-
1
-
-
78650475398
-
Phenotypic landscape of a bacterial cell
-
Nichols RJ, Sen S, Choo YJ, Beltrao P, Zietek M, Chaba R, Lee S, Kazmierczak KM, Lee KJ, Wong A, Shales M, Lovett S, Winkler ME, Krogan NJ, Typas A, Gross CA: Phenotypic landscape of a bacterial cell. Cell 2011, 144(1):143-156.
-
(2011)
Cell
, vol.144
, Issue.1
, pp. 143-156
-
-
Nichols, R.J.1
Sen, S.2
Choo, Y.J.3
Beltrao, P.4
Zietek, M.5
Chaba, R.6
Lee, S.7
Kazmierczak, K.M.8
Lee, K.J.9
Wong, A.10
Shales, M.11
Lovett, S.12
Winkler, M.E.13
Krogan, N.J.14
Typas, A.15
Gross, C.A.16
-
2
-
-
0037062951
-
RNA interference
-
Hannon GJ: RNA interference. Nature 2002, 418(6894):244-251.
-
(2002)
Nature
, vol.418
, Issue.6894
, pp. 244-251
-
-
Hannon, G.J.1
-
4
-
-
35948989284
-
The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration
-
Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 2007, 25(11):1251-1255.
-
(2007)
Nat Biotechnol
, vol.25
, Issue.11
, pp. 1251-1255
-
-
Smith, B.1
Ashburner, M.2
Rosse, C.3
Bard, J.4
Bug, W.5
Ceusters, W.6
Goldberg, L.J.7
Eilbeck, K.8
Ireland, A.9
Mungall, C.J.10
Leontis, N.11
Rocca-Serra, P.12
Ruttenberg, A.13
Sansone, S.A.14
Scheuermann, R.H.15
Shah, N.16
Whetzel, P.L.17
Lewis, S.18
-
5
-
-
56649105354
-
Prosecutor: Parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources
-
Blom EJ, Breitling R, Hofstede KJ, Roerdink JB, Van Hijum SA, Kuipers OP: Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources. BMC Genomics 2008, 9:495.
-
(2008)
BMC Genomics
, vol.9
, pp. 495
-
-
Blom, E.J.1
Breitling, R.2
Hofstede, K.J.3
Roerdink, J.B.4
Van Hijum, S.A.5
Kuipers, O.P.6
-
6
-
-
55449125498
-
The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function
-
Punta M, Ofran Y: The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function. PLoS Comput Biol 2008, 4(10):e1000160.
-
(2008)
PLoS Comput Biol
, vol.4
, Issue.10
-
-
Punta, M.1
Ofran, Y.2
-
7
-
-
84987680729
-
Standardized description of scientific evidence using the Evidence Ontology (ECO)
-
Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M: Standardized description of scientific evidence using the Evidence Ontology (ECO). Database 2014, 2014:bau075.
-
(2014)
Database
, vol.2014
, pp. bau075
-
-
Chibucos, M.C.1
Mungall, C.J.2
Balakrishnan, R.3
Christie, K.R.4
Huntley, R.P.5
White, O.6
Blake, J.A.7
Lewis, S.E.8
Giglio, M.9
-
8
-
-
22344437098
-
A chromosomally integrated bacteriophage in invasive meningococci
-
Bille E, Zahar JR, Perrin A, Morelle S, Kriz P, Jolley KA, Maiden MC, Dervin C, Nassif X, Tinsley CR: A chromosomally integrated bacteriophage in invasive meningococci. J Exp Med 2005, 201(12):1905-1913.
-
(2005)
J Exp Med
, vol.201
, Issue.12
, pp. 1905-1913
-
-
Bille, E.1
Zahar, J.R.2
Perrin, A.3
Morelle, S.4
Kriz, P.5
Jolley, K.A.6
Maiden, M.C.7
Dervin, C.8
Nassif, X.9
Tinsley, C.R.10
-
9
-
-
32644456040
-
The adult mouse anatomical dictionary: A tool for annotating and integrating data
-
Hayamizu TF, Mangan M, Corradi JP, Kadin JA, Ringwald M: The adult mouse anatomical dictionary: a tool for annotating and integrating data. Genome Biol 2005, 6(3):R29.
-
(2005)
Genome Biol
, vol.6
, Issue.3
, pp. R29
-
-
Hayamizu, T.F.1
Mangan, M.2
Corradi, J.P.3
Kadin, J.A.4
Ringwald, M.5
-
10
-
-
33644873681
-
FlyBase: Anatomical data, images and queries
-
Grumbling G, Strelets V: FlyBase: anatomical data, images and queries. Nucleic Acids Res 2006, 34(Database issue):D484-D488.
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.DATABASE ISSUE
, pp. D484-D488
-
-
Grumbling, G.1
Strelets, V.2
-
11
-
-
78751642348
-
Worm phenotype ontology: Integrating phenotype data within and beyond the C
-
Schindelman G, Fernandes JS, Bastiani CA, Yook K, Sternberg PW: Worm phenotype ontology: integrating phenotype data within and beyond the C. Elegans community. BMC Bioinformatics 2011, 12:32.
-
(2011)
Elegans Community. BMC Bioinformatics
, vol.12
, pp. 32
-
-
Schindelman, G.1
Fernandes, J.S.2
Bastiani, C.A.3
Yook, K.4
Sternberg, P.W.5
-
12
-
-
84907961999
-
The zebrafish anatomy and stage ontologies: Representing the anatomy and development of Danio rerio
-
Van Slyke CE, Bradford YM, Westerfield M, Haendel MA: The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio. J Biomedical Semantics 2014, 5(1):12.
-
(2014)
J Biomedical Semantics
, vol.5
, Issue.1
, pp. 12
-
-
Van Slyke, C.E.1
Bradford, Y.M.2
Westerfield, M.3
Haendel, M.A.4
-
13
-
-
34247192074
-
The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant
-
Ilic K, Kellogg EA, Jaiswal P, Zapata F, Stevens PF, Vincent LP, Avraham S, Reiser L, Pujar A, Sachs MM, Whitman NT, McCouch SR, Schaeffer ML, Ware DH, Stein LD, Rhee SY: The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiol 2007, 143(2):587-599.
-
(2007)
Plant Physiol
, vol.143
, Issue.2
, pp. 587-599
-
-
Ilic, K.1
Kellogg, E.A.2
Jaiswal, P.3
Zapata, F.4
Stevens, P.F.5
Vincent, L.P.6
Avraham, S.7
Reiser, L.8
Pujar, A.9
Sachs, M.M.10
Whitman, N.T.11
McCouch, S.R.12
Schaeffer, M.L.13
Ware, D.H.14
Stein, L.D.15
Rhee, S.Y.16
-
14
-
-
84879944114
-
FYPO: The fission yeast phenotype ontology
-
Harris MA, Lock A, Bahler J, Oliver SG, Wood V: FYPO: the fission yeast phenotype ontology. Bioinformatics 2013, 29(13):1671-1678.
-
(2013)
Bioinformatics
, vol.29
, Issue.13
, pp. 1671-1678
-
-
Harris, M.A.1
Lock, A.2
Bahler, J.3
Oliver, S.G.4
Wood, V.5
-
15
-
-
75549087626
-
Saccharomyces genome database provides mutant phenotype data
-
Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, Dwight SS, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Livstone MS, Miyasato SR, Nash R, Oughtred R, Park J, Skrzypek MS, Weng S, Wong ED, Dolinski K, Botstein D, Cherry JM: Saccharomyces genome database provides mutant phenotype data. Nucleic Acids Res 2010, 38(Database issue):D433-D436.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.DATABASE ISSUE
, pp. D433-D436
-
-
Engel, S.R.1
Balakrishnan, R.2
Binkley, G.3
Christie, K.R.4
Costanzo, M.C.5
Dwight, S.S.6
Fisk, D.G.7
Hirschman, J.E.8
Hitz, B.C.9
Hong, E.L.10
Krieger, C.J.11
Livstone, M.S.12
Miyasato, S.R.13
Nash, R.14
Oughtred, R.15
Park, J.16
Skrzypek, M.S.17
Weng, S.18
Wong, E.D.19
Dolinski, K.20
Botstein, D.21
Cherry, J.M.22
more..
-
18
-
-
0019381724
-
Suppressor mutations that restore export of a protein with a defective signal sequence
-
Emr SD, Hanley-Way S, Silhavy TJ: Suppressor mutations that restore export of a protein with a defective signal sequence. Cell 1981, 23(1):79-88.
-
(1981)
Cell
, vol.23
, Issue.1
, pp. 79-88
-
-
Emr, S.D.1
Hanley-Way, S.2
Silhavy, T.J.3
-
19
-
-
0025959707
-
Use of a screen for synthetic lethal and multicopy suppressee mutants to identify two new genes involved in morphogenesis in Saccharomyces cerevisiae
-
Bender A, Pringle JR: Use of a screen for synthetic lethal and multicopy suppressee mutants to identify two new genes involved in morphogenesis in Saccharomyces cerevisiae. Mol Cell Biol 1991, 11(3):1295-1305.
-
(1991)
Mol Cell Biol
, vol.11
, Issue.3
, pp. 1295-1305
-
-
Bender, A.1
Pringle, J.R.2
-
20
-
-
34147217542
-
Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map
-
Collins SR, Miller KM, Maas NL, Roguev A, Fillingham J, Chu CS, Schuldiner M, Gebbia M, Recht J, Shales M, Ding H, Xu H, Han J, Ingvarsdottir K, Cheng B, Andrews B, Boone C, Berger SL, Hieter P, Zhang Z, Brown GW, Ingles CJ, Emili A, Allis CD, Toczyski DP, Weissman JS, Greenblatt JF, Krogan NJ: Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 2007, 446(7137):806-810.
-
(2007)
Nature
, vol.446
, Issue.7137
, pp. 806-810
-
-
Collins, S.R.1
Miller, K.M.2
Maas, N.L.3
Roguev, A.4
Fillingham, J.5
Chu, C.S.6
Schuldiner, M.7
Gebbia, M.8
Recht, J.9
Shales, M.10
Ding, H.11
Xu, H.12
Han, J.13
Ingvarsdottir, K.14
Cheng, B.15
Andrews, B.16
Boone, C.17
Berger, S.L.18
Hieter, P.19
Zhang, Z.20
Brown, G.W.21
Ingles, C.J.22
Emili, A.23
Allis, C.D.24
Toczyski, D.P.25
Weissman, J.S.26
Greenblatt, J.F.27
Krogan, N.J.28
more..
-
21
-
-
50849125711
-
High-throughput, quantitative analyses of genetic interactions in E coli
-
Typas A, Nichols RJ, Siegele DA, Shales M, Collins SR, Lim B, Braberg H, Yamamoto N, Takeuchi R, Wanner BL, Mori H, Weissman JS, Krogan NJ, Gross CA: High-throughput, quantitative analyses of genetic interactions in E. coli. Nat Methods 2008, 5(9):781-787.
-
(2008)
Nat Methods
, vol.5
, Issue.9
, pp. 781-787
-
-
Typas, A.1
Nichols, R.J.2
Siegele, D.A.3
Shales, M.4
Collins, S.R.5
Lim, B.6
Braberg, H.7
Yamamoto, N.8
Takeuchi, R.9
Wanner, B.L.10
Mori, H.11
Weissman, J.S.12
Krogan, N.J.13
Gross, C.A.14
-
22
-
-
50849098825
-
ESGA: Ec coli synthetic genetic array analysis
-
Butland G, Babu M, Diaz-Mejia JJ, Bohdana F, Phanse S, Gold B, Yang W, Li J, Gagarinova AG, Pogoutse O, Mori H, Wanner BL, Lo H, Wasniewski J, Christopolous C, Ali M, Venn P, Safavi-Naini A, Sourour N, Caron S, Choi JY, Laigle L, Nazarians-Armavil A, Deshpande A, Joe S, Datsenko KA, Yamamoto N, Andrews BJ, Boone C, Ding H, et al: eSGA: Ec coli synthetic genetic array analysis. Nat Methods 2008, 5(9):789-795.
-
(2008)
Nat Methods
, vol.5
, Issue.9
, pp. 789-795
-
-
Butland, G.1
Babu, M.2
Diaz-Mejia, J.J.3
Bohdana, F.4
Phanse, S.5
Gold, B.6
Yang, W.7
Li, J.8
Gagarinova, A.G.9
Pogoutse, O.10
Mori, H.11
Wanner, B.L.12
Lo, H.13
Wasniewski, J.14
Christopolous, C.15
Ali, M.16
Venn, P.17
Safavi-Naini, A.18
Sourour, N.19
Caron, S.20
Choi, J.Y.21
Laigle, L.22
Nazarians-Armavil, A.23
Deshpande, A.24
Joe, S.25
Datsenko, K.A.26
Yamamoto, N.27
Andrews, B.J.28
Boone, C.29
Ding, H.30
more..
-
23
-
-
33644532256
-
Formal ontology for natural language processing and the integration of biomedical databases
-
Simon J, Dos Santos M, Fielding J, Smith B: Formal ontology for natural language processing and the integration of biomedical databases. Int J Med Inform 2006, 75(3-4):224-231.
-
(2006)
Int J Med Inform
, vol.75
, Issue.3-4
, pp. 224-231
-
-
Simon, J.1
Dos Santos, M.2
Fielding, J.3
Smith, B.4
-
24
-
-
20844433631
-
Using ontologies to describe mouse phenotypes
-
Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D: Using ontologies to describe mouse phenotypes. Genome Biol 2005, 6(1):R8.
-
(2005)
Genome Biol
, vol.6
, Issue.1
, pp. R8
-
-
Gkoutos, G.V.1
Green, E.C.2
Mallon, A.M.3
Hancock, J.M.4
Davidson, D.5
-
26
-
-
84874253819
-
Gene Ontology annotations and resources
-
Gene Ontology Consortium, Blake JA, Dolan M, Drabkin H, Hill DP, Li N, Sitnikov D, Bridges S, Burgess S, Buza T, McCarthy F, Peddinti D, Pillai L, Carbon S, Dietze H, Ireland A, Lewis SE, Mungall CJ, Gaudet P, Chrisholm RL, Fey P, Kibbe WA, Basu S, Siegele DA, McIntosh BK, Renfro DP, Zweifel AE, Hu JC, Brown NH, Tweedie S, et al: Gene Ontology annotations and resources. Nucleic Acids Res 2013, 41(Database issue):D530-D535.
-
(2013)
Nucleic Acids Res
, vol.41
, Issue.DATABASE ISSUE
, pp. D530-D535
-
-
Gene Ontology Consortium1
Blake, J.A.2
Dolan, M.3
Drabkin, H.4
Hill, D.P.5
Li, N.6
Sitnikov, D.7
Bridges, S.8
Burgess, S.9
Buza, T.10
McCarthy, F.11
Peddinti, D.12
Pillai, L.13
Carbon, S.14
Dietze, H.15
Ireland, A.16
Lewis, S.E.17
Mungall, C.J.18
Gaudet, P.19
Chrisholm, R.L.20
Fey, P.21
Kibbe, W.A.22
Basu, S.23
Siegele, D.A.24
McIntosh, B.K.25
Renfro, D.P.26
Zweifel, A.E.27
Hu, J.C.28
Brown, N.H.29
Tweedie, S.30
more..
-
28
-
-
67649803191
-
Genetic suppressors and recovery of repressed biochemical memory
-
Beckwith J: Genetic suppressors and recovery of repressed biochemical memory. J Biol Chem 2009, 284(19):12585-12592.
-
(2009)
J Biol Chem
, vol.284
, Issue.19
, pp. 12585-12592
-
-
Beckwith, J.1
-
30
-
-
22044433259
-
Relations in biomedical ontologies
-
Smith B, Ceusters W, Klagges B, Kohler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector AL, Rosse C: Relations in biomedical ontologies. Genome Biol 2005, 6(5):R46.
-
(2005)
Genome Biol
, vol.6
, Issue.5
, pp. R46
-
-
Smith, B.1
Ceusters, W.2
Klagges, B.3
Kohler, J.4
Kumar, A.5
Lomax, J.6
Mungall, C.7
Neuhaus, F.8
Rector, A.L.9
Rosse, C.10
-
31
-
-
77349112447
-
Integrating phenotype ontologies across multiple species
-
Mungall CJ, Gkoutos GV, Smith CL, Haendel MA, Lewis SE, Ashburner M: Integrating phenotype ontologies across multiple species. Genome Biol 2010, 11(1):R2.
-
(2010)
Genome Biol
, vol.11
, Issue.1
, pp. R2
-
-
Mungall, C.J.1
Gkoutos, G.V.2
Smith, C.L.3
Haendel, M.A.4
Lewis, S.E.5
Ashburner, M.6
-
32
-
-
84884238012
-
The intrinsic resistome of bacterial pathogens
-
Olivares J, Bernardini A, Garcia-Leon G, Corona F, B Sanchez M, Martinez JL: The intrinsic resistome of bacterial pathogens. Front Microbiol 2013, 4:103.
-
(2013)
Front Microbiol
, vol.4
, pp. 103
-
-
Olivares, J.1
Bernardini, A.2
Garcia-Leon, G.3
Corona, F.4
Sanchez, B.M.5
Martinez, J.L.6
-
33
-
-
84897083269
-
Metabolic flux analysis of Escherichia coli knockouts: Lessons from the Keio collection and future outlook
-
Long CP, Antoniewicz MR: Metabolic flux analysis of Escherichia coli knockouts: lessons from the Keio collection and future outlook. Curr Opin Biotechnol 2014, 28C:127-133.
-
(2014)
Curr Opin Biotechnol
, vol.28 C
, pp. 127-133
-
-
Long, C.P.1
Antoniewicz, M.R.2
-
34
-
-
67849128700
-
BioPortal: Ontologies and integrated data resources at the click of a mouse
-
Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL, Storey MA, Chute CG, Musen MA: BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res 2009, 37(Web Server issue):W170-W173.
-
(2009)
Nucleic Acids Res
, vol.37
, Issue.WEB SERVER ISSUE
, pp. W170-W173
-
-
Noy, N.F.1
Shah, N.H.2
Whetzel, P.L.3
Dai, B.4
Dorf, M.5
Griffith, N.6
Jonquet, C.7
Rubin, D.L.8
Storey, M.A.9
Chute, C.G.10
Musen, M.A.11
-
36
-
-
34548595489
-
OBO-Edit-an ontology editor for biologists
-
Day-Richter J, Harris MA, Haendel M, Gene Ontology OBO-Edit Working Group, Lewis S: OBO-Edit-an ontology editor for biologists. Bioinformatics 2007, 23(16):2198-2200.
-
(2007)
Bioinformatics
, vol.23
, Issue.16
, pp. 2198-2200
-
-
Day-Richter, J.1
Harris, M.A.2
Haendel, M.3
Lewis, S.4
-
37
-
-
84862156604
-
GONUTS: The gene ontology normal usage tracking system
-
Renfro DP, McIntosh BK, Venkatraman A, Siegele DA, Hu JC: GONUTS: the gene ontology normal usage tracking system. Nucleic Acids Res 2012, 40(Database issue):D1262-D1269.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.DATABASE ISSUE
, pp. D1262-D1269
-
-
Renfro, D.P.1
McIntosh, B.K.2
Venkatraman, A.3
Siegele, D.A.4
Hu, J.C.5
-
38
-
-
84858588614
-
Saccharomyces genome database: The genomics resource of budding yeast
-
Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Karra K, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Simison M, Weng S, Wong ED: Saccharomyces genome database: the genomics resource of budding yeast. Nucleic Acids Res 2012, 40(Database issue):D700-D705.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.DATABASE ISSUE
, pp. D700-D705
-
-
Cherry, J.M.1
Hong, E.L.2
Amundsen, C.3
Balakrishnan, R.4
Binkley, G.5
Chan, E.T.6
Christie, K.R.7
Costanzo, M.C.8
Dwight, S.S.9
Engel, S.R.10
Fisk, D.G.11
Hirschman, J.E.12
Hitz, B.C.13
Karra, K.14
Krieger, C.J.15
Miyasato, S.R.16
Nash, R.S.17
Park, J.18
Skrzypek, M.S.19
Simison, M.20
Weng, S.21
Wong, E.D.22
more..
-
39
-
-
84858305675
-
PomBase: A comprehensive online resource for fission yeast
-
Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, Aslett M, Lock A, Bahler J, Kersey PJ, Oliver SG: PomBase: a comprehensive online resource for fission yeast. Nucleic Acids Res 2012, 40(Database issue): D695-D699.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.DATABASE ISSUE
, pp. D695-D699
-
-
Wood, V.1
Harris, M.A.2
McDowall, M.D.3
Rutherford, K.4
Vaughan, B.W.5
Staines, D.M.6
Aslett, M.7
Lock, A.8
Bahler, J.9
Kersey, P.J.10
Oliver, S.G.11
-
40
-
-
0014649257
-
Escherichia coli mutants defective in chemotaxis toward specific chemicals
-
Hazelbauer GL, Mesibov RE, Adler J: Escherichia coli mutants defective in chemotaxis toward specific chemicals. Proc Natl Acad Sci USA 1969, 64(4):1300-1307.
-
(1969)
Proc Natl Acad Sci USA
, vol.64
, Issue.4
, pp. 1300-1307
-
-
Hazelbauer, G.L.1
Mesibov, R.E.2
Adler, J.3
|