| Year |
Citation |
Score |
| 2023 |
Wichers-Misterek JS, Krumkamp R, Held J, von Thien H, Wittmann I, Höppner YD, Ruge JM, Moser K, Dara A, Strauss J, Esen M, Fendel R, Sulyok Z, Jeninga MD, Kremsner PG, ... ... Otto TD, et al. The exception that proves the rule: Virulence gene expression at the onset of Plasmodium falciparum blood stage infections. Plos Pathogens. 19: e1011468. PMID 37384799 DOI: 10.1371/journal.ppat.1011468 |
0.307 |
|
| 2023 |
Simmons C, Gibbons J, Wang C, Pires CV, Zhang M, Siddiqui F, Oberstaller J, Casandra D, Seyfang A, Cui L, Otto TD, Adams JH. A novel Modulator of Ring Stage Translation (MRST) gene alters artemisinin sensitivity in . Msphere. e0015223. PMID 37219373 DOI: 10.1128/msphere.00152-23 |
0.307 |
|
| 2023 |
Koutros S, Kiemeney LA, Pal Choudhury P, Milne RL, Lopez de Maturana E, Ye Y, Joseph V, Florez-Vargas O, Dyrskjøt L, Figueroa J, Dutta D, Giles GG, Hildebrandt MAT, Offit K, Kogevinas M, ... ... Otto T, et al. Genome-wide Association Study of Bladder Cancer Reveals New Biological and Translational Insights. European Urology. PMID 37210288 DOI: 10.1016/j.eururo.2023.04.020 |
0.304 |
|
| 2023 |
Chawla J, Goldowitz I, Oberstaller J, Zhang M, Pires CV, Navarro F, Sollelis L, Wang CCQ, Seyfang A, Dvorin J, Otto TD, Rayner JC, Marti M, Adams JH. Phenotypic Screens Identify Genetic Factors Associated with Gametocyte Development in the Human Malaria Parasite Plasmodium falciparum. Microbiology Spectrum. e0416422. PMID 37154686 DOI: 10.1128/spectrum.04164-22 |
0.323 |
|
| 2023 |
Britton C, Laing R, McNeilly TN, Perez MG, Otto TD, Hildersley KA, Maizels RM, Devaney E, Gillan V. New technologies to study helminth development and host-parasite interactions. International Journal For Parasitology. PMID 36931423 DOI: 10.1016/j.ijpara.2022.11.012 |
0.308 |
|
| 2022 |
Hentzschel F, Gibbins MP, Attipa C, Beraldi D, Moxon CA, Otto TD, Marti M. Host cell maturation modulates parasite invasion and sexual differentiation in . Science Advances. 8: eabm7348. PMID 35476438 DOI: 10.1126/sciadv.abm7348 |
0.304 |
|
| 2022 |
Mackenzie G, Jensen RW, Lavstsen T, Otto TD. Varia: a tool for prediction, analysis and visualisation of variable genes. Bmc Bioinformatics. 23: 52. PMID 35073845 DOI: 10.1186/s12859-022-04573-6 |
0.338 |
|
| 2021 |
Minassian AM, Themistocleous Y, Silk SE, Barrett JR, Kemp A, Quinkert D, Nielsen CM, Edwards NJ, Rawlinson TA, Ramos Lopez F, Roobsoong W, Ellis KJ, Cho JS, Aunin E, Otto TD, et al. Controlled human malaria infection with a clone of Plasmodium vivax with high quality genome assembly. Jci Insight. PMID 34609964 DOI: 10.1172/jci.insight.152465 |
0.427 |
|
| 2021 |
Zhang M, Wang C, Oberstaller J, Thomas P, Otto TD, Casandra D, Boyapalle S, Adapa SR, Xu S, Button-Simons K, Mayho M, Rayner JC, Ferdig MT, Jiang RHY, Adams JH. The apicoplast link to fever-survival and artemisinin-resistance in the malaria parasite. Nature Communications. 12: 4563. PMID 34315897 DOI: 10.1038/s41467-021-24814-1 |
0.381 |
|
| 2021 |
Wichers JS, Tonkin-Hill G, Thye T, Krumkamp R, Kreuels B, Strauss J, von Thien H, Scholz JA, Smedegaard Hansson H, Weisel Jensen R, Turner L, Lorenz FR, Schöllhorn A, Bruchhaus I, Tannich E, ... ... Otto TD, et al. Common virulence gene expression in adult first-time infected malaria patients and severe cases. Elife. 10. PMID 33908865 DOI: 10.7554/eLife.69040 |
0.314 |
|
| 2021 |
Oberstaller J, Otto TD, Rayner JC, Adams JH. Essential Genes of the Parasitic Apicomplexa. Trends in Parasitology. PMID 33419671 DOI: 10.1016/j.pt.2020.11.007 |
0.396 |
|
| 2020 |
Otto TD, Gilabert A, Crellen T, Böhme U, Arnathau C, Sanders M, Oyola SO, Okouga AP, Boundenga L, Willaume E, Ngoubangoye B, Moukodoum ND, Paupy C, Durand P, Rougeron V, et al. Author Correction: Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria. Nature Microbiology. PMID 32796922 DOI: 10.1038/S41564-020-0787-9 |
0.585 |
|
| 2020 |
Akkaya M, Bansal A, Sheehan PW, Pena M, Cimperman CK, Qi CF, Yazew T, Otto TD, Billker O, Miller LH, Pierce SK. Testing the impact of a single nucleotide polymorphism in a Plasmodium berghei ApiAP2 transcription factor on experimental cerebral malaria in mice. Scientific Reports. 10: 13630. PMID 32788672 DOI: 10.1038/S41598-020-70617-7 |
0.309 |
|
| 2020 |
Chappell L, Ross P, Orchard L, Russell TJ, Otto TD, Berriman M, Rayner JC, Llinás M. Refining the transcriptome of the human malaria parasite Plasmodium falciparum using amplification-free RNA-seq. Bmc Genomics. 21: 395. PMID 32513207 DOI: 10.1186/S12864-020-06787-5 |
0.552 |
|
| 2019 |
Otto TD, Assefa SA, Böhme U, Sanders MJ, Kwiatkowski D, Berriman M, Newbold C. Evolutionary analysis of the most polymorphic gene family in malaria. Wellcome Open Research. 4: 193. PMID 32055709 DOI: 10.12688/wellcomeopenres.15590.1 |
0.584 |
|
| 2019 |
Sloan MA, Brooks K, Otto TD, Sanders MJ, Cotton JA, Ligoxygakis P. Transcriptional and genomic parallels between the monoxenous parasite Herpetomonas muscarum and Leishmania. Plos Genetics. 15: e1008452. PMID 31710597 DOI: 10.1371/Journal.Pgen.1008452 |
0.359 |
|
| 2019 |
Böhme U, Otto TD, Sanders M, Newbold CI, Berriman M. Progression of the canonical reference malaria parasite genome from 2002-2019. Wellcome Open Research. 4: 58. PMID 31080894 DOI: 10.12688/wellcomeopenres.15194.1 |
0.652 |
|
| 2019 |
Woodford J, Collins KA, Odedra A, Wang C, Kyung JI, Domingo GJ, Watts R, Marquart L, Berriman M, Otto TD, McCarthy JS. An experimental human blood stage model for studying Plasmodium malariae infection. The Journal of Infectious Diseases. PMID 30852586 DOI: 10.1093/Infdis/Jiz102 |
0.532 |
|
| 2018 |
Tarr SJ, Díaz-Ingelmo O, Stewart LB, Hocking SE, Murray L, Duffy CW, Otto TD, Chappell L, Rayner JC, Awandare GA, Conway DJ. Schizont transcriptome variation among clinical isolates and laboratory-adapted clones of the malaria parasite Plasmodium falciparum. Bmc Genomics. 19: 894. PMID 30526479 DOI: 10.1186/S12864-018-5257-X |
0.339 |
|
| 2018 |
Mendes AM, Reuling IJ, Andrade CM, Otto TD, Machado M, Teixeira F, Pissarra J, Gonçalves-Rosa N, Bonaparte D, Sinfrónio J, Sanders M, Janse CJ, Khan SM, Newbold CI, Berriman M, et al. Pre-clinical evaluation of a -based whole-sporozoite malaria vaccine candidate. Npj Vaccines. 3: 54. PMID 30510775 DOI: 10.1038/s41541-018-0091-3 |
0.528 |
|
| 2018 |
Campino S, Marin-Menendez A, Kemp A, Cross N, Drought L, Otto TD, Benavente ED, Ravenhall M, Schwach F, Girling G, Manske M, Theron M, Gould K, Drury E, Clark TG, et al. A forward genetic screen reveals a primary role for Plasmodium falciparum Reticulocyte Binding Protein Homologue 2a and 2b in determining alternative erythrocyte invasion pathways. Plos Pathogens. 14: e1007436. PMID 30496294 DOI: 10.1371/Journal.Ppat.1007436 |
0.321 |
|
| 2018 |
Duffy CW, Amambua-Ngwa A, Ahouidi AD, Diakite M, Awandare GA, Ba H, Tarr SJ, Murray L, Stewart LB, D'Alessandro U, Otto TD, Kwiatkowski DP, Conway DJ. Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development. Scientific Reports. 8: 15763. PMID 30361631 DOI: 10.1038/S41598-018-34078-3 |
0.431 |
|
| 2018 |
Müller LSM, Cosentino RO, Förstner KU, Guizetti J, Wedel C, Kaplan N, Janzen CJ, Arampatzi P, Vogel J, Steinbiss S, Otto TD, Saliba AE, Sebra RP, Siegel TN. Genome organization and DNA accessibility control antigenic variation in trypanosomes. Nature. 563: 121-125. PMID 30333624 DOI: 10.1038/S41586-018-0619-8 |
0.412 |
|
| 2018 |
Wyllie S, Thomas M, Patterson S, Crouch S, De Rycker M, Lowe R, Gresham S, Urbaniak MD, Otto TD, Stojanovski L, Simeons FRC, Manthri S, MacLean LM, Zuccotto F, Homeyer N, et al. Cyclin-dependent kinase 12 is a drug target for visceral leishmaniasis. Nature. PMID 30046105 DOI: 10.1038/S41586-018-0356-Z |
0.43 |
|
| 2018 |
Lee HJ, Georgiadou A, Walther M, Nwakanma D, Stewart LB, Levin M, Otto TD, Conway DJ, Coin LJ, Cunnington AJ. Integrated pathogen load and dual transcriptome analysis of systemic host-pathogen interactions in severe malaria. Science Translational Medicine. 10. PMID 29950443 DOI: 10.1126/Scitranslmed.Aar3619 |
0.35 |
|
| 2018 |
Otto TD, Böhme U, Sanders M, Reid A, Bruske EI, Duffy CW, Bull PC, Pearson RD, Abdi A, Dimonte S, Stewart LB, Campino S, Kekre M, Hamilton WL, Claessens A, et al. Long read assemblies of geographically dispersed isolates reveal highly structured subtelomeres. Wellcome Open Research. 3: 52. PMID 29862326 DOI: 10.12688/wellcomeopenres.14571.1 |
0.614 |
|
| 2018 |
Otto TD, Gilabert A, Crellen T, Böhme U, Arnathau C, Sanders M, Oyola SO, Okouga AP, Boundenga L, Willaume E, Ngoubangoye B, Moukodoum ND, Paupy C, Durand P, Rougeron V, et al. Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria. Nature Microbiology. PMID 29784978 DOI: 10.1038/S41564-018-0162-2 |
0.659 |
|
| 2018 |
Zhang M, Wang C, Otto TD, Oberstaller J, Liao X, Adapa SR, Udenze K, Bronner IF, Casandra D, Mayho M, Brown J, Li S, Swanson J, Rayner JC, Jiang RHY, et al. Uncovering the essential genes of the human malaria parasite by saturation mutagenesis. Science (New York, N.Y.). 360. PMID 29724925 DOI: 10.1126/Science.Aap7847 |
0.382 |
|
| 2018 |
Lee HJ, Georgiadou A, Otto TD, Levin M, Coin LJ, Conway DJ, Cunnington AJ. Transcriptomic Studies of Malaria: a Paradigm for Investigation of Systemic Host-Pathogen Interactions. Microbiology and Molecular Biology Reviews : Mmbr. 82. PMID 29695497 DOI: 10.1128/Mmbr.00071-17 |
0.305 |
|
| 2018 |
Böhme U, Otto TD, Cotton J, Steinbiss S, Sanders M, Oyola SO, Nicot A, Gandon S, Patra KP, Herd C, Bushell E, Modrzynska KK, Billker O, Vinetz JM, Rivero A, et al. Complete avian malaria parasite genomes reveal features associated with lineage specific evolution in birds and mammals. Genome Research. PMID 29500236 DOI: 10.1101/Gr.218123.116 |
0.667 |
|
| 2017 |
Pasini EM, Böhme U, Rutledge GG, Voorberg-Van der Wel A, Sanders M, Berriman M, Kocken CH, Otto TD. An improved Plasmodium cynomolgi genome assembly reveals an unexpected methyltransferase gene expansion. Wellcome Open Research. 2: 42. PMID 28748222 DOI: 10.12688/wellcomeopenres.11864.1 |
0.677 |
|
| 2017 |
Rutledge GG, Marr I, Huang GKL, Auburn S, Marfurt J, Sanders M, White NJ, Berriman M, Newbold CI, Anstey NM, Otto TD, Price RN. Genomic Characterization of Recrudescent Plasmodium malariae after Treatment with Artemether/Lumefantrine. Emerging Infectious Diseases. 23. PMID 28430103 DOI: 10.3201/Eid2308.161582 |
0.601 |
|
| 2017 |
Sutherland CJ, Lansdell P, Sanders M, Muwanguzi J, van Schalkwyk DA, Kaur H, Nolder D, Tucker J, Bennett HM, Otto TD, Berriman M, Patel TA, Lynn R, Gkrania-Klotsas E, Chiodini PL. Pfk13-independent treatment failure in four imported cases of Plasmodium falciparum malaria given artemether-lumefantrine in the UK. Antimicrobial Agents and Chemotherapy. PMID 28137810 DOI: 10.1128/Aac.02382-16 |
0.491 |
|
| 2017 |
Rutledge GG, Böhme U, Sanders M, Reid AJ, Cotton JA, Maiga-Ascofare O, Djimdé AA, Apinjoh TO, Amenga-Etego L, Manske M, Barnwell JW, Renaud F, Ollomo B, Prugnolle F, Anstey NM, ... ... Otto TD, et al. Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution. Nature. PMID 28117441 DOI: 10.1038/Nature21038 |
0.62 |
|
| 2016 |
Auburn S, Böhme U, Steinbiss S, Trimarsanto H, Hostetler J, Sanders M, Gao Q, Nosten F, Newbold CI, Berriman M, Price RN, Otto TD. A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes. Wellcome Open Research. 1: 4. PMID 28008421 DOI: 10.12688/wellcomeopenres.9876.1 |
0.645 |
|
| 2016 |
Oyola SO, Ariani CV, Hamilton WL, Kekre M, Amenga-Etego LN, Ghansah A, Rutledge GG, Redmond S, Manske M, Jyothi D, Jacob CG, Otto TD, Rockett K, Newbold CI, Berriman M, et al. Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification. Malaria Journal. 15: 597. PMID 27998271 DOI: 10.1186/S12936-016-1641-7 |
0.62 |
|
| 2016 |
Hamilton WL, Claessens A, Otto TD, Kekre M, Fairhurst RM, Rayner JC, Kwiatkowski D. Extreme mutation bias and high AT content in Plasmodium falciparum. Nucleic Acids Research. PMID 27994033 DOI: 10.1093/Nar/Gkw1259 |
0.401 |
|
| 2016 |
Klemm EJ, Gkrania-Klotsas E, Hadfield J, Forbester JL, Harris SR, Hale C, Heath JN, Wileman T, Clare S, Kane L, Goulding D, Otto TD, Kay S, Doffinger R, Cooke FJ, et al. Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host. Nature Microbiology. 1: 15023. PMID 27572160 DOI: 10.1038/nmicrobiol.2015.23 |
0.367 |
|
| 2016 |
Klemm EJ, Gkrania-Klotsas E, Hadfield J, Forbester JL, Harris SR, Hale C, Heath JN, Wileman T, Clare S, Kane L, Goulding D, Otto TD, Kay S, Doffinger R, Cooke FJ, et al. Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host. Nature Microbiology. 1. PMID 27127642 DOI: 10.1038/nmicrobiol.2015.23 |
0.366 |
|
| 2016 |
Steinbiss S, Silva-Franco F, Brunk B, Foth B, Hertz-Fowler C, Berriman M, Otto TD. Companion: a web server for annotation and analysis of parasite genomes. Nucleic Acids Research. PMID 27105845 DOI: 10.1093/Nar/Gkw292 |
0.66 |
|
| 2015 |
Jackson AP, Otto TD, Aslett M, Armstrong SD, Bringaud F, Schlacht A, Hartley C, Sanders M, Wastling JM, Dacks JB, Acosta-Serrano A, Field MC, Ginger ML, Berriman M. Kinetoplastid Phylogenomics Reveals the Evolutionary Innovations Associated with the Origins of Parasitism. Current Biology : Cb. PMID 26725202 DOI: 10.1016/J.Cub.2015.11.055 |
0.666 |
|
| 2015 |
Hunt M, Silva ND, Otto TD, Parkhill J, Keane JA, Harris SR. Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biology. 16: 294. PMID 26714481 DOI: 10.1186/s13059-015-0849-0 |
0.406 |
|
| 2015 |
Woo YH, Ansari H, Otto TD, Klinger CM, Kolisko M, Michálek J, Saxena A, Shanmugam D, Tayyrov A, Veluchamy A, Ali S, Bernal A, del Campo J, Cihlář J, Flegontov P, et al. Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites. Elife. 4: e06974. PMID 26175406 DOI: 10.7554/Elife.06974 |
0.442 |
|
| 2015 |
Ramaprasad A, Mourier T, Naeem R, Malas TB, Moussa E, Panigrahi A, Vermont SJ, Otto TD, Wastling J, Pain A. Comprehensive evaluation of Toxoplasma gondii VEG and Neospora caninum LIV genomes with tachyzoite stage transcriptome and proteome defines novel transcript features. Plos One. 10: e0124473. PMID 25875305 DOI: 10.1371/journal.pone.0124473 |
0.455 |
|
| 2015 |
Pinheiro MM, Ahmed MA, Millar SB, Sanderson T, Otto TD, Lu WC, Krishna S, Rayner JC, Cox-Singh J. Plasmodium knowlesi genome sequences from clinical isolates reveal extensive genomic dimorphism. Plos One. 10: e0121303. PMID 25830531 DOI: 10.1371/Journal.Pone.0121303 |
0.493 |
|
| 2015 |
Weerdenburg EM, Abdallah AM, Rangkuti F, Abd El Ghany M, Otto TD, Adroub SA, Molenaar D, Ummels R, Ter Veen K, van Stempvoort G, van der Sar AM, Ali S, Langridge GC, Thomson NR, Pain A, et al. Genome-wide transposon mutagenesis indicates that Mycobacterium marinum customizes its virulence mechanisms for survival and replication in different hosts. Infection and Immunity. 83: 1778-88. PMID 25690095 DOI: 10.1128/IAI.03050-14 |
0.329 |
|
| 2015 |
Otto TD. From sequence mapping to genome assemblies. Methods in Molecular Biology (Clifton, N.J.). 1201: 19-50. PMID 25388106 DOI: 10.1007/978-1-4939-1438-8_2 |
0.368 |
|
| 2014 |
Claessens A, Hamilton WL, Kekre M, Otto TD, Faizullabhoy A, Rayner JC, Kwiatkowski D. Generation of antigenic diversity in Plasmodium falciparum by structured rearrangement of Var genes during mitosis. Plos Genetics. 10: e1004812. PMID 25521112 DOI: 10.1371/Journal.Pgen.1004812 |
0.445 |
|
| 2014 |
Vaidya AB, Morrisey JM, Zhang Z, Das S, Daly TM, Otto TD, Spillman NJ, Wyvratt M, Siegl P, Marfurt J, Wirjanata G, Sebayang BF, Price RN, Chatterjee A, Nagle A, et al. Pyrazoleamide compounds are potent antimalarials that target Na+ homeostasis in intraerythrocytic Plasmodium falciparum. Nature Communications. 5: 5521. PMID 25422853 DOI: 10.1038/Ncomms6521 |
0.545 |
|
| 2014 |
Foth BJ, Otto TD. Genomics illuminates parasite biology. Nature Reviews. Microbiology. 12: 727. PMID 25402362 DOI: 10.1038/nrmicro3368 |
0.455 |
|
| 2014 |
Otto TD, Böhme U, Jackson AP, Hunt M, Franke-Fayard B, Hoeijmakers WA, Religa AA, Robertson L, Sanders M, Ogun SA, Cunningham D, Erhart A, Billker O, Khan SM, Stunnenberg HG, et al. A comprehensive evaluation of rodent malaria parasite genomes and gene expression. Bmc Biology. 12: 86. PMID 25359557 DOI: 10.1186/S12915-014-0086-0 |
0.687 |
|
| 2014 |
Otto TD, Rayner JC, Böhme U, Pain A, Spottiswoode N, Sanders M, Quail M, Ollomo B, Renaud F, Thomas AW, Prugnolle F, Conway DJ, Newbold C, Berriman M. Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts. Nature Communications. 5: 4754. PMID 25203297 DOI: 10.1038/Ncomms5754 |
0.673 |
|
| 2014 |
Reid AJ, Blake DP, Ansari HR, Billington K, Browne HP, Bryant J, Dunn M, Hung SS, Kawahara F, Miranda-Saavedra D, Malas TB, Mourier T, Naghra H, Nair M, Otto TD, et al. Genomic analysis of the causative agents of coccidiosis in domestic chickens. Genome Research. 24: 1676-85. PMID 25015382 DOI: 10.1101/Gr.168955.113 |
0.622 |
|
| 2014 |
Jackson AP, Otto TD, Darby A, Ramaprasad A, Xia D, Echaide IE, Farber M, Gahlot S, Gamble J, Gupta D, Gupta Y, Jackson L, Malandrin L, Malas TB, Moussa E, et al. The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction. Nucleic Acids Research. 42: 7113-31. PMID 24799432 DOI: 10.1093/Nar/Gku322 |
0.617 |
|
| 2014 |
Hunt M, Newbold C, Berriman M, Otto TD. A comprehensive evaluation of assembly scaffolding tools. Genome Biology. 15: R42. PMID 24581555 DOI: 10.1186/Gb-2014-15-3-R42 |
0.575 |
|
| 2014 |
Sinha A, Hughes KR, Modrzynska KK, Otto TD, Pfander C, Dickens NJ, Religa AA, Bushell E, Graham AL, Cameron R, Kafsack BF, Williams AE, Llinás M, Berriman M, Billker O, et al. A cascade of DNA-binding proteins for sexual commitment and development in Plasmodium. Nature. 507: 253-7. PMID 24572359 DOI: 10.1038/Nature12970 |
0.51 |
|
| 2013 |
Lemieux JE, Kyes SA, Otto TD, Feller AI, Eastman RT, Pinches RA, Berriman M, Su XZ, Newbold CI. Genome-wide profiling of chromosome interactions in Plasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation. Molecular Microbiology. 90: 519-37. PMID 23980881 DOI: 10.1111/Mmi.12381 |
0.515 |
|
| 2013 |
Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, ... ... Otto TD, et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience. 2: 10. PMID 23870653 DOI: 10.1186/2047-217X-2-10 |
0.409 |
|
| 2013 |
Hunt M, Kikuchi T, Sanders M, Newbold C, Berriman M, Otto TD. REAPR: a universal tool for genome assembly evaluation. Genome Biology. 14: R47. PMID 23710727 DOI: 10.1186/Gb-2013-14-5-R47 |
0.608 |
|
| 2013 |
Ning J, Otto TD, Pfander C, Schwach F, Brochet M, Bushell E, Goulding D, Sanders M, Lefebvre PA, Pei J, Grishin NV, Vanderlaan G, Billker O, Snell WJ. Comparative genomics in Chlamydomonas and Plasmodium identifies an ancient nuclear envelope protein family essential for sexual reproduction in protists, fungi, plants, and vertebrates. Genes & Development. 27: 1198-215. PMID 23699412 DOI: 10.1101/Gad.212746.112 |
0.308 |
|
| 2013 |
Oyola SO, Gu Y, Manske M, Otto TD, O'Brien J, Alcock D, Macinnis B, Berriman M, Newbold CI, Kwiatkowski DP, Swerdlow HP, Quail MA. Efficient depletion of host DNA contamination in malaria clinical sequencing. Journal of Clinical Microbiology. 51: 745-51. PMID 23224084 DOI: 10.1128/Jcm.02507-12 |
0.566 |
|
| 2013 |
Pasini EM, Braks JA, Fonager J, Klop O, Aime E, Spaccapelo R, Otto TD, Berriman M, Hiss JA, Thomas AW, Mann M, Janse CJ, Kocken CH, Franke-Fayard B. Proteomic and genetic analyses demonstrate that Plasmodium berghei blood stages export a large and diverse repertoire of proteins. Molecular & Cellular Proteomics : McP. 12: 426-48. PMID 23197789 DOI: 10.1074/Mcp.M112.021238 |
0.53 |
|
| 2013 |
Carver T, Harris SR, Otto TD, Berriman M, Parkhill J, McQuillan JA. BamView: visualizing and interpretation of next-generation sequencing read alignments. Briefings in Bioinformatics. 14: 203-12. PMID 22253280 DOI: 10.1093/Bib/Bbr073 |
0.574 |
|
| 2012 |
Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. Bmc Genomics. 13: 341. PMID 22827831 DOI: 10.1186/1471-2164-13-341 |
0.382 |
|
| 2012 |
Swain MT, Tsai IJ, Assefa SA, Newbold C, Berriman M, Otto TD. A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nature Protocols. 7: 1260-84. PMID 22678431 DOI: 10.1038/Nprot.2012.068 |
0.62 |
|
| 2012 |
Lawton J, Brugat T, Yan YX, Reid AJ, Böhme U, Otto TD, Pain A, Jackson A, Berriman M, Cunningham D, Preiser P, Langhorne J. Characterization and gene expression analysis of the cir multi-gene family of Plasmodium chabaudi chabaudi (AS). Bmc Genomics. 13: 125. PMID 22458863 DOI: 10.1186/1471-2164-13-125 |
0.571 |
|
| 2012 |
Jackson AP, Berry A, Aslett M, Allison HC, Burton P, Vavrova-Anderson J, Brown R, Browne H, Corton N, Hauser H, Gamble J, Gilderthorp R, Marcello L, McQuillan J, Otto TD, et al. Antigenic diversity is generated by distinct evolutionary mechanisms in African trypanosome species. Proceedings of the National Academy of Sciences of the United States of America. 109: 3416-21. PMID 22331916 DOI: 10.1073/Pnas.1117313109 |
0.566 |
|
| 2012 |
Protasio AV, Tsai IJ, Babbage A, Nichol S, Hunt M, Aslett MA, De Silva N, Velarde GS, Anderson TJ, Clark RC, Davidson C, Dillon GP, Holroyd NE, LoVerde PT, Lloyd C, ... ... Otto TD, et al. A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni. Plos Neglected Tropical Diseases. 6: e1455. PMID 22253936 DOI: 10.1371/Journal.Pntd.0001455 |
0.666 |
|
| 2012 |
Oyola SO, Otto TD, Gu Y, Maslen G, Manske M, Campino S, Turner DJ, Macinnis B, Kwiatkowski DP, Swerdlow HP, Quail MA. Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. Bmc Genomics. 13: 1. PMID 22214261 DOI: 10.1186/1471-2164-13-1 |
0.355 |
|
| 2011 |
Rogers MB, Hilley JD, Dickens NJ, Wilkes J, Bates PA, Depledge DP, Harris D, Her Y, Herzyk P, Imamura H, Otto TD, Sanders M, Seeger K, Dujardin JC, Berriman M, et al. Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania. Genome Research. 21: 2129-42. PMID 22038252 DOI: 10.1101/Gr.122945.111 |
0.516 |
|
| 2011 |
Pfander C, Anar B, Schwach F, Otto TD, Brochet M, Volkmann K, Quail MA, Pain A, Rosen B, Skarnes W, Rayner JC, Billker O. A scalable pipeline for highly effective genetic modification of a malaria parasite. Nature Methods. 8: 1078-82. PMID 22020067 DOI: 10.1038/Nmeth.1742 |
0.346 |
|
| 2011 |
Kikuchi T, Cotton JA, Dalzell JJ, Hasegawa K, Kanzaki N, McVeigh P, Takanashi T, Tsai IJ, Assefa SA, Cock PJ, Otto TD, Hunt M, Reid AJ, Sanchez-Flores A, Tsuchihara K, et al. Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus. Plos Pathogens. 7: e1002219. PMID 21909270 DOI: 10.1371/Journal.Ppat.1002219 |
0.612 |
|
| 2011 |
Otto TD, Dillon GP, Degrave WS, Berriman M. RATT: Rapid Annotation Transfer Tool. Nucleic Acids Research. 39: e57. PMID 21306991 DOI: 10.1093/Nar/Gkq1268 |
0.632 |
|
| 2010 |
Hunt P, Martinelli A, Modrzynska K, Borges S, Creasey A, Rodrigues L, Beraldi D, Loewe L, Fawcett R, Kumar S, Thomson M, Trivedi U, Otto TD, Pain A, Blaxter M, et al. Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites. Bmc Genomics. 11: 499. PMID 20846421 DOI: 10.1186/1471-2164-11-499 |
0.387 |
|
| 2010 |
Nygaard S, Braunstein A, Malsen G, Van Dongen S, Gardner PP, Krogh A, Otto TD, Pain A, Berriman M, McAuliffe J, Dermitzakis ET, Jeffares DC. Long- and short-term selective forces on malaria parasite genomes. Plos Genetics. 6: e1001099. PMID 20838588 DOI: 10.1371/Journal.Pgen.1001099 |
0.624 |
|
| 2010 |
Otto TD, Sanders M, Berriman M, Newbold C. Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. Bioinformatics (Oxford, England). 26: 1704-7. PMID 20562415 DOI: 10.1093/Bioinformatics/Btq269 |
0.579 |
|
| 2010 |
Tsai IJ, Otto TD, Berriman M. Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biology. 11: R41. PMID 20388197 DOI: 10.1186/Gb-2010-11-4-R41 |
0.591 |
|
| 2010 |
Sutherland CJ, Tanomsing N, Nolder D, Oguike M, Jennison C, Pukrittayakamee S, Dolecek C, Hien TT, do Rosário VE, Arez AP, Pinto J, Michon P, Escalante AA, Nosten F, Burke M, ... ... Otto TD, et al. Two nonrecombining sympatric forms of the human malaria parasite Plasmodium ovale occur globally. The Journal of Infectious Diseases. 201: 1544-50. PMID 20380562 DOI: 10.1086/652240 |
0.351 |
|
| 2010 |
Otto TD, Wilinski D, Assefa S, Keane TM, Sarry LR, Böhme U, Lemieux J, Barrell B, Pain A, Berriman M, Newbold C, Llinás M. New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq. Molecular Microbiology. 76: 12-24. PMID 20141604 DOI: 10.1111/J.1365-2958.2009.07026.X |
0.588 |
|
| 2010 |
Carver T, Böhme U, Otto TD, Parkhill J, Berriman M. BamView: viewing mapped read alignment data in the context of the reference sequence. Bioinformatics (Oxford, England). 26: 676-7. PMID 20071372 DOI: 10.1093/Bioinformatics/Btq010 |
0.587 |
|
| 2009 |
Assefa S, Keane TM, Otto TD, Newbold C, Berriman M. ABACAS: algorithm-based automatic contiguation of assembled sequences. Bioinformatics (Oxford, England). 25: 1968-9. PMID 19497936 DOI: 10.1093/Bioinformatics/Btp347 |
0.593 |
|
| 2008 |
Otto TD, Gomes LH, Alves-Ferreira M, de Miranda AB, Degrave WM. ReRep: computational detection of repetitive sequences in genome survey sequences (GSS). Bmc Bioinformatics. 9: 366. PMID 18782453 DOI: 10.1186/1471-2105-9-366 |
0.364 |
|
| Show low-probability matches. |