-
1
-
-
80052014384
-
On the biological and genetic diversity in Neospora caninum
-
Al-Qassab S.E., Reichel M.P., Ellis J.T. On the biological and genetic diversity in Neospora caninum. Diversity 2010, 2:411-438.
-
(2010)
Diversity
, vol.2
, pp. 411-438
-
-
Al-Qassab, S.E.1
Reichel, M.P.2
Ellis, J.T.3
-
2
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders S., Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010, 11:R106.
-
(2010)
Genome Biol.
, vol.11
, pp. R106
-
-
Anders, S.1
Huber, W.2
-
3
-
-
9144232912
-
UniProt: the Universal Protein knowledgebase
-
Apweiler R., Bairoch A., Wu C.H., Barker W.C., Boeckmann B., Ferro S., Gasteiger E., Huang H.Z., Lopez R., Magrane M., Martin M.J., Natale D.A., O'Donovan C., Redaschi N., Yeh L.S.L. UniProt: the Universal Protein knowledgebase. Nucleic Acids Res. 2004, 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.Z.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.L.15
-
4
-
-
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., Innamorato F., Iodice J., Kissinger J.C., Kraemer E.T., Li W., Miller J.A., Nayak V., Pennington C., Pinney D.F., Roos D.S., Ross C., Srinivasamoorthy G., Stoeckert C.J., Thibodeau R., Treatman C., Wang H. EuPathDB: a portal to eukaryotic pathogen databases. Nucleic Acids Res. 2010, 38:D415-D419.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. D415-D419
-
-
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
Innamorato, F.11
Iodice, J.12
Kissinger, J.C.13
Kraemer, E.T.14
Li, W.15
Miller, J.A.16
Nayak, V.17
Pennington, C.18
Pinney, D.F.19
Roos, D.S.20
Ross, C.21
Srinivasamoorthy, G.22
Stoeckert, C.J.23
Thibodeau, R.24
Treatman, C.25
Wang, H.26
more..
-
5
-
-
78049360815
-
Importance of nonenteric protozoan infections in immunocompromised people
-
Barratt J.L.N., Harkness J., Marriott D., Ellis J.T., Stark D. Importance of nonenteric protozoan infections in immunocompromised people. Clin. Microbiol. Rev. 2010, 23:795-836.
-
(2010)
Clin. Microbiol. Rev.
, vol.23
, pp. 795-836
-
-
Barratt, J.L.N.1
Harkness, J.2
Marriott, D.3
Ellis, J.T.4
Stark, D.5
-
6
-
-
79551487629
-
Alternative translation start sites are conserved in eukaryotic genomes
-
Bazykin G.A., Kochetov A.V. Alternative translation start sites are conserved in eukaryotic genomes. Nucleic Acids Res. 2011, 39:567-577.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 567-577
-
-
Bazykin, G.A.1
Kochetov, A.V.2
-
7
-
-
84869104652
-
Introns in UTRs: why we should stop ignoring them
-
Bicknell A.A., Cenik C., Chua H.N., Roth F.P., Moore M.J. Introns in UTRs: why we should stop ignoring them. Bioessays 2012, 34:1025-1034.
-
(2012)
Bioessays
, vol.34
, pp. 1025-1034
-
-
Bicknell, A.A.1
Cenik, C.2
Chua, H.N.3
Roth, F.P.4
Moore, M.J.5
-
8
-
-
0026271395
-
Evidence that Neospora caninum is identical to the Toxoplasma-like parasite of Norwegian dogs
-
Bjerkas I., Dubey J.P. Evidence that Neospora caninum is identical to the Toxoplasma-like parasite of Norwegian dogs. Acta Vet. Scand. 1991, 32:407-410.
-
(1991)
Acta Vet. Scand.
, vol.32
, pp. 407-410
-
-
Bjerkas, I.1
Dubey, J.P.2
-
9
-
-
0028004414
-
Intrinsic and extrinsic approaches for detecting genes in a bacterial genome
-
Borodovsky M., Rudd K.E., Koonin E.V. Intrinsic and extrinsic approaches for detecting genes in a bacterial genome. Nucleic Acids Res. 1994, 22:4756-4767.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 4756-4767
-
-
Borodovsky, M.1
Rudd, K.E.2
Koonin, E.V.3
-
10
-
-
0034326362
-
Analysis of canonical and non-canonical splice sites in mammalian genomes
-
Burset M., Seledtsov I.A., Solovyev V.V. Analysis of canonical and non-canonical splice sites in mammalian genomes. Nucleic Acids Res. 2000, 28:4364-4375.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 4364-4375
-
-
Burset, M.1
Seledtsov, I.A.2
Solovyev, V.V.3
-
11
-
-
74049108922
-
BLAST plus: architecture and applications
-
Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K., Madden T.L. BLAST plus: architecture and applications. BMC Bioinf. 2009, 10:421.
-
(2009)
BMC Bioinf.
, vol.10
, pp. 421
-
-
Camacho, C.1
Coulouris, G.2
Avagyan, V.3
Ma, N.4
Papadopoulos, J.5
Bealer, K.6
Madden, T.L.7
-
12
-
-
78651108767
-
Comprehensive proteomic analysis of membrane proteins in Toxoplasma gondii
-
Che F.-Y., Madrid-Aliste C., Burd B., Zhang H., Nieves E., Kim K., Fiser A., Angeletti R.H., Weiss L.M. Comprehensive proteomic analysis of membrane proteins in Toxoplasma gondii. Mol Cell Prot. 2010, 10(M110):000745.
-
(2010)
Mol Cell Prot.
, vol.10
, Issue.M110
, pp. 000745
-
-
Che, F.-Y.1
Madrid-Aliste, C.2
Burd, B.3
Zhang, H.4
Nieves, E.5
Kim, K.6
Fiser, A.7
Angeletti, R.H.8
Weiss, L.M.9
-
13
-
-
77951226627
-
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
-
Cock P.J.A., Fields C.J., Goto N., Heuer M.L., Rice P.M. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2010, 38:1767-1771.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 1767-1771
-
-
Cock, P.J.A.1
Fields, C.J.2
Goto, N.3
Heuer, M.L.4
Rice, P.M.5
-
14
-
-
84891783174
-
Activities at the Universal Protein Resource (UniProt)
-
Consortium T.U. Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2014, 42:D191-D198.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D191-D198
-
-
Consortium, T.U.1
-
15
-
-
84878194846
-
Reverse vaccinology in the 21st century: improvements over the original design
-
Donati C., Rappuoli R. Reverse vaccinology in the 21st century: improvements over the original design. Ann. N. Y. Acad. Sci. 2013, 1285:115-132.
-
(2013)
Ann. N. Y. Acad. Sci.
, vol.1285
, pp. 115-132
-
-
Donati, C.1
Rappuoli, R.2
-
16
-
-
67349215111
-
History of the discovery of the life cycle of Toxoplasma gondii
-
Dubey J.P. History of the discovery of the life cycle of Toxoplasma gondii. Int. J. Parasitol. 2009, 39:877-882.
-
(2009)
Int. J. Parasitol.
, vol.39
, pp. 877-882
-
-
Dubey, J.P.1
-
17
-
-
0024004904
-
Newly recognized fatal protozoan disease of dogs
-
Dubey J.P., Carpenter J.L., Speer C.A., Topper M.J., Uggla A. Newly recognized fatal protozoan disease of dogs. J. Am. Vet. Med. Assoc. 1988, 192:1269-1285.
-
(1988)
J. Am. Vet. Med. Assoc.
, vol.192
, pp. 1269-1285
-
-
Dubey, J.P.1
Carpenter, J.L.2
Speer, C.A.3
Topper, M.J.4
Uggla, A.5
-
18
-
-
0028176104
-
The phylogeny of Neospora-caninum
-
Ellis J., Luton K., Baverstock P.R., Brindley P.J., Nimmo K.A., Johnson A.M. The phylogeny of Neospora-caninum. Mol. Biochem. Parasitol. 1994, 64:303-311.
-
(1994)
Mol. Biochem. Parasitol.
, vol.64
, pp. 303-311
-
-
Ellis, J.1
Luton, K.2
Baverstock, P.R.3
Brindley, P.J.4
Nimmo, K.A.5
Johnson, A.M.6
-
19
-
-
34248531753
-
Locating proteins in the cell using TargetP, SignalP and related tools
-
Emanuelsson O., Brunak S., von Heijne G., Nielsen H. Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc. 2007, 2:953-971.
-
(2007)
Nat Protoc.
, vol.2
, pp. 953-971
-
-
Emanuelsson, O.1
Brunak, S.2
von Heijne, G.3
Nielsen, H.4
-
20
-
-
0030218799
-
Finding genes by computer: the state of the art
-
Fickett J.W. Finding genes by computer: the state of the art. Trends Genet. 1996, 12:316-320.
-
(1996)
Trends Genet.
, vol.12
, pp. 316-320
-
-
Fickett, J.W.1
-
21
-
-
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., Pinney D.F., Roos D.S., Stoeckert C.J., Wang H., Brunk B.P. ToxoDB: an integrated Toxoplasma gondii database resource. Nucleic Acids Res. 2008, 36:D553-D556.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. D553-D556
-
-
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
Pinney, D.F.11
Roos, D.S.12
Stoeckert, C.J.13
Wang, H.14
Brunk, B.P.15
-
22
-
-
84870596055
-
Evaluating high-throughput ab initio gene finders to discover proteins encoded in eukaryotic pathogen genomes missed by laboratory techniques
-
Goodswen S.J., Kennedy P.J., Ellis J.T. Evaluating high-throughput ab initio gene finders to discover proteins encoded in eukaryotic pathogen genomes missed by laboratory techniques. PLoS ONE 2012, 7:e50609.
-
(2012)
PLoS ONE
, vol.7
, pp. e50609
-
-
Goodswen, S.J.1
Kennedy, P.J.2
Ellis, J.T.3
-
23
-
-
84886737285
-
A novel strategy for classifying the output from an in silico vaccine discovery pipeline for eukaryotic pathogens using machine learning algorithms
-
Goodswen S., Kennedy P., Ellis J. A novel strategy for classifying the output from an in silico vaccine discovery pipeline for eukaryotic pathogens using machine learning algorithms. BMC Bioinf. 2013, 14:315.
-
(2013)
BMC Bioinf.
, vol.14
, pp. 315
-
-
Goodswen, S.1
Kennedy, P.2
Ellis, J.3
-
24
-
-
84887669298
-
A guide to in silico vaccine discovery for eukaryotic pathogens
-
Goodswen S.J., Kennedy P.J., Ellis J.T. A guide to in silico vaccine discovery for eukaryotic pathogens. Brief Bioinf. 2013, 14:753-774.
-
(2013)
Brief Bioinf.
, vol.14
, pp. 753-774
-
-
Goodswen, S.J.1
Kennedy, P.J.2
Ellis, J.T.3
-
25
-
-
79960264362
-
Full-length transcriptome assembly from RNA-Seq data without a reference genome
-
Grabherr M.G., Haas B.J., Yassour M., Levin J.Z., Thompson D.A., Amit I., Adiconis X., Fan L., Raychowdhury R., Zeng Q., Chen Z., Mauceli E., Hacohen N., Gnirke A., Rhind N., di Palma F., Birren B.W., Nusbaum C., Lindblad-Toh K., Friedman N., Regev A. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol. 2011, 29:644-652.
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 644-652
-
-
Grabherr, M.G.1
Haas, B.J.2
Yassour, M.3
Levin, J.Z.4
Thompson, D.A.5
Amit, I.6
Adiconis, X.7
Fan, L.8
Raychowdhury, R.9
Zeng, Q.10
Chen, Z.11
Mauceli, E.12
Hacohen, N.13
Gnirke, A.14
Rhind, N.15
di Palma, F.16
Birren, B.W.17
Nusbaum, C.18
Lindblad-Toh, K.19
Friedman, N.20
Regev, A.21
more..
-
26
-
-
33645979674
-
Using multiple alignments to improve gene prediction
-
Gross S., Brent M. Using multiple alignments to improve gene prediction. J. Comput. Biol. 2006, 13:379-393.
-
(2006)
J. Comput. Biol.
, vol.13
, pp. 379-393
-
-
Gross, S.1
Brent, M.2
-
27
-
-
0141905891
-
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
-
Haas B.J., Delcher A.L., Mount S.M., Wortman J.R., Smith R.K., Hannick L.I., Maiti R., Ronning C.M., Rusch D.B., Town C.D., Salzberg S.L., White O. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 2003, 31:5654-5666.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 5654-5666
-
-
Haas, B.J.1
Delcher, A.L.2
Mount, S.M.3
Wortman, J.R.4
Smith, R.K.5
Hannick, L.I.6
Maiti, R.7
Ronning, C.M.8
Rusch, D.B.9
Town, C.D.10
Salzberg, S.L.11
White, O.12
-
28
-
-
84880266648
-
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
-
Haas B.J., Papanicolaou A., Yassour M., Grabherr M., Blood P.D., Bowden J., Couger M.B., Eccles D., Li B., Lieber M., MacManes M.D., Ott M., Orvis J., Pochet N., Strozzi F., Weeks N., Westerman R., William T., Dewey C.N., Henschel R., Leduc R.D., Friedman N., Regev A. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013, 8:1494-1512.
-
(2013)
Nat Protoc.
, vol.8
, pp. 1494-1512
-
-
Haas, B.J.1
Papanicolaou, A.2
Yassour, M.3
Grabherr, M.4
Blood, P.D.5
Bowden, J.6
Couger, M.B.7
Eccles, D.8
Li, B.9
Lieber, M.10
MacManes, M.D.11
Ott, M.12
Orvis, J.13
Pochet, N.14
Strozzi, F.15
Weeks, N.16
Westerman, R.17
William, T.18
Dewey, C.N.19
Henschel, R.20
Leduc, R.D.21
Friedman, N.22
Regev, A.23
more..
-
29
-
-
77952231080
-
Advancing RNA-Seq analysis
-
Haas B.J., Zody M.C. Advancing RNA-Seq analysis. Nat. Biotechnol. 2010, 28:421-423.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 421-423
-
-
Haas, B.J.1
Zody, M.C.2
-
30
-
-
34547560275
-
WoLF PSORT: protein localization predictor
-
Horton P., Park K.-J., Obayashi T., Fujita N., Harada H., Adams-Collier C.J., Nakai K. WoLF PSORT: protein localization predictor. Nucleic Acids Res. 2007, 35:W585-W587.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. W585-W587
-
-
Horton, P.1
Park, K.-J.2
Obayashi, T.3
Fujita, N.4
Harada, H.5
Adams-Collier, C.J.6
Nakai, K.7
-
31
-
-
2142657817
-
A combined transmembrane topology and signal peptide prediction method
-
Kall L., Krogh A., Sonnhammer E.L.L. A combined transmembrane topology and signal peptide prediction method. J. Mol. Biol. 2004, 338:1027-1036.
-
(2004)
J. Mol. Biol.
, vol.338
, pp. 1027-1036
-
-
Kall, L.1
Krogh, A.2
Sonnhammer, E.L.L.3
-
33
-
-
0036226603
-
BLAT-the BLAST-like alignment tool
-
Kent W.J. BLAT-the BLAST-like alignment tool. Genome Res. 2002, 12:656-664.
-
(2002)
Genome Res.
, vol.12
, pp. 656-664
-
-
Kent, W.J.1
-
34
-
-
84876996918
-
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
-
Kim D., Pertea G., Trapnell C., Pimentel H., Kelley R., Salzberg S.L. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013, 14:R36.
-
(2013)
Genome Biol.
, vol.14
, pp. R36
-
-
Kim, D.1
Pertea, G.2
Trapnell, C.3
Pimentel, H.4
Kelley, R.5
Salzberg, S.L.6
-
35
-
-
1542285447
-
Toxoplasma gondii: the model apicomplexan
-
Kim K., Weiss L.M. Toxoplasma gondii: the model apicomplexan. Int. J. Parasitol. 2004, 34:423-432.
-
(2004)
Int. J. Parasitol.
, vol.34
, pp. 423-432
-
-
Kim, K.1
Weiss, L.M.2
-
36
-
-
84864424747
-
Immune epitope database analysis resource
-
Kim Y., Ponomarenko J., Zhu Z., Tamang D., Wang P., Greenbaum J., Lundegaard C., Sette A., Lund O., Bourne P.E., Nielsen M., Peters B. Immune epitope database analysis resource. Nucleic Acids Res. 2012, 40:W525-W530.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. W525-W530
-
-
Kim, Y.1
Ponomarenko, J.2
Zhu, Z.3
Tamang, D.4
Wang, P.5
Greenbaum, J.6
Lundegaard, C.7
Sette, A.8
Lund, O.9
Bourne, P.E.10
Nielsen, M.11
Peters, B.12
-
37
-
-
81255156922
-
Applications for T-cell epitope queries and tools in the Immune Epitope Database and Analysis Resource
-
Kim Y., Sette A., Peters B. Applications for T-cell epitope queries and tools in the Immune Epitope Database and Analysis Resource. J. Immunol. Methods 2011, 374:62-69.
-
(2011)
J. Immunol. Methods
, vol.374
, pp. 62-69
-
-
Kim, Y.1
Sette, A.2
Peters, B.3
-
38
-
-
4143115768
-
Characterization of the splice sites in GT-AG and GC-AG introns in higher eukaryotes using full-length cDNAs
-
Kitamura-Abe S., Itoh H., Washio T., Tsutsumi A., Tomita M. Characterization of the splice sites in GT-AG and GC-AG introns in higher eukaryotes using full-length cDNAs. J. Bioinf. Comput. Biol. 2004, 2:309-331.
-
(2004)
J. Bioinf. Comput. Biol.
, vol.2
, pp. 309-331
-
-
Kitamura-Abe, S.1
Itoh, H.2
Washio, T.3
Tsutsumi, A.4
Tomita, M.5
-
39
-
-
27144555357
-
Regulation of translation via mRNA structure in prokaryotes and eukaryotes
-
Kozak M. Regulation of translation via mRNA structure in prokaryotes and eukaryotes. Gene 2005, 361:13-37.
-
(2005)
Gene
, vol.361
, pp. 13-37
-
-
Kozak, M.1
-
40
-
-
0035910270
-
Predicting transmembrane protein topology with a hidden markov model: application to complete genomes
-
Krogh A., Larsson B., von Heijne G., Sonnhammer E.L.L. Predicting transmembrane protein topology with a hidden markov model: application to complete genomes. J. Mol. Biol. 2001, 305:567-580.
-
(2001)
J. Mol. Biol.
, vol.305
, pp. 567-580
-
-
Krogh, A.1
Larsson, B.2
von Heijne, G.3
Sonnhammer, E.L.L.4
-
41
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B., Trapnell C., Pop M., Salzberg S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009, 10:R25.
-
(2009)
Genome Biol.
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
42
-
-
84889483068
-
Genome mining and reverse vaccinology
-
Wiley-VCH Verlag GmbH & Co., Weinheim, M. Frosch, M.C.J. Maiden (Eds.)
-
Leuzzi R., Savino S., Pizza M., Rappuoli R. Genome mining and reverse vaccinology. Handbook of Meningococcal Disease 2006, 391-402. Wiley-VCH Verlag GmbH & Co., Weinheim. M. Frosch, M.C.J. Maiden (Eds.).
-
(2006)
Handbook of Meningococcal Disease
, pp. 391-402
-
-
Leuzzi, R.1
Savino, S.2
Pizza, M.3
Rappuoli, R.4
-
43
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., Genome Project Data P. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 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
Genome Project Data, P.10
-
44
-
-
84864483625
-
RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics
-
Lohse M., Bolger A.M., Nagel A., Fernie A.R., Lunn J.E., Stitt M., Usadel B. RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res. 2012, 40:W622-W627.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. W622-W627
-
-
Lohse, M.1
Bolger, A.M.2
Nagel, A.3
Fernie, A.R.4
Lunn, J.E.5
Stitt, M.6
Usadel, B.7
-
45
-
-
34548258281
-
Limitations and pitfalls in protein identification by mass spectrometry
-
Lubec G., Afjehi-Sadat L. Limitations and pitfalls in protein identification by mass spectrometry. Chem. Rev. 2007, 107:3568-3584.
-
(2007)
Chem. Rev.
, vol.107
, pp. 3568-3584
-
-
Lubec, G.1
Afjehi-Sadat, L.2
-
46
-
-
8844252293
-
TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders
-
Majoros W.H., Pertea M., Salzberg S.L. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 2004, 20:2878-2879.
-
(2004)
Bioinformatics
, vol.20
, pp. 2878-2879
-
-
Majoros, W.H.1
Pertea, M.2
Salzberg, S.L.3
-
47
-
-
80255127234
-
Cutadapt removes adapter sequences from high-throughput sequencing reads
-
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 2011, 17:10-12.
-
(2011)
EMBnet. J.
, vol.17
, pp. 10-12
-
-
Martin, M.1
-
49
-
-
33748681096
-
Microbial genomes and vaccine design: refinements to the classical reverse vaccinology approach
-
Mora M., Donati C., Medini D., Covacci A., Rappuoli R. Microbial genomes and vaccine design: refinements to the classical reverse vaccinology approach. Curr Opin Microbiol 2006, 9:532-536.
-
(2006)
Curr Opin Microbiol
, vol.9
, pp. 532-536
-
-
Mora, M.1
Donati, C.2
Medini, D.3
Covacci, A.4
Rappuoli, R.5
-
50
-
-
0013462065
-
A highly conserved repetitive DNA-sequence, (TTAGGG)N, present at the telomeres of human-chromosomes
-
Moyzis R.K., Buckingham J.M., Cram L.S., Dani M., Deaven L.L., Jones M.D., Meyne J., Ratliff R.L., Wu J.R. A highly conserved repetitive DNA-sequence, (TTAGGG)N, present at the telomeres of human-chromosomes. Proc Nat Acad Sci USA 1988, 85:6622-6626.
-
(1988)
Proc Nat Acad Sci USA
, vol.85
, pp. 6622-6626
-
-
Moyzis, R.K.1
Buckingham, J.M.2
Cram, L.S.3
Dani, M.4
Deaven, L.L.5
Jones, M.D.6
Meyne, J.7
Ratliff, R.L.8
Wu, J.R.9
-
51
-
-
0034764307
-
SSAHA: A fast search method for large DNA databases
-
Ning Z.M., Cox A.J., Mullikin J.C. SSAHA: A fast search method for large DNA databases. Genome Res. 2001, 11:1725-1729.
-
(2001)
Genome Res.
, vol.11
, pp. 1725-1729
-
-
Ning, Z.M.1
Cox, A.J.2
Mullikin, J.C.3
-
52
-
-
54049089560
-
Using GlimmerM to find genes in eukaryotic genomes
-
00:4.4:4.4.1-4.4.20
-
Pertea M., Salzberg S.L. Using GlimmerM to find genes in eukaryotic genomes. Curr. Protoc. Bioinf. 2002, 00:4.4:4.4.1-4.4.20.
-
(2002)
Curr. Protoc. Bioinf.
-
-
Pertea, M.1
Salzberg, S.L.2
-
53
-
-
80053345905
-
SignalP 4.0: discriminating signal peptides from transmembrane regions
-
Petersen T.N., Brunak S., von Heijne G., Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods 2011, 8:785-786.
-
(2011)
Nat. Methods
, vol.8
, pp. 785-786
-
-
Petersen, T.N.1
Brunak, S.2
von Heijne, G.3
Nielsen, H.4
-
54
-
-
84873140040
-
What is the global economic impact of Neospora caninum in cattle - the billion dollar question
-
Reichel M.P., Alejandra Ayanegui-Alcerreca M., Gondim L.F.P., Ellis J.T. What is the global economic impact of Neospora caninum in cattle - the billion dollar question. Int. J. Parasitol. 2013, 43:133-142.
-
(2013)
Int. J. Parasitol.
, vol.43
, pp. 133-142
-
-
Reichel, M.P.1
Alejandra Ayanegui-Alcerreca, M.2
Gondim, L.F.P.3
Ellis, J.T.4
-
55
-
-
33750053595
-
If control of Neospora caninum infection is technically feasible does it make economic
-
Reichel M.P., Ellis J.T. If control of Neospora caninum infection is technically feasible does it make economic. Vet. Parasitol. 2006, 142:23-34.
-
(2006)
Vet. Parasitol.
, vol.142
, pp. 23-34
-
-
Reichel, M.P.1
Ellis, J.T.2
-
56
-
-
50349101879
-
Re-evaluating the economics of neosporosis control
-
Reichel M.P., Ellis J.T. Re-evaluating the economics of neosporosis control. Vet. Parasitol. 2008, 156:361-362.
-
(2008)
Vet. Parasitol.
, vol.156
, pp. 361-362
-
-
Reichel, M.P.1
Ellis, J.T.2
-
57
-
-
84861207409
-
Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: coccidia differing in host range and transmission strategy
-
Reid A.J., Vermont S.J., Cotton J.A., Harris D., Hill-Cawthorne G.A., Könen-Waisman S., Latham S.M., Mourier T., Norton R., Quail M.A., Sanders M., Shanmugam D., Sohal A., Wasmuth J.D., Brunk B., Grigg M.E., Howard J.C., Parkinson J., Roos D.S., Trees A.J., Berriman M., Pain A., Wastling J.M. Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: coccidia differing in host range and transmission strategy. PLoS Pathog. 2012, 8:e1002567.
-
(2012)
PLoS Pathog.
, vol.8
, pp. e1002567
-
-
Reid, A.J.1
Vermont, S.J.2
Cotton, J.A.3
Harris, D.4
Hill-Cawthorne, G.A.5
Könen-Waisman, S.6
Latham, S.M.7
Mourier, T.8
Norton, R.9
Quail, M.A.10
Sanders, M.11
Shanmugam, D.12
Sohal, A.13
Wasmuth, J.D.14
Brunk, B.15
Grigg, M.E.16
Howard, J.C.17
Parkinson, J.18
Roos, D.S.19
Trees, A.J.20
Berriman, M.21
Pain, A.22
Wastling, J.M.23
more..
-
58
-
-
32244442042
-
The presence of GC-AG introns in Neurospora crassa and other euascomycetes determined from analyses of complete genomes: Implications for automated gene prediction
-
Rep M., Duyvesteijn R.G.E., Gale L., Usgaard T., Cornelissen B.J.C., Ma L.J., Ward T.J. The presence of GC-AG introns in Neurospora crassa and other euascomycetes determined from analyses of complete genomes: Implications for automated gene prediction. Genomics 2006, 87:338-347.
-
(2006)
Genomics
, vol.87
, pp. 338-347
-
-
Rep, M.1
Duyvesteijn, R.G.E.2
Gale, L.3
Usgaard, T.4
Cornelissen, B.J.C.5
Ma, L.J.6
Ward, T.J.7
-
59
-
-
0034781576
-
Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a 'weak' context of the start codon
-
Rogozin I.B., Kochetov A.V., Kondrashov F.A., Koonin E.V., Milanesi L. Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a 'weak' context of the start codon. Bioinformatics 2001, 17:890-900.
-
(2001)
Bioinformatics
, vol.17
, pp. 890-900
-
-
Rogozin, I.B.1
Kochetov, A.V.2
Kondrashov, F.A.3
Koonin, E.V.4
Milanesi, L.5
-
60
-
-
21644467683
-
Themes and variations in apicomplexan parasite biology
-
Roos D.S. Themes and variations in apicomplexan parasite biology. Science 2005, 309:72-73.
-
(2005)
Science
, vol.309
, pp. 72-73
-
-
Roos, D.S.1
-
61
-
-
0030889496
-
Consensus sequence of translational initiation sites from Toxoplasma gondii genes
-
Seeber F. Consensus sequence of translational initiation sites from Toxoplasma gondii genes. Parasitol. Res. 1997, 83:309-311.
-
(1997)
Parasitol. Res.
, vol.83
, pp. 309-311
-
-
Seeber, F.1
-
62
-
-
84890694181
-
Reverse vaccinology: revolutionizing the approach to vaccine design
-
Wiley-VCH Verlag GmbH & Co., Weinheim, J. Hacker, U. Dobrindt (Eds.)
-
Serino L., Pizza M., Rappuoli R. Reverse vaccinology: revolutionizing the approach to vaccine design. Pathogenomics: Genome Analysis of Pathogenic Microbes 2006, 533-554. Wiley-VCH Verlag GmbH & Co., Weinheim. J. Hacker, U. Dobrindt (Eds.).
-
(2006)
Pathogenomics: Genome Analysis of Pathogenic Microbes
, pp. 533-554
-
-
Serino, L.1
Pizza, M.2
Rappuoli, R.3
-
63
-
-
0142075770
-
Recent origins among ancient parasites
-
Sibley L.D. Recent origins among ancient parasites. Vet. Parasitol. 2003, 115:185-198.
-
(2003)
Vet. Parasitol.
, vol.115
, pp. 185-198
-
-
Sibley, L.D.1
-
64
-
-
3242889577
-
AUGUSTUS: a web server for gene finding in eukaryotes
-
Stanke M., Steinkamp R., Waack S., Morgenstern B. AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Res. 2004, 32:W309-W312.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. W309-W312
-
-
Stanke, M.1
Steinkamp, R.2
Waack, S.3
Morgenstern, B.4
-
65
-
-
33748674197
-
AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome
-
Stanke M., Tzvetkova A., Morgenstern B. AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome. Genome Biol. 2006, 7:S11.
-
(2006)
Genome Biol.
, vol.7
, pp. S11
-
-
Stanke, M.1
Tzvetkova, A.2
Morgenstern, B.3
-
66
-
-
0347091255
-
Recent expansion of Toxoplasma through enhanced oral transmission
-
Su C., Evans D., Cole R.H., Kissinger J.C., Ajioka J.W., Sibley L.D. Recent expansion of Toxoplasma through enhanced oral transmission. Science 2003, 299:414-416.
-
(2003)
Science
, vol.299
, pp. 414-416
-
-
Su, C.1
Evans, D.2
Cole, R.H.3
Kissinger, J.C.4
Ajioka, J.W.5
Sibley, L.D.6
-
67
-
-
84859885816
-
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
-
Trapnell C., Roberts A., Goff L., Pertea G., Kim D., Kelley D.R., Pimentel H., Salzberg S.L., Rinn J.L., Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 2012, 7:562-578.
-
(2012)
Nat. Protoc.
, vol.7
, pp. 562-578
-
-
Trapnell, C.1
Roberts, A.2
Goff, L.3
Pertea, G.4
Kim, D.5
Kelley, D.R.6
Pimentel, H.7
Salzberg, S.L.8
Rinn, J.L.9
Pachter, L.10
-
68
-
-
84932193897
-
Using N-SCAN or TWINSCAN to predict gene structures in genomic DNA sequences
-
20:4.8:4.8.1-4.8.16
-
van Baren M.J., Koebbe B.C., Brent M.R. Using N-SCAN or TWINSCAN to predict gene structures in genomic DNA sequences. Curr. Protoc. Bioinf. 2002, 20:4.8:4.8.1-4.8.16.
-
(2002)
Curr. Protoc. Bioinf.
-
-
van Baren, M.J.1
Koebbe, B.C.2
Brent, M.R.3
-
69
-
-
40849147099
-
Computer-aided biotechnology: from immuno-informatics to reverse vaccinology
-
Vivona S., Gardy J.L., Ramachandran S., Brinkman F.S.L., Raghava G.P.S., Flower D.R., Filippini F. Computer-aided biotechnology: from immuno-informatics to reverse vaccinology. Trends Biotechnol. 2008, 26:190-200.
-
(2008)
Trends Biotechnol.
, vol.26
, pp. 190-200
-
-
Vivona, S.1
Gardy, J.L.2
Ramachandran, S.3
Brinkman, F.S.L.4
Raghava, G.P.S.5
Flower, D.R.6
Filippini, F.7
-
70
-
-
57749195712
-
RNA-Seq: a revolutionary tool for transcriptomics
-
Wang Z., Gerstein M., Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev Genet. 2009, 10:57-63.
-
(2009)
Nat. Rev Genet.
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
71
-
-
18744383071
-
GMAP: a genomic mapping and alignment program for mRNA and EST sequences
-
Wu T., Watanabe C. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 2005, 21:1859-1875.
-
(2005)
Bioinformatics
, vol.21
, pp. 1859-1875
-
-
Wu, T.1
Watanabe, C.2
-
72
-
-
79251564926
-
GC content around splice sites affects splicing through pre-mRNA secondary structures
-
Zhang J., Kuo C.C.J., Chen L. GC content around splice sites affects splicing through pre-mRNA secondary structures. BMC Genomics 2011, 12:90.
-
(2011)
BMC Genomics
, vol.12
, pp. 90
-
-
Zhang, J.1
Kuo, C.C.J.2
Chen, L.3
|