-
1
-
-
84862198590
-
The Sequence Read Archive: explosive growth of sequencing data
-
10.1093/nar/gkr854, 3245110, 22009675
-
Kodama Y, Shumway M, Leinonen R. The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res 2012, 40:D54-D56. 10.1093/nar/gkr854, 3245110, 22009675.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Kodama, Y.1
Shumway, M.2
Leinonen, R.3
-
2
-
-
79957842166
-
Computational methods for transcriptome annotation and quantification using RNA-seq
-
10.1038/nmeth.1613, 21623353
-
Garber M, Grabherr MG, Guttman M, Trapnell C. Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods 2011, 8:469-477. 10.1038/nmeth.1613, 21623353.
-
(2011)
Nat Methods
, vol.8
, pp. 469-477
-
-
Garber, M.1
Grabherr, M.G.2
Guttman, M.3
Trapnell, C.4
-
3
-
-
80052960863
-
Next-generation transcriptome assembly
-
10.1038/nrg3068, 21897427
-
Martin JA, Wang Z. Next-generation transcriptome assembly. Nat Rev Genet 2011, 12:671-682. 10.1038/nrg3068, 21897427.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 671-682
-
-
Martin, J.A.1
Wang, Z.2
-
4
-
-
67650711615
-
SOAP2: an improved ultrafast tool for short read alignment
-
10.1093/bioinformatics/btp336, 19497933
-
Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 2009, 25:1966-1967. 10.1093/bioinformatics/btp336, 19497933.
-
(2009)
Bioinformatics
, vol.25
, pp. 1966-1967
-
-
Li, R.1
Yu, C.2
Li, Y.3
Lam, T.W.4
Yiu, S.M.5
Kristiansen, K.6
Wang, J.7
-
5
-
-
78049346632
-
De novo assembly and analysis of RNA-seq data
-
10.1038/nmeth.1517, 20935650
-
Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ, Griffith M, Raymond A, Thiessen N, Cezard T, Butterfield YS, Newsome R, Chan SK, She R, Varhol R, Kamoh B, Prabhu AL, Tam A, Zhao Y, Moore RA, Hirst M, Marra MA, Jones SJ, Hoodless PA, Birol I. De novo assembly and analysis of RNA-seq data. Nat Methods 2010, 7:909-912. 10.1038/nmeth.1517, 20935650.
-
(2010)
Nat Methods
, vol.7
, pp. 909-912
-
-
Robertson, G.1
Schein, J.2
Chiu, R.3
Corbett, R.4
Field, M.5
Jackman, S.D.6
Mungall, K.7
Lee, S.8
Okada, H.M.9
Qian, J.Q.10
Griffith, M.11
Raymond, A.12
Thiessen, N.13
Cezard, T.14
Butterfield, Y.S.15
Newsome, R.16
Chan, S.K.17
She, R.18
Varhol, R.19
Kamoh, B.20
Prabhu, A.L.21
Tam, A.22
Zhao, Y.23
Moore, R.A.24
Hirst, M.25
Marra, M.A.26
Jones, S.J.27
Hoodless, P.A.28
Birol, I.29
more..
-
6
-
-
84859768479
-
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels
-
10.1093/bioinformatics/bts094, 3324515, 22368243
-
Schulz MH, Zerbino DR, Vingron M, Birney E. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics 2012, 28:1086-1092. 10.1093/bioinformatics/bts094, 3324515, 22368243.
-
(2012)
Bioinformatics
, vol.28
, pp. 1086-1092
-
-
Schulz, M.H.1
Zerbino, D.R.2
Vingron, M.3
Birney, E.4
-
7
-
-
69449099392
-
Comparison of next generation sequencing technologies for transcriptome characterization
-
10.1186/1471-2164-10-347, 2907694, 19646272
-
Wall PK, Leebens-Mack J, Chanderbali AS, Barakat A, Wolcott E, Liang H, Landherr L, Tomsho LP, Hu Y, Carlson JE, Ma H, Schuster SC, Soltis DE, Soltis PS, Altman N, dePamphilis CW. Comparison of next generation sequencing technologies for transcriptome characterization. BMC Genomics 2009, 10:347. 10.1186/1471-2164-10-347, 2907694, 19646272.
-
(2009)
BMC Genomics
, vol.10
, pp. 347
-
-
Wall, P.K.1
Leebens-Mack, J.2
Chanderbali, A.S.3
Barakat, A.4
Wolcott, E.5
Liang, H.6
Landherr, L.7
Tomsho, L.P.8
Hu, Y.9
Carlson, J.E.10
Ma, H.11
Schuster, S.C.12
Soltis, D.E.13
Soltis, P.S.14
Altman, N.15
dePamphilis, C.W.16
-
8
-
-
84860485003
-
Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study
-
Zhao QY, Wang Y, Kong YM, Luo D, Li X, Hao P. Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinformatics 2011, 12:S2.
-
(2011)
BMC Bioinformatics
, vol.12
-
-
Zhao, Q.Y.1
Wang, Y.2
Kong, Y.M.3
Luo, D.4
Li, X.5
Hao, P.6
-
9
-
-
34547588704
-
KAAS: an automatic genome annotation and pathway reconstruction server
-
10.1093/nar/gkm321, 1933193, 17526522
-
Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007, 35:W182-W185. 10.1093/nar/gkm321, 1933193, 17526522.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Moriya, Y.1
Itoh, M.2
Okuda, S.3
Yoshizawa, A.C.4
Kanehisa, M.5
-
10
-
-
79953315365
-
B2G-FAR, a species-centered GO annotation repository
-
10.1093/bioinformatics/btr059, 3065692, 21335611
-
Gotz S, Arnold R, Sebastian-Leon P, Martin-Rodriguez S, Tischler P, Jehl MA, Dopazo J, Rattei T, Conesa A. B2G-FAR, a species-centered GO annotation repository. Bioinformatics 2011, 27:919-924. 10.1093/bioinformatics/btr059, 3065692, 21335611.
-
(2011)
Bioinformatics
, vol.27
, pp. 919-924
-
-
Gotz, S.1
Arnold, R.2
Sebastian-Leon, P.3
Martin-Rodriguez, S.4
Tischler, P.5
Jehl, M.A.6
Dopazo, J.7
Rattei, T.8
Conesa, A.9
-
11
-
-
84859048706
-
The Transcriptome Analysis and Comparison Explorer-T-ACE: a platform-independent, graphical tool to process large RNAseq datasets of non-model organisms
-
10.1093/bioinformatics/bts056, 22285826
-
Philipp EE, Kraemer L, Mountfort D, Schilhabel M, Schreiber S, Rosenstiel P. The Transcriptome Analysis and Comparison Explorer-T-ACE: a platform-independent, graphical tool to process large RNAseq datasets of non-model organisms. Bioinformatics 2012, 28:777-783. 10.1093/bioinformatics/bts056, 22285826.
-
(2012)
Bioinformatics
, vol.28
, pp. 777-783
-
-
Philipp, E.E.1
Kraemer, L.2
Mountfort, D.3
Schilhabel, M.4
Schreiber, S.5
Rosenstiel, P.6
-
12
-
-
80055080319
-
Comparative transcriptomics of Eastern African cichlid fishes shows signs of positive selection and a large contribution of untranslated regions to genetic diversity
-
10.1093/gbe/evr047, 3296448, 21617250
-
Baldo L, Santos ME, Salzburger W. Comparative transcriptomics of Eastern African cichlid fishes shows signs of positive selection and a large contribution of untranslated regions to genetic diversity. Genome Biol Evol 2011, 3:443-455. 10.1093/gbe/evr047, 3296448, 21617250.
-
(2011)
Genome Biol Evol
, vol.3
, pp. 443-455
-
-
Baldo, L.1
Santos, M.E.2
Salzburger, W.3
-
13
-
-
83655181424
-
A de novo transcriptome of the Asian tiger mosquito, Aedes albopictus, to identify candidate transcripts for diapause preparation
-
10.1186/1471-2164-12-619, 3258294, 22185595
-
Poelchau MF, Reynolds JA, Denlinger DL, Elsik CG, Armbruster PA. A de novo transcriptome of the Asian tiger mosquito, Aedes albopictus, to identify candidate transcripts for diapause preparation. BMC Genomics 2011, 12:619. 10.1186/1471-2164-12-619, 3258294, 22185595.
-
(2011)
BMC Genomics
, vol.12
, pp. 619
-
-
Poelchau, M.F.1
Reynolds, J.A.2
Denlinger, D.L.3
Elsik, C.G.4
Armbruster, P.A.5
-
14
-
-
84864388751
-
Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles
-
Tzika AC, Helaers R, Schramm G, Milinkovitch MC. Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles. Evodevo 2012, 2:19.
-
(2012)
Evodevo
, vol.2
, pp. 19
-
-
Tzika, A.C.1
Helaers, R.2
Schramm, G.3
Milinkovitch, M.C.4
-
15
-
-
18744378026
-
Exploring the plant transcriptome through phylogenetic profiling
-
10.1104/pp.104.054700, 548836, 15644465
-
Vandepoele K, Van de Peer Y. Exploring the plant transcriptome through phylogenetic profiling. Plant Physiol 2005, 137:31-42. 10.1104/pp.104.054700, 548836, 15644465.
-
(2005)
Plant Physiol
, vol.137
, pp. 31-42
-
-
Vandepoele, K.1
Van de Peer, Y.2
-
16
-
-
84855167751
-
RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data
-
10.1093/bioinformatics/btr595, 3244761, 22039206
-
Zhao Y, Tang H, Ye Y. RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinformatics 2012, 28:125-126. 10.1093/bioinformatics/btr595, 3244761, 22039206.
-
(2012)
Bioinformatics
, vol.28
, pp. 125-126
-
-
Zhao, Y.1
Tang, H.2
Ye, Y.3
-
17
-
-
84856569514
-
Dissecting plant genomes with the PLAZA comparative genomics platform
-
10.1104/pp.111.189514, 3271752, 22198273
-
Van Bel M, Proost S, Wischnitzki E, Movahedi S, Scheerlinck C, Van de Peer Y, Vandepoele K. Dissecting plant genomes with the PLAZA comparative genomics platform. Plant Physiol 2012, 158:590-600. 10.1104/pp.111.189514, 3271752, 22198273.
-
(2012)
Plant Physiol
, vol.158
, pp. 590-600
-
-
Van Bel, M.1
Proost, S.2
Wischnitzki, E.3
Movahedi, S.4
Scheerlinck, C.5
Van de Peer, Y.6
Vandepoele, K.7
-
18
-
-
33644787447
-
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups
-
10.1093/nar/gkj123, 1347485, 16381887
-
Chen F, Mackey AJ, Stoeckert CJ, Roos DS. OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res 2006, 34:D363-D368. 10.1093/nar/gkj123, 1347485, 16381887.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Chen, F.1
Mackey, A.J.2
Stoeckert, C.J.3
Roos, D.S.4
-
19
-
-
37849023306
-
Assessing performance of orthology detection strategies applied to eukaryotic genomes
-
10.1371/journal.pone.0000383, 1849888, 17440619
-
Chen F, Mackey AJ, Vermunt JK, Roos DS. Assessing performance of orthology detection strategies applied to eukaryotic genomes. PLoS One 2007, 2:e383. 10.1371/journal.pone.0000383, 1849888, 17440619.
-
(2007)
PLoS One
, vol.2
-
-
Chen, F.1
Mackey, A.J.2
Vermunt, J.K.3
Roos, D.S.4
-
20
-
-
80053299004
-
Plant protein-coding gene families: emerging bioinformatics approaches
-
10.1016/j.tplants.2011.06.003, 21757395
-
Martinez M. Plant protein-coding gene families: emerging bioinformatics approaches. Trends Plant Sci 2011, 16:558-567. 10.1016/j.tplants.2011.06.003, 21757395.
-
(2011)
Trends Plant Sci
, vol.16
, pp. 558-567
-
-
Martinez, M.1
-
21
-
-
75649134588
-
PLAZA: a comparative genomics resource to study gene and genome evolution in plants
-
10.1105/tpc.109.071506, 2814516, 20040540
-
Proost S, Van Bel M, Sterck L, Billiau K, Van Parys T, Van de Peer Y, Vandepoele K. PLAZA: a comparative genomics resource to study gene and genome evolution in plants. Plant Cell 2009, 21:3718-3731. 10.1105/tpc.109.071506, 2814516, 20040540.
-
(2009)
Plant Cell
, vol.21
, pp. 3718-3731
-
-
Proost, S.1
Van Bel, M.2
Sterck, L.3
Billiau, K.4
Van Parys, T.5
Van de Peer, Y.6
Vandepoele, K.7
-
22
-
-
61449124151
-
FrameDP: sensitive peptide detection on noisy matured sequences
-
10.1093/bioinformatics/btp024, 2647831, 19153134
-
Gouzy J, Carrere S, Schiex T. FrameDP: sensitive peptide detection on noisy matured sequences. Bioinformatics 2009, 25:670-671. 10.1093/bioinformatics/btp024, 2647831, 19153134.
-
(2009)
Bioinformatics
, vol.25
, pp. 670-671
-
-
Gouzy, J.1
Carrere, S.2
Schiex, T.3
-
23
-
-
3042666256
-
MUSCLE: multiple sequence alignment with high accuracy and high throughput
-
10.1093/nar/gkh340, 390337, 15034147
-
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-1797. 10.1093/nar/gkh340, 390337, 15034147.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
24
-
-
65449188232
-
Jalview Version 2-a multiple sequence alignment editor and analysis workbench
-
10.1093/bioinformatics/btp033, 2672624, 19151095
-
Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ. Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics 2009, 25:1189-1191. 10.1093/bioinformatics/btp033, 2672624, 19151095.
-
(2009)
Bioinformatics
, vol.25
, pp. 1189-1191
-
-
Waterhouse, A.M.1
Procter, J.B.2
Martin, D.M.3
Clamp, M.4
Barton, G.J.5
-
25
-
-
77949718257
-
FastTree 2-approximately maximum-likelihood trees for large alignments
-
10.1371/journal.pone.0009490, 2835736, 20224823
-
Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One 2010, 5:e9490. 10.1371/journal.pone.0009490, 2835736, 20224823.
-
(2010)
PLoS One
, vol.5
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
26
-
-
77950806408
-
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
-
10.1093/sysbio/syq010, 20525638
-
Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010, 59:307-321. 10.1093/sysbio/syq010, 20525638.
-
(2010)
Syst Biol
, vol.59
, pp. 307-321
-
-
Guindon, S.1
Dufayard, J.F.2
Lefort, V.3
Anisimova, M.4
Hordijk, W.5
Gascuel, O.6
-
27
-
-
0036699481
-
Increased taxon sampling greatly reduces phylogenetic error
-
10.1080/10635150290102339, 12228001
-
Zwickl DJ, Hillis DM. Increased taxon sampling greatly reduces phylogenetic error. Syst Biol 2002, 51:588-598. 10.1080/10635150290102339, 12228001.
-
(2002)
Syst Biol
, vol.51
, pp. 588-598
-
-
Zwickl, D.J.1
Hillis, D.M.2
-
28
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
-
(1990)
J Mol Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
29
-
-
13244256972
-
Prot4EST: translating expressed sequence tags from neglected genomes
-
10.1186/1471-2105-5-187, 543579, 15571632
-
Wasmuth JD, Blaxter ML. prot4EST: translating expressed sequence tags from neglected genomes. BMC Bioinformatics 2004, 5:187. 10.1186/1471-2105-5-187, 543579, 15571632.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 187
-
-
Wasmuth, J.D.1
Blaxter, M.L.2
-
30
-
-
84869018936
-
Gamma Paleohexaploidy in the Stem Lineage of Core Eudicots: Significance for MADS-Box Gene and Species Diversification
-
10.1093/molbev/mss183, 22821009
-
Vekemans D, Proost S, Vanneste K, Coenen H, Viaene T, Ruelens P, Maere S, Van de Peer Y, Geuten K. Gamma Paleohexaploidy in the Stem Lineage of Core Eudicots: Significance for MADS-Box Gene and Species Diversification. Mol Biol Evol 2012, 29:3793-3806. 10.1093/molbev/mss183, 22821009.
-
(2012)
Mol Biol Evol
, vol.29
, pp. 3793-3806
-
-
Vekemans, D.1
Proost, S.2
Vanneste, K.3
Coenen, H.4
Viaene, T.5
Ruelens, P.6
Maere, S.7
Van de Peer, Y.8
Geuten, K.9
-
31
-
-
33846059234
-
The TIGR Plant Transcript Assemblies database
-
10.1093/nar/gkl785, 1669722, 17088284
-
Childs KL, Hamilton JP, Zhu W, Ly E, Cheung F, Wu H, Rabinowicz PD, Town CD, Buell CR, Chan AP. The TIGR Plant Transcript Assemblies database. Nucleic Acids Res 2007, 35:D846-D851. 10.1093/nar/gkl785, 1669722, 17088284.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Childs, K.L.1
Hamilton, J.P.2
Zhu, W.3
Ly, E.4
Cheung, F.5
Wu, H.6
Rabinowicz, P.D.7
Town, C.D.8
Buell, C.R.9
Chan, A.P.10
-
32
-
-
84861529088
-
Transcriptome analysis and gene expression atlas for Panicum hallii var. filipes, a diploid model for biofuel research
-
10.1111/j.1365-313X.2012.04938.x, 22324449
-
Meyer E, Logan TL, Juenger TE. Transcriptome analysis and gene expression atlas for Panicum hallii var. filipes, a diploid model for biofuel research. Plant J 2012, 70:879-890. 10.1111/j.1365-313X.2012.04938.x, 22324449.
-
(2012)
Plant J
, vol.70
, pp. 879-890
-
-
Meyer, E.1
Logan, T.L.2
Juenger, T.E.3
-
33
-
-
84856562355
-
The NCBI Taxonomy database
-
10.1093/nar/gkr1178, 3245000, 22139910
-
Federhen S. The NCBI Taxonomy database. Nucleic Acids Res 2012, 40:D136-D143. 10.1093/nar/gkr1178, 3245000, 22139910.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Federhen, S.1
-
34
-
-
84891491330
-
FTP TRAPID
-
FTP TRAPID. [ftp://ftp.psb.ugent.be/pub/trapid/].
-
-
-
-
35
-
-
71749099862
-
PhyloXML: XML for evolutionary biology and comparative genomics
-
10.1186/1471-2105-10-356, 2774328, 19860910
-
Han MV, Zmasek CM. phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics 2009, 10:356. 10.1186/1471-2105-10-356, 2774328, 19860910.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 356
-
-
Han, M.V.1
Zmasek, C.M.2
-
36
-
-
84891481560
-
CakePHP official website
-
CakePHP official website. [http://www.cakephp.org].
-
-
-
-
37
-
-
84891493823
-
MySQL official website
-
MySQL official website. [http://www.mysql.com/].
-
-
-
-
38
-
-
84891492596
-
URL TRAPID
-
URL TRAPID. [http://bioinformatics.psb.ugent.be/webtools/trapid].
-
-
-
-
39
-
-
84891495001
-
TRAPID source code on GitHub
-
TRAPID source code on GitHub. [https://github.com/CIGUGent/TRAPID/tree/master/src].
-
-
-
-
40
-
-
84891481427
-
TRAPID source code on TRAPID FTP
-
TRAPID source code on TRAPID FTP. [ftp://ftp.psb.ugent.be/pub/trapid/src/].
-
-
-
|