-
1
-
-
77951640946
-
A method and server for predicting damaging missense mutations
-
Adzhubei, I. A., S. Schmidt, L. Peshkin, V. E. Ramensky, A. Gerasimova, P. Bork, A. S. Kondrashov et al. 2010. A method and server for predicting damaging missense mutations. Nature Methods 7:248-249.
-
(2010)
Nature Methods
, vol.7
, pp. 248-249
-
-
Adzhubei, I.A.1
Schmidt, S.2
Peshkin, L.3
Ramensky, V.E.4
Gerasimova, A.5
Bork, P.6
Kondrashov, A.S.7
-
2
-
-
84880957747
-
Glossina fuscipes populations provide insights for human African trypanosomiasis transmission in Uganda
-
Aksoy, S., A. Caccone, A. P. Galvani, and L. M. Okedi 2013. Glossina fuscipes populations provide insights for human African trypanosomiasis transmission in Uganda. Trends in Parasitology 29:394-406.
-
(2013)
Trends in Parasitology
, vol.29
, pp. 394-406
-
-
Aksoy, S.1
Caccone, A.2
Galvani, A.P.3
Okedi, L.M.4
-
3
-
-
84856955769
-
High-throughput decoding of antitrypanosomal drug efficacy and resistance
-
Alsford, S., S. Eckert, N. Baker, L. Glover, A. Sanchez-Flores, K. F. Leung, D. J. Turner et al. 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
-
4
-
-
84856282851
-
FastQC a quality control tool for high throughput sequence data
-
Available from(accessed on 24 September 2013).
-
Andrews, S. 2010. FastQC a quality control tool for high throughput sequence data. Available from http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (accessed on 24 September 2013).
-
(2010)
-
-
Andrews, S.1
-
5
-
-
75549088870
-
TriTrypDB: a functional genomic resource for the Trypanosomatidae
-
Aslett, M., C. Aurrecoechea, M. Berriman, J. Brestelli, B. P. Brunk, M. Carrington, D. P. Depledge et al. 2010. TriTrypDB: a functional genomic resource for the Trypanosomatidae. Nucleic Acids Research 38:D457-D462.
-
(2010)
Nucleic Acids Research
, vol.38
, pp. D457-D462
-
-
Aslett, M.1
Aurrecoechea, C.2
Berriman, M.3
Brestelli, J.4
Brunk, B.P.5
Carrington, M.6
Depledge, D.P.7
-
6
-
-
84863585771
-
Aquaglyceroporin 2 controls susceptibility to melarsoprol and pentamidine in African trypanosomes
-
Baker, N., L. Glover, J. C. Munday, D. Aguinaga Andres, M. P. Barrett, H. P. de Koning, and D. Horn 2012. Aquaglyceroporin 2 controls susceptibility to melarsoprol and pentamidine in African trypanosomes. Proceedings of the National Academy of Sciences of the United States of America 109:10996-11001.
-
(2012)
Proceedings of the National Academy of Sciences of the United States of America
, vol.109
, pp. 10996-11001
-
-
Baker, N.1
Glover, L.2
Munday, J.C.3
Aguinaga Andres, D.4
Barrett, M.P.5
de Koning, H.P.6
Horn, D.7
-
7
-
-
52949124400
-
Multiple-strain infections of Trypanosoma brucei across Africa
-
Balmer, O., and A. Caccone 2008. Multiple-strain infections of Trypanosoma brucei across Africa. Acta Tropica 107:275-279.
-
(2008)
Acta Tropica
, vol.107
, pp. 275-279
-
-
Balmer, O.1
Caccone, A.2
-
8
-
-
0034986380
-
Clinical description of encephalopathic syndromes and risk factors for their occurrence and outcome during melarsoprol treatment of human African trypanosomiasis
-
Blum, J., S. Nkunku, and C. Burri 2001. Clinical description of encephalopathic syndromes and risk factors for their occurrence and outcome during melarsoprol treatment of human African trypanosomiasis. Tropical Medicine and International Health 6:390-400.
-
(2001)
Tropical Medicine and International Health
, vol.6
, pp. 390-400
-
-
Blum, J.1
Nkunku, S.2
Burri, C.3
-
9
-
-
0036464010
-
A new, expressed multigene family containing a hot spot for insertion of retroelements is associated with polymorphic subtelomeric regions of Trypanosoma brucei
-
Bringaud, F., N. Biteau, S. E. Melville, S. Hez, N. M. El-Sayed, V. Leech, M. Berriman et al. 2002. A new, expressed multigene family containing a hot spot for insertion of retroelements is associated with polymorphic subtelomeric regions of Trypanosoma brucei. Eukaryotic Cell 1:137-151.
-
(2002)
Eukaryotic Cell
, vol.1
, pp. 137-151
-
-
Bringaud, F.1
Biteau, N.2
Melville, S.E.3
Hez, S.4
El-Sayed, N.M.5
Leech, V.6
Berriman, M.7
-
10
-
-
34547100092
-
SNAP: predict effect of non-synonymous polymorphisms on function
-
Bromberg, Y., and B. Rost 2007. SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Research 35:3823-3835.
-
(2007)
Nucleic Acids Research
, vol.35
, pp. 3823-3835
-
-
Bromberg, Y.1
Rost, B.2
-
11
-
-
0027500261
-
Arsenical-resistant trypanosomes lack an unusual adenosine transporter
-
Carter, N. S., and A. H. Fairlamb 1993. Arsenical-resistant trypanosomes lack an unusual adenosine transporter. Nature 361:173-176.
-
(1993)
Nature
, vol.361
, pp. 173-176
-
-
Carter, N.S.1
Fairlamb, A.H.2
-
12
-
-
84862506964
-
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3
-
Cingolani, P., A. Platts, L. Wang le, M. Coon, T. Nguyen, L. Wang, S. J. Land et al. 2012. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6:80-92.
-
(2012)
Fly (Austin)
, vol.6
, pp. 80-92
-
-
Cingolani, P.1
Platts, A.2
Wang le, L.3
Coon, M.4
Nguyen, T.5
Wang, L.6
Land, S.J.7
-
13
-
-
84866790716
-
MESSA: MEta-server for protein sequence analysis
-
Cong, Q., and N. V. Grishin 2012. MESSA: MEta-server for protein sequence analysis. BMC Biology 10:82.
-
(2012)
BMC Biology
, vol.10
, pp. 82
-
-
Cong, Q.1
Grishin, N.V.2
-
14
-
-
84883732474
-
Monitoring the use of nifurtimox-eflornithine combination therapy (NECT) in the treatment of second stage gambiense human African trypanosomiasis
-
Franco, J. R., P. P. Simarro, A. Diarra, J. Ruiz-Postigo, M. Samo, and J. Jannin 2012. Monitoring the use of nifurtimox-eflornithine combination therapy (NECT) in the treatment of second stage gambiense human African trypanosomiasis. Research and Reports in Tropical Medicine 3:93-101.
-
(2012)
Research and Reports in Tropical Medicine
, vol.3
, pp. 93-101
-
-
Franco, J.R.1
Simarro, P.P.2
Diarra, A.3
Ruiz-Postigo, J.4
Samo, M.5
Jannin, J.6
-
15
-
-
84887310584
-
Aquaporin 2 mutations in Trypanosoma brucei gambiense field isolates correlate with decreased susceptibility to pentamidine and melarsoprol
-
Graf, F. E., P. Ludin, T. Wenzler, M. Kaiser, R. Brun, P. P. Pyana, P. Buscher et al. 2013. Aquaporin 2 mutations in Trypanosoma brucei gambiense field isolates correlate with decreased susceptibility to pentamidine and melarsoprol. PLoS Neglected Tropical Diseases 7:e2475.
-
(2013)
PLoS Neglected Tropical Diseases
, vol.7
, pp. e2475
-
-
Graf, F.E.1
Ludin, P.2
Wenzler, T.3
Kaiser, M.4
Brun, R.5
Pyana, P.P.6
Buscher, P.7
-
16
-
-
77952329013
-
The genome sequence of Trypanosoma brucei gambiense, causative agent of chronic human African trypanosomiasis
-
Jackson, A. P., M. Sanders, A. Berry, J. McQuillan, M. A. Aslett, M. A. Quail, B. Chukualim et al. 2010. The genome sequence of Trypanosoma brucei gambiense, causative agent of chronic human African trypanosomiasis. PLoS Neglected Tropical Diseases 4:e658.
-
(2010)
PLoS Neglected Tropical Diseases
, vol.4
, pp. e658
-
-
Jackson, A.P.1
Sanders, M.2
Berry, A.3
McQuillan, J.4
Aslett, M.A.5
Quail, M.A.6
Chukualim, B.7
-
17
-
-
70450253253
-
Widespread variation in transcript abundance within and across developmental stages of Trypanosoma brucei
-
Jensen, B. C., D. Sivam, C. T. Kifer, P. J. Myler, and M. Parsons 2009. Widespread variation in transcript abundance within and across developmental stages of Trypanosoma brucei. BMC Genomics 10:482.
-
(2009)
BMC Genomics
, vol.10
, pp. 482
-
-
Jensen, B.C.1
Sivam, D.2
Kifer, C.T.3
Myler, P.J.4
Parsons, M.5
-
18
-
-
80054949793
-
adegenet 1.3-1: new tools for the analysis of genome-wide SNP data
-
Jombart, T., and I. Ahmed 2011. adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics 27:3070-3071.
-
(2011)
Bioinformatics
, vol.27
, pp. 3070-3071
-
-
Jombart, T.1
Ahmed, I.2
-
19
-
-
77957919360
-
Discriminant analysis of principal components: a new method for the analysis of genetically structured populations
-
Jombart, T., S. Devillard, and F. Balloux 2010. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics 11:94.
-
(2010)
BMC Genetics
, vol.11
, pp. 94
-
-
Jombart, T.1
Devillard, S.2
Balloux, F.3
-
20
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead, B., and S. L. Salzberg 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9:357-359.
-
(2012)
Nature Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
21
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li, H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth et al. 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
-
22
-
-
0032811332
-
A high level of mixed Trypanosoma brucei infections in tsetse flies detected by three hypervariable minisatellites
-
MacLeod, A., C. M. Turner, and A. Tait 1999. A high level of mixed Trypanosoma brucei infections in tsetse flies detected by three hypervariable minisatellites. Molecular and Biochemical Parasitology 102:237-248.
-
(1999)
Molecular and Biochemical Parasitology
, vol.102
, pp. 237-248
-
-
MacLeod, A.1
Turner, C.M.2
Tait, A.3
-
23
-
-
35348915954
-
Genotypic and phenotypic characterization of Trypanosoma brucei gambiense isolates from Ibba, South Sudan, an area of high melarsoprol treatment failure rate
-
Maina, N., K. J. Maina, P. Maser, and R. Brun 2007. Genotypic and phenotypic characterization of Trypanosoma brucei gambiense isolates from Ibba, South Sudan, an area of high melarsoprol treatment failure rate. Acta Tropica 104:84-90.
-
(2007)
Acta Tropica
, vol.104
, pp. 84-90
-
-
Maina, N.1
Maina, K.J.2
Maser, P.3
Brun, R.4
-
24
-
-
84863982076
-
Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing
-
Manske, M., O. Miotto, S. Campino, S. Auburn, J. Almagro-Garcia, G. Maslen, J. O'Brien et al. 2012. Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature 487:375-379.
-
(2012)
Nature
, vol.487
, pp. 375-379
-
-
Manske, M.1
Miotto, O.2
Campino, S.3
Auburn, S.4
Almagro-Garcia, J.5
Maslen, G.6
O'Brien, J.7
-
25
-
-
0037834651
-
A nucleoside transporter from Trypanosoma brucei involved in drug resistance
-
Maser, P., C. Sutterlin, A. Kralli, and R. Kaminsky 1999. A nucleoside transporter from Trypanosoma brucei involved in drug resistance. Science 285:242-244.
-
(1999)
Science
, vol.285
, pp. 242-244
-
-
Maser, P.1
Sutterlin, C.2
Kralli, A.3
Kaminsky, R.4
-
26
-
-
0034985389
-
Melarsoprol refractory T. b. gambiense from Omugo, north-western Uganda
-
Matovu, E., J. C. Enyaru, D. Legros, C. Schmid, T. Seebeck, and R. Kaminsky 2001a. Melarsoprol refractory T. b. gambiense from Omugo, north-western Uganda. Tropical Medicine and International Health 6:407-411.
-
(2001)
Tropical Medicine and International Health
, vol.6
, pp. 407-411
-
-
Matovu, E.1
Enyaru, J.C.2
Legros, D.3
Schmid, C.4
Seebeck, T.5
Kaminsky, R.6
-
27
-
-
0034852287
-
Genetic variants of the TbAT1 adenosine transporter from African trypanosomes in relapse infections following melarsoprol therapy
-
Matovu, E., F. Geiser, V. Schneider, P. Maser, J. C. Enyaru, R. Kaminsky, S. Gallati et al. 2001b. Genetic variants of the TbAT1 adenosine transporter from African trypanosomes in relapse infections following melarsoprol therapy. Molecular and Biochemical Parasitology 117:73-81.
-
(2001)
Molecular and Biochemical Parasitology
, vol.117
, pp. 73-81
-
-
Matovu, E.1
Geiser, F.2
Schneider, V.3
Maser, P.4
Enyaru, J.C.5
Kaminsky, R.6
Gallati, S.7
-
28
-
-
77956295988
-
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
-
McKenna, A., M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis, A. Kernytsky, K. Garimella et al. 2010. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research 20:1297-1303.
-
(2010)
Genome Research
, 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
-
29
-
-
84885911072
-
Population genomics of rapid adaptation by soft selective sweeps
-
Messer, P. W., and D. A. Petrov 2013. Population genomics of rapid adaptation by soft selective sweeps. Trends in Ecology and Evolution 28:659-669.
-
(2013)
Trends in Ecology and Evolution
, vol.28
, pp. 659-669
-
-
Messer, P.W.1
Petrov, D.A.2
-
31
-
-
75649107641
-
How to shorten patient follow-up after treatment for Trypanosoma brucei gambiense sleeping sickness
-
Mumba Ngoyi, D., V. Lejon, P. Pyana, M. Boelaert, M. Ilunga, J. Menten, J. P. Mulunda et al. 2010. How to shorten patient follow-up after treatment for Trypanosoma brucei gambiense sleeping sickness. Journal of Infectious Diseases 201:453-463.
-
(2010)
Journal of Infectious Diseases
, vol.201
, pp. 453-463
-
-
Mumba Ngoyi, D.1
Lejon, V.2
Pyana, P.3
Boelaert, M.4
Ilunga, M.5
Menten, J.6
Mulunda, J.P.7
-
32
-
-
67649635323
-
Nifurtimox-eflornithine combination therapy for second-stage African Trypanosoma brucei gambiense trypanosomiasis: a multicentre, randomised, phase III, non-inferiority trial
-
Priotto, G., S. Kasparian, W. Mutombo, D. Ngouama, S. Ghorashian, U. Arnold, S. Ghabri et al. 2009. Nifurtimox-eflornithine combination therapy for second-stage African Trypanosoma brucei gambiense trypanosomiasis: a multicentre, randomised, phase III, non-inferiority trial. Lancet 374:56-64.
-
(2009)
Lancet
, vol.374
, pp. 56-64
-
-
Priotto, G.1
Kasparian, S.2
Mutombo, W.3
Ngouama, D.4
Ghorashian, S.5
Arnold, U.6
Ghabri, S.7
-
33
-
-
84920118789
-
Melarsoprol sensitivity profile of Trypanosoma brucei gambiense isolates from cured and relapsed sleeping sickness patients from the Democratic Republic of the Congo
-
Pyana Pati, P., N. Van Reet, D. Mumba Ngoyi, I. Ngay Lukusa, S. Karhemere Bin Shamamba, and P. Buscher 2014. Melarsoprol sensitivity profile of Trypanosoma brucei gambiense isolates from cured and relapsed sleeping sickness patients from the Democratic Republic of the Congo. PLoS Neglected Tropical Diseases 8:e3212.
-
(2014)
PLoS Neglected Tropical Diseases
, vol.8
, pp. e3212
-
-
Pyana Pati, P.1
Van Reet, N.2
Mumba Ngoyi, D.3
Ngay Lukusa, I.4
Karhemere Bin Shamamba, S.5
Buscher, P.6
-
34
-
-
79955847165
-
Isolation of Trypanosoma brucei gambiense from cured and relapsed sleeping sickness patients and adaptation to laboratory mice
-
Pyana, P. P., I. Ngay Lukusa, D. Mumba Ngoyi, N. Van Reet, M. Kaiser, S. Karhemere Bin Shamamba, and P. Buscher 2011. Isolation of Trypanosoma brucei gambiense from cured and relapsed sleeping sickness patients and adaptation to laboratory mice. PLoS Neglected Tropical Diseases 5:e1025.
-
(2011)
PLoS Neglected Tropical Diseases
, vol.5
, pp. e1025
-
-
Pyana, P.P.1
Ngay Lukusa, I.2
Mumba Ngoyi, D.3
Van Reet, N.4
Kaiser, M.5
Karhemere Bin Shamamba, S.6
Buscher, P.7
-
35
-
-
84874427856
-
Adaptive genetic variation on the landscape: methods and cases
-
Schoville, S. D., A. Bonin, O. François, S. Lobreaux, C. Melodelima, and S. Manel 2012. Adaptive genetic variation on the landscape: methods and cases. Annual Review of Ecology, Evolution, and Systematics 43:23-43.
-
(2012)
Annual Review of Ecology, Evolution, and Systematics
, vol.43
, pp. 23-43
-
-
Schoville, S.D.1
Bonin, A.2
François, O.3
Lobreaux, S.4
Melodelima, C.5
Manel, S.6
-
36
-
-
0036223214
-
Overexpression of the putative thiol conjugate transporter TbMRPA causes melarsoprol resistance in Trypanosoma brucei
-
Shahi, S. K., R. L. Krauth-Siegel, and C. E. Clayton 2002. Overexpression of the putative thiol conjugate transporter TbMRPA causes melarsoprol resistance in Trypanosoma brucei. Molecular Microbiology 43:1129-1138.
-
(2002)
Molecular Microbiology
, vol.43
, pp. 1129-1138
-
-
Shahi, S.K.1
Krauth-Siegel, R.L.2
Clayton, C.E.3
-
37
-
-
84861909705
-
Update on field use of the available drugs for the chemotherapy of human African trypanosomiasis
-
Simarro, P. P., J. Franco, A. Diarra, J. A. Postigo, and J. Jannin 2012. Update on field use of the available drugs for the chemotherapy of human African trypanosomiasis. Parasitology 139:842-846.
-
(2012)
Parasitology
, vol.139
, pp. 842-846
-
-
Simarro, P.P.1
Franco, J.2
Diarra, A.3
Postigo, J.A.4
Jannin, J.5
-
38
-
-
84985947309
-
Comparative genomics reveals multiple genetic backgrounds of human pathogenicity in the Trypanosoma brucei complex
-
Sistrom, M., B. Evans, R. Bjornson, W. Gibson, O. Balmer, P. Maser, S. Aksoy, et al. 2014. Comparative genomics reveals multiple genetic backgrounds of human pathogenicity in the Trypanosoma brucei complex. Genome Biology and Evolution 6:2811-2819.
-
(2014)
Genome Biology and Evolution
, vol.6
, pp. 2811-2819
-
-
Sistrom, M.1
Evans, B.2
Bjornson, R.3
Gibson, W.4
Balmer, O.5
Maser, P.6
Aksoy, S.7
-
39
-
-
84964995809
-
RepeatMasker Open-4.0
-
2015. Available from(accessed on 11 February 2014).
-
Smit, A. F. A., R. Hubley, and P. Green 2013-2015. RepeatMasker Open-4.0. Available from http://www.repeatmasker.org (accessed on 11 February 2014).
-
(2013)
-
-
Smit, A.F.A.1
Hubley, R.2
Green, P.3
-
41
-
-
84907820354
-
From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline
-
Van der Auwera, G. A., M. O. Carneiro, C. Hartl, R. Poplin, G. Del Angel, A. Levy-Moonshine, T. Jordan et al. 2013. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Current Protocols in Bioinformatics 11:1-33.
-
(2013)
Current Protocols in Bioinformatics
, vol.11
, pp. 1-33
-
-
Van der Auwera, G.A.1
Carneiro, M.O.2
Hartl, C.3
Poplin, R.4
Del Angel, G.5
Levy-Moonshine, A.6
Jordan, T.7
-
42
-
-
77649318621
-
Digital gene expression analysis of two life cycle stages of the human-infective parasite, Trypanosoma brucei gambiense reveals differentially expressed clusters of co-regulated genes
-
Veitch, N. J., P. C. Johnson, U. Trivedi, S. Terry, D. Wildridge, and A. MacLeod 2010. Digital gene expression analysis of two life cycle stages of the human-infective parasite, Trypanosoma brucei gambiense reveals differentially expressed clusters of co-regulated genes. BMC Genomics 11:124.
-
(2010)
BMC Genomics
, vol.11
, pp. 124
-
-
Veitch, N.J.1
Johnson, P.C.2
Trivedi, U.3
Terry, S.4
Wildridge, D.5
MacLeod, A.6
|