Xiaoyan Wang, David Elashoff, So Young Kang, Su Mi Kim, Kyoung Kim, Sung Kim, David Chia, Xinshu Xiao, Joel S. Rozowsky, David T. W. Wong
2018	J	`jnl`	Rank Projection Trees for Multilevel Neural Network Interpretation. CoRR Jonathan Warrell, Hussein Mohsen, Mark Gerstein
2017	J	`jnl`	HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps. Bioinform. Koon-Kiu Yan, Galip Gürkan Yardimci, Chengfei Yan, William S. Noble, Mark Gerstein
2017	J	`jnl`	MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions. PLoS Comput. Biol. Koon-Kiu Yan, Shaoke Lou, Mark Gerstein
2016	J	`jnl`	DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks. PLoS Comput. Biol. Daifeng Wang, Fei He, Sergei Maslov, Mark Gerstein
2015	J	`jnl`	High-order neural networks and kernel methods for peptide-MHC binding prediction. Bioinform. Pavel P. Kuksa, Martin Renqiang Min, Rishabh Dugar, Mark Gerstein
2014	J	`jnl`	Comparative analysis of regulatory information and circuits across distant species Open. Nat. Alan P. Boyle, Carlos L. Araya, Cathleen Brdlik, Philip Cayting, Chao Cheng, Yong Cheng, Kathryn Gardner, LaDeana W. Hillier, Judith Janette, Lixia Jiang, Dionna Kasper, Trupti Kawli, Pouya Kheradpour, Anshul Kundaje, Jingyi Jessica Li, Lijia Ma, Wei Niu, E. Jay Rehm, Joel S. Rozowsky, Matthew Slattery, Rebecca Spokony, Robert Terrell, Dionne Vafeados, Daifeng Wang, Peter Weisdepp, Yi-Chieh Wu, Dan Xie, Koon-Kiu Yan, Elise A. Feingold, Peter J. Good, Michael J. Pazin, Haiyan Huang, Peter J. Bickel, Steven E. Brenner, Valerie Reinke, Robert H. Waterston, Mark Gerstein, Kevin P. White, Manolis Kellis, Michael Snyder
2014	A	`conf`	Interpretable Sparse High-Order Boltzmann Machines. AISTATS Martin Renqiang Min, Xia Ning, Chao Cheng, Mark Gerstein
2013	—	`conf`	Comparative network analysis of gene co-expression networks reveals the conserved and species-specific functions of cell-wall related genes between Arabidopsis and Poplar. BCB Daifeng Wang, Eric Pan, Gang Fang, Sunita Kumari, Fei He, Doreen Ware, Sergei Maslov, Mark Gerstein
2013	J	`jnl`	Identification of yeast cell cycle regulated genes based on genomic features. BMC Syst. Biol. Chao Cheng, Yao Fu, Linsheng Shen, Mark Gerstein
2013	J	`jnl`	Interpretation of Genomic Variants Using a Unified Biological Network Approach. PLoS Comput. Biol. Ekta Khurana, Yao Fu, Jieming Chen, Mark Gerstein
2012	J	`jnl`	VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment. Bioinform. Lukas Habegger, Suganthi Balasubramanian, David Z. Chen, Ekta Khurana, Andrea Sboner, Arif Ozgun Harmanci, Joel S. Rozowsky, Declan Clarke, Michael Snyder, Mark Gerstein
2011	J	`jnl`	ACT: aggregation and correlation toolbox for analyses of genome tracks. Bioinform. Justin Jee, Joel S. Rozowsky, Kevin Y. Yip, Lucas Lochovsky, Robert D. Bjornson, Guoneng Zhong, Zhengdong D. Zhang, Yutao Fu, Jie Wang, Zhiping Weng, Mark Gerstein
2011	J	`jnl`	AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision. Bioinform. Alexej Abyzov, Mark Gerstein
2011	J	`jnl`	Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data. PLoS Comput. Biol. Chao Cheng, Koon-Kiu Yan, Woochang Hwang, Jiang Qian, Nitin Bhardwaj, Joel S. Rozowsky, Zhi John Lu, Wei Niu, Pedro Alves, Masaomi Kato, Michael Snyder, Mark Gerstein
2011	J	`jnl`	Genomics and Privacy: Implications of the New Reality of Closed Data for the Field. PLoS Comput. Biol. Dov Greenbaum, Andrea Sboner, Xinmeng Jasmine Mu, Mark Gerstein
2011	J	`jnl`	RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries. Bioinform. Lukas Habegger, Andrea Sboner, Tara A. Gianoulis, Joel S. Rozowsky, Ashish Agarwal, Michael Snyder, Mark Gerstein
2011	J	`jnl`	TIP: A probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles. Bioinform. Chao Cheng, Renqiang Min, Mark Gerstein
2011	J	`jnl`	Tiling array data analysis: a multiscale approach using wavelets. BMC Bioinform. Alexander Karpikov, Joel S. Rozowsky, Mark Gerstein
2010	J	`jnl`	3V: cavity, channel and cleft volume calculator and extractor. Nucleic Acids Res. Neil Voss, Mark Gerstein
2010	—	`conf`	Analysis of molecular networks. BCB Mark Gerstein
2010	—	`conf`	Dynamic and static analysis of transcriptional regulatory networks in a hierarchical context. GENSiPS Nitin Bhardwaj, Mark Gerstein
2010	J	`jnl`	Genome-wide sequence-based prediction of peripheral proteins using a novel semi-supervised learning technique. BMC Bioinform. Nitin Bhardwaj, Mark Gerstein, Hui Lu
2010	—	`conf`	Hierarchical analysis of regulatory networks and cross-disciplinary comparison with the Linux call graph. GENSiPS Koon-Kiu Yan, Mark Gerstein
2010	J	`jnl`	Using semantic web rules to reason on an ontology of pseudogenes. Bioinform. Matthew Holford, Ekta Khurana, Kei-Hoi Cheung, Mark Gerstein
2009	J	`jnl`	Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels. BMC Bioinform. Kevin Y. Yip, Philip M. Kim, Drew McDermott, Mark Gerstein
2009	J	`jnl`	Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions. Bioinform. Kevin Y. Yip, Mark Gerstein
2008	J	`jnl`	An integrated system for studying residue coevolution in proteins. Bioinform. Kevin Y. Yip, Prianka Patel, Philip M. Kim, Donald M. Engelman, Drew McDermott, Mark Gerstein
2008	J	`jnl`	Modeling ChIP Sequencing In Silico with Applications. PLoS Comput. Biol. Zhengdong D. Zhang, Joel S. Rozowsky, Michael Snyder, Joseph T. Chang, Mark Gerstein
2008	J	`jnl`	Open Access: Taking Full Advantage of the Content. PLoS Comput. Biol. Philip E. Bourne, J. Lynn Fink, Mark Gerstein
2007	J	`jnl`	An interdepartmental Ph.D. program in computational biology and bioinformatics: The Yale perspective. J. Biomed. Informatics Mark Gerstein, Dov Greenbaum, Kei-Hoi Cheung, Perry L. Miller
2007	J	`jnl`	Assessing the need for sequence-based normalization in tiling microarray experiments. Bioinform. Thomas E. Royce, Joel S. Rozowsky, Mark Gerstein
2007	J	`jnl`	FlexOracle: predicting flexible hinges by identification of stable domains. BMC Bioinform. Samuel Flores, Mark Gerstein
2007	J	`jnl`	Hinge Atlas: relating protein sequence to sites of structural flexibility. BMC Bioinform. Samuel Flores, Long J. Lu, Julie Yang, Nicholas Carriero, Mark Gerstein
2007	J	`jnl`	Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics. Bioinform. Andrew K. Smith, Kei-Hoi Cheung, Michael Krauthammer, Martin H. Schultz, Mark Gerstein
2007	J	`jnl`	LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics. BMC Bioinform. Andrew K. Smith, Kei-Hoi Cheung, Kevin Y. Yip, Martin H. Schultz, Mark Gerstein
2007	J	`jnl`	PARE: A tool for comparing protein abundance and mRNA expression data. BMC Bioinform. Eric Z. Yu, Anne E. Counterman Burba, Mark Gerstein
2007	J	`jnl`	Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Res. John E. Karro, Yangpan Yan, Deyou Zheng, Zhaolei Zhang, Nicholas Carriero, Philip Cayting, Paul M. Harrison, Mark Gerstein
2007	J	`jnl`	RNAi Development. PLoS Comput. Biol. Mark Gerstein, Shawn M. Douglas
2007	J	`jnl`	The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics. PLoS Comput. Biol. Haiyuan Yu, Philip M. Kim, Emmett Sprecher, Valery Trifonov, Mark Gerstein
2007	J	`jnl`	The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks. Bioinform. Kevin Y. Yip, Haiyuan Yu, Philip M. Kim, Martin H. Schultz, Mark Gerstein
2007	J	`jnl`	Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications. Bioinform. Haiyuan Yu, Ronald Jansen, Gustavo Stolovitzky, Mark Gerstein
2006	J	`jnl`	A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge. Bioinform. Jiang Du, Joel S. Rozowsky, Jan O. Korbel, Zhengdong D. Zhang, Thomas E. Royce, Martin H. Schultz, Michael Snyder, Mark Gerstein
2006	J	`jnl`	An Integrative Genomic Approach to Uncover Molecular Mechanisms of Prokaryotic Traits. PLoS Comput. Biol. Yang Liu, Jianrong Li, Lee T. Sam, Chern-Sing Goh, Mark Gerstein, Yves A. Lussier
2006	Misc	`conf`	Design Issues in Implementing a Portable Sample Tracking and Analysis Research Support (STARS) System for PCR Based Microarray Research. CISS Frederick G. Sayward, Jin Yang, Kenneth Nelson, Ghia Euskirchen, Alexander E. Urban, Paul Bertone, John Rinn, Sherman Weissman, Mark Gerstein, Michael Snyder, Perry L. Miller
2006	J	`jnl`	Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins. Bioinform. Anne E. Counterman Burba, Ursula Lehnert, Eric Z. Yu, Mark Gerstein
2006	J	`jnl`	Predicting interactions in protein networks by completing defective cliques. Bioinform. Haiyuan Yu, Alberto Paccanaro, Valery Trifonov, Mark Gerstein
2006	J	`jnl`	PseudoPipe: an automated pseudogene identification pipeline. Bioinform. Zhaolei Zhang, Nicholas Carriero, Deyou Zheng, John E. Karro, Paul M. Harrison, Mark Gerstein
2006	J	`jnl`	The Database of Macromolecular Motions: new features added at the decade mark. Nucleic Acids Res. Samuel Flores, Nathaniel Echols, Duncan Milburn, Brandon Hespenheide, Kevin Keating, Jason Lu, Stephen Wells, Eric Z. Yu, Michael Thorpe, Mark Gerstein
2006	J	`jnl`	The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks. Bioinform. Kevin Y. Yip, Haiyuan Yu, Philip M. Kim, Martin H. Schultz, Mark Gerstein
2005	—	`conf`	Analysis of Genomic Tiling Microarrays for Transcript Mapping and the Identification of Transcription Factor Binding Sites. BSB Joel S. Rozowsky, Paul Bertone, Thomas E. Royce, Sherman Weissman, Michael Snyder, Mark Gerstein
2005	J	`jnl`	Case Report: A High Productivity/Low Maintenance Approach to High-performance Computation for Biomedicine: Four Case Studies. J. Am. Medical Informatics Assoc. Nicholas Carriero, Michael V. Osier, Kei-Hoi Cheung, Perry L. Miller, Mark Gerstein, Hongyu Zhao, Baolin Wu, Scott Rifkin, Joseph T. Chang, Heping Zhang, Kevin P. White, Kenneth R. Williams, Martin H. Schultz
2005	J	`jnl`	Editorial. Nucleic Acids Res. Dov Greenbaum, Andrew K. Smith, Mark Gerstein
2005	B	`conf`	Inferring protein-protein interactions using interaction network topologies. IJCNN Alberto Paccanaro, Valery Trifonov, Haiyuan Yu, Mark Gerstein
2005	—	`ch.`	Protein Interaction Prediction by Integrating Genomic Features and Protein Interaction Network Analysis. Data Analysis and Visualization in Genomics and Proteomics Long J. Lu, Yu Xia, Haiyuan Yu, Alexander Rives, Haoxin Lu, Falk Schubert, Mark Gerstein
2005	—	`conf`	YeastHub: a semantic web use case for integrating data in the life sciences domain. ISMB (Supplement of Bioinformatics) Kei-Hoi Cheung, Kevin Y. Yip, Andrew K. Smith, Remko de Knikker, Andy Masiar, Mark Gerstein
2004	—	`conf`	A XML-Based Approach to Integrating Heterogeneous Yeast Genome Data. METMBS Kei-Hoi Cheung, Deyun Pan, Andrew K. Smith, Michael R. Seringhaus, Shawn M. Douglas, Mark Gerstein
2004	J	`jnl`	Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search. J. Comput. Biol. Piotr Berman, Paul Bertone, Bhaskar DasGupta, Mark Gerstein, Ming-Yang Kao, Michael Snyder
2004	J	`jnl`	Information assessment on predicting protein-protein interactions. BMC Bioinform. Nan Lin, Baolin Wu, Ronald Jansen, Mark Gerstein, Hongyu Zhao
2004	J	`jnl`	Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures. BMC Bioinform. Vadim Alexandrov, Mark Gerstein
2003	—	`conf`	Computational Proteomics: Genome-scale Analysis of Protein Structure, Function, & Evolution(Invited Talk). German Conference on Bioinformatics Mark Gerstein
2003	J	`jnl`	ExpressYourself: a modular platform for processing and visualizing microarray data Nucleic Acids Res. Nicholas M. Luscombe, Thomas E. Royce, Paul Bertone, Nathaniel Echols, Christine E. Horak, Joseph T. Chang, Michael Snyder, Mark Gerstein
2003	J	`jnl`	MolMovDB: analysis and visualization of conformational change and structural flexibility. Nucleic Acids Res. Nathaniel Echols, Duncan Milburn, Mark Gerstein
2003	J	`jnl`	Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. Bioinform. Jiang Qian, C. Jimmy Lin, Nicholas M. Luscombe, Haiyuan Yu, Mark Gerstein
2002	J	`jnl`	Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts. Bioinform. Dov Greenbaum, Ronald Jansen, Mark Gerstein
2002	J	`jnl`	Calculations of protein volumes: sensitivity analysis and parameter database. Bioinform. Jerry Tsai, Mark Gerstein
2002	C	`conf`	Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search. WABI Piotr Berman, Paul Bertone, Bhaskar DasGupta, Mark Gerstein, Ming-Yang Kao, Michael Snyder
2002	J	`jnl`	Toward a systematic definition of protein function that scales to the genome level: defining function in terms of interactions. Proc. IEEE Ning Lan, Ronald Jansen, Mark Gerstein
2002	Misc	`conf`	YMD: a microarray database for large-scale gene expression analysis. AMIA Kei-Hoi Cheung, Kevin P. White, Janet Hager, Mark Gerstein, Valerie Reinke, Kenneth Nelson, Peter Masiar, Ranjana Srivastava, Yuli Li, Ju Li, Hongyu Zhao, Jinming Li, David B. Allison, Michael Snyder, Perry L. Miller, Kenneth R. Williams
2001	C	`conf`	An XML Application For Genomic Data Interoperation. BIBE Kei-Hoi Cheung, Yang Liu, Anuj Kumar, Michael Snyder, Mark Gerstein, Perry L. Miller
2001	J	`jnl`	Determining the minimum number of types necessary to represent the sizes of protein atoms. Bioinform. Jerry Tsai, Neil Voss, Mark Gerstein
2001	J	`jnl`	SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics. Nucleic Acids Res. Paul Bertone, Yuval Kluger, Ning Lan, Deyou Zheng, Dinesh Christendat, Adelinda Yee, Aled M. Edwards, Cheryl H. Arrowsmith, Gaetano T. Montelione, Mark Gerstein
1999	J	`jnl`	E-publishing on the Web: promises, pitfalls, and payoffs for bioinformatics. Bioinform. Mark Gerstein
1998	J	`jnl`	Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence. Bioinform. Mark Gerstein
1998	—	`conf`	[Invited Lecture] A Structural Census of Genomes: Comparing Bacterial, Eukaryotic, and Archaea Genomes in Terms of Protein Structure. German Conference on Bioinformatics Mark Gerstein
1996	A	`conf`	Using Iterative Dynamic Programming to Obtain Accurate Pairwise and Multiple Alignments of Protein Structures. ISMB Mark Gerstein, Michael Levitt
1995	J	`jnl`	Using a measure of structural variation to define a core for the globins. Comput. Appl. Biosci. Mark Gerstein, Russ B. Altman
1994	A	`conf`	Finding an Average Core Structure: Application to the Globins. ISMB Russ B. Altman, Mark Gerstein