Mark Gerstein

ORCID

Publication Activity (10 Years)

Years Active: 1994-2024
Publications (10 Years): 52

Top Venues

Publications

Xiangru Tang, Anni Zou, Zhuosheng Zhang, Ziming Li, Yilun Zhao, Xingyao Zhang, Arman Cohan, Mark Gerstein
MedAgents: Large Language Models as Collaborators for Zero-shot Medical Reasoning. ACL (Findings) (2024)
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
Prioritizing Safeguarding Over Autonomy: Risks of LLM Agents for Science. CoRR (2024)
Xiangru Tang, Howard Dai, Elizabeth Knight, Fang Wu, Yunyang Li, Tianxiao Li, Mark Gerstein
drug design: new frontiers in molecule and protein generation. Briefings Bioinform. 25 (4) (2024)
Chunyuan Deng, Xiangru Tang, Yilun Zhao, Hanming Wang, Haoran Wang, Wangchunshu Zhou, Arman Cohan, Mark Gerstein
MIMIR: A Streamlined Platform for Personalized Agent Tuning in Domain Expertise. CoRR (2024)
Xiangru Tang, Howard Dai, Elizabeth Knight, Fang Wu, Yunyang Li, Tianxiao Li, Mark Gerstein
A Survey of Generative AI for De Novo Drug Design: New Frontiers in Molecule and Protein Generation. CoRR (2024)
Yin Fang, Kangwei Liu, Ningyu Zhang, Xinle Deng, Penghui Yang, Zhuo Chen, Xiangru Tang, Mark Gerstein, Xiaohui Fan, Huajun Chen
ChatCell: Facilitating Single-Cell Analysis with Natural Language. CoRR (2024)
Xiangru Tang, Xingyao Zhang, Yanjun Shao, Jie Wu, Yilun Zhao, Arman Cohan, Ming Gong, Dongmei Zhang, Mark Gerstein
Step-Back Profiling: Distilling User History for Personalized Scientific Writing. CoRR (2024)
Chunyuan Deng, Yilun Zhao, Xiangru Tang, Mark Gerstein, Arman Cohan
Investigating Data Contamination in Modern Benchmarks for Large Language Models. NAACL-HLT (2024)
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
ToolLLM: Facilitating Large Language Models to Master 16000+ Real-world APIs. ICLR (2024)
Xiangru Tang, Bill Qian, Rick Gao, Jiakang Chen, Xinyun Chen, Mark Gerstein
BioCoder: A Benchmark for Bioinformatics Code Generation with Contextual Pragmatic Knowledge. CoRR (2023)
Shaoke Lou, Mingjun Yang, Tianxiao Li, Weihao Zhao, Hannah Cevasco, Yucheng T. Yang, Mark 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 Comput. Biol. 19 (7) (2023)
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
ToolLLM: Facilitating Large Language Models to Master 16000+ Real-world APIs. CoRR (2023)
Chunyuan Deng, Yilun Zhao, Xiangru Tang, Mark Gerstein, Arman Cohan
Investigating Data Contamination in Modern Benchmarks for Large Language Models. CoRR (2023)
Xiangru Tang, Andrew Tran, Jeffrey Tan, Mark Gerstein
GersteinLab at MEDIQA-Chat 2023: Clinical Note Summarization from Doctor-Patient Conversations through Fine-tuning and In-context Learning. CoRR (2023)
Tianxiao Li, Hongyu Guo, Filippo Grazioli, Mark Gerstein, Martin Renqiang Min
Disentangled Wasserstein Autoencoder for T-Cell Receptor Engineering. NeurIPS (2023)
Xiangru Tang, Andrew Tran, Jeffrey Tan, Mark Gerstein
GersteinLab at MEDIQA-Chat 2023: Clinical Note Summarization from Doctor-Patient Conversations through Fine-tuning and In-context Learning. ClinicalNLP@ACL (2023)
Xiangru Tang, Anni Zou, Zhuosheng Zhang, Yilun Zhao, Xingyao Zhang, Arman Cohan, Mark Gerstein
MedAgents: Large Language Models as Collaborators for Zero-shot Medical Reasoning. CoRR (2023)
Ziqi Chen, Baoyi Zhang, Hongyu Guo, Prashant S. Emani, Trevor Clancy, Chongming Jiang, Mark Gerstein, Xia Ning, Chao Cheng, Martin Renqiang Min
Binding peptide generation for MHC Class I proteins with deep reinforcement learning. Bioinform. 39 (2) (2023)
Xiangru Tang, Yiming Zong, Jason Phang, Yilun Zhao, Wangchunshu Zhou, Arman Cohan, Mark Gerstein
Struc-Bench: Are Large Language Models Really Good at Generating Complex Structured Data? CoRR (2023)
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
FAVOR: functional annotation of variants online resource and annotator for variation across the human genome. Nucleic Acids Res. 51 (D1) (2023)
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
ML-Bench: Large Language Models Leverage Open-source Libraries for Machine Learning Tasks. CoRR (2023)
Xiangru Tang, Arman Cohan, Mark Gerstein
Aligning Factual Consistency for Clinical Studies Summarization through Reinforcement Learning. ClinicalNLP@ACL (2023)
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
GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Res. 51 (D1) (2023)
Zhuosheng Zhang, Yao Yao, Aston Zhang, Xiangru Tang, Xinbei Ma, Zhiwei He, Yiming Wang, Mark Gerstein, Rui Wang, Gongshen Liu, Hai Zhao
Igniting Language Intelligence: The Hitchhiker's Guide From Chain-of-Thought Reasoning to Language Agents. CoRR (2023)
Amol Khanna, Vincent Schaffer, Gamze Gürsoy, Mark Gerstein
Privacy-preserving Model Training for Disease Prediction Using Federated Learning with Differential Privacy. EMBC (2022)
Esha Sarkar, Eduardo Chielle, Gamze Gürsoy, Leo Chen, Mark Gerstein, Michail Maniatakos
Scalable privacy-preserving cancer type prediction with homomorphic encryption. CoRR (2022)
Cheyu Lee, Yuhang Chen, Ziheng Duan, Min Xu, Matthew J. Girgenti, Ke Xu, Mark Gerstein, Jing Zhang
Venus: An efficient virus infection detection and fusion site discovery method using single-cell and bulk RNA-seq data. PLoS Comput. Biol. 18 (10) (2022)
Jonathan Warrell, Mark Gerstein
Higher-Order Generalization Bounds: Learning Deep Probabilistic Programs via PAC-Bayes Objectives. CoRR (2022)
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
Bayesian structural time series for biomedical sensor data: A flexible modeling framework for evaluating interventions. PLoS Comput. Biol. 17 (8) (2021)
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
GENCODE 2021. Nucleic Acids Res. 49 (Database-Issue) (2021)
Gamze Gürsoy, Charlotte M. Brannon, Fabio C. P. Navarro, Mark Gerstein
FANCY: fast estimation of privacy risk in functional genomics data. Bioinform. 36 (21) (2021)
Zhanlin Chen, Philip Tuckman, Jeremy Goldwasser, Jing Zhang, Mark Gerstein
Forest Fire Clustering: Cluster-oriented Label Propagation Clustering and Monte Carlo Verification Inspired by Forest Fire Dynamics. CoRR (2021)
Zhanlin Chen, Jing Zhang, Jason Liu, Yi Dai, Donghoon Lee, Martin Renqiang Min, Min Xu, Mark Gerstein
DECODE: a Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays. Bioinform. 37 (Supplement) (2021)
Esha Sarkar, Eduardo Chielle, Gamze Gürsoy, Oleg Mazonka, Mark Gerstein, Michail Maniatakos
Fast and Scalable Private Genotype Imputation Using Machine Learning and Partially Homomorphic Encryption. IEEE Access 9 (2021)
Shaoke Lou, Tianxiao Li, Jason Liu, Mark Gerstein
Gene Tracer: a smart, interactive, voice-controlled Alexa skill For gene information retrieval and browsing, mutation annotation and network visualization. Bioinform. 37 (18) (2021)
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 Gonzalez-Perez, 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 G. Gut, David Haan, Arif O. 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
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578 (7793) (2020)
Cheng Ye, Alberto Paccanaro, Mark Gerstein, Koon-Kiu Yan
The corrected gene proximity map for analyzing the 3D genome organization using Hi-C data. BMC Bioinform. 21 (1) (2020)
William Meyerson, John Leisman, Fabio C. P. Navarro, Mark Gerstein
Origins and characterization of variants shared between databases of somatic and germline human mutations. BMC Bioinform. 21 (1) (2020)
Jing Zhang, Jason Liu, Donghoon Lee, Shaoke Lou, Zhanlin Chen, Gamze Gürsoy, Mark Gerstein
DiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring. BMC Bioinform. 21 (1) (2020)
Jing Zhang, Jason Liu, Patrick D. McGillivray, Caroline Yi, Lucas Lochovsky, Donghoon Lee, Mark Gerstein
NIMBus: a negative binomial regression based Integrative Method for mutation Burden Analysis. BMC Bioinform. 21 (1) (2020)
Shaoke Lou, Tianxiao Li, Xiangmeng Kong, Jing Zhang, Jason Liu, Donghoon Lee, Mark Gerstein
TopicNet: a framework for measuring transcriptional regulatory network change. Bioinform. 36 (Supplement-1) (2020)
Shaoke Lou, Tianxiao Li, Daniel Spakowicz, Xiting Yan, Geoffrey Lowell Chupp, Mark Gerstein
Latent-space embedding of expression data identifies gene signatures from sputum samples of asthmatic patients. BMC Bioinform. 21 (1) (2020)
Edwin Yu-Kiu Ho, Qin Cao, Mengting Gu, Ricky Wai-Lun Chan, Qiong Wu, Mark Gerstein, Kevin Y. Yip
Shaping the nebulous enhancer in the era of high-throughput assays and genome editing. Briefings Bioinform. 21 (3) (2020)
Donghoon Lee, Jing Zhang, Jason Liu, Mark Gerstein
Epigenome-based splicing prediction using a recurrent neural network. PLoS Comput. Biol. 16 (6) (2020)
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
GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res. 47 (Database-Issue) (2019)
Lucas Lochovsky, Jing Zhang, Mark Gerstein
MOAT: efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool. Bioinform. 34 (6) (2018)
Pedro Alves, Shuang Liu, Daifeng Wang, Mark Gerstein
Multiple-Swarm Ensembles: Improving the Predictive Power and Robustness of Predictive Models and Its Use in Computational Biology. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (3) (2018)
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
Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development. Bioinform. 34 (1) (2018)
Jonathan Warrell, Hussein Mohsen, Mark Gerstein
Rank Projection Trees for Multilevel Neural Network Interpretation. CoRR (2018)
Koon-Kiu Yan, Galip Gürkan Yardimci, Chengfei Yan, William S. Noble, Mark Gerstein
HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps. Bioinform. 33 (14) (2017)
Koon-Kiu Yan, Shaoke Lou, Mark Gerstein
MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions. PLoS Comput. Biol. 13 (7) (2017)
Daifeng Wang, Fei He, Sergei Maslov, Mark Gerstein
DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks. PLoS Comput. Biol. 12 (10) (2016)
Pavel P. Kuksa, Martin Renqiang Min, Rishabh Dugar, Mark Gerstein
High-order neural networks and kernel methods for peptide-MHC binding prediction. Bioinform. 31 (22) (2015)
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
Comparative analysis of regulatory information and circuits across distant species Open. Nat. 512 (7515) (2014)
Martin Renqiang Min, Xia Ning, Chao Cheng, Mark Gerstein
Interpretable Sparse High-Order Boltzmann Machines. AISTATS (2014)
Daifeng Wang, Eric Pan, Gang Fang, Sunita Kumari, Fei He, Doreen Ware, Sergei Maslov, Mark Gerstein
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 (2013)
Chao Cheng, Yao Fu, Linsheng Shen, Mark Gerstein
Identification of yeast cell cycle regulated genes based on genomic features. BMC Syst. Biol. 7 (2013)
Ekta Khurana, Yao Fu, Jieming Chen, Mark Gerstein
Interpretation of Genomic Variants Using a Unified Biological Network Approach. PLoS Comput. Biol. 9 (3) (2013)
Lukas Habegger, Suganthi Balasubramanian, David Z. Chen, Ekta Khurana, Andrea Sboner, Arif O. Harmanci, Joel S. Rozowsky, Declan Clarke, Michael Snyder, Mark Gerstein
VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment. Bioinform. 28 (17) (2012)
Alexej Abyzov, Mark Gerstein
AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision. Bioinform. 27 (5) (2011)
Alexander Karpikov, Joel S. Rozowsky, Mark Gerstein
Tiling array data analysis: a multiscale approach using wavelets. BMC Bioinform. 12 (2011)
Dov Greenbaum, Andrea Sboner, Xinmeng Jasmine Mu, Mark Gerstein
Genomics and Privacy: Implications of the New Reality of Closed Data for the Field. PLoS Comput. Biol. 7 (12) (2011)
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
ACT: aggregation and correlation toolbox for analyses of genome tracks. Bioinform. 27 (8) (2011)
Chao Cheng, Renqiang Min, Mark Gerstein
TIP: A probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles. Bioinform. 27 (23) (2011)
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
Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data. PLoS Comput. Biol. 7 (11) (2011)
Lukas Habegger, Andrea Sboner, Tara A. Gianoulis, Joel S. Rozowsky, Ashish Agarwal, Michael Snyder, Mark Gerstein
RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries. Bioinform. 27 (2) (2011)
Koon-Kiu Yan, Mark Gerstein
Hierarchical analysis of regulatory networks and cross-disciplinary comparison with the Linux call graph. GENSiPS (2010)
Nitin Bhardwaj, Mark Gerstein, Hui Lu
Genome-wide sequence-based prediction of peripheral proteins using a novel semi-supervised learning technique. BMC Bioinform. 11 (S-1) (2010)
Nitin Bhardwaj, Mark Gerstein
Dynamic and static analysis of transcriptional regulatory networks in a hierarchical context. GENSiPS (2010)
Mark Gerstein
Analysis of molecular networks. BCB (2010)
Neil Voss, Mark Gerstein
3V: cavity, channel and cleft volume calculator and extractor. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Matthew Holford, Ekta Khurana, Kei-Hoi Cheung, Mark Gerstein
Using semantic web rules to reason on an ontology of pseudogenes. Bioinform. 26 (12) (2010)
Kevin Y. Yip, Mark Gerstein
Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions. Bioinform. 25 (2) (2009)
Kevin Y. Yip, Philip M. Kim, Drew McDermott, Mark Gerstein
Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels. BMC Bioinform. 10 (2009)
Philip E. Bourne, J. Lynn Fink, Mark Gerstein
Open Access: Taking Full Advantage of the Content. PLoS Comput. Biol. 4 (3) (2008)
Kevin Y. Yip, Prianka Patel, Philip M. Kim, Donald M. Engelman, Drew McDermott, Mark Gerstein
An integrated system for studying residue coevolution in proteins. Bioinform. 24 (2) (2008)
Zhengdong D. Zhang, Joel S. Rozowsky, Michael Snyder, Joseph T. Chang, Mark Gerstein
Modeling ChIP Sequencing In Silico with Applications. PLoS Comput. Biol. 4 (8) (2008)
Mark Gerstein, Dov Greenbaum, Kei-Hoi Cheung, Perry L. Miller
An interdepartmental Ph.D. program in computational biology and bioinformatics: The Yale perspective. J. Biomed. Informatics 40 (1) (2007)
Haiyuan Yu, Philip M. Kim, Emmett Sprecher, Valery Trifonov, Mark Gerstein
The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics. PLoS Comput. Biol. 3 (4) (2007)
Andrew K. Smith, Kei-Hoi Cheung, Kevin Y. Yip, Martin H. Schultz, Mark Gerstein
LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics. BMC Bioinform. 8 (S-3) (2007)
Eric Z. Yu, Anne E. Counterman Burba, Mark Gerstein
PARE: A tool for comparing protein abundance and mRNA expression data. BMC Bioinform. 8 (2007)
Mark Gerstein, Shawn M. Douglas
RNAi Development. PLoS Comput. Biol. 3 (4) (2007)
Kevin Y. Yip, Haiyuan Yu, Philip M. Kim, Martin H. Schultz, Mark Gerstein
The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks. Bioinform. 23 (8) (2007)
Andrew K. Smith, Kei-Hoi Cheung, Michael Krauthammer, Martin H. Schultz, Mark Gerstein
Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics. Bioinform. 23 (22) (2007)
Thomas E. Royce, Joel S. Rozowsky, Mark Gerstein
Assessing the need for sequence-based normalization in tiling microarray experiments. Bioinform. 23 (8) (2007)
John E. Karro, Yangpan Yan, Deyou Zheng, Zhaolei Zhang, Nicholas Carriero, Philip Cayting, Paul M. Harrison, Mark Gerstein
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Res. 35 (Database-Issue) (2007)
Samuel Flores, Long J. Lu, Julie Yang, Nicholas Carriero, Mark Gerstein
Hinge Atlas: relating protein sequence to sites of structural flexibility. BMC Bioinform. 8 (2007)
Samuel Flores, Mark Gerstein
FlexOracle: predicting flexible hinges by identification of stable domains. BMC Bioinform. 8 (2007)
Haiyuan Yu, Ronald Jansen, Gustavo Stolovitzky, Mark Gerstein
Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications. Bioinform. 23 (16) (2007)
Samuel Flores, Nathaniel Echols, Duncan Milburn, Brandon Hespenheide, Kevin Keating, Jason Lu, Stephen Wells, Eric Z. Yu, Michael Thorpe, Mark Gerstein
The Database of Macromolecular Motions: new features added at the decade mark. Nucleic Acids Res. 34 (Database-Issue) (2006)
Haiyuan Yu, Alberto Paccanaro, Valery Trifonov, Mark Gerstein
Predicting interactions in protein networks by completing defective cliques. Bioinform. 22 (7) (2006)
Jiang Du, Joel S. Rozowsky, Jan O. Korbel, Zhengdong D. Zhang, Thomas E. Royce, Martin H. Schultz, Michael Snyder, Mark Gerstein
A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge. Bioinform. 22 (24) (2006)
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
Design Issues in Implementing a Portable Sample Tracking and Analysis Research Support (STARS) System for PCR Based Microarray Research. CISS (2006)
Yang Liu, Jianrong Li, Lee T. Sam, Chern-Sing Goh, Mark Gerstein, Yves A. Lussier
An Integrative Genomic Approach to Uncover Molecular Mechanisms of Prokaryotic Traits. PLoS Comput. Biol. 2 (11) (2006)
Anne E. Counterman Burba, Ursula Lehnert, Eric Z. Yu, Mark Gerstein
Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins. Bioinform. 22 (22) (2006)
Kevin Y. Yip, Haiyuan Yu, Philip M. Kim, Martin H. Schultz, Mark Gerstein
The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks. Bioinform. 22 (23) (2006)
Zhaolei Zhang, Nicholas Carriero, Deyou Zheng, John E. Karro, Paul M. Harrison, Mark Gerstein
PseudoPipe: an automated pseudogene identification pipeline. Bioinform. 22 (12) (2006)
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
Case Report: A High Productivity/Low Maintenance Approach to High-performance Computation for Biomedicine: Four Case Studies. J. Am. Medical Informatics Assoc. 12 (1) (2005)
Kei-Hoi Cheung, Kevin Y. Yip, Andrew K. Smith, Remko de Knikker, Andy Masiar, Mark Gerstein
YeastHub: a semantic web use case for integrating data in the life sciences domain. ISMB (Supplement of Bioinformatics) (2005)
Dov Greenbaum, Andrew K. Smith, Mark Gerstein
Editorial. Nucleic Acids Res. 33 (Database-Issue) (2005)

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Mark Gerstein