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Mark Gerstein
Mark B. Gerstein
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- affiliation: Yale University
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2020 – today
- 2024
- [j104]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) - [c25]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 - [c24]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 - [c23]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 - [c22]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 - [i17]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) - [i16]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) - [i15]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) - [i14]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) - 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
Binding peptide generation for MHC Class I proteins with deep reinforcement learning. Bioinform. 39(2) (2023) - [j101]Adam Frankish
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
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) - [c21]Xiangru Tang, Arman Cohan, Mark Gerstein:
Aligning Factual Consistency for Clinical Studies Summarization through Reinforcement Learning. ClinicalNLP@ACL 2023: 48-58 - [c20]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 - [c19]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
Struc-Bench: Are Large Language Models Really Good at Generating Complex Structured Data? CoRR abs/2309.08963 (2023) - [i9]Ho-Joon Lee
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
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) - [c18]Amol Khanna
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
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
FANCY: fast estimation of privacy risk in functional genomics data. Bioinform. 36(21): 5145-5150 (2021) - [j95]Shaoke Lou, Tianxiao Li
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
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
GENCODE 2021. Nucleic Acids Res. 49(Database-Issue): D916-D923 (2021) - [j92]Jason Liu
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
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
TopicNet: a framework for measuring transcriptional regulatory network change. Bioinform. 36(Supplement-1): i474-i481 (2020) - [j89]Cheng Ye, Alberto Paccanaro
The corrected gene proximity map for analyzing the 3D genome organization using Hi-C data. BMC Bioinform. 21(1): 222 (2020) - [j88]William Meyerson
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
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
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
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nat. 578(7793): 102-111 (2020) - [j83]Donghoon Lee
Epigenome-based splicing prediction using a recurrent neural network. PLoS Comput. Biol. 16(6) (2020) - [j82]Bian Li
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
GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res. 47(Database-Issue): D766-D773 (2019) - [j80]Fabio C. P. Navarro
TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements. PLoS Comput. Biol. 15(8) (2019) - 2018
- [j79]Karolina Elzbieta Kaczor-Urbanowicz
Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development. Bioinform. 34(1): 1-8 (2018) - [j78]Lucas Lochovsky
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
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
Landscape and variation of novel retroduplications in 26 human populations. PLoS Comput. Biol. 13(6) (2017) - [j74]Koon-Kiu Yan
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
Extending gene ontology in the context of extracellular RNA and vesicle communication. J. Biomed. Semant. 7: 19 (2016) - [j72]Daifeng Wang, Fei He
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
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
MetaSV: an accurate and integrative structural-variant caller for next generation sequencing. Bioinform. 31(16): 2741-2744 (2015) - [j69]Pavel P. Kuksa
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
Loregic: A Method to Characterize the Cooperative Logic of Regulatory Factors. PLoS Comput. Biol. 11(4) (2015) - 2014
- [j67]Alan P. Boyle
Comparative analysis of regulatory information and circuits across distant species Open. Nat. 512(7515): 453-456 (2014) - [c17]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
Interpretation of Genomic Variants Using a Unified Biological Network Approach. PLoS Comput. Biol. 9(3) (2013) - [c16]Daifeng Wang, Eric Pan, Gang Fang, Sunita Kumari, Fei He, Doreen Ware, Sergei Maslov
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
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
RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries. Bioinform. 27(2): 281-283 (2011) - [j62]Alexej Abyzov
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
ACT: aggregation and correlation toolbox for analyses of genome tracks. Bioinform. 27(8): 1152-1154 (2011) - [j60]Chao Cheng, Renqiang Min
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
Tiling array data analysis: a multiscale approach using wavelets. BMC Bioinform. 12: 57 (2011) - [j58]Samuel Flores
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
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
Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data. PLoS Comput. Biol. 7(11) (2011) - [j55]Dov Greenbaum
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
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
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
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
Analysis of Combinatorial Regulation: Scaling of Partnerships between Regulators with the Number of Governed Targets. PLoS Comput. Biol. 6(5) (2010) - [c15]Mark Gerstein:
Analysis of molecular networks. BCB 2010: 1 - [c14]Nitin Bhardwaj, Mark Gerstein:
Dynamic and static analysis of transcriptional regulatory networks in a hierarchical context. GENSiPS 2010: 1 - [c13]Koon-Kiu Yan, Mark Gerstein:
Hierarchical analysis of regulatory networks and cross-disciplinary comparison with the Linux call graph. GENSiPS 2010: 1 - [c12]Mark B. Gerstein:
Human Genome Annotation. ISBRA 2010: 50-51
2000 – 2009
- 2009
- [j46]Kevin Y. Yip
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
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
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
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
Getting Started in Text Mining: Part Two. PLoS Comput. Biol. 5(7) (2009) - 2008
- [j39]Kevin Y. Yip
An integrated system for studying residue coevolution in proteins. Bioinform. 24(2): 290-292 (2008) - [j38]Philip E. Bourne, J. Lynn Fink
Open Access: Taking Full Advantage of the Content. PLoS Comput. Biol. 4(3) (2008) - [j37]Zhengdong D. Zhang, Joel S. Rozowsky
Modeling ChIP Sequencing In Silico with Applications. PLoS Comput. Biol. 4(8) (2008) - 2007
- [j36]Thomas E. Royce, Joel S. Rozowsky
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
Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics. Bioinform. 23(22): 3073-3079 (2007) - [j32]Samuel Flores
FlexOracle: predicting flexible hinges by identification of stable domains. BMC Bioinform. 8 (2007) - [j31]Samuel Flores
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
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
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
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
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
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
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
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) - [c11]Frederick G. Sayward, Jin Yang, Kenneth Nelson, Ghia Euskirchen, Alexander E. Urban, Paul Bertone
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
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
Editorial. Nucleic Acids Res. 33(Database-Issue): 3-4 (2005) - [c10]Kei-Hoi Cheung, Kevin Y. Yip
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
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
Information assessment on predicting protein-protein interactions. BMC Bioinform. 5: 154 (2004) - [j11]Piotr Berman, Paul Bertone
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
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
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
Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search. WABI 2002: 419-433 - 2001
- [j4]Jerry Tsai, Neil Voss
Determining the minimum number of types necessary to represent the sizes of protein atoms. Bioinform. 17(10): 949-956 (2001) - [j3]Paul Bertone
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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