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J. Michael Cherry

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2008
25EEEurie L. Hong, Rama Balakrishnan, Qing Dong, Karen R. Christie, Julie Park, Gail Binkley, Maria C. Costanzo, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Benjamin C. Hitz, Cynthia J. Krieger, Michael S. Livstone, Stuart R. Miyasato, Robert S. Nash, Rose Oughtred, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Kathy K. Zhu, Kara Dolinski, David Botstein, J. Michael Cherry: Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Research 36(Database-Issue): 577-581 (2008)
2007
24EEColleen E. Crangle, J. Michael Cherry, Eurie L. Hong, Alex Zbyslaw: Mining experimental evidence of molecular function claims from the literature. Bioinformatics 23(23): 3232-3240 (2007)
23EERobert S. Nash, Shuai Weng, Benjamin C. Hitz, Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Michael S. Livstone, Rose Oughtred, Julie Park, Marek S. Skrzypek, Chandra L. Theesfeld, Gail Binkley, Qing Dong, Christopher Lane, Stuart R. Miyasato, Anand Sethuraman, Mark Schroeder, Kara Dolinski, David Botstein, J. Michael Cherry: Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Research 35(Database-Issue): 468-471 (2007)
2006
22EEJodi E. Hirschman, Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Eurie L. Hong, Michael S. Livstone, Robert S. Nash, Julie Park, Rose Oughtred, Marek S. Skrzypek, Barry Starr, Chandra L. Theesfeld, Jennifer Williams, Rey Andrada, Gail Binkley, Qing Dong, Christopher Lane, Stuart R. Miyasato, Anand Sethuraman, Mark Schroeder, Mayank K. Thanawala, Shuai Weng, Kara Dolinski, David Botstein, J. Michael Cherry: Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Research 34(Database-Issue): 442-445 (2006)
21EENicholas A. Stover, Cynthia J. Krieger, Gail Binkley, Qing Dong, Dianna G. Fisk, Robert S. Nash, Anand Sethuraman, Shuai Weng, J. Michael Cherry: Tetrahymena Genome Database (TGD): a new genomic resource for Tetrahymena thermophila research. Nucleic Acids Research 34(Database-Issue): 500-503 (2006)
2005
20EERama Balakrishnan, Karen R. Christie, Maria C. Costanzo, Kara Dolinski, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Robert S. Nash, Rose Oughtred, Marek S. Skrzypek, Chandra L. Theesfeld, Gail Binkley, Qing Dong, Christopher Lane, Anand Sethuraman, Shuai Weng, David Botstein, J. Michael Cherry: Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD). Nucleic Acids Research 33(Database-Issue): 374-377 (2005)
19EEThomas Yan, Danny Yoo, Tanya Z. Berardini, Lukas A. Mueller, Dan C. Weems, Shuai Weng, J. Michael Cherry, Seung Yon Rhee: PatMatch: a program for finding patterns in peptide and nucleotide sequences. Nucleic Acids Research 33(Web-Server-Issue): 262-266 (2005)
2004
18EEElizabeth I. Boyle, Shuai Weng, Jeremy Gollub, Heng Jin, David Botstein, J. Michael Cherry, Gavin Sherlock: GO: : TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 20(18): 3710-3715 (2004)
17EEC. Wiederkehr, R. Basavaraj, Cyril Sarrauste de Menthière, R. Koch, U. Schlecht, Leandro Hermida, Benjamin Masdoua, R. Ishii, V. Cassen, M. Yamamoto, Christopher Lane, J. Michael Cherry, N. Lamb, Michael Primig: Database model and specification of GermOnline Release 2.0, a cross-species community annotation knowledgebase on germ cell differentiation. Bioinformatics 20(5): 808-811 (2004)
16 Selina S. Dwight, Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, Kara Dolinski, Stacia R. Engel, Becket Feierbach, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Laurie Issel-Tarver, Robert S. Nash, Anand Sethuraman, Barry Starr, Chandra L. Theesfeld, Rey Andrada, Gail Binkley, Qing Dong, Christopher Lane, Mark Schroeder, Shuai Weng, David Botstein, J. Michael Cherry: Saccharomyces genome database: Underlying principles and organisation. Briefings in Bioinformatics 5(1): 9-22 (2004)
15EEMichael Bada, Robert Stevens, Carole A. Goble, Yolanda Gil, Michael Ashburner, Judith A. Blake, J. Michael Cherry, Midori A. Harris, Suzanna Lewis: A short study on the success of the Gene Ontology. J. Web Sem. 1(2): 235-240 (2004)
14 Karen R. Christie, Shuai Weng, Rama Balakrishnan, Maria C. Costanzo, Kara Dolinski, Selina S. Dwight, Stacia R. Engel, Becket Feierbach, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Laurie Issel-Tarver, Robert S. Nash, Anand Sethuraman, Barry Starr, Chandra L. Theesfeld, Rey Andrada, Gail Binkley, Qing Dong, Christopher Lane, Mark Schroeder, David Botstein, J. Michael Cherry: Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. Nucleic Acids Research 32(Database-Issue): 311-314 (2004)
13 C. Wiederkehr, R. Basavaraj, Cyril Sarrauste de Menthière, Leandro Hermida, R. Koch, U. Schlecht, A. Amon, Sophie Brachat, Michael Breitenbach, Peter Briza, Sandrine Caburet, J. Michael Cherry, R. Davis, A. Deutschbauer, H. G. Dickinson, T. Dumitrescu, M. Fellous, A. Goldman, J. Anton Grootegoed, R. Scott Hawley, R. Ishii, B. Jégou, R. J. Kaufman, F. Klein, N. Lamb, B. Maro, K. Nasmyth, A. Nicolas, T. Orr-Weaver, Peter Philippsen, C. Pineau, K. P. Rabitsch, V. Reinke, H. Roest, W. Saunders, M. Schröder, T. Schedl, M. Siep, A. Villeneuve, Debra J. Wolgemuth, M. Yamamoto, D. Zickler, R. E. Esposito, Michael Primig: GermOnline, a cross-species community knowledgebase on germ cell differentiation. Nucleic Acids Research 32(Database-Issue): 560-567 (2004)
2003
12EEQing Dong, Rama Balakrishnan, Gail Binkley, Karen R. Christie, Maria C. Costanzo, Kara Dolinski, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Robert S. Nash, Laurie Issel-Tarver, Anand Sethuraman, Chandra L. Theesfeld, Shuai Weng, David Botstein, J. Michael Cherry: Gene Function, Metabolic Pathways and Comparative Genomics in Yeast. CSB 2003: 437-438
11 Shuai Weng, Qing Dong, Rama Balakrishnan, Karen R. Christie, Maria C. Costanzo, Kara Dolinski, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Eurie L. Hong, Laurie Issel-Tarver, Anand Sethuraman, Chandra L. Theesfeld, Rey Andrada, Gail Binkley, Christopher Lane, Mark Schroeder, David Botstein, J. Michael Cherry: Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins. Nucleic Acids Research 31(1): 216-218 (2003)
10 Maximilian Diehn, Gavin Sherlock, Gail Binkley, Heng Jin, John C. Matese, Tina Hernandez-Boussard, Christian A. Rees, J. Michael Cherry, David Botstein, Patrick O. Brown, Ash A. Alizadeh: SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Nucleic Acids Research 31(1): 219-223 (2003)
2002
9 Selina S. Dwight, Midori A. Harris, Kara Dolinski, Catherine A. Ball, Gail Binkley, Karen R. Christie, Dianna G. Fisk, Laurie Issel-Tarver, Mark Schroeder, Gavin Sherlock, Anand Sethuraman, Shuai Weng, David Botstein, J. Michael Cherry: Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Research 30(1): 69-72 (2002)
2001
8 Rob M. Ewing, J. Michael Cherry: Visualization of expression clusters using Sammon's non-linear mapping. Bioinformatics 17(7): 658-659 (2001)
7 Gavin Sherlock, Tina Hernandez-Boussard, Andrew Kasarskis, Gail Binkley, John C. Matese, Selina S. Dwight, Miroslava Kaloper, Shuai Weng, Heng Jin, Catherine A. Ball, Michael B. Eisen, Paul T. Spellman, Patrick O. Brown, David Botstein, J. Michael Cherry: The Stanford Microarray Database. Nucleic Acids Research 29(1): 152-155 (2001)
6 Catherine A. Ball, Heng Jin, Gavin Sherlock, Shuai Weng, John C. Matese, Rey Andrada, Gail Binkley, Kara Dolinski, Selina S. Dwight, Midori A. Harris, Laurie Issel-Tarver, Mark Schroeder, David Botstein, J. Michael Cherry: Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data. Nucleic Acids Research 29(1): 80-81 (2001)
2000
5 Catherine A. Ball, Kara Dolinski, Selina S. Dwight, Midori A. Harris, Laurie Issel-Tarver, Andrew Kasarskis, Charles R. Scafe, Gavin Sherlock, Gail Binkley, Heng Jin, Miroslava Kaloper, Sidney D. Orr, Mark Schroeder, Shuai Weng, Yan Zhu, David Botstein, J. Michael Cherry: Integrating functional genomic information into the Saccharomyces Genome Database. Nucleic Acids Research 28(1): 77-80 (2000)
1999
4 Stephen A. Chervitz, Erich T. Hester, Catherine A. Ball, Kara Dolinski, Selina S. Dwight, Midori A. Harris, Gail Juvik, Alice Malekian, Shannon Roberts, TaiYun Roe, Charles R. Scafe, Mark Schroeder, Gavin Sherlock, Shuai Weng, Yan Zhu, J. Michael Cherry, David Botstein: Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure. Nucleic Acids Research 27(1): 74-78 (1999)
3 Seung Yon Rhee, Shuai Weng, Deverie K. Bongard-Pierce, Margarita Garcia-Hernandez, Alice Malekian, David J. Flanders, J. Michael Cherry: Unified display of Arabidopsis thaliana physical maps from AtDB, the A.thaliana database. Nucleic Acids Research 27(1): 79-84 (1999)
1998
2 J. Michael Cherry, Caroline Adler, Catherine A. Ball, Stephen A. Chervitz, Selina S. Dwight, Erich T. Hester, Yankai Jia, Gail Juvik, TaiYun Roe, Mark Schroeder, Shuai Weng, David Botstein: SGD: Saccharomyces Genome Database. Nucleic Acids Research 26(1): 73-79 (1998)
1 David J. Flanders, Shuai Weng, Fabien X. Petel, J. Michael Cherry: AtDB, the Arabidopsis thaliana database, and graphical-web-display of progress by the Arabidopsis Genome Initiative. Nucleic Acids Research 26(1): 80-84 (1998)

Coauthor Index

1Caroline Adler [2]
2Ash A. Alizadeh [10]
3A. Amon [13]
4Rey Andrada [6] [11] [14] [16] [22]
5Michael Ashburner [15]
6Michael Bada [15]
7Rama Balakrishnan [11] [12] [14] [16] [20] [22] [23] [25]
8Catherine A. Ball [2] [4] [5] [6] [7] [9]
9R. Basavaraj [13] [17]
10Tanya Z. Berardini [19]
11Gail Binkley [5] [6] [7] [9] [10] [11] [12] [14] [16] [20] [21] [22] [23] [25]
12Judith A. Blake [15]
13Deverie K. Bongard-Pierce [3]
14David Botstein [2] [4] [5] [6] [7] [9] [10] [11] [12] [14] [16] [18] [20] [22] [23] [25]
15Elizabeth I. Boyle [18]
16Sophie Brachat [13]
17Michael Breitenbach [13]
18Peter Briza [13]
19Patrick O. Brown [7] [10]
20Sandrine Caburet [13]
21V. Cassen [17]
22Stephen A. Chervitz [2] [4]
23Karen R. Christie [9] [11] [12] [14] [16] [20] [22] [23] [25]
24Maria C. Costanzo [11] [12] [14] [16] [20] [22] [23] [25]
25Colleen E. Crangle [24]
26R. Davis [13]
27A. Deutschbauer [13]
28H. G. Dickinson [13]
29Maximilian Diehn [10]
30Kara Dolinski [4] [5] [6] [9] [11] [12] [14] [16] [20] [22] [23] [25]
31Qing Dong [11] [12] [14] [16] [20] [21] [22] [23] [25]
32T. Dumitrescu [13]
33Selina S. Dwight [2] [4] [5] [6] [7] [9] [11] [12] [14] [16] [20] [22] [23] [25]
34Michael B. Eisen [7]
35Stacia R. Engel [11] [12] [14] [16] [20] [22] [23] [25]
36R. E. Esposito [13]
37Rob M. Ewing [8]
38Becket Feierbach [14] [16]
39M. Fellous [13]
40Dianna G. Fisk [9] [11] [12] [14] [16] [20] [21] [22] [23] [25]
41David J. Flanders [1] [3]
42Margarita Garcia-Hernandez [3]
43Yolanda Gil [15]
44Carole A. Goble [15]
45A. Goldman [13]
46Jeremy Gollub [18]
47J. Anton Grootegoed [13]
48Midori A. Harris [4] [5] [6] [9] [15]
49R. Scott Hawley [13]
50Leandro Hermida [13] [17]
51Tina Hernandez-Boussard [7] [10]
52Erich T. Hester [2] [4]
53Jodi E. Hirschman [12] [14] [16] [20] [22] [23] [25]
54Benjamin C. Hitz [23] [25]
55Eurie L. Hong [11] [12] [14] [16] [20] [22] [23] [24] [25]
56R. Ishii [13] [17]
57Laurie Issel-Tarver [5] [6] [9] [11] [12] [14] [16]
58B. Jégou [13]
59Yankai Jia [2]
60Heng Jin [5] [6] [7] [10] [18]
61Gail Juvik [2] [4]
62Miroslava Kaloper [5] [7]
63Andrew Kasarskis [5] [7]
64R. J. Kaufman [13]
65F. Klein [13]
66R. Koch [13] [17]
67Cynthia J. Krieger [21] [25]
68N. Lamb [13] [17]
69Christopher Lane [11] [14] [16] [17] [20] [22] [23]
70Suzanna Lewis [15]
71Michael S. Livstone [22] [23] [25]
72Alice Malekian [3] [4]
73B. Maro [13]
74Benjamin Masdoua [17]
75John C. Matese [6] [7] [10]
76Cyril Sarrauste de Menthière [13] [17]
77Stuart R. Miyasato [22] [23] [25]
78Lukas A. Mueller [19]
79Robert S. Nash [12] [14] [16] [20] [21] [22] [23] [25]
80K. Nasmyth [13]
81A. Nicolas [13]
82Sidney D. Orr [5]
83T. Orr-Weaver [13]
84Rose Oughtred [20] [22] [23] [25]
85Julie Park [22] [23] [25]
86Fabien X. Petel [1]
87Peter Philippsen [13]
88C. Pineau [13]
89Michael Primig [13] [17]
90K. P. Rabitsch [13]
91Christian A. Rees [10]
92V. Reinke [13]
93Seung Yon Rhee [3] [19]
94Shannon Roberts [4]
95TaiYun Roe [2] [4]
96H. Roest [13]
97W. Saunders [13]
98Charles R. Scafe [4] [5]
99T. Schedl [13]
100U. Schlecht [13] [17]
101M. Schröder [13]
102Mark Schroeder [2] [4] [5] [6] [9] [11] [14] [16] [22] [23]
103Anand Sethuraman [9] [11] [12] [14] [16] [20] [21] [22] [23]
104Gavin Sherlock [4] [5] [6] [7] [9] [10] [18]
105M. Siep [13]
106Marek S. Skrzypek [20] [22] [23] [25]
107Paul T. Spellman [7]
108Barry Starr [14] [16] [22]
109Robert Stevens (Robert D. Stevens) [15]
110Nicholas A. Stover [21]
111Mayank K. Thanawala [22]
112Chandra L. Theesfeld [11] [12] [14] [16] [20] [22] [23]
113A. Villeneuve [13]
114Dan C. Weems [19]
115Shuai Weng [1] [2] [3] [4] [5] [6] [7] [9] [11] [12] [14] [16] [18] [19] [20] [21] [22] [23] [25]
116C. Wiederkehr [13] [17]
117Jennifer Williams [22]
118Debra J. Wolgemuth [13]
119Edith D. Wong [25]
120M. Yamamoto [13] [17]
121Thomas Yan [19]
122Danny Yoo [19]
123Alex Zbyslaw [24]
124Kathy K. Zhu [25]
125Yan Zhu [4] [5]
126D. Zickler [13]

Colors in the list of coauthors

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