-
1
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ 1990. Basic local alignment search tool. J Mol Biol 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
-
2
-
-
9144232912
-
UniProt: The Universal Protein knowledgebase
-
Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O’Donovan C, Redaschi N, Yeh L-SL 2004. UniProt: the Universal Protein knowledgebase. Nucleic Acids Res 32: D115-D119.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. D115-D119
-
-
Apweiler, R.1
Bairoch, A.2
Wu, C.H.3
Barker, W.C.4
Boeckmann, B.5
Ferro, S.6
Gasteiger, E.7
Huang, H.8
Lopez, R.9
Magrane, M.10
Martin, M.J.11
Natale, D.A.12
O’Donovan, C.13
Redaschi, N.14
Yeh, L.-S.15
-
3
-
-
84860771820
-
SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing
-
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin A V, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19: 455-477.
-
(2012)
J Comput Biol
, vol.19
, pp. 455-477
-
-
Bankevich, A.1
Nurk, S.2
Antipov, D.3
Gurevich, A.A.4
Dvorkin, M.5
Kulikov, A.S.6
Lesin, V.M.7
Nikolenko, S.I.8
Pham, S.9
Prjibelski, A.D.10
Pyshkin, A.V.11
Sirotkin, A.V.12
Vyahhi, N.13
Tesler, G.14
Alekseyev, M.A.15
Pevzner, P.A.16
-
4
-
-
0344983453
-
Leptospirosis: A zoonotic disease of global importance
-
Bharti AR, Nally JE, Ricaldi JN, Matthias MA, Diaz MM, Lovett MA, Levett PN, Gilman RH, Willig MR, Gotuzzo E, Vinetz JM 2003. Leptospirosis: a zoonotic disease of global importance. Lancet Infect Dis 3: 757-771.
-
(2003)
Lancet Infect Dis
, vol.3
, pp. 757-771
-
-
Bharti, A.R.1
Nally, J.E.2
Ricaldi, J.N.3
Matthias, M.A.4
Diaz, M.M.5
Lovett, M.A.6
Levett, P.N.7
Gilman, R.H.8
Willig, M.R.9
Gotuzzo, E.10
Vinetz, J.M.11
-
5
-
-
78349238864
-
Ray: Simultaneous assembly of reads from a mix of high-throughput sequencing technologies
-
Boisvert S, Laviolette F, Corbeil J 2010. Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. J Comput Biol 17: 1519-1533.
-
(2010)
J Comput Biol
, vol.17
, pp. 1519-1533
-
-
Boisvert, S.1
Laviolette, F.2
Corbeil, J.3
-
6
-
-
84905049901
-
Trimmomatic: A flexible trimmer for Illumina sequence data
-
Bolger AM, Lohse M, Usadel B 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120.
-
(2014)
Bioinformatics
, vol.30
, pp. 2114-2120
-
-
Bolger, A.M.1
Lohse, M.2
Usadel, B.3
-
7
-
-
84873493253
-
A single multilocus sequence typing (MLST) scheme for seven pathogenic Leptospira species
-
Boonsilp S, Thaipadungpanit J, Amornchai P, Wuthiekanun V, Bailey MS, Holden MTG, Zhang C, Jiang X, Koizumi N, Taylor K, Galloway R, Hoffmaster AR, Craig S, Smythe LD, Hartskeerl RA, Day NP, Chantratita N, Feil EJ, Aanensen DM, Spratt BG, Peacock SJ 2013. A single multilocus sequence typing (MLST) scheme for seven pathogenic Leptospira species. PLoS Negl Trop Dis 7: e1954.
-
(2013)
Plos Negl Trop Dis
, vol.7
-
-
Boonsilp, S.1
Thaipadungpanit, J.2
Amornchai, P.3
Wuthiekanun, V.4
Bailey, M.S.5
Holden, M.6
Zhang, C.7
Jiang, X.8
Koizumi, N.9
Taylor, K.10
Galloway, R.11
Hoffmaster, A.R.12
Craig, S.13
Smythe, L.D.14
Hartskeerl, R.A.15
Day, N.P.16
Chantratita, N.17
Feil, E.J.18
Aanensen, D.M.19
Spratt, B.G.20
Peacock, S.J.21
more..
-
8
-
-
84916209474
-
Leptospira mayottensis sp. Nov., a pathogenic species of the genus Leptospira isolated from humans
-
Bourhy P, Collet L, Brisse S, Picardeau M 2014. Leptospira mayottensis sp. nov., a pathogenic species of the genus Leptospira isolated from humans. Int J Syst Evol Microbiol 64: 4061-4067.
-
(2014)
Int J Syst Evol Microbiol
, vol.64
, pp. 4061-4067
-
-
Bourhy, P.1
Collet, L.2
Brisse, S.3
Picardeau, M.4
-
9
-
-
84897373393
-
A model system for studying the transcriptomic and physiological changes associated with mammalian host-adaptation by Leptospira interrogans serovar Copenhageni
-
Caimano MJ, Sivasankaran SK, Allard A, Hurley D, Hokamp K, Grassmann AA, Hinton JCD, Nally JE 2014. A model system for studying the transcriptomic and physiological changes associated with mammalian host-adaptation by Leptospira interrogans serovar Copenhageni. PLoS Pathog 10: e1004004.
-
(2014)
Plos Pathog
, vol.10
-
-
Caimano, M.J.1
Sivasankaran, S.K.2
Allard, A.3
Hurley, D.4
Hokamp, K.5
Grassmann, A.A.6
Hinton, J.7
Nally, J.E.8
-
10
-
-
74049108922
-
BLAST+: Architecture and applications
-
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL 2009. BLAST+: architecture and applications. BMC Bioinformatics 10: 421.
-
(2009)
BMC Bioinformatics
, vol.10
-
-
Camacho, C.1
Coulouris, G.2
Avagyan, V.3
Ma, N.4
Papadopoulos, J.5
Bealer, K.6
Madden, T.L.7
-
11
-
-
84864030677
-
-
Database (Oxford) 2012: bas003
-
Eberhardt RY, Haft DH, Punta M, Martin M, O’Donovan C, Bateman A 2012. AntiFam: a tool to help identify spurious ORFs in protein annotation. Database (Oxford) 2012: bas003.
-
(2012)
Antifam: A Tool to Help Identify Spurious Orfs in Protein Annotation
-
-
Eberhardt, R.Y.1
Haft, D.H.2
Punta, M.3
Martin, M.4
O’Donovan, C.5
Bateman, A.6
-
12
-
-
80055082271
-
Accelerated profile HMM searches
-
Eddy SR 2011. Accelerated profile HMM searches. PLoS Comput Biol 7: e1002195.
-
(2011)
Plos Comput Biol
, vol.7
-
-
Eddy, S.R.1
-
13
-
-
0023049324
-
Isolation of leptospires from the genital tract and kidneys of aborted sows
-
Ellis WA, McParland PJ, Bryson DG, Thiermann AB, Montgomery J 1986. Isolation of leptospires from the genital tract and kidneys of aborted sows. Vet Rec 118: 294-295.
-
(1986)
Vet Rec
, vol.118
, pp. 294-295
-
-
Ellis, W.A.1
McParland, P.J.2
Bryson, D.G.3
Thiermann, A.B.4
Montgomery, J.5
-
14
-
-
84900424434
-
A putative regulatory genetic locus modulates virulence in the pathogen Leptospira interrogans
-
Eshghi A, Becam J, Lambert A, Sismeiro O, Dillies M-A, Jagla B, Wunder EA, Ko AI, Coppee J-Y, Goarant C, Picardeau M 2014. A putative regulatory genetic locus modulates virulence in the pathogen Leptospira interrogans. Infect Immun 82: 2542-2552.
-
(2014)
Infect Immun
, vol.82
, pp. 2542-2552
-
-
Eshghi, A.1
Becam, J.2
Lambert, A.3
Sismeiro, O.4
Dillies, M.-A.5
Jagla, B.6
Wunder, E.A.7
Ko, A.I.8
Coppee, J.-Y.9
Goarant, C.10
Picardeau, M.11
-
15
-
-
77957582069
-
Leptospira as an emerging pathogen: A review of its biology, pathogenesis, and host immune responses
-
Evangelista KV, Coburn J 2010. Leptospira as an emerging pathogen: a review of its biology, pathogenesis, and host immune responses. Future Microbiol 5: 1413-1425.
-
(2010)
Future Microbiol
, vol.5
, pp. 1413-1425
-
-
Evangelista, K.V.1
Coburn, J.2
-
16
-
-
0037252684
-
Rfam: An RNA family database
-
Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR 2003. Rfam: an RNA family database. Nucleic Acids Res 31: 439-441.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 439-441
-
-
Griffiths-Jones, S.1
Bateman, A.2
Marshall, M.3
Khanna, A.4
Eddy, S.R.5
-
17
-
-
84883552754
-
Leptospirosis: Public health perspectives
-
Guerra MA 2013. Leptospirosis: public health perspectives. Biologicals 41: 295-297.
-
(2013)
Biologicals
, vol.41
, pp. 295-297
-
-
Guerra, M.A.1
-
19
-
-
0032849859
-
CAP3: A DNA sequence assembly program
-
Huang X, Madan A 1999. CAP3: A DNA sequence assembly program. Genome Res 9: 868-877.
-
(1999)
Genome Res
, vol.9
, pp. 868-877
-
-
Huang, X.1
Madan, A.2
-
20
-
-
77952299957
-
Prodigal: Prokaryotic gene recognition and translation initiation site identification
-
Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW, Hauser LJ 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: 119.
-
(2010)
BMC Bioinformatics
, vol.11
-
-
Hyatt, D.1
Chen, G.-L.2
Locascio, P.F.3
Land, M.L.4
Larimer, F.W.5
Hauser, L.J.6
-
21
-
-
84865989688
-
Detection of virulence factors and molecular typing of pathogenic Leptospira from capybara (Hydrochaeris hydrochaeris)
-
Jorge S, Monte LG, Coimbra MA, Albano AP, Hartwig DD, Lucas C, Seixas FK, Dellagostin OA, Hartleben CP 2012. Detection of virulence factors and molecular typing of pathogenic Leptospira from capybara (Hydrochaeris hydrochaeris). Curr Microbiol 65: 461-464.
-
(2012)
Curr Microbiol
, vol.65
, pp. 461-464
-
-
Jorge, S.1
Monte, L.G.2
Coimbra, M.A.3
Albano, A.P.4
Hartwig, D.D.5
Lucas, C.6
Seixas, F.K.7
Dellagostin, O.A.8
Hartleben, C.P.9
-
22
-
-
85008452744
-
Draft genome sequences of Leptospira santarosai strains U160, U164, and U233, isolated from asymptomatic cattle
-
Kremer FS, Eslabão MR, Provisor M, Woloski RDS, Ramires OV, Moreno LZ, Moreno AM, Hamond C, Lilenbaum W, Dellagostin OA 2015. Draft genome sequences of Leptospira santarosai strains U160, U164, and U233, isolated from asymptomatic cattle. Genome Announc 3: e00910-e00915.
-
(2015)
Genome Announc
, vol.3
, pp. e00910-e00915
-
-
Kremer, F.S.1
Eslabão, M.R.2
Provisor, M.3
Woloski, R.4
Ramires, O.V.5
Moreno, L.Z.6
Moreno, A.M.7
Hamond, C.8
Lilenbaum, W.9
Dellagostin, O.A.10
-
23
-
-
34250665888
-
RNAmmer: Consistent and rapid annotation of ribosomal RNA genes
-
Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T, Ussery DW 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35: 3100-3108.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 3100-3108
-
-
Lagesen, K.1
Hallin, P.2
Rødland, E.A.3
Staerfeldt, H.-H.4
Rognes, T.5
Ussery, D.W.6
-
24
-
-
1242297827
-
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences
-
Laslett D 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32: 11-16.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 11-16
-
-
Laslett, D.1
-
25
-
-
84887307424
-
Pathogenomic inference of virulence-associated genes in Leptospira interrogans
-
Lehmann JS, Fouts DE, Haft DH, Cannella AP, Ricaldi JN, Brinkac L, Harkins D, Durkin S, Sanka R, Sutton G, Moreno A, Vinetz JM, Matthias MA 2013. Pathogenomic inference of virulence-associated genes in Leptospira interrogans. PLoS Negl Trop Dis 7: e2468.
-
(2013)
Plos Negl Trop Dis
, vol.7
-
-
Lehmann, J.S.1
Fouts, D.E.2
Haft, D.H.3
Cannella, A.P.4
Ricaldi, J.N.5
Brinkac, L.6
Harkins, D.7
Durkin, S.8
Sanka, R.9
Sutton, G.10
Moreno, A.11
Vinetz, J.M.12
Matthias, M.A.13
-
27
-
-
84875546384
-
CISA: Contig integrator for sequence assembly of bacterial genomes
-
Lin S-H, Liao Y-C 2013. CISA: contig integrator for sequence assembly of bacterial genomes. PLoS ONE 8: e60843.
-
(2013)
Plos ONE
, vol.8
-
-
Lin, S.-H.1
Liao, Y.-C.2
-
28
-
-
0030854739
-
TRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
-
Lowe TM, Eddy SR 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 955-964
-
-
Lowe, T.M.1
Eddy, S.R.2
-
29
-
-
84866175144
-
Differential in vivo gene expression of major Leptospira proteins in resistant or susceptible animal models
-
Matsui M, Soupé M-E, Becam J, Goarant C 2012. Differential in vivo gene expression of major Leptospira proteins in resistant or susceptible animal models. Appl Environ Microbiol 78: 6372-6376.
-
(2012)
Appl Environ Microbiol
, vol.78
, pp. 6372-6376
-
-
Matsui, M.1
Soupé, M.-E.2
Becam, J.3
Goarant, C.4
-
30
-
-
84874932374
-
Molecular characterization of virulent Leptospira interrogans serogroup icterohaemorrhagiae isolated from Cavia aperea
-
Monte LG, Jorge S, Xavier MA, Leal FMA, Amaral MG, Seixas FK, Dellagostin OA, Hartleben CP 2013. Molecular characterization of virulent Leptospira interrogans serogroup icterohaemorrhagiae isolated from Cavia aperea. Acta Trop 126: 164-166.
-
(2013)
Acta Trop
, vol.126
, pp. 164-166
-
-
Monte, L.G.1
Jorge, S.2
Xavier, M.A.3
Leal, F.4
Amaral, M.G.5
Seixas, F.K.6
Dellagostin, O.A.7
Hartleben, C.P.8
-
31
-
-
84929705948
-
Immunological and molecular characterization of Leptospira interrogans isolated from a bovine foetus
-
Monte LG, Ridieri KF, Jorge S, Oliveira NR, Hartwig DD, Amaral MG, Hartleben CP, Dellagostin OA 2015. Immunological and molecular characterization of Leptospira interrogans isolated from a bovine foetus. Comp Immunol Microbiol Infect Dis 40: 41-45.
-
(2015)
Comp Immunol Microbiol Infect Dis
, vol.40
, pp. 41-45
-
-
Monte, L.G.1
Ridieri, K.F.2
Jorge, S.3
Oliveira, N.R.4
Hartwig, D.D.5
Amaral, M.G.6
Hartleben, C.P.7
Dellagostin, O.A.8
-
33
-
-
0033635022
-
Artemis: Sequence visualization and annotation
-
Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream M-A, Barrell B 2000. Artemis: sequence visualization and annotation. Bioinformatics 16: 944-945.
-
(2000)
Bioinformatics
, vol.16
, pp. 944-945
-
-
Rutherford, K.1
Parkhill, J.2
Crook, J.3
Horsnell, T.4
Rice, P.5
Rajandream, M.-A.6
Barrell, B.7
-
34
-
-
84857838310
-
Efficient de novo assembly of large genomes using compressed data structures
-
Simpson JT, Durbin R 2012. Efficient de novo assembly of large genomes using compressed data structures. Genome Res 22: 549-556.
-
(2012)
Genome Res
, vol.22
, pp. 549-556
-
-
Simpson, J.T.1
Durbin, R.2
|