2008 |
35 | EE | Kevin Y. Yip,
Prianka Patel,
Philip M. Kim,
Donald M. Engelman,
Drew McDermott,
Mark Gerstein:
An integrated system for studying residue coevolution in proteins.
Bioinformatics 24(2): 290-292 (2008) |
2007 |
34 | EE | Haiyuan Yu,
Ronald Jansen,
Gustavo Stolovitzky,
Mark Gerstein:
Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications.
Bioinformatics 23(16): 2163-2173 (2007) |
33 | EE | Andrew Smith,
Kei Cheung,
Michael Krauthammer,
Martin H. Schultz,
Mark Gerstein:
Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics.
Bioinformatics 23(22): 3073-3079 (2007) |
32 | EE | 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.
Bioinformatics 23(8): 1048 (2007) |
31 | EE | Thomas E. Royce,
Joel S. Rozowsky,
Mark Gerstein:
Assessing the need for sequence-based normalization in tiling microarray experiments.
Bioinformatics 23(8): 988-997 (2007) |
30 | EE | Mark Gerstein,
Dov Greenbaum,
Kei Cheung,
Perry L. Miller:
An interdepartmental Ph.D. program in computational biology and bioinformatics: The Yale perspective.
Journal of Biomedical Informatics 40(1): 73-79 (2007) |
29 | EE | 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 Research 35(Database-Issue): 55-60 (2007) |
2006 |
28 | EE | Zhaolei Zhang,
Nicholas Carriero,
Deyou Zheng,
John E. Karro,
Paul M. Harrison,
Mark Gerstein:
PseudoPipe: an automated pseudogene identification pipeline.
Bioinformatics 22(12): 1437-1439 (2006) |
27 | EE | 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.
Bioinformatics 22(22): 2735-2738 (2006) |
26 | EE | 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.
Bioinformatics 22(23): 2968-2970 (2006) |
25 | EE | 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.
Bioinformatics 22(24): 3016-3024 (2006) |
24 | EE | Haiyuan Yu,
Alberto Paccanaro,
Valery Trifonov,
Mark Gerstein:
Predicting interactions in protein networks by completing defective cliques.
Bioinformatics 22(7): 823-829 (2006) |
23 | EE | 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 Research 34(Database-Issue): 296-301 (2006) |
2005 |
22 | EE | 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 |
21 | EE | Kei-Hoi Cheung,
Kevin Y. Yip,
Andrew 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 |
20 | EE | Dov Greenbaum,
Andrew Smith,
Mark Gerstein:
Editorial.
Nucleic Acids Research 33(Database-Issue): 3-4 (2005) |
2004 |
19 | | Kei-Hoi Cheung,
Deyun Pan,
Andrew Smith,
Michael Seringhaus,
Shawn M. Douglas,
Mark Gerstein:
A XML-Based Approach to Integrating Heterogeneous Yeast Genome Data.
METMBS 2004: 236-242 |
18 | EE | Nan Lin,
Baolin Wu,
Ronald Jansen,
Mark Gerstein,
Hongyu Zhao:
Information assessment on predicting protein-protein interactions.
BMC Bioinformatics 5: 154 (2004) |
17 | EE | Vadim Alexandrov,
Mark Gerstein:
Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures.
BMC Bioinformatics 5: 2 (2004) |
16 | EE | 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.
Journal of Computational Biology 11(4): 766-785 (2004) |
2003 |
15 | | Mark Gerstein:
Computational Proteomics: Genome-scale Analysis of Protein Structure, Function, & Evolution(Invited Talk).
German Conference on Bioinformatics 2003: 53 |
14 | | Jiang Qian,
Jimmy Lin,
Nicholas M. Luscombe,
Haiyuan Yu,
Mark Gerstein:
Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data.
Bioinformatics 19(15): 1917-1926 (2003) |
13 | | Nathaniel Echols,
Duncan Milburn,
Mark Gerstein:
MolMovDB: analysis and visualization of conformational change and structural flexibility.
Nucleic Acids Research 31(1): 478-482 (2003) |
12 | | 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 Research 31(13): 3477-3482 (2003) |
2002 |
11 | EE | 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 |
10 | | 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.
Bioinformatics 18(4): 585-596 (2002) |
9 | | Jerry Tsai,
Mark Gerstein:
Calculations of protein volumes: sensitivity analysis and parameter database.
Bioinformatics 18(7): 985-995 (2002) |
2001 |
8 | | 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 |
7 | | Jerry Tsai,
Neil Voss,
Mark Gerstein:
Determining the minimum number of types necessary to represent the sizes of protein atoms.
Bioinformatics 17(10): 949-956 (2001) |
6 | | 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 Research 29(13): 2884-2898 (2001) |
1998 |
5 | | 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 |
4 | | Mark Gerstein:
Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence.
Bioinformatics 14(8): 707-714 (1998) |
1996 |
3 | | Mark Gerstein,
Michael Levitt:
Using Iterative Dynamic Programming to Obtain Accurate Pairwise and Multiple Alignments of Protein Structures.
ISMB 1996: 59-67 |
1995 |
2 | | Mark Gerstein,
Russ B. Altman:
Using a measure of structural variation to define a core for the globins.
Computer Applications in the Biosciences 11(6): 633-644 (1995) |
1994 |
1 | | Russ B. Altman,
Mark Gerstein:
Finding an Average Core Structure: Application to the Globins.
ISMB 1994: 19-27 |