-
1
-
-
75549083482
-
EuPathDB: A portal to eukaryotic pathogen databases
-
Aurrecoechea, C., Brestelli, J., Brunk, B.P., Fischer, S., Gajria, B., Gao, X., Gingle, A., Grant, G., Harb, O.S., Heiges, M. et al. (2010) EuPathDB: a portal to eukaryotic pathogen databases. Nucleic Acids Res., 38, D415-D419.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Aurrecoechea, C.1
Brestelli, J.2
Brunk, B.P.3
Fischer, S.4
Gajria, B.5
Gao, X.6
Gingle, A.7
Grant, G.8
Harb, O.S.9
Heiges, M.10
-
2
-
-
84867723807
-
Influenza Research Database: An integrated bioinformatics resource for influenza research and surveillance
-
Squires, R.B., Noronha, J., Hunt, V., García Sastre, A., Macken, C., Baumgarth, N., Suarez, D., Pickett, B.E., Zhang, Y., Larsen, C.N. et al. (2012) Influenza Research Database: an integrated bioinformatics resource for influenza research and surveillance. Influenza Other Respi Viruses, 6, 404-416.
-
(2012)
Influenza Other Respi Viruses
, vol.6
, pp. 404-416
-
-
Squires, R.B.1
Noronha, J.2
Hunt, V.3
García Sastre, A.4
Macken, C.5
Baumgarth, N.6
Suarez, D.7
Pickett, B.E.8
Zhang, Y.9
Larsen, C.N.10
-
3
-
-
84862167820
-
ViPR: An open bioinformatics database and analysis resource for virology research
-
Pickett, B.E., Sadat, E.L., Zhang, Y., Noronha, J.M., Squires, R.B., Hunt, V., Liu, M., Kumar, S., Zaremba, S., Gu, Z. et al. (2011) ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Res., 40, D593-D598.
-
(2011)
Nucleic Acids Res.
, vol.40
-
-
Pickett, B.E.1
Sadat, E.L.2
Zhang, Y.3
Noronha, J.M.4
Squires, R.B.5
Hunt, V.6
Liu, M.7
Kumar, S.8
Zaremba, S.9
Gu, Z.10
-
4
-
-
84858286227
-
VectorBase: Improvements to a bioinformatics resource for invertebrate vector genomics
-
Megy, K., Emrich, S.J., Lawson, D., Campbell, D., Dialynas, E., Hughes, D.S.T., Koscielny, G., Louis, C., Maccallum, R.M., Redmond, S.N. et al. (2012) VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics. Nucleic Acids Res., 40, D729-D734.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Megy, K.1
Emrich, S.J.2
Lawson, D.3
Campbell, D.4
Dialynas, E.5
Hughes, D.S.T.6
Koscielny, G.7
Louis, C.8
Maccallum, R.M.9
Redmond, S.N.10
-
5
-
-
80855134793
-
PATRIC: The comprehensive bacterial bioinformatics resource with a focus on human pathogenic species
-
Gillespie, J.J., Wattam, A.R., Cammer, S.A., Gabbard, J.L., Shukla, M.P., Dalay, O., Driscoll, T., Hix, D., Mane, S.P., Mao, C. et al. (2011) PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. Infect. Immun., 79, 4286-4298.
-
(2011)
Infect. Immun.
, vol.79
, pp. 4286-4298
-
-
Gillespie, J.J.1
Wattam, A.R.2
Cammer, S.A.3
Gabbard, J.L.4
Shukla, M.P.5
Dalay, O.6
Driscoll, T.7
Hix, D.8
Mane, S.P.9
Mao, C.10
-
6
-
-
34447271298
-
National institute of allergy and infectious diseases bioinformatics resource centers: New assets for pathogen informatics
-
Greene, J.M., Collins, F., Lefkowitz, E.J., Roos, D., Scheuermann, R.H., Sobral, B., Stevens, R., White, O. and Di Francesco, V. (2007) National Institute of Allergy and Infectious Diseases Bioinformatics Resource Centers: New Assets for Pathogen Informatics. Infect Immun, 75, 3212-3219.
-
(2007)
Infect Immun
, vol.75
, pp. 3212-3219
-
-
Greene, J.M.1
Collins, F.2
Lefkowitz, E.J.3
Roos, D.4
Scheuermann, R.H.5
Sobral, B.6
Stevens, R.7
White, O.8
Di Francesco, V.9
-
7
-
-
84862208151
-
GeneDB - An annotation database for pathogens
-
Logan-Klumpler, F.J., De Silva, N., Boehme, U., Rogers, M.B., Velarde, G., McQuillan, J.A., Carver, T., Aslett, M., Olsen, C., Subramanian, S. et al. (2012) GeneDB - an annotation database for pathogens. Nucleic Acids Res., 40, D98-D108.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Logan-Klumpler, F.J.1
De Silva, N.2
Boehme, U.3
Rogers, M.B.4
Velarde, G.5
McQuillan, J.A.6
Carver, T.7
Aslett, M.8
Olsen, C.9
Subramanian, S.10
-
8
-
-
75549088870
-
TriTrypDB: A functional genomic resource for the Trypanosomatidae
-
Aslett, M., Aurrecoechea, C., Berriman, M., Brestelli, J., Brunk, B.P., Carrington, M., Depledge, D.P., Fischer, S., Gajria, B., Gao, X. et al. (2009) TriTrypDB: a functional genomic resource for the Trypanosomatidae. Nucleic Acids Res, 38, D457-D462.
-
(2009)
Nucleic Acids Res
, vol.38
-
-
Aslett, M.1
Aurrecoechea, C.2
Berriman, M.3
Brestelli, J.4
Brunk, B.P.5
Carrington, M.6
Depledge, D.P.7
Fischer, S.8
Gajria, B.9
Gao, X.10
-
9
-
-
33644875511
-
CryptoDB: A Cryptosporidium bioinformatics resource update
-
Heiges, M., Wang, H., Robinson, E., Aurrecoechea, C., Gao, X., Kaluskar, N., Rhodes, P., Wang, S., He, C.-Z., Su, Y. et al. (2006) CryptoDB: a Cryptosporidium bioinformatics resource update. Nucleic Acids Res., 34, D419-D422.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Heiges, M.1
Wang, H.2
Robinson, E.3
Aurrecoechea, C.4
Gao, X.5
Kaluskar, N.6
Rhodes, P.7
Wang, S.8
He, C.-Z.9
Su, Y.10
-
10
-
-
38549128700
-
ToxoDB: An integrated Toxoplasma gondii database resource
-
Gajria, B., Bahl, A., Brestelli, J., Dommer, J., Fischer, S., Gao, X., Heiges, M., Iodice, J., Kissinger, J.C., Mackey, A.J. et al. (2008) ToxoDB: an integrated Toxoplasma gondii database resource. Nucleic Acids Res., 36, D553-D556.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Gajria, B.1
Bahl, A.2
Brestelli, J.3
Dommer, J.4
Fischer, S.5
Gao, X.6
Heiges, M.7
Iodice, J.8
Kissinger, J.C.9
Mackey, A.J.10
-
11
-
-
78651323941
-
AmoebaDB and MicrosporidiaDB: Functional genomic resources for Amoebozoa and Microsporidia species
-
Aurrecoechea, C., Barreto, A., Brestelli, J., Brunk, B.P., Caler, E.V., Fischer, S., Gajria, B., Gao, X., Gingle, A., Grant, G. et al. (2011) AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species. Nucleic Acids Res., 39, D612-D619.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Aurrecoechea, C.1
Barreto, A.2
Brestelli, J.3
Brunk, B.P.4
Caler, E.V.5
Fischer, S.6
Gajria, B.7
Gao, X.8
Gingle, A.9
Grant, G.10
-
12
-
-
58149200936
-
GiardiaDB and TrichDB: Integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis
-
Aurrecoechea, C., Brestelli, J., Brunk, B.P., Carlton, J.M., Dommer, J., Fischer, S., Gajria, B., Gao, X., Gingle, A., Grant, G. et al. (2009) GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis. Nucleic Acids Res., 37, D526-D530.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Aurrecoechea, C.1
Brestelli, J.2
Brunk, B.P.3
Carlton, J.M.4
Dommer, J.5
Fischer, S.6
Gajria, B.7
Gao, X.8
Gingle, A.9
Grant, G.10
-
13
-
-
33644787447
-
OrthoMCL-DB: Querying a comprehensive multi-species collection of ortholog groups
-
Chen, F., Mackey, A.J., Stoeckert, C.J. and Roos, D.S. (2006) OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res., 34, D363-D368.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Chen, F.1
Mackey, A.J.2
Stoeckert, C.J.3
Roos, D.S.4
-
14
-
-
80053484719
-
The Strategies WDK: A graphical search interface and web development kit for functional genomics databases
-
Fischer, S., Aurrecoechea, C., Brunk, B.P., Gao, X., Harb, O.S., Kraemer, E.T., Pennington, C., Treatman, C., Kissinger, J.C., Roos, D.S. et al. (2011) The Strategies WDK: a graphical search interface and web development kit for functional genomics databases. Database, 2011, bar027.
-
(2011)
Database
, vol.2011
-
-
Fischer, S.1
Aurrecoechea, C.2
Brunk, B.P.3
Gao, X.4
Harb, O.S.5
Kraemer, E.T.6
Pennington, C.7
Treatman, C.8
Kissinger, J.C.9
Roos, D.S.10
-
15
-
-
84862214345
-
FungiDB: An integrated functional genomics database for fungi
-
Stajich, J.E., Harris, T., Brunk, B.P., Brestelli, J., Fischer, S., Harb, O.S., Kissinger, J.C., Li, W., Nayak, V., Pinney, D.F. et al. (2012) FungiDB: an integrated functional genomics database for fungi. Nucleic Acids Res., 40, D675-D681.
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Stajich, J.E.1
Harris, T.2
Brunk, B.P.3
Brestelli, J.4
Fischer, S.5
Harb, O.S.6
Kissinger, J.C.7
Li, W.8
Nayak, V.9
Pinney, D.F.10
-
16
-
-
58149194614
-
SchistoDB: A Schistosoma mansoni genome resource
-
Zerlotini, A., Heiges, M., Wang, H., Moraes, R.L.V., Dominitini, A.J., Ruiz, J.C., Kissinger, J.C. and Oliveira, G. (2009) SchistoDB: a Schistosoma mansoni genome resource. Nucleic Acids Res., 37, D579-D582.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Zerlotini, A.1
Heiges, M.2
Wang, H.3
Moraes, R.L.V.4
Dominitini, A.J.5
Ruiz, J.C.6
Kissinger, J.C.7
Oliveira, G.8
-
17
-
-
77955712976
-
TB database 2010: Overview and update
-
Galagan, J.E., Sisk, P., Stolte, C., Weiner, B., Koehrsen, M., Wymore, F., Reddy, T.B.K., Zucker, J.D., Engels, R., Gellesch, M. et al. (2010) TB database 2010: overview and update. Tuberculosis, 90, 225-235.
-
(2010)
Tuberculosis
, vol.90
, pp. 225-235
-
-
Galagan, J.E.1
Sisk, P.2
Stolte, C.3
Weiner, B.4
Koehrsen, M.5
Wymore, F.6
Reddy, T.B.K.7
Zucker, J.D.8
Engels, R.9
Gellesch, M.10
-
18
-
-
33846056827
-
EPConDB: A web resource for gene expression related to pancreatic development, beta-cell function and diabetes
-
Mazzarelli, J.M., Brestelli, J., Gorski, R.K., Liu, J., Manduchi, E., Pinney, D.F., Schug, J., White, P., Kaestner, K.H. and Stoeckert, C.J. (2007) EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes. Nucleic Acids Res., 35, D751-D755.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Mazzarelli, J.M.1
Brestelli, J.2
Gorski, R.K.3
Liu, J.4
Manduchi, E.5
Pinney, D.F.6
Schug, J.7
White, P.8
Kaestner, K.H.9
Stoeckert, C.J.10
-
19
-
-
80051600636
-
Attenuation of virulence in an apicomplexan hemoparasite results in reduced genome diversity at the population level
-
Lau, A.O., Kalyanaraman, A., Echaide, I., Palmer, G.H., Bock, R., Pedroni, M.J., Rameshkumar, M., Ferreira, M.B., Fletcher, T.I. and McElwain, T.F. (2011) Attenuation of virulence in an apicomplexan hemoparasite results in reduced genome diversity at the population level. BMC Genomics, 12, 410.
-
(2011)
BMC Genomics
, vol.12
, pp. 410
-
-
Lau, A.O.1
Kalyanaraman, A.2
Echaide, I.3
Palmer, G.H.4
Bock, R.5
Pedroni, M.J.6
Rameshkumar, M.7
Ferreira, M.B.8
Fletcher, T.I.9
McElwain, T.F.10
-
20
-
-
0034800374
-
InterProScan - An integration platform for the signature-recognition methods in InterPro
-
Zdobnov, E.M. and Apweiler, R. (2001) InterProScan - an integration platform for the signature-recognition methods in InterPro. Bioinformatics, 17, 847-848.
-
(2001)
Bioinformatics
, vol.17
, pp. 847-848
-
-
Zdobnov, E.M.1
Apweiler, R.2
-
21
-
-
18644378331
-
The generic genome browser: A building block for a model organism system database
-
Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A. et al. (2002) The generic genome browser: a building block for a model organism system database. Genome Res., 12, 1599-1610.
-
(2002)
Genome Res.
, vol.12
, pp. 1599-1610
-
-
Stein, L.D.1
Mungall, C.2
Shu, S.3
Caudy, M.4
Mangone, M.5
Day, A.6
Nickerson, E.7
Stajich, J.E.8
Harris, T.W.9
Arva, A.10
-
22
-
-
80054901700
-
The phosphoproteomes of Plasmodium falciparum and Toxoplasma gondii reveal unusual adaptations within and beyond the parasites' boundaries
-
Treeck, M., Sanders, J.L., Elias, J.E. and Boothroyd, J.C. (2011) The phosphoproteomes of Plasmodium falciparum and Toxoplasma gondii reveal unusual adaptations within and beyond the parasites' boundaries. Cell Host Microbe, 10, 410-419.
-
(2011)
Cell Host Microbe
, vol.10
, pp. 410-419
-
-
Treeck, M.1
Sanders, J.L.2
Elias, J.E.3
Boothroyd, J.C.4
-
23
-
-
80052745094
-
Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)
-
Grant, G.R., Farkas, M.H., Pizarro, A.D., Lahens, N.F., Schug, J., Brunk, B.P., Stoeckert, C.J., Hogenesch, J.B. and Pierce, E.A. (2011) Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinformatics, 27, 2518-2528.
-
(2011)
Bioinformatics
, vol.27
, pp. 2518-2528
-
-
Grant, G.R.1
Farkas, M.H.2
Pizarro, A.D.3
Lahens, N.F.4
Schug, J.5
Brunk, B.P.6
Stoeckert, C.J.7
Hogenesch, J.B.8
Pierce, E.A.9
-
24
-
-
79953177468
-
Aligning short sequencing reads with Bowtie
-
Chapter 11, Unit 11.7
-
Langmead, B. (2010) Aligning short sequencing reads with Bowtie. Curr. Protoc. Bioinformatics, Chapter 11, Unit 11.7.
-
(2010)
Curr. Protoc. Bioinformatics
-
-
Langmead, B.1
-
25
-
-
68549104404
-
The Sequence Alignment/map format and SAMtools
-
1000 Genome Project Data Processing Subgroup
-
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G. and Durbin, R. 1000 Genome Project Data Processing Subgroup (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
26
-
-
77956295988
-
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
-
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M. et al. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res., 20, 1297-1303.
-
(2010)
Genome Res.
, vol.20
, pp. 1297-1303
-
-
McKenna, A.1
Hanna, M.2
Banks, E.3
Sivachenko, A.4
Cibulskis, K.5
Kernytsky, A.6
Garimella, K.7
Altshuler, D.8
Gabriel, S.9
Daly, M.10
-
27
-
-
69949122158
-
VarScan: Variant detection in massively parallel sequencing of individual and pooled samples
-
Koboldt, D.C., Chen, K., Wylie, T., Larson, D.E., McLellan, M.D., Mardis, E.R., Weinstock, G.M., Wilson, R.K. and Ding, L. (2009) VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics, 25, 2283-2285.
-
(2009)
Bioinformatics
, vol.25
, pp. 2283-2285
-
-
Koboldt, D.C.1
Chen, K.2
Wylie, T.3
Larson, D.E.4
McLellan, M.D.5
Mardis, E.R.6
Weinstock, G.M.7
Wilson, R.K.8
Ding, L.9
-
28
-
-
54749157466
-
Regulatory hotspots in the malaria parasite genome dictate transcriptional variation
-
Gonzales, J.M., Patel, J.J., Ponmee, N., Jiang, L., Tan, A., Maher, S.P., Wuchty, S., Rathod, P.K. and Ferdig, M.T. (2008) Regulatory hotspots in the malaria parasite genome dictate transcriptional variation. PLoS Biol., 6, e238.
-
(2008)
PLoS Biol.
, vol.6
-
-
Gonzales, J.M.1
Patel, J.J.2
Ponmee, N.3
Jiang, L.4
Tan, A.5
Maher, S.P.6
Wuchty, S.7
Rathod, P.K.8
Ferdig, M.T.9
-
29
-
-
84856955769
-
High-throughput decoding of antitrypanosomal drug efficacy and resistance
-
Alsford, S., Eckert, S., Baker, N., Glover, L., Sanchez-Flores, A., Leung, K.F., Turner, D.J., Field, M.C., Berriman, M. and Horn, D. (2012) High-throughput decoding of antitrypanosomal drug efficacy and resistance. Nature, 482, 232-236.
-
(2012)
Nature
, vol.482
, pp. 232-236
-
-
Alsford, S.1
Eckert, S.2
Baker, N.3
Glover, L.4
Sanchez-Flores, A.5
Leung, K.F.6
Turner, D.J.7
Field, M.C.8
Berriman, M.9
Horn, D.10
-
30
-
-
77955801615
-
Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
-
Galaxy Team. (2010)
-
Goecks, J., Nekrutenko, A. and Taylor, J. (2010). Galaxy Team. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, R86.
-
(2010)
Genome Biol.
, vol.11
-
-
Goecks, J.1
Nekrutenko, A.2
Taylor, J.3
|