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CBIO Publications: 2009 - 2013

2013
  1. Duarte J, Serufuri J-M, Mulder N, Blackburn J. "Protein Function Microarrays: Design, Use and Bioinformatic Analysis in Cancer Biomarker Discovery and Quantitation", In: Bioinformatics of Human Proteomics Translational Bioinformatics Springer Science+Business Media Dordrecht, 3:39-74.
  2. Barton C, Iliopoulos CS, Mulder N, Watson B. "Identification of all exact and approximate inverted repeats in regular and weighted sequences". Communications in Computer and Information Science. Volume 384: 11-19.
  3. Mulder NJ, Mazandu GK, Rapanoel HA et al "Using Host-Pathogen functional interactions for filtering potential drug targets in Mycobacterium tuberculosis". Mycobacterial Diseases. 3: 126, doi: 10.4172/2161-1068.1000126.
  4. Chimusa ER, Zaitlen N, Daya M, Möller M, Mulder NJ, Price AL, Hoal EG. "Genome-wide association study of ancestry-specific TB risk in the South African Coloured population". Human Molecular Genetics, 23(3):796-809. doi: 10.1093/hmg/ddt462.
  5. Mazandu GK, Mulder NJ. DaGO-Fun: "Tool for Gene Ontology-based functional analysis using term information content measures". BMC Bioinformatics 14:284. DOI: 10.1186/10.1186/1471-2105-14-284. 
  6. Akinola RO, Mazandu GK, Mulder NJ. "A Systems Level Comparison of Mycobacterium tuberculosis, Mycobacterium leprae and Mycobacterium smegmatis based on Functional Interaction Network Analysis". Journal of Bacteriology and Parasitology. 4(4):173, doi: 10.4172/2155-9597.1000173.
  7. Magombedze G, Dowdy D, Mulder NJ. "Latent Tuberculosis: Models, Computational efforts and the Pathogen's regulatory mechanisms during dormancy". Frontiers Bioeng. Biotechnol., 1:4 doi: 10.3389/fbioe.2013.00004.
  8. Mazandu GK, Mulder NJ. "Information content-based Gene Ontology semantic similarity approaches: Toward a unified framework theory". BioMed Research International. vol. 2013, Article ID 292063, 11 pages, 2013. doi:10.1155/2013/292063. 
  9. Chimusa ER, Daya M, Möller M, Ramesar R, Henn BM, van Helden PD, Mulder NJ, Hoal EG. "Determining Ancestry Proportions in Complex Admixture Scenarios in South Africa using a novel Proxy Ancestry Selection Method". PLOS ONE, 8(9): e73971. doi:10.1371/journal.pone.0073971.
  10. Deffur A, Mulder N, Wilkinson R. "Co-infection with Mycobacterium tuberculosis and Human Immunodeficiency Virus: an overview and motivation for systems approaches". Pathogens and Disease, doi: 10.1111/2049-632X.12060. 
  11. Rapanoel HA, Mazandu GK, Mulder NJ. "Predicting and analyzing interactions between Mycobacterium tuberculosis and its human host". PloSOne, 8(7): e67472. doi:10.1371/journal.pone.0067472.
  12. Jimenez RC, Albar JP, Bhak J, Blatter M-C, Blicher T, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, van Driel M, Dunn MJ, Fernandes PL, van Gelder CWG, Hermjakob H, Ioannidis V, Judge DP, Kahlem P, Korpelainen E, Kraus HJ, Loveland J, Mayer C, McDowall J, Moran F, Mulder N, Nyronen T, Rother K, Salazar GA, Schneider MV, Schneider R, Via A, Villaveces JM, Yu P, Attwood TK, Corpas M. "iAnn: An Informatics Platform for Scientific Event Sharing", Bioinformatics, 29(15):1919-1921. 
  13. Via A, Blatter M-C, Blicher T, Brazas M, Brooksbank C, Budd A, Dreyer J, Fernandes P, van de Gelder C, Jacob J, Jimenez R, Judge DP, Loveland J, McDowall J, Moran F, Mulder N, Nyroren T, de Las Rivas J, Rother K, Vlahovicek K, Schneider MV and Attwood TK. "Best Practices in Bioinformatics Training for Life Scientists", Briefings in Bioinformatics, 14 (5): 528-537. doi: 10.1093/bib/bbt043.
  14. Riedel A, Mofolo B, Avota E, Schneider-Schaulies S, Meintjes A, Mulder N and Kneitz S. "Accumulation of splice variants and transcripts in response to PI3K inhibition in T cells". PLOS ONE, 2013;8(2):e50695. doi: 10.1371/journal.pone.0050695.
  15. Mulder NJ. "Protein Family Databases", In: eLS. John Wiley & Sons, Ltd: Chichester.DOI: 10.1002/9780470015902.a0003058.pub3. 
  16. Magombedze G, Mulder N. "Understanding TB latency using computational and dynamic modelling procedures". Infection, Genetics and Evolution. 13: 267–283 DOI: 10.1016/j.meegid.2012.09.017.
2012
  1. Mazandu GK, Mulder NJ., "Using the underlying biological organization of the Mycobacterium tuberculosis functional network for protein function prediction", Infection, Genetics and Evolution. 12(5):922-932.
  2. Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJA, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C and Yong S-Y. , "InterPro in 2011: new developments in the family and domain prediction database", Nucleic Acids Research 40(1):D306-312.
  3. Burge S, Kelly E, Lonsdale D, Mutowo-Muellenet P, McAnulla C, Mitchell A, Sangrador-Vegas A, Yong S-Y, Mulder N and Hunter S., "Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation", Database, Vol. 2012, doi:10.1093/database/bar068.
  4. Mazandu GK, Mulder NJ. , "A Topology-based Metric for Measuring Term Similarity in the Gene Ontology (GO)", Advances in Bioinformatics, Volume 2012 Article ID 975783
  5. Mazandu GK, Mulder NJ., "Function Prediction and Analysis of Mycobacterium tuberculosis Hypothetical Proteins", International Journal of Molecular Sciences. 13:7283-7302
  6. Pande, D.; Kraberger, S.; Lefeuvre, P.; Lett, J.M.; Shepherd, D.N.; Varsani, A.; Martin, D.P.; , "A novel maize-infecting mastrevirus from La Réunion Island", Archives of Virology
  7. Dayaram, A.; Opong, A.; Jäschke, A.; Hadfield, J.; Baschiera, M.; Dobson, R.C.J.; Offei, S.K.; Shepherd, D.N.; Martin, D.P.; Varsani, A.; , "Molecular characterisation of a novel cassava associated circular ssDNA virus", Virus Research
  8. Hadfield, J.; Thomas, J.E.; Schwinghamer, M.W.; Kraberger, S.; Stainton, D.; Dayaram, A.; Parry, J.N.; Pande, D.; Martin, D.P.; Varsani, A.; , "Molecular characterisation of dicot-infecting mastreviruses from Australia", Virus Research
  9. Thierry, M.; Lefeuvre, P.; Hoareau, M.; Péréfarres, F.; Delatte, H.; Reynaud, B.; Martin, DP; Lett, J.M.; , "Differential disease phenotype of begomoviruses associated with tobacco leaf curl disease in Comoros", Archives of Virology
  10. Piasecki, T.; Kurenbach, B.; Chrząstek, K.; Bednarek, K.; Kraberger, S.; Martin, D.P.; Varsani, A.; , "Molecular characterisation of an avihepadnavirus isolated from Psittacula krameri (ring-necked parrot)", Archives of Virology
  11. Singh, L.; Hallan, V.; Martin, DP; Ram, R.; Zaidi, AA; , "Genomic sequence analysis of four new chrysanthemum virus B isolates: evidence of RNA recombination", Archives of Virology
  12. Stainton, D.; Kraberger, S.; Walters, M.; Wiltshire, E.J.; Rosario, K.; Lolohea, S.; Katoa, I.; Tu'amelie, H.F.; Aholelei, W.; Taufa, L.; John E Thomas, David A Collings, Darren P Martin, Arvind Varsani, "Evidence of inter-component recombination, intra-component recombination and reassortment in Banana bunchy top virus", Journal of General Virology
  13. Albuquerque, L.C.; Varsani, A.; Fernandes, F.R.; Pinheiro, B.; Martin, D.P.; de Tarso Oliveira Ferreira, P.; Lemos, T.O.; Inoue-Nagata, A.K.; , "Further characterization of tomato-infecting begomoviruses in Brazil", Archives of Virology
2011
  1. Mazandu GK, Mulder NJ, "Scoring Protein Relationships in Functional Interaction Networks Predicted from Sequence Data", PLoS One, 2011, 6:4 e18607
  2. Salazar GA, Jimenez RC, Garcia A, Hermjakob H, Mulder N, Blake E, "DAS Writeback: A Collaborative Annotation System"BMC Bioinformatics 2011, 12:143
  3. Faure AJ, Seoighe C, Mulder N, "Investigating the effect of paralogs on microarray gene-set analysis"BMC Bioinformatics 2011, 12:29.
  4. Mazandu GK, Oppap K, Mulder N, "Contribution of Microarray Data to the Advancement of Knowledge on the Mycobacterium tuberculosis Interactome: use of the random Partial Least Squares approach", Infection, Genetics and Evolution 2011, 11: 181-189.
  5. Hadfield J, Martin DP, Stainton D, Kraberger S, Owor BE, Shepherd DN, Lakay F, Markham PG, Greber RS, Briddon RW, Varsani A, "Bromus catharticus striate mosaic virus: a new mastrevirus infecting Bromus catharticus from Australia"Arch Virol. 2011, 156(2):335-41.
  6. Martin DP, Briddon RW, Varsani A, "Recombination patterns in dicot-infecting mastreviruses mirror those found in monocot-infecting mastreviruses"Arch Virol. 2011
  7. Rosario K, Marinov M, Stainton D, Kraberger S, Wiltshire EJ, Collings DA, Walters M, Martin DP, Breitbart M, Varsani A, "Dragonfly cyclovirus, a novel single-stranded DNA virus discovered in dragonflies (Odonata: Anisoptera)"J Gen Virol 2011
  8. van der Sanden S, van Eek J, Martin DP, van der Avoort H, Vennema H, Koopmans M, "Detection of recombination breakpoints in the genomes of human enterovirus 71 strains isolated in the Netherlands in epidemic and non-epidemic years, 1963-2010"Infect Genet Evol. 2011
  9. Mumtaz H, Kumari SG, Mansoor S, Martin DP, Briddon RW, "Analysis of the sequence of a dicot-infecting mastrevirus (family Geminiviridae) originating from Syria"Virus Genes. 2011
  10. Owor Betty, Martin D P, Rybicki Edward, Thomson Jennifer, Bezuidenhout Marion, Lakay, Francisco, Shepherd Dionne Natalie, "A rep-based hairpin inhibits replication of diverse maize streak virus isolates in a transient assay"Journal of General Virology
  11. Martin D P, Lemey Philippe, Posada, David, "Analysing recombination in nucleotide sequences", Molecular Ecology Resources
  12. Darren P. Martin, Pierre Lefeuvre, Arvind Varsani, Murielle Hoareau, Jean-Yves Semegni, Betty Dijoux, Claire Vincent, Bernard Reynaud, Jean-Michel Lett, "Complex Recombination Patterns Arising during Geminivirus Coinfections Preserve and Demarcate Biologically Important Intra-Genome Interaction Networks", PLOS Pathogens
  13. Villaveces, Jose. Rafael, Jimenez. Garcia, Leyla. Salazar, Gustavo. Gel, Bernat.Mulder, Nicola Jane. Martin, Maria. Alexander, Garcia. Hermjakob, Henning, "Dasty3, a WEB framework for DAS"Bioinformatics
  14. Hiller, Luisa. Eutsey, Rory. Powell, Evan. Earl, Joshua. Janto, Benjamin. Martin, D P. Dawid, Suzanne. Ahmed, Azad. Longwell, Mark. Dahlgren, Margaret.Ezzo, Suzanne. Tettelin, Herve.Daugherty, Sean. Mitchell, Timothy. Hillaman, Todd. buchinsky, Farrel.Tomasz, Alexander. De Lencastre, Heminia. Sa-Leao, Raquel. Post, Christopher. Hu, Fen Zu. Ehrlich, Garth, "Differences in genotype and virulence among four multidrug-resistant strptococcus pneumoniae isolates belonging to the PMEN1 clone", PLoS One
  15. Lefeuvre, Pierre. Harkins, Gordon W. Lett, Jean-Michel. Briddon, Rob.Chase, Mark.Moury, Benoit. Martin, D P, "Evolutionary time-scale of the begomviruses: eviodence from intergrated sequences in the nicotiana genome"PLoS One
  16. Geistlinger, Ludwig. Csaba, Gergely. Kuffner, Robert.Mulder, Nicola Jane.Zimmer, Ralf, "From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems"Bioinformatics
  17. Monjane, Aderito Luis. Van der Walt, E. Varsani, Arvind. Rybicki, Edward.Martin, D P, "Recombination hotspots and host susceptibility modulate the adaptive value of recombination during maize streak virus evolution", BMC Evolutionary Biology
  18. Martin, D P.Biagini, Phillipe. Lefeuvre, Pierre.Golden , Michael. Roumagnac, Philippe. Varsani, Arvind, "Recombination in Eukaryotic single stranded DNA viruses"Viruses-Basel
  19. Chopera, Denis Rutendo.Mlotshwa, Mandla.Woodman, Zenda.Mlisana, Koleka. de Assis Rosa, Debra. Martin, D P. Abdool Karim, Quarraisha.Gray, Clive. Williamson, Carolyn.caprisa 002 study team, caprisa 002 study team, "Virological and Immunological Factors Associated with HIV-1 differential disease progression in HLA-B* 58:01- Positive individuals"Journal of Virology
  20. Corpas M, Doumbia S, Gascuel O, Mulder N., "Bamako 2009 conference on the bioinformatics of infectious diseases", Infect Genet Evol.
  21. Mazandu GK, Mulder NJ. , "Generation and analysis of large-scale data driven Mycobacterium tuberculosis functional networks for drug target identification"Advances in Bioinformatics
  22. Magombedze G, Mulder N. , "A mathematical representation of the development of Mycobacterium tuberculosis active, latent and dormant stages"Journal of Theoretical Biology. 292: 44-59
  23. Jimenez RC, Salazar GA, Gel B, Bevan P, Dopazo J, Mulder N, Corpas M. , "myKaryoView: A Light-Weight Client for Visualization of Genomic Data"PLoS ONE. 6(10):e26345.
  24. Rybicki, EP; Martin, DP; , "Virus-Derived ssDNA Vectors for the Expression of Foreign Proteins in Plants", Current Topics in Microbiology and Immunology
  25. Monjane, A.L.; Harkins, G.W.; Martin, D.P.; Lemey, P.; Lefeuvre, P.; Shepherd, D.N.; Oluwafemi, S.; Simuyandi, M.; Zinga, I.; Komba, E.K.; Didier P Lakoutene, Noella Mandakombo, Joseph Mboukoulida, Silla Semballa, Appolinaire Tagne, Fidèle Tiendrébéogo, Julia B Erdmann, Tania van Antwerpen, Betty E Owor, Bradley Flett, Moses Ramusi, Oliver P Windram, Rizwan Syed, Jean-Michel Lett, Rob W Briddon, Peter G Markham, Edward P Rybicki, Arvind Varsani, "Reconstructing the history of Maize streak virus strain A dispersal to reveal diversification hot spots and its origin in southern Africa"Journal of virology
  26. Martin, D.P.; Linderme, D.; Lefeuvre, P.; Shepherd, D.N.; Varsani, A.; , "Eragrostis minor streak virus: an Asian streak virus in Africa", Archives of Virology
  27. Semegni, JY; Wamalwa, M.; Gaujoux, R.; Harkins, GW; Gray, A.; Martin, DP; , "NASP: a parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments"Bioinformatics
2010
  1. Treurnicht FK, Seoighe C, Martin DP, Wood N, Abrahams MR, Rosa Dde A, Bredell H, Woodman Z, Hide W, Mlisana K, Karim SA, Gray CM, Williamson C, "Adaptive changes in HIV-1 subtype C proteins during early infection are driven by changes in HLA-associated immune pressure", Virology. 2010, 396(2):213-25.
  2. Kanapin AA, Mulder N, Kuznetsov VA, "Projection of gene-protein networks to the functional space of the proteome and its application to analysis of organism complexity", BMC Genomics 2010, 11:S4.
  3. Gaujoux R and Seoighe C, "A flexible R package for nonnegative matrix factorization", BMC Bioinformatics 2010, 11:367.
  4. De Wit E, Delport W, Rugamika CE, Meintjes A, Möller M, van Helden PD, Seoighe C, Hoal EG, "Genome-Wide Analysis of the Structure of the South African Coloured Population in the Western Cape", Hum Genetics 2010, 128(2):145-53.
  5. Mulder NJ, "Protein Domain Architectures", Methods in Molecular Biology 2010, 609:83-95.
  6. Lefeuvre P, Martin DP, Harkins G, Lemey P, Gray AJ, Meredith S, Lakay F, Monjane A, Lett JM, Varsani A, Heydarnejad J, "The spread of tomato yellow leaf curl virus from the Middle East to the world", PLoS Pathogens 2010, 6(10):e1001164.
  7. Simon-Loriere E, Martin DP, Weeks KM, Negroni M, "RNA structures facilitate recombination-mediated gene swapping in HIV-1", J Virol. 2010, 84:12675-12682
  8. Hiller NL, Ahmed A, Powell E, Martin DP, Eutsey R, Earl J, Janto B, Boissy RJ, Hogg J, Barbadora K, Sampath R, Lonergan S, Post JC, Hu FZ, Ehrlich GD, "Generation of genic diversity among Streptococcus pneumoniae strains via horizontal gene transfer during a chronic polyclonal pediatric infection", PLoS Pathogens 2010, 6(9). pii: e1001108.
  9. Prasanna HC, Sinha DP, Verma A, Singh M, Singh B, Rai M, Martin DP, "The population genomics of begomoviruses: global scale population structure and gene flow", Virol J. 2010, 7:220.
  10. Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P, "RDP3: a flexible and fast computer program for analyzing recombination", Bioinformatics 2010, 26:2462-2363
  11. Briddon RW, Martin DP, Owor BE, Donaldson L, Markham PG, Greber RS, Varsani A, "A novel species of mastrevirus (family Geminiviridae) isolated from Digitaria didactyla grass from Australia", Arch Virol. 2010, 155:1529-1534
  12. Briddon RW, Heydarnejad J, Khosrowfar F, Massumi H, Martin DP, Varsani A, "Turnip curly top virus, a highly divergent geminivirus infecting turnip in Iran", Virus Res. 2010, 152:169-175
2009
  1. Ngandu NK, Seoighe C, Scheffler K, "Evidence of HIV-1 adaptation to host HLA alleles following chimp-to-human transmission", Virol J. 2009, 6:164.
  2. Illing N, Klak C, Johnson C, Brito D, Negrao N, Baine F, van Kets V, Ramchurn KR, Seoighe C, Roden L, "Duplication of the Asymmetric Leaves1/Rough Sheath 2/Phantastica (ARP) gene precedes the explosive radiation of the Ruschioideae", Dev Genes Evol. 2009, 219(6):331-8.
  3. Wood N, Bhattacharya T, Keele BF, Giorgi E, Liu M, Gaschen B, Daniels M, Ferrari G, Haynes BF, McMichael A, Shaw GM, Hahn BH, Korber B, Seoighe C, "HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC", PLoS Pathog. 2009, 5(5):e1000414.
  4. Berman P, Collins M, Baumgarten I, Seoighe C, Jennings CL, Joffe Y, Lambert EV, Levitt NS, Faulenbach MV, Kahn SE, Goedecke JH, "Association between the 4 bp proinsulin gene insertion polymorphism (IVS-69) and body composition in black South African women", Obesity (Silver Spring) 2009, 17(6):1298-300
  5. Abrahams MR, Anderson JA, Giorgi EE, Seoighe C, Mlisana K, Ping LH, Athreya GS, Treurnicht FK, Keele BF, Wood N, Salazar-Gonzalez JF, Bhattacharya T, Chu H, Hoffman I, Galvin S, Mapanje C, Kazembe P, Thebus R, Fiscus S, Hide W, Cohen MS, Karim SA, Haynes BF, Shaw GM, Hahn BH, Korber BT, Swanstrom R, Williamson C; CAPRISA Acute Infection Study Team; Center for HIV-AIDS Vaccine Immunology Consortium, "Quantitating the multiplicity of infection with human immunodeficiency virus type 1 subtype C reveals a non-poisson distribution of transmitted variants", J Virol. 2009, 83(8):3556-67.
  6. Cross S, Kuttel MM, Stone JE, Gain JE, "Visualisation of cyclic and multi-branched molecules with VMD", J Mol Graph Model. 2009, 28(2):131-9.
  7. Zawaira A, Gallotta M, Beeton-Kempen N, Coulson L, Marais P, Kuttel M,Blackburn J, "Exhaustive computational search of ionic-charge clusters that mediate interactions between mammalian cytochrome P450 (CYP) and P450-oxidoreductase (POR) proteins", Comput Biol Chem. 2010, 34(1):42-52.
  8. Delport W, Scheffler K, Seoighe C, "Models of coding sequence evolution", Brief Bioinform. 2009, 10(1):97-109.
  9. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJA, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH and Yeats C, "InterPro: the integrative protein signature database", Nucleic Acids Res. 2009, 37(1):D211-215.
  10. Mulder N, Rabiu H, Jamieson G, Vuppu V, "Comparative analysis of microbial genomes to study unique and expanded gene families in Mycobacterium tuberculosis", Infect Genet Evol. 2009, 9(3):314-21