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ORCIDMark Gerstein
Mark B. Gerstein
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- affiliation: Yale University
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2020 – today
- 2025
[j110]Eric Ni, Elizabeth Knight, Mark Gerstein:
Scalable and efficient on-chain data management in blockchain for large biomedical data. J. Biomed. Informatics 165: 104818 (2025)- [c27]Yunyang Li, Zaishuo Xia, Lin Huang, Xinran Wei, Samuel Harshe, Han Yang, Erpai Luo, Zun Wang, Jia Zhang, Chang Liu, Bin Shao, Mark Gerstein:
Enhancing the Scalability and Applicability of Kohn-Sham Hamiltonians for Molecular Systems. ICLR 2025 - [i22]Xiangru Tang, Tianyu Hu, Muyang Ye, Yanjun Shao, Xunjian Yin, Siru Ouyang, Wangchunshu Zhou, Pan Lu, Zhuosheng Zhang
, Yilun Zhao, Arman Cohan, Mark Gerstein:
ChemAgent: Self-updating Library in Large Language Models Improves Chemical Reasoning. CoRR abs/2501.06590 (2025) - [i21]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:
E2Former: A Linear-time Efficient and Equivariant Transformer for Scalable Molecular Modeling. CoRR abs/2501.19216 (2025) - [i20]Yunyang Li, Zaishuo Xia, Lin Huang, Xinran Wei, Han Yang, Sam Harshe, Zun Wang, Chang Liu, Jia Zhang, Bin Shao, Mark B. Gerstein:
Enhancing the Scalability and Applicability of Kohn-Sham Hamiltonians for Molecular Systems. CoRR abs/2502.19227 (2025) - [i19]Xiangru Tang, Daniel Shao, Jiwoong Sohn, Jiapeng Chen, Jiayi Zhang, Jinyu Xiang, Fang Wu, Yilun Zhao, Chenglin Wu, Wenqi Shi, Arman Cohan, Mark Gerstein:
MedAgentsBench: Benchmarking Thinking Models and Agent Frameworks for Complex Medical Reasoning. CoRR abs/2503.07459 (2025) - 2024
- [j109]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. Briefings Bioinform. 25(4) (2024) - [j108]Xiangru Tang, Bill Qian, Rick Gao, Jiakang Chen, Xinyun Chen, Mark B. Gerstein:
BioCoder: a benchmark for bioinformatics code generation with large language models. Bioinform. 40(Supplement_1): i266-i276 (2024) - [j107]Xiangru Tang, Andrew Tran, Jeffrey Tan, Mark B. Gerstein:
MolLM: a unified language model for integrating biomedical text with 2D and 3D molecular representations. Bioinform. 40(Supplement_1): i357-i368 (2024) - [j106]Tianci Song, Eric Cosatto, Gaoyuan Wang, Rui Kuang, Mark Gerstein, Martin Renqiang Min, Jonathan Warrell:
Predicting spatially resolved gene expression via tissue morphology using adaptive spatial GNNs. Bioinform. 40(Supplement_2): ii111-ii119 (2024) - [j105]Ho-Joon Lee, Prashant S. Emani, Mark B. Gerstein:
Improved Prediction of Ligand-Protein Binding Affinities by Meta-modeling. J. Chem. Inf. Model. 64(23): 8684-8704 (2024) - [j104]Yumeng Zhang, Zhikang Wang, Yunzhe Jiang, Dene R. Littler, Mark Gerstein, Anthony W. Purcell, Jamie Rossjohn, Hong-Yu Ou, Jiangning Song:
Epitope-anchored contrastive transfer learning for paired CD8+ T cell receptor-antigen recognition. Nat. Mac. Intell. 6(11): 1344-1358 (2024) - [c26]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: 599-621 - [c25]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 - [c24]Xiangru Tang, Yiming Zong, Jason Phang, Yilun Zhao, Wangchunshu Zhou, Arman Cohan, Mark Gerstein:
Struc-Bench: Are Large Language Models Good at Generating Complex Structured Tabular Data? NAACL (Short Papers) 2024: 12-34 - [c23]Chunyuan Deng, Yilun Zhao, Xiangru Tang, Mark Gerstein, Arman Cohan:
Investigating Data Contamination in Modern Benchmarks for Large Language Models. NAACL-HLT 2024: 8706-8719 - [i18]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 abs/2402.04247 (2024) - [i17]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 abs/2402.08703 (2024) - [i16]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 abs/2404.04285 (2024) - [i15]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 abs/2406.14275 (2024) - [i14]Haochen Zhao, Xiangru Tang, Ziran Yang, Xiao Han, Xuanzhi Feng, Yueqing Fan, Senhao Cheng, Di Jin, Yilun Zhao, Arman Cohan, Mark Gerstein:
ChemSafetyBench: Benchmarking LLM Safety on Chemistry Domain. CoRR abs/2411.16736 (2024) - 2023
- [j103]Bayo Lau, Prashant S. Emani, Jackson Chapman, Lijing Yao, Tarsus Lam, Paul Merrill, Jonathan Warrell, Mark B. Gerstein, Hugo Y. K. Lam:
Insights from incorporating quantum computing into drug design workflows. Bioinform. 39(1) (2023) - [j102]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) - [j101]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): 942-949 (2023) - [j100]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): 1300-1311 (2023) - [j99]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) - [c22]Xiangru Tang, Arman Cohan, Mark Gerstein:
Aligning Factual Consistency for Clinical Studies Summarization through Reinforcement Learning. ClinicalNLP@ACL 2023: 48-58 - [c21]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: 546-554 - [c20]Tianxiao Li, Hongyu Guo, Filippo Grazioli, Mark Gerstein, Martin Renqiang Min:
Disentangled Wasserstein Autoencoder for T-Cell Receptor Engineering. NeurIPS 2023 - [i13]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 abs/2305.05001 (2023) - [i12]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 abs/2307.16789 (2023) - [i11]Xiangru Tang, Bill Qian, Rick Gao, Jiakang Chen, Xinyun Chen, Mark Gerstein:
BioCoder: A Benchmark for Bioinformatics Code Generation with Contextual Pragmatic Knowledge. CoRR abs/2308.16458 (2023) - [i10]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 abs/2309.08963 (2023) - [i9]Ho-Joon Lee, Prashant S. Emani, Mark B. Gerstein:
Improved prediction of ligand-protein binding affinities by meta-modeling. CoRR abs/2310.03946 (2023) - [i8]Chunyuan Deng, Yilun Zhao, Xiangru Tang, Mark Gerstein, Arman Cohan:
Investigating Data Contamination in Modern Benchmarks for Large Language Models. CoRR abs/2311.09783 (2023) - [i7]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 abs/2311.09835 (2023) - [i6]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 abs/2311.10537 (2023) - [i5]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 abs/2311.11797 (2023) - 2022
- [j98]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): 1010636 (2022) - [c19]Amol Khanna, Vincent Schaffer, Gamze Gürsoy, Mark Gerstein:
Privacy-preserving Model Training for Disease Prediction Using Federated Learning with Differential Privacy. EMBC 2022: 1358-1361 - [i4]Jonathan Warrell, Mark Gerstein:
Higher-Order Generalization Bounds: Learning Deep Probabilistic Programs via PAC-Bayes Objectives. CoRR abs/2203.15972 (2022) - [i3]Esha Sarkar, Eduardo Chielle, Gamze Gürsoy, Leo Chen, Mark Gerstein, Michail Maniatakos:
Scalable privacy-preserving cancer type prediction with homomorphic encryption. CoRR abs/2204.05496 (2022) - 2021
- [j97]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: 93097-93110 (2021) - [j96]Gamze Gürsoy, Charlotte M. Brannon, Fabio C. P. Navarro, Mark Gerstein:
FANCY: fast estimation of privacy risk in functional genomics data. Bioinform. 36(21): 5145-5150 (2021) - [j95]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): 2998-3000 (2021) - [j94]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): 280-288 (2021) - [j93]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): D916-D923 (2021) - [j92]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) - [i2]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 abs/2103.11802 (2021) - 2020
- [j91]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): 836-850 (2020) - [j90]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): i474-i481 (2020) - [j89]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): 222 (2020) - [j88]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): 227 (2020) - [j87]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): 281 (2020) - [j86]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): 457 (2020) - [j85]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): 474 (2020) - [j84]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 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:
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578(7793): 102-111 (2020) - [j83]Donghoon Lee, Jing Zhang, Jason Liu, Mark Gerstein:
Epigenome-based splicing prediction using a recurrent neural network. PLoS Comput. Biol. 16(6) (2020) - [j82]Bian Li, Yucheng T. Yang, John A. Capra, Mark B. Gerstein:
Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks. PLoS Comput. Biol. 16(11) (2020)
2010 – 2019
- 2019
- [j81]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): D766-D773 (2019) - [j80]Fabio C. P. Navarro, Jacob Hoops, Lauren Bellfy, Eliza Cerveira, Qihui Zhu, Chengsheng Zhang, Charles Lee, Mark B. Gerstein:
TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements. PLoS Comput. Biol. 15(8) (2019) - 2018
- [j79]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): 1-8 (2018) - [j78]Lucas Lochovsky, Jing Zhang, Mark Gerstein:
MOAT: efficient detection of highly mutated regions with the Mutations Overburdening Annotations Tool. Bioinform. 34(6): 1031-1033 (2018) - [j77]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): 926-933 (2018) - [i1]Jonathan Warrell, Hussein Mohsen, Mark Gerstein:
Rank Projection Trees for Multilevel Neural Network Interpretation. CoRR abs/1812.00172 (2018) - 2017
- [j76]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): 2199-2201 (2017) - [j75]Yan Zhang, Shantao Li, Alexej Abyzov, Mark B. Gerstein:
Landscape and variation of novel retroduplications in 26 human populations. PLoS Comput. Biol. 13(6) (2017) - [j74]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) - 2016
- [j73]Kei-Hoi Cheung, Shivakumar Keerthikumar, Paola Roncaglia, Sai Lakshmi Subramanian, Matthew E. Roth, Monisha Samuel, Sushma Anand, Lahiru Gangoda, Stephen Gould, Roger Alexander, David Galas, Mark B. Gerstein, Andrew F. Hill, Robert R. Kitchen, Jan Lötvall, Tushar Patel:
Extending gene ontology in the context of extracellular RNA and vesicle communication. J. Biomed. Semant. 7: 19 (2016) - [j72]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) - 2015
- [j71]John C. Mu, Marghoob Mohiyuddin, Jian Li, Narges Bani Asadi, Mark B. Gerstein, Alexej Abyzov, Wing H. Wong, Hugo Y. K. Lam:
VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications. Bioinform. 31(9): 1469-1471 (2015) - [j70]Marghoob Mohiyuddin, John C. Mu, Jian Li, Narges Bani Asadi, Mark B. Gerstein, Alexej Abyzov, Wing H. Wong, Hugo Y. K. Lam:
MetaSV: an accurate and integrative structural-variant caller for next generation sequencing. Bioinform. 31(16): 2741-2744 (2015) - [j69]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): 3600-3607 (2015) - [j68]Daifeng Wang, Koon-Kiu Yan, Cristina Sisu, Chao Cheng, Joel S. Rozowsky, William Meyerson, Mark B. Gerstein:
Loregic: A Method to Characterize the Cooperative Logic of Regulatory Factors. PLoS Comput. Biol. 11(4) (2015) - 2014
- [j67]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): 453-456 (2014) - [c18]Martin Renqiang Min, Xia Ning, Chao Cheng, Mark Gerstein:
Interpretable Sparse High-Order Boltzmann Machines. AISTATS 2014: 614-622 - 2013
- [j66]Chao Cheng, Yao Fu, Linsheng Shen, Mark Gerstein:
Identification of yeast cell cycle regulated genes based on genomic features. BMC Syst. Biol. 7: 70 (2013) - [j65]Ekta Khurana, Yao Fu, Jieming Chen, Mark Gerstein:
Interpretation of Genomic Variants Using a Unified Biological Network Approach. PLoS Comput. Biol. 9(3) (2013) - [c17]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: 689 - 2012
- [j64]Lukas Habegger, Suganthi Balasubramanian, David Z. Chen, Ekta Khurana, Andrea Sboner, Arif Ozgun 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): 2267-2269 (2012) - 2011
- [j63]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): 281-283 (2011) - [j62]Alexej Abyzov, Mark Gerstein:
AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision. Bioinform. 27(5): 595-603 (2011) - [j61]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): 1152-1154 (2011) - [j60]Chao Cheng, Renqiang Min, Mark Gerstein:
TIP: A probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles. Bioinform. 27(23): 3221-3227 (2011) - [j59]Alexander Karpikov, Joel S. Rozowsky, Mark Gerstein:
Tiling array data analysis: a multiscale approach using wavelets. BMC Bioinform. 12: 57 (2011) - [j58]Samuel Flores, Mark B. Gerstein:
Predicting protein ligand binding motions with the Conformation Explorer. BMC Bioinform. 12: 417 (2011) - [j57]Chong Shou, Nitin Bhardwaj, Hugo Y. K. Lam, Koon-Kiu Yan, Philip M. Kim, Michael Snyder, Mark B. Gerstein:
Measuring the Evolutionary Rewiring of Biological Networks. PLoS Comput. Biol. 7(1) (2011) - [j56]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) - [j55]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) - 2010
- [j54]Matthew Holford, Ekta Khurana, Kei-Hoi Cheung, Mark Gerstein:
Using semantic web rules to reason on an ontology of pseudogenes. Bioinform. 26(12): 71-78 (2010) - [j53]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): 6 (2010) - [j52]Hugo Y. K. Lam, Philip M. Kim, Janine Mok, Raffi Tonikian, Sachdev S. Sidhu, Benjamin E. Turk, Michael Snyder, Mark B. Gerstein:
MOTIPS: Automated Motif Analysis for Predicting Targets of Modular Protein Domains. BMC Bioinform. 11: 243 (2010) - [j51]Zhengdong D. Zhang, Mark B. Gerstein:
Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model. BMC Bioinform. 11: 539 (2010) - [j50]Neil Voss, Mark Gerstein:
3V: cavity, channel and cleft volume calculator and extractor. Nucleic Acids Res. 38(Web-Server-Issue): 555-562 (2010) - [j49]Gang Fang, Nitin Bhardwaj, Rebecca Robilotto, Mark B. Gerstein:
Getting Started in Gene Orthology and Functional Analysis. PLoS Comput. Biol. 6(3) (2010) - [j48]Younghee Lee, Xinan Yang, Yong Huang, Hanli Fan, Qingbei Zhang, Youngfei Wu, Jianrong Li, Rifat Hasina, Chao Cheng, Mark W. Lingen, Mark B. Gerstein, Ralph R. Weichselbaum, H. Rosie Xing, Yves A. Lussier:
Network Modeling Identifies Molecular Functions Targeted by miR-204 to Suppress Head and Neck Tumor Metastasis. PLoS Comput. Biol. 6(4) (2010) - [j47]Nitin Bhardwaj, Matthew B. Carson, Alexej Abyzov, Koon-Kiu Yan, Hui Lu, Mark B. Gerstein:
Analysis of Combinatorial Regulation: Scaling of Partnerships between Regulators with the Number of Governed Targets. PLoS Comput. Biol. 6(5) (2010) - [c16]Mark Gerstein:
Analysis of molecular networks. BCB 2010: 1 - [c15]Nitin Bhardwaj, Mark Gerstein:
Dynamic and static analysis of transcriptional regulatory networks in a hierarchical context. GENSiPS 2010: 1 - [c14]Koon-Kiu Yan, Mark Gerstein:
Hierarchical analysis of regulatory networks and cross-disciplinary comparison with the Linux call graph. GENSiPS 2010: 1 - [c13]Mark B. Gerstein:
Human Genome Annotation. ISBRA 2010: 50-51
2000 – 2009
- 2009
- [j46]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): 243-250 (2009) - [j45]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) - [j44]Hugo Y. K. Lam, Ekta Khurana, Gang Fang, Philip Cayting, Nicholas Carriero, Kei-Hoi Cheung, Mark B. Gerstein:
Pseudofam: the pseudogene families database. Nucleic Acids Res. 37(Database-Issue): 738-743 (2009) - [j43]Yu Xia, Eric A. Franzosa, Mark B. Gerstein:
Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate. PLoS Comput. Biol. 5(6) (2009) - [j42]Jiang Du, Robert D. Bjornson, Zhengdong D. Zhang, Yong Kong, Michael Snyder, Mark B. Gerstein:
Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants. PLoS Comput. Biol. 5(7) (2009) - [j41]Xingyi Guo, Zhaolei Zhang, Mark B. Gerstein, Deyou Zheng:
Small RNAs Originated from Pseudogenes: cis- or trans-Acting? PLoS Comput. Biol. 5(7) (2009) - [j40]Andrey Rzhetsky, Michael R. Seringhaus, Mark B. Gerstein:
Getting Started in Text Mining: Part Two. PLoS Comput. Biol. 5(7) (2009) - 2008
- [j39]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): 290-292 (2008) - [j38]Philip E. Bourne, J. Lynn Fink, Mark Gerstein:
Open Access: Taking Full Advantage of the Content. PLoS Comput. Biol. 4(3) (2008) - [j37]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) - 2007
- [j36]Thomas E. Royce, Joel S. Rozowsky, Mark Gerstein:
Assessing the need for sequence-based normalization in tiling microarray experiments. Bioinform. 23(8): 988-997 (2007) - [j35]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): 1048 (2007) - [j34]Haiyuan Yu, Ronald Jansen, Gustavo Stolovitzky, Mark Gerstein:
Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications. Bioinform. 23(16): 2163-2173 (2007) - [j33]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): 3073-3079 (2007) - [j32]Samuel Flores, Mark Gerstein:
FlexOracle: predicting flexible hinges by identification of stable domains. BMC Bioinform. 8 (2007) - [j31]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) - [j30]Thomas E. Royce, Nicholas Carriero, Mark B. Gerstein:
An efficient pseudomedian filter for tiling microrrays. BMC Bioinform. 8 (2007) - [j29]Michael R. Seringhaus, Mark B. Gerstein:
Publishing perishing? Towards tomorrow's information architecture. BMC Bioinform. 8 (2007) - [j28]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) - [j27]Eric Z. Yu, Anne E. Counterman Burba, Mark Gerstein:
PARE: A tool for comparing protein abundance and mRNA expression data. BMC Bioinform. 8 (2007) - [j26]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): 73-79 (2007) - [j25]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): 55-60 (2007) - [j24]Mark Gerstein, Shawn M. Douglas:
RNAi Development. PLoS Comput. Biol. 3(4) (2007) - [j23]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) - 2006
- [j22]Haiyuan Yu, Alberto Paccanaro, Valery Trifonov, Mark Gerstein:
Predicting interactions in protein networks by completing defective cliques. Bioinform. 22(7): 823-829 (2006) - [j21]Zhaolei Zhang, Nicholas Carriero, Deyou Zheng, John E. Karro, Paul M. Harrison, Mark Gerstein:
PseudoPipe: an automated pseudogene identification pipeline. Bioinform. 22(12): 1437-1439 (2006) - [j20]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): 2735-2738 (2006) - [j19]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): 2968-2970 (2006) - [j18]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): 3016-3024 (2006) - [j17]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): 296-301 (2006) - [j16]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) - [c12]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: 1578-1598 - 2005
- [j15]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): 90-98 (2005) - [j14]Dov Greenbaum, Andrew K. Smith, Mark Gerstein:
Editorial. Nucleic Acids Res. 33(Database-Issue): 3-4 (2005) - [c11]Alberto Paccanaro, Valery Trifonov, Haiyuan Yu, Mark Gerstein:
Inferring protein-protein interactions using interaction network topologies. IJCNN 2005: 161-166 - [c10]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: 85-96 - [c9]Joel S. Rozowsky, Paul Bertone, Thomas E. Royce, Sherman Weissman, Michael Snyder, Mark Gerstein:
Analysis of Genomic Tiling Microarrays for Transcript Mapping and the Identification of Transcription Factor Binding Sites. BSB 2005: 28-29 - [p1]Long J. Lu, Yu Xia, Haiyuan Yu, Alexander Rives, Haoxin Lu, Falk Schubert, Mark Gerstein:
Protein Interaction Prediction by Integrating Genomic Features and Protein Interaction Network Analysis. Data Analysis and Visualization in Genomics and Proteomics 2005: 61-81 - 2004
- [j13]Vadim Alexandrov, Mark Gerstein:
Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures. BMC Bioinform. 5: 2 (2004) - [j12]Nan Lin, Baolin Wu, Ronald Jansen, Mark Gerstein, Hongyu Zhao:
Information assessment on predicting protein-protein interactions. BMC Bioinform. 5: 154 (2004) - [j11]Piotr Berman, Paul Bertone, Bhaskar DasGupta, Mark Gerstein, Ming-Yang Kao, Michael Snyder:
Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search. J. Comput. Biol. 11(4): 766-785 (2004) - [c8]Kei-Hoi Cheung, Deyun Pan, Andrew K. Smith, Michael R. Seringhaus, Shawn M. Douglas, Mark Gerstein:
A XML-Based Approach to Integrating Heterogeneous Yeast Genome Data. METMBS 2004: 236-242 - 2003
- [j10]Jiang Qian, C. Jimmy Lin, Nicholas M. Luscombe, Haiyuan Yu, Mark Gerstein:
Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. Bioinform. 19(15): 1917-1926 (2003) - [j9]Nathaniel Echols, Duncan Milburn, Mark Gerstein:
MolMovDB: analysis and visualization of conformational change and structural flexibility. Nucleic Acids Res. 31(1): 478-482 (2003) - [j8]Nicholas M. Luscombe, Thomas E. Royce, Paul Bertone, Nathaniel Echols, Christine E. Horak, Joseph T. Chang, Michael Snyder, Mark Gerstein:
ExpressYourself: a modular platform for processing and visualizing microarray data. Nucleic Acids Res. 31(13): 3477-3482 (2003) - [c7]Mark Gerstein:
Computational Proteomics: Genome-scale Analysis of Protein Structure, Function, & Evolution(Invited Talk). German Conference on Bioinformatics 2003: 53 - 2002
- [j7]Dov Greenbaum, Ronald Jansen, Mark Gerstein:
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. 18(4): 585-596 (2002) - [j6]Jerry Tsai, Mark Gerstein:
Calculations of protein volumes: sensitivity analysis and parameter database. Bioinform. 18(7): 985-995 (2002) - [j5]Ning Lan, Ronald Jansen, Mark Gerstein:
Toward a systematic definition of protein function that scales to the genome level: defining function in terms of interactions. Proc. IEEE 90(12): 1848-1858 (2002) - [c6]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:
YMD: a microarray database for large-scale gene expression analysis. AMIA 2002 - [c5]Piotr Berman, Paul Bertone, Bhaskar DasGupta, Mark Gerstein, Ming-Yang Kao, Michael Snyder:
Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search. WABI 2002: 419-433 - 2001
- [j4]Jerry Tsai, Neil Voss, Mark Gerstein:
Determining the minimum number of types necessary to represent the sizes of protein atoms. Bioinform. 17(10): 949-956 (2001) - [j3]Paul Bertone, Yuval Kluger, Ning Lan, Deyou Zheng, Dinesh Christendat, Adelinda Yee, Aled M. Edwards, Cheryl H. Arrowsmith, Gaetano T. Montelione, Mark Gerstein:
SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics. Nucleic Acids Res. 29(13): 2884-2898 (2001) - [c4]Kei-Hoi Cheung, Yang Liu, Anuj Kumar, Michael Snyder, Mark Gerstein, Perry L. Miller:
An XML Application For Genomic Data Interoperation. BIBE 2001: 97-103
1990 – 1999
- 1998
- [j2]Mark Gerstein:
Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence. Bioinform. 14(8): 707-714 (1998) - [c3]Mark Gerstein:
[Invited Lecture] A Structural Census of Genomes: Comparing Bacterial, Eukaryotic, and Archaea Genomes in Terms of Protein Structure. German Conference on Bioinformatics 1998 - 1996
- [c2]Mark Gerstein, Michael Levitt:
Using Iterative Dynamic Programming to Obtain Accurate Pairwise and Multiple Alignments of Protein Structures. ISMB 1996: 59-67 - 1995
- [j1]Mark Gerstein, Russ B. Altman:
Using a measure of structural variation to define a core for the globins. Comput. Appl. Biosci. 11(6): 633-644 (1995) - 1994
- [c1]Russ B. Altman, Mark Gerstein:
Finding an Average Core Structure: Application to the Globins. ISMB 1994: 19-27
Coauthor Index
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