Mark Gerstein

Mark B. Gerstein

	2009
44		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 Bioinformatics 10: (2009)
43		Kevin Y. Yip, Mark Gerstein: Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions. Bioinformatics 25(2): 243-250 (2009)
42		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 Research 37(Database-Issue): 738-743 (2009)
	2008
41		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
40		Thomas E. Royce, Nicholas Carriero, Mark B. Gerstein: An efficient pseudomedian filter for tiling microrrays. BMC Bioinformatics 8: (2007)
39		Samuel Flores, Mark Gerstein: FlexOracle: predicting flexible hinges by identification of stable domains. BMC Bioinformatics 8: (2007)
38		Samuel Flores, Long J. Lu, Julie Yang, Nicholas Carriero, Mark Gerstein: Hinge Atlas: relating protein sequence to sites of structural flexibility. BMC Bioinformatics 8: (2007)
37		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 Bioinformatics 8(S-3): (2007)
36		Eric Z. Yu, Anne E. Counterman Burba, Mark Gerstein: PARE: A tool for comparing protein abundance and mRNA expression data. BMC Bioinformatics 8: (2007)
35		Michael R. Seringhaus, Mark B. Gerstein: Publishing perishing? Towards tomorrow's information architecture. BMC Bioinformatics 8: (2007)
34		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		Andrew K. 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		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		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		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		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		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		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		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		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		Haiyuan Yu, Alberto Paccanaro, Valery Trifonov, Mark Gerstein: Predicting interactions in protein networks by completing defective cliques. Bioinformatics 22(7): 823-829 (2006)
23		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		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		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
20		Dov Greenbaum, Andrew K. Smith, Mark Gerstein: Editorial. Nucleic Acids Research 33(Database-Issue): 3-4 (2005)
	2004
19		Kei-Hoi Cheung, Deyun Pan, Andrew K. Smith, Michael B. Seringhaus, Shawn M. Douglas, Mark Gerstein: A XML-Based Approach to Integrating Heterogeneous Yeast Genome Data. METMBS 2004: 236-242
18		Nan Lin, Baolin Wu, Ronald Jansen, Mark Gerstein, Hongyu Zhao: Information assessment on predicting protein-protein interactions. BMC Bioinformatics 5: 154 (2004)
17		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		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 J. 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		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

Coauthor Index

1	Vadim Alexandrov	[17]
2	Russ B. Altman	[1] [2]
3	Cheryl H. Arrowsmith	[6]
4	Piotr Berman	[11] [16]
5	Paul Bertone	[6] [11] [12] [16] [22]
6	Anne E. Counterman Burba	[27] [36]
7	Nicholas Carriero	[28] [29] [38] [40] [42]
8	Philip Cayting	[29] [42]
9	Joseph T. Chang	[12]
10	Kei Cheung	[30] [33]
11	Kei-Hoi Cheung	[8] [19] [21] [37] [42]
12	Dinesh Christendat	[6]
13	Bhaskar DasGupta	[11] [16]
14	Shawn M. Douglas	[19]
15	Jiang Du	[25]
16	Nathaniel Echols	[12] [13] [23]
17	Aled M. Edwards	[6]
18	Donald M. Engelman	[41]
19	Gang Fang	[42]
20	Samuel Flores	[23] [38] [39]
21	Dov Greenbaum	[10] [20] [30]
22	Paul M. Harrison	[28] [29]
23	Brandon Hespenheide	[23]
24	Christine E. Horak	[12]
25	Ronald Jansen	[10] [18] [34]
26	Ming-Yang Kao	[11] [16]
27	John E. Karro	[28] [29]
28	Kevin Keating	[23]
29	Ekta Khurana	[42]
30	Philip M. Kim	[26] [32] [41] [44]
31	Yuval Kluger	[6]
32	Remko de Knikker	[21]
33	Jan O. Korbel	[25]
34	Michael Krauthammer	[33]
35	Anuj Kumar	[8]
36	Hugo Y. K. Lam	[42]
37	Ning Lan	[6]
38	Ursula Lehnert	[27]
39	Michael Levitt	[3]
40	Jimmy J. Lin	[14]
41	Nan Lin	[18]
42	Yang Liu	[8]
43	Jason Lu	[23]
44	Long J. Lu	[38]
45	Nicholas M. Luscombe	[12] [14]
46	Andy Masiar	[21]
47	Drew McDermott	[41] [44]
48	Duncan Milburn	[13] [23]
49	Perry L. Miller	[8] [30]
50	Gaetano T. Montelione	[6]
51	Alberto Paccanaro	[24]
52	Deyun Pan	[19]
53	Prianka Patel	[41]
54	Jiang Qian	[14]
55	Thomas E. Royce	[12] [22] [25] [31] [40]
56	Joel S. Rozowsky	[22] [25] [31]
57	Martin H. Schultz	[25] [26] [32] [33] [37]
58	Michael B. Seringhaus	[19]
59	Michael R. Seringhaus	[35]
60	Andrew K. Smith	[19] [20] [21] [33] [37]
61	Michael Snyder	[8] [11] [12] [16] [22] [25]
62	Gustavo Stolovitzky	[34]
63	Michael Thorpe	[23]
64	Valery Trifonov	[24]
65	Jerry Tsai	[7] [9]
66	Neil Voss	[7]
67	Sherman Weissman	[22]
68	Stephen Wells	[23]
69	Baolin Wu	[18]
70	Yangpan Yan	[29]
71	Julie Yang	[38]
72	Adelinda Yee	[6]
73	Kevin Y. Yip	[21] [26] [32] [37] [41] [43] [44]
74	Eric Z. Yu	[23] [27] [36]
75	Haiyuan Yu	[14] [24] [26] [32] [34]
76	Zhaolei Zhang	[28] [29]
77	Zhengdong D. Zhang	[25]
78	Hongyu Zhao	[18]
79	Deyou Zheng	[6] [28] [29]

Colors in the list of coauthors