Publications

One of the core principles of SANBI is to publish high quality and relevant academic papers. On this page you will be able to find a collection of these.

2017
  • A practical guide to filtering and prioritizing genetic variants.
    Mahjoubeh Jalali, Junaid Gamieldien.
    January 2017 · BioTechniques 01/2017; 62(1)
    DOI:10.2144/000114492
  • Virome Assembly and Annotation: A Surprise in the Namib Desert.
    Uljana Hesse, Peter van Heusden, Bronwyn Michelle Kirby, Israel Olonade, Marla Tuffin.
    January 2017 Frontiers in Microbiology 8
    DOI: 10.3389/fmicb.2017.00013.
  • Metagenomics-based discovery and molecular characterization of novel geminiviruses from two Mediterranean-climate biodiversity hotspots.
    Galzi Serge, Bernardo Pauline, Fernandez Emmanuel, Julian Charlotte, Ferdinand Romain, Harkins Gordon William, Peterschmitt Michel, Martin Darren Patrick, Filloux Denis, Roumagnac Philippe.
    16th Meeting of Plant Virology. 15 – 19 January 2017. Aussois, France
  • The role of Kenya in the trans-African spread of maize streak virus strain A.
    Daniel Pande, Eugene Madzokere, Penelope Hartnady, Simona Kraberger, James Hadfield, Karyna Rosario, Anja Jäschke, Adérito L Monjane, Betty E Owor, Mathews M Dida, Dionne N Shepherd, Darren P Martin, Arvind Varsani, Gordon W Harkins.
    Feb 2017 · Virus Research 232:69-76
    DOI: 10.1016/j.virusres.2017.02.005
  • Accessing Biospecimens from the H3Africa Consortium.
    Christine M. Beiswanger, Alash’le Abimiku, Nadia Carstens, Alan Christoffels, Jantina de Vries, Audrey Duncanson, Morne du Plessis, Maria Giovanni, Katherine Littler, Nicola Mulder, Jennifer Troyer, Louise Wideroff and H3Africa Data and Biospecimen Sharing Organizing Committee.
    April 2017 · Biopreservation and Biobanking 04/2017; 15(2). · DOI:10.1089/bio.2017.0008
  • Baobab Laboratory Information Management System: Development of an Open-Source Laboratory Information Management System for Biobanking.
    Hocine Bendou, Lunga Sizani, Tim Reid, Carmen Swanepoel, Toluwaleke Ademuyiwa,Roxana Merino-Martinez, Heimo Meuller, Akin Abayomi and Alan Christoffels.
    Biopreservation and Biobanking Volume 15, Number 2, 2017
    DOI: 10.1089/bio.2017.0014
  • Selecting a Laboratory Information Management System for Biorepositories in Low- and Middle-Income Countries: The H3Africa Experience and Lessons Learned.
    Kyobe Samuel, Musinguzi Henry, Lwanga Newton, Kezimbira Dafala, Kigozi Edgar, Katabazi Fred Ashaba, Wayengera Misaki, Joloba Moses Lutaakome, Abayomi Emmanuel Akin, Swanepoel Carmen, Abimiku Alash’le, Croxton Talishiea, Ozumba Petronilla, Thankgod Anazodo, Christoffels Alan, van Zyl Lizelle, Mayne Elizabeth Sarah, Kader Mukthar, Swartz Garth, and H3Africa Biorepository PI Working Group.
    Biopreservation and Biobanking. April 2017, 15(2): 111-115. https://doi.org/10.1089/bio.2017.0006
  • Delineating Transcriptomic Profiles in PTSD: An RNAseq Investigation.
    Sian Hemmings, Laetitia Dicks, Mahjoubeh Jalali, Junaid Gamieldien, Soraya Seedat.
    May 2017 Biological Psychiatry 81 (10), S222-S223
    DOI:10.1016/j.biopsych.2017.02.1158
  • Structural and functional effects of nucleotide variation on the human TB drug metabolizing enzyme arylamine N-acetyltransferase 1.
    Ruben Cloete, Wisdom A. Akurugu, Cedric J. Werely, Paul D. van Helden, Alan Christoffels.
    Journal of Molecular Graphics and Modelling 75 (2017) 330–339
  • Exome sequencing identifies targets in the treatment-resistant ophthalmoplegic subphenotype of myasthenia gravis.
    Melissa Nel, Mahjoubeh Jalali Sefid Dashti, Junaid Gamieldien, Jeannine M. Heckmann.
    Neuromuscular Disorders 27 (2017) 816–825
  • The role of microRNAs in the therapeutic action of D-cycloserine in a post-traumatic stress disorder animal model: an exploratory study.
    Malan-Müller, Stefanie; Fairbairn, Lorren; Hart, Stephanie; Daniels, Willie M.U.; Jalali Sefid Dashti, Mahjoubeh; Kidd, Martin; Seedat, Soraya; Gamieldien, Junaid; Hemmings, Sîan M.J.
    Psychiatric Genetics 2017 Aug;27(4):139-151. doi: 10.1097/YPG.0000000000000176.

    Biopreservation and Biobanking Volume 15, Number 2, 2017
    DOI: 10.1089/bio.2017.0014

  • The Transcription Factor 7-Like 2–Peroxisome Proliferator-Activated Receptor Gamma Coactivator-1 Alpha Axis Connects Mitochondrial Biogenesis and Metabolic Shift with Stem Cell Commitment to Hepatic Differentiation.
    Ana’is Wanet, Marino Caruso, Jean-Baka Domelevo Entfellner, Mehdi Najar, Antoine Fattaccioli, Catherine Demazy, Jonathan Evraerts, Hoda El-Kehdy, Guillaume Pourcher, Etienne Sokal, Thierry Arnould, Nicki Tiffin, Mustapha Najimi, Patricia Renard.
    Stem Cells 2017
    AlphaMed Press 1066-5099/2017/$30.00/0
    http://dx.doi.org/10.1002/stem.2688
  • Exploring the potential of T7 bacteriophage protein Gp2 as a novel inhibitor of mycobacterial RNA polymerase.
    J du Plessis, R.Cloete, L.Burchell, P.Sarkar, R.M.Warren, A.Christoffels, S Wigneshweraraj, S.L.Sampson.
    Tuberculosis, Volume 106, September 2017 Pages 82 – 90.
  • The interaction of polymorphisms in extracellular matrix genes and underlying miRNA motifs that modulate susceptibility to anterior cruciate ligament rupture.
    Kyle Willard, Sasha Mannion, Colleen J. Saunders, Malcolm Collins, Alison V. September.
    Journal of Science and Medicine in Sport
    DOI: http://dx.doi.org/10.1016/j.jsams.2017.08.017
  • Designing a course model for distance-based online bioinformatics training in Africa: The H3ABioNet experience.
    Kim T. Gurwitz , Shaun Aron , Sumir Panji, Suresh Maslamoney, Pedro L. Fernandes, David P. Judge, Amel Ghouila, Jean-Baka Domelevo Entfellner, Fatma Z. Guerfali, Colleen Saunders, Ahmed Mansour Alzohairy, Samson P. Salifu, Rehab Ahmed, Ruben Cloete, Jonathan Kayondo, Deogratius Ssemwanga, Nicola Mulder , H3ABioNet Consortium’s Education Training and Working Group as members of the H3Africa Consortium.
    October 2017. PLoS Comput Biol 13(10): e1005715. https://doi.org/10.1371/journal.pcbi.1005715
  • Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale.
    Pauline Bernardo, Tristan Charles-Dominique, Mohamed Barakat, Philippe Ortet, Emmanuel Fernandez, Denis Filloux, Penelope Hartnady, Tony A Rebelo, Stephen R Cousins, François Mesleard, Damien Cohez, Nicole Yavercovski, Arvind Varsani, Gordon W Harkins, Michel Peterschmitt, Carolyn M Malmstrom, Darren P Martin and Philippe Roumagnac.
    October 2017. The ISME Journal (2017), 1–12
  • Whole-genome sequencing for an enhanced understanding of genetic variation among South Africans.
    Ananyo Choudhury, Michèle Ramsay, Scott Hazelhurst, Shaun Aron, Soraya Bardien, Gerrit Botha, Emile R. Chimusa, Alan Christoffels, Junaid Gamieldien, Mahjoubeh J. Sefid-Dashti, Fourie Joubert, Ayton Meintjes, Nicola Mulder, Raj Ramesar, Jasper Rees, Kathrine Scholtz, Dhriti Sengupta, Himla Soodyall, Philip Venter, Louise Warnich, Michael S. Pepper.
    December 2017. Nature Communications.
    DOI: 10.1038/s41467-017-00663-9
  • An integrated and comparative approach towards identification, characterization and functional annotation of candidate genes for drought tolerance in sorghum (Sorghum bicolor (L.) Moench).
    Abdi Woldesemayat, Adugna,  van Heusden, Peter, Ndimba, Bongani, Christoffels, Alan.
    December 2017. BMC Genetics. 18. DOI 10.1186/s12863-017-0584-5

2016
  • Exploration of Scaffolds from Natural Products with Antiplasmodial Activities, Currently Registered Antimalarial Drugs and Public Malarial Screen Data.
    Egieyeh S, Syce J, Christoffels A, Malan SF.
    Molecules. 2016 Jan 16;21(1):104.
    doi: 10.3390/molecules21010104
  • Semantic interrogation of a multi knowledge domain ontological model of tendinopathy identifies four strong candidate risk genes.
    Saunders CJ, Jalali Sefid Dashti M, Gamieldien J.
    Scientific Report 2016 Jan 25;6:19820.
    doi: 10.1038/srep19820
  • Prioritization of anti-malarial hits from nature: chemo-informatic profiling of natural products with in vitro antiplasmodial activities and currently registered anti-malarial drugs.
    Egieyeh SA, Syce J, Malan SF, Christoffels A.
    Malaria Journal. 2016 Jan 29;15:50.
    doi: 10.1186/s12936-016-1087-y.
  • The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt.
    Mulder NJ, Christoffels A, de Oliveira T, Gamieldien J, Hazelhurst S, Joubert F, Kumuthini J, Pillay CS, Snoep JL, Tastan Bishop Ö, Tiffin N.
    PLoS Computational Biology. 2016 Feb 4;12(2):e1004395.
    doi: 10.1371/journal.pcbi.1004395.
  • Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis.
    Cloete R, Oppon E, Murungi E, Schubert WD, Christoffels A.
    BMC Bioinformatics. 2016 Feb 8;17:75.
    doi: 10.1186/s12859-016-0898-8
  • Genome-Wide Comparative Analysis of Chemosensory Gene Families in Five Tsetse Fly Species.
    Macharia R, Mireji P, Murungi E, Murilla G, Christoffels A, Aksoy S, Masiga D.
    PLoS Negl Tropical Diseases. 2016 Feb 17;10(2):e0004421.
    doi: 10.1371/journal.pntd.0004421.
  • NetCapDB: measuring bioinformatics capacity development in Africa.
    Bendou H, Entfellner JB, van Heusden P, Gamieldien J, Tiffin N; H3ABioNet Consortium, as members of the H3Africa Consortium.
    BMC Research Notes. 2016 Mar 5;9:144.
    doi: 10.1186/s13104-016-1950-5
  • Molecular characterization and prevalence of two capulaviruses: Alfalfa leaf curl virus from France and Euphorbia caput-medusae latent virus from South Africa.
    Bernardo P, Muhire B, François S, Deshoux M, Hartnady P, Farkas K, Kraberger S, Filloux D, Fernandez E, Galzi S, Ferdinand R, Granier M, Marais A, Monge Blasco P, Candresse T, Escriu F, Varsani A, Harkins GW, Martin DP, Roumagnac P.
    Virology. 2016 Jun;493:142-53.
    doi: 10.1016/j.virol.2016.03.016.
  • Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding.
    Vij S, Kuhl H, Kuznetsova IS, Komissarov A, Yurchenko AA, Van Heusden P, Singh S, Thevasagayam NM, Prakki SR, Purushothaman K, Saju JM, Jiang J, Mbandi SK, Jonas M, Hin Yan Tong A, Mwangi S, Lau D, Ngoh SY, Liew WC, Shen X, Hon LS, Drake JP, Boitano M, Hall R, Chin CS, Lachumanan R, Korlach J, Trifonov V, Kabilov M, Tupikin A, Green D, Moxon S, Garvin T, Sedlazeck FJ, Vurture GW, Gopalapillai G, Kumar Katneni V, Noble TH, Scaria V, Sivasubbu S, Jerry DR, O’Brien SJ, Schatz MC, Dalmay T, Turner SW, Lok S, Christoffels A, Orbán L.
    PLoS Genetics. 2016 Apr 15;12(4):e1005954.
  • A new tool for prioritization of sequence variants from whole exome sequencing data.
    Glanzmann B, Herbst H, Kinnear CJ, Möller M, Gamieldien J, Bardien S.
    Source Code Biol Med. 2016 Jul 1;11:10.
    doi: 10.1186/s13029-016-0056-8.
  • Identification of phenotype-relevant differentially expressed genes in breast cancer demonstrates enhanced quantile discretization protocol’s utility in multi-platform microarray data integration.
    Mapiye DS, Christoffels AG, Gamieldien J.
    J Bioinform Computational Biology. 2016 Jul 13:1650022.
    [Epub ahead of print]
  • Genome-Wide DNA Methylation in Mixed Ancestry Individuals with Diabetes and Prediabetes from South Africa.
    Matsha TE, Pheiffer C, Humphries SE, Gamieldien J, Erasmus RT, Kengne AP.
    International Journal Endocrinology. 2016;2016:3172093.
    doi: 10.1155/2016/3172093.
    Epub 2016 Jul 31.
  • Mycobacterium tuberculosis strains exhibit differential and strain-specific molecular signatures in pulmonary epithelial cells.
    Mvubu NE, Pillay B, Gamieldien J, Bishai W, Pillay M.
    Dev Comp Immunol. 2016 Dec;65:321-9.
    doi: 10.1016/j.dci.2016.07.022.
    [Epub ahead of print]
  • Computational characterization of Iron metabolism in the Tsetse disease vector, Glossina morsitans: IRE stem-loops.
    Dashti ZJ, Gamieldien J, Christoffels A.
    BMC Genomics. 2016 Aug 8;17:561.
    doi: 10.1186/s12864-016-2932-7
  • Structure of an N276-Dependent HIV-1 Neutralizing Antibody Targeting a Rare V5 Glycan Hole Adjacent to the CD4 Binding Site.
    Wibmer CK, Gorman J, Anthony CS, Mkhize NN, Druz A, York T, Schmidt SD, Labuschagne P, Louder MK, Bailer RT, Abdool Karim SS, Mascola JR, Williamson C, Moore PL, Kwong PD, Morris L.
    Journal of Virology
    2016 vol: 90 (22) pp: 10220-10235
    doi:10.1128/JVI.01357-16.
  • Divergent evolutionary and epidemiological dynamics of cassava mosaic geminiviruses in Madagascar.
    De Bruyn A, Harimalala M, Zinga I, Mabvakure BM, Hoareau M, Ravigné V, Walters M, Reynaud B, Varsani A, Harkins GW, Martin DP, Lett JM, Lefeuvre P.
    BMC Evol Biol. 2016 Sep 6;16:182.
    doi: 10.1186/s12862-016-0749-2.
  • Ongoing geographical spread of Tomato yellow leaf curl virus.
    Mabvakure B, Martin DP, Kraberger S, Cloete L, van Brunschot S, Geering AD, Thomas JE, Bananej K, Lett JM, Lefeuvre P, Varsani A, Harkins GW.
    Virology. 2016 Nov;498:257-64.
    doi: 10.1016/j.virol.2016.08.033.
    Epub 2016 Sep 15.
  • SNiPhunter. A SNP based search engine.
    Werner Veldsman and Alan Christoffels.
    Data, 1, 17 doi:10.3390/data1030017
  • Identification and characterization of microRNAs expressed in the African malaria vector Anopheles funestus life stages using high throughput sequencing.
    Mushal Allam, Belinda L. Spillings, Hiba Abdalla, Darlington Mapiye, Lizette L. Koekemoer and Alan Christoffels
    Malaria Journal 2016 15:542
    DOI: 10.1186/s12936-016-1591-0
    [Epub ahead of print]
  • Chinks in the armor of the HIV-1 Envelope glycan shield: Implications for immune escape from anti-glycan broadly neutralizing antibodies
    Thandeka Moyo, Roux-Cil Ferreira, Reyaaz Davids, Zarinah Sonday, Penny L. Moore, Simon A. Travers, Natasha T. Wood, Jeffrey R. Dorfman
    Virology Journal
    doi: 10.1016/j.virol.2016.10.026.
    Epub 2016 Nov 13.

2015
  • Daisy Stainton, Darren P. Martin, Brejnev M. Muhire, Samiuela Lolohea, Mana’ia Halafihi, Pascale Lepoint, Guy Blomme, Kathleen S.Crew, Murray Sharman, Simona Kraberger, Anisha Dayaram, Matthew Walters, David A. Collings, Batsirai Mabvakure, Philippe Lemey, Gordon W. Harkins, John E. Thomas, Arvind Varsani
    The global distribution of Banana bunchy top virus reveals little evidence for frequent recent, human-mediated long distance dispersal events
    Virus Evolution, 2015, Vol. 1, No. 1
    DOI: http://dx.doi.org/10.1093/ve/vev009
    01 January
  • Kotze MJ, Lückhoff HK, Peeters AV, Baatjes K, Schoemann M, van der Merwe L, Grant KA, Fisher LR,  van der Merwe N, Pretorius J, van Velden DP, Ettienne J Myburgh E J, Pienaar FM, van Rensburg SJ, Yako YY, September AV,  Moremi KE, Cronje FJ, Tiffin N, Bouwens CSH, Bezuidenhout J, Apffelstaedt JP, Hough FS, Erasmus RT, Schneider JW.
    Genomic medicine and risk prediction across the disease spectrum.
    Critical Reviews in Clinical Laboratory Sciences, 2015 Jan 19:1-18.
    19 January
  • Budd A, Dinkel H, Corpas M, Fuller JC, Rubinat L, Devos DP, Khoueiry PH, Forstner KU, Georgatos F, Rowland F, Sharan M, Binder JX, Grace T, Traphagen K, Gristwood A, Wood NT.
    Ten simple rules for organizing an unconference.
    PLoS Computational Biology 2015; 11(1):e1003905.
    29 January
  • Stanley Kimbung Mbandi, Uljana Hesse, Peter van Heusden and Alan Christoffels.
    Inferring bona fide transfrags in RNA-Seq derived-transcriptome assemblies of non-model organisms.
    BMC Bioinformatics 2015, 16:58
    doi:10.1186/s12859-015-0492-5
    21 February
  • Fadhal E, Gamieldien J, Mwambene EC.
    Self-similarity of human protein interaction networks: a novel strategy of distinguishing proteins.
    Scientific Reports 2015; 5: 7628.
    27 February
  • Michael Berry, Junaid Gamieldien,  and Burtram C. Fielding.
    Identification of New Respiratory Viruses in the New Millennium.
    Viruses 2015, 7, 996-1019; doi:10.3390/v7030996
    6 March
  • Celia van der Merwe, Zahra Jalali Sefid Dashti, Alan Christoffels, Ben Loos, Soraya Bardien (2015).
    Evidence for a common biological pathway linking three Parkinson’s Disease causing genes: Parkin, PINK1 and DJ-1.
    European Journal of Neurosciences 41(9): DOI: 10.1111/ejn.12872
    11 March
  • Scheepers C, Shrestha RK, Lambson BE, Jackson KJ, Wright IA, Naicker D, Goosen M, Berrie L, Ismail A, Garrett N, Abdool Karim Q, Abdool Karim SS, Moore PL, Travers SA, Morris L.
    Ability To Develop Broadly Neutralizing HIV-1 Antibodies Is Not Restricted by the Germline Ig Gene Repertoire.
    Journal of Immunology 2015. pii: 1500118.
    30 March
  • Michael Berry, Burtram Fielding and Junaid Gamieldien.
    Human coronavirus OC43 3CL protease and the potential of ML188 as a broad-spectrum lead compound: Homology modelling and molecular dynamic studies.
    BMC Structural Biology (2015) 15:8 DOI 10.1186/s12900-015-0035-3
    28 April
  • Charlotte Osafo, Yemi Raheem Raji, David Burke, Bamidele O Tayo, Nicki Tiffin, Marva M Moxey-Mims, Rebekah S Rasooly, Paul L Kimmel, Akinlolu Ojo, Dwomoa Adu, Rulan S Parekh.
    Human Heredity and Health (H3) in Africa Kidney Disease Research Network: A Focus on Methods in Sub-Saharan Africa
    Clinical Journal of the American Society of Nephrology, CJN. 11951214
    02 July
  • Azeez Butali, Peter Anthony Mossey, Nikki Tiffin, Wasiu Lanre Adeyemo, Mekonen Abebe Eshete, Chrispinanus Mumena, Rosemary Audu, Chika Onwuamah, Pius Agbenorku, Mobolanle Olugbenga Ogunlewe, Adetokunbo Raphael Adebola, Hecto Oladapo Olasoji, Babatunde Aregbesola, Ramat Oyebunmi Braimah, Abimibola Victoria Oladugba, Ifeanyichukwu Igwilo Onah, Ezekiel Adebiyi, Peter Babatunde Olaitan, Lukman Olajide Abdur-Rahman, Adebowale Adeyemo.
    Multidisciplinary approach to genomics research in Africa: the AfriCRAN model. 
    The Pan African Medical Journal. 2015;21:229
  • Xiaowei Jiang, Felix Feyertag, Conor Meehan, Grace McCormack, Simon A Travers, Charles Craig, Mike Westby, Marilyn Lewis, David L Robertson
    Characterising the diverse mutational pathways associated with R5-tropic maraviroc resistance: HIV-1 that uses the drug-bound CCR5 coreceptor.
    J Virol 89:11457–11472.
    doi:10.1128/JVI.01384-15
    02 September
  • Sarah Mwangi, Geoffrey Attardo, Yutaka Suzuki, Serap Aksoy and Alan Christoffels
    TSS seq based core promoter architecture in blood feeding Tsetse fly (Glossina morsitans morsitans) vector of Trypanosomiasis.
    BMC Genomics (2015) 16:722
    DOI 10.1186/s12864-015-1921-6
    22 September
  • B Hodkinson, D Mapiye, D Jayne , A Kalla, N Tiffin and I Okpechi
    The African Lupus Genetics Network (ALUGEN) registry: standardized, prospective follow-up studies in African patients with systemic lupus erythematosus.
    Lupus (2015) 0, 1–6
    24 September
  • Malan-Müller S, Fairbairn L, Daniels WM, Dashti MJ, Oakeley EJ, Altorfer M, Kidd M, Seedat S, Gamieldien J, Hemmings SM.
    Molecular mechanisms of D-cycloserine in facilitating fear extinction: insights from RNAseq.
    Metabolic Brain Disease Sep 2015 10.1007/s11011-015-9727-4
    23 September
  • Nicola J Mulder, · Ezekiel Adebiyi, · Raouf Alami, · Alia Benkahla, · James Brandful, · Seydou Doumbia, · Dean Everett, · Faisal M Fadlelmola, · Fatima Gaboun, · Simani Gaseitsiwe ,· Odile Ouwe Missi Oukem-Boyer ,· Ellis Owusu-Dabo, · Sumir Panji ,· Hugh Patterton, · Fouzia Radouani, · Khalid Sadki ,· Fouad Seghrouchni, · Özlem Tastan Bishop, · Nicki Tiffin, · Nzovu Ulenga.
    H3ABioNet, a sustainable Pan-African Bioinformatics Network for Human Heredity and Health in Africa.
    Genome Research 12/2015; DOI:10.1101/gr.196295.115
    04 December
  • Lindisa Mbuli, Darlington Mapiye, Ikechi Okpechi.
    Lupus nephritis is associated with poor pregnancy outcomes in pregnant SLE patients in Cape Town: a retrospective analysis.
    Pan African Medical Journal 01/2015; 22.
    DOI: 10.11604/pamj.2015.22.365.7897
    15 December
  • Nontobeko Eunice Mvubu, Bala Pillay, Junaid Gamieldien, William Bishai, Manormoney Pillay
    Canonical Pathways, Networks and Transcriptional Factor Regulation by Clinical Strains of M. tuberculosis in Pulmonary Alveolar Epithelial Cells.
    Tuberculosis 12/2015; DOI: 10.1016/j.tube.2015.12.002
    December 2015
  • Michael Berry, Burtram Clinton Fielding, Junaid Gamieldien
    Potential broad spectrum inhibitors of the coronavirus 3CLpro: A virtual screening and structure based drug design study.
    Viruses 12/2015; 7(12):6642-6660.. DOI: 10.3390/v7122963
    December 2015
  • N Tiffin, J Gamieldien.
    A Prioritization Analysis of Disease Association by Data-mining of Functional Annotation of Human Genes.
    Book chapter in Sakharkar, K.R., Sakharkar, M.K., and Chandra, R. (2015).
    Post-Genomic Approaches in Drug and Vaccine Development.
    River Publishers
    ISBN: 9788793102842
    http://www.riverpublishers.com/view_details.php?book_id=291
  • Michael Berry, Burtram Fielding, Junaid Gamieldien
    Practical Considerations in Virtual Screening and Molecular Docking
    Book chapter in: Emerging Trends in Computational Biology, Bioinformatic and Systems Biology (2015)
    Edition: 1st Edition,
    Chapter: 27,
    Publisher: Elsevier (MK imprints),
    Editors: Q.N. Tran, H.R. Arabnia
    DOI: 10.1016/B978-0-12-802508-6.00027-2 In book

2014
  • Emad Fadhal, Junaid Gamieldien and Eric C Mwambene
    Protein interaction networks as metric spaces: a novel perspective on distribution of hubs.
    BMC Systems Biology 01/2014 8(1):6.
    doi:10.1186/1752-0509-8-6
    http://www.biomedcentral.com/1752-0509/8/6
  • Ram Krishna Shrestha, Baruch Lubinsky, Vijay B Bansode, Mónica BJ Moinz, Grace P McCormack and Simon A Travers.
    QTrim: a novel tool for the quality trimming of sequence reads generated using the Roche/454 sequencing platform.
    BMC Bioinformatics 2014, 15:33
    http://www.biomedcentral.com/1471-2105/15/33
    doi:10.1186/1471-2105-15-33
  • Gordon W. Harkins, Darren P. Martin, Alan Christoffels, Arvind Varsani.
    Towards inferring the global movement of beak and feather disease virus.
    Virology 450-451 (2014) 24–33
    http://dx.doi.org/10.1016/j.virol.2013.11.033
  • Stanley Kimbung Mbandi, Uljana Hesse, D. Jasper G. Rees and Alan Christoffels.
    A glance at quality score: implication for denovo transcriptomes reconstruction of Illumina reads.
    Frontiers in Genetics. 2014 Feb 12;5:17
    doi: 10.3389/fgene.2014.00017
  • Muhire B.M, Golden M, Murrel B, Lefeuvre P, Lett J.M, Gray A, Poon A, Ngandu N.K, Semengi Y, Tanov E, Monjane A.L, Harkins G.W, Varsani A, Shepherd D. N, Martin DP. (2014).
    Evidence of Pervasive Biologically-Functional Secondary-Structures Within the Genomes of Single-Stranded DNA Viruses.
    Journal of Virology: 2014:88 (4): 1972-1989 doi:10.1128/JVI.0303113.
  • Britt I Drogemoller, Galen E B Wright & Louise Warnich
    Considerations for rare variants in drug metabolism genes and the clinical implications.
    Expert Opinion Drug Metabolism Toxicology (2014) Early Online:1-12
    10.1517/17425255.2014.903239
    ISSN 1742-5255, e-ISSN 1744-7607 1
  • Nicki Tiffin
    Unique considerations for advancing genomic medicine in African populations.
    Personalized Medicine (2014) 11(2), 187–196
    10.2217/PME.13.105 © 2014 Future Medicine Ltd
  • Edwin Murungi, Lael D. Barlow, Divya Venkatesh, Vincent O. Adung’a, Joel B. Dacks, Mark C. Field, Alan Christoffels.
    A Comparative analysis of trypanosomatid SNARE proteins.
    Parasitology International 63(2014) 341 – 348
  • George Fredrick Obiero, Steven R.G Njanjom, Paul O. Mireji, Alan Christoffels, Hugh Robertson and Daniel K. Masiga.
    Odorant and gustatory receptors in the tsetse fly Glossina morsitans morsitans.
    PLoS Negl Trop Dis. 8(4):e2663.
    doi: 10.1371/journal.pntd.0002663
  • Serap Aksoy, Geoffrey Attardo, Matt Berriman, Alan Christoffels, Mike Lehane, Dan Masiga and Yeya Toure.
    Human African Trypanosomiasis Research Gets a Boost: Unraveling the Tsetse Genome.
    PLoS Negl Trop Dis 8(4):e2624.
    doi:10.1371/journal.pntd.0002624
  • International Glossina Genome Initiative (including Alan Christoffels and Gordon Harkins).
    Genome Sequence of the Tsetse Fly (Glossina morsitans): Vector of African Trypanosomiasis.
    Science Vol. 344 no. 6182 pp. 380-386
    DOI:10.1126/science.1249656
  • Monjane AL, Martin DP, Lakay F, Muhire BM, Pande D, Varsani A, Harkins G, Shepherd DN, Rybicki EP.
    Extensive recombination-induced disruption of genetic interactions is highly deleterious but can be partially reversed by small numbers of secondary recombination events.
    J Virol. 2014 Jul;88(14):7843-51.
    doi: 10.1128/JVI.00709-14.
  • Imogen A. Wright and Simon A. Travers
    RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA.
    Nucleic Acids Research, 2014 1 doi: 10.1093/nar/gku473
  • Ananyo Choudhury, Scott Hazelhurst, Ayton Meintjes, Ovokeraye Achinike-Oduaran, Shaun Aron, Junaid Gamieldien, Mahjoubeh Jalali Sefid Dashti, Nicola Mulder, Nicki Tiffin, Michèle Ramsay.
    Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance.
    BMC Genomics 2014, 15:437
    doi:10.1186/1471-2164-15-437
  • Emad Fadhal, Eric C Mwambene, Junaid Gamieldien
    Modeling human protein interaction networks as metric spaces has potential in disease research and drug target discovery.
    BMC Systems Biology 2014, 8:68
    doi:10.1186/1752-0509-8-68
  • The H3Africa Consortium (including Alan Christoffels, Junaid Gamieldien and Nicki Tiffin).
    Enabling the genomic revolution in Africa.
    Science Vol. 344 no. 6190 pp. 1346-1348
    DOI: 10.1126/science.1251546
  • Daniel Masiga, George Obiero, Rosaline Macharia, Paul Mireji and Alan Christoffels.
    Chemosensory receptors in tsetse flies provide link between chemical and behavioural ecology.
    Trends in Parasitology, Volume 30, Issue 9, Pages 426–428
    DOI: 10.1016/j.pt.2014.06.007
  • Ramon A. Tamayo Isla, Darlington Mapiye, Charles R. Swanepoel, Nadiya Rozumyk, Jerome E. Hubahib, and Ikechi G. Okpechi.
    Continuous ambulatory Peritoneal Dialysis in Limpopo South Africa: Predictors of patient and technique survival.
    Peritoneal Dialysis International July-August 2014 34:518-525
    doi: 10.3747/pdi.2013.00334
  • Barbara Picone and Alan Christoffels.
    Molecular Evolution of Key Receptor Genes in Primates and Non-Human Primates.
    International Journal of Genetics and Genomics 2014; 2(4): 57-61
    doi: 10.11648/j.ijgg.20140204.12
  • Christoffels A, Masiga D, Berriman M, Lehane M, Toure´ Y, et al. (2014)
    International Glossina Genome Initiative 2004 – 2014: A Driver for Post-Genomic Era Research on the African Continent.
    PLoS Neglected Tropical Diseases 8(8): e3024.
    doi:10.1371/journal.pntd.0003024
  • Barbara Picone, Uljana Hesse, Sumir Panji, Peter van Heusden, Mario Jonas and Alan Christoffels.
    Taste and Odorant Receptors of the Coelacanth – A Gene Repertoire in Transition.
    Journal of Experimental Zoology (Part B: Molecular and Developmental Evolution) 322(6): 403-414
    doi: 10.1002/jez.b.22531
  • Leendert J Cloete, Emil P Tanov, Brejnev M Muhire, Darren P Martin and Gordon W Harkins.
    The influence of secondary structure, selection and recombination on rubella virus nucleotide substitution rate estimates.
    Virology Journal 2014, 11:166  doi:10.1186/1743-422X-11-166.
  • Ishla Seager, Simon A. Travers, Michael D. Leeson, Amelia C. Crampin, Neil French, Judith R. Glynn and Grace P. McCormack.
    Coreceptor Usage, Diversity, and Divergence in Drug-Naive and Drug-Exposed Individuals from Malawi, Infected with HIV-1 Subtype C for More Than 20 Years.
    AIDS Research and Human Retroviruses, Volume 30, Number 10, 2014
  • Wright G, Adeyemo AA, Tiffin N. Informed consent and ethical re-use of African genomic data. Human Genomics. 2014 Oct 22;8(1):18.
  • Ayesha B.M. Kharsany, Thulasizwe John Buthelezi, Janet A. Frohlich, Nonhlanhla Yende-Zuma, Natasha Samsunder, Gethwana Mahlase, Carolyn Williamson, Simon A. Travers, Jinny C. Marais, Rachael Dellar, Salim S. Abdool Karim and Quarraisha Abdool Karim.
    HIV Infection in High School Students in Rural South Africa: Role of Transmissions Among Students.
    AIDS Research and Human Retroviruses, Volume 30, Number 10, 2014.
  • Kraberger S, Kumari SG, Hamed AA, Gronenborn B, Thomas JE, Sharman M, Harkins GW, Muhire BM, Martin DP, Varsani A.
    Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: High rates of intra-species recombination – a driving force in the emergence of new strains.
    Infection, Genetics and Evolution/:(29) 2013-2015, 2015
    doi: 10.1016/j.meegid.2014.11.024.
  • Bosch J, Noubiap JJ, Dandara C, Makubalo N, Wright G, Entfellner JB, Tiffin N, Wonkam A.Sequencing of GJB2 in Cameroonians and Black South Africans and comparison to 1000 Genomes Project Data Support Need to Revise Strategy for Discovery of Nonsyndromic Deafness Genes in Africans. OMICS A Journal of Integrative Biology Volume 18, Number 11, 2014:705-10. doi: 10.1089/omi.2014.0063.
  • Edwin K. Murungi, Henry M. Kariithi, Vincent Adunga, Meshack Obonyo and Alan Christoffels. Evolution and Structural Analyses of Glossina morsitans (Diptera; Glossinidae) Tetraspanins. Insects 2014, 5, 885-908
    doi:10.3390/insects5040885

2013
  • Nicki Tiffin, Adebowale Adeyemo and Ikechi Okpechi.
    A diverse array of genetic factors contribute to the pathogenesis of Systemic Lupus Erythematosus.
    Orphanet Journal of Rare Diseases 2013, 8:2
    http://www.ojrd.com/content/8/1/2
  • Laurel Julian, Tomasz Piasecki, Klaudia Chrzastek, Matthew Walters, Brejnev Muhire, Gordon W. Harkins, Darren P. Martin and Arvind Varsani.
    Extensive recombination detected among beak and feather disease virus isolates from breeding facilities in Poland.
    Journal of General Virology (2013), 94, 1086–1095
    DOI 10.1099/vir.0.050179-0
  • Vijay Bansode, Grace P McCormack, Amelia C Crampin, Bagrey Ngwira, Ram K Shrestha, Neil French, Judith R Glynn and Simon A Travers.
    Characterizing the emergence and persistence of drug resistant mutations in HIV-1 subtype C infections using 454 ultra deep pyrosequencing.
    BMC Infectious Diseases 2013, 13 :52
    http://www.biomedcentral.com/1471-2334/13/52
  • Tomasz Piasecki, Gordon W. Harkins, Klaudia Chrząstek, Laurel Julian, Darren P. Martin, Arvind Varsani.
    Avihepadnavirus diversity in parrots is comparable to that found amongst all other avian species.
    Virology (Volume 438, Issue 2, Pages 98–105)
    http://dx.doi.org/10.1016/j.virol.2013.01.009
  • Chris T. Amemiya, Jessica Alföldi, Alison P. Lee, Shaohua Fan,  Hervé Philippe,  Iain MacCallum,  Ingo Braasch, Tereza Manousaki,  Igor Schneider,  Nicolas Rohner,  Chris Organ,  Domitille Chalopin,  Jeramiah J. Smith,  Mark Robinson,  Rosemary A. Dorrington,  Marco Gerdol, Bronwen Aken, Maria Assunta Biscotti, Marco Barucca, Denis Baurain, Aaron M. Berlin, Gregory L. Blatch,  Francesco Buonocore, Thorsten Burmester, Michael S. Campbell, Adriana Canapa, John P. Cannon,   Alan Christoffels, De Moro G, Edkins AL, Fan L, Fausto AM, Feiner N, Forconi M, Junaid Gamieldien, et al.
    The African coelacanth genome provides insights into tetrapod evolution.
    Nature 496, 311–316
  • Gordon W. Harkins, Maria E. D’Amato and Mark J. Gibbons.
    Self-maintaining or continuously refreshed? The genetic structure of Euphausia lucens populations in the Benguela upwelling ecosystem.
    Journal of Plankton Research (2013)
    doi: 10.1093/plankt/fbt046
    http://plankt.oxfordjournals.org/content/early/2013/05/24/plankt.fbt046.abstract
  • Galen EB Wright, Pieter GJ Koornhof, Adebowale A Adeyemo and Nicki Tiffin.
    Ethical and legal implications of whole genome and whole exome sequencing in African populations.
    BMC Medical Ethics 2013, 14:21
    doi:10.1186/1472-6939-14-21
    http://www.biomedcentral.com/1472-6939/14/21
  • Simona Kraberger, Gordon W. Harkins, Safaa G.Kumari, John E.Thomas, Mark W. Schwinghamer, Murray Sharman, David A. Collings, Rob W. Briddon, Darren P. Martin, Arvind Varsani.
    Evidence that dicot-infecting mastreviruses are particularly prone to inter-species recombination and have likely been circulating in Australia for longer than in Africa and the Middle East.
    Virology 444 (2013) 282 – 291
    http://dx.doi.org/10.1016/j.virol.2013.06.024
  • Gert U. Van Zyl, Tommy F. Liu, Mathilda Claassen, Susan Engelbrecht, Tulio de Oliveira, Wolfgang Preiser, Natasha T. Wood, Simon Travers, Robert W. Shafer.
    Trends in Genotypic HIV-1 Antiretroviral Resistance between 2006 and 2012 in South African Patients Receiving First- and Second-Line Antiretroviral Treatment Regimens.
    PLoS ONE 8(6): e67188
    doi:10.1371/journal.pone.0067188
  • Ikechi Gareth Okpechi, Innocent Ijezie Chukwuonye, Nicki Tiffin, Okechukwu Ojoemelam Madukwe, Ugochukwu Uchenna Onyeonoro, Theophilus Ifeanyichukwu Umeizudike, Okechukwu, Samuel Ogah.
    Blood Pressure Gradients and Cardiovascular Risk Factors in Urban and Rural Populations in Abia State South Eastern Nigeria Using the WHO STEPwise Approach.
    PLoS ONE 8(9): e73403.
    doi:10.1371/journal.pone.0073403
  • Rabhi I, Rabhi S, Ben-Othman R, Aniba MR; Sysco Consortium (includes N Tiffin) et al.
    Comparative analysis of resistant and susceptible macrophage gene expression response to Leishmania major parasite.
    BMC Genomics. Oct 22;14:723.
  • Nicki Tiffin, Bridget Hodkinson, Ikechi Okpechi.
    Lupus in Africa: can we dispel the myths and face the challenges? Lupus January 2014 vol. 23 no. 1 102-111
  • Rajini Sreenivasan, Junhui Jiang, Xingang Wang, Richard Bartfai, Hsiao Yuen Kwan, Alan Christoffels, and Laszlo Orban.
    Gonad Differentiation in Zebrafish Is Regulated by the Canonical Wnt Signaling.
    Biology of Reproduction biolreprod.113.110874 doi:10.1095/biolreprod.113.110874
  • Akin Abayomi, Alan Christoffels, Ravnit Grewal, Locunda A. Karam, Catherine Rossouw, Ciara Staunton, Carmen Swanepoel, Beverley van Rooyen.
    Challenges of Biobanking in South Africa to facilitate indigenous research in an environment burdened with HIV, TB and emerging non-communicable diseases.
    Biopreservation and Biobanking 11: 347-354
    DOI: 10.1089/bio.2013.0049
  • Natasha T. Wood, Elisa Fadda,  Robert Davis, Oliver C. Grant, Joanne C. Martin,  Robert J. Woods,  Simon A. Travers.
    The Influence of N-Linked Glycans on the Molecular Dynamics of the HIV-1 gp120 V3 Loop.
    PLOS One. 10.1371/journal.pone.0080301
  • Brejnev Muhizi Muhire,  Michael Golden, Ben Murrell, Pierre Lefeuvre, Jean-Michel Lett, Alistair Gray, Art Y. F. Poon, Nobubelo Kwanele Ngandu, Yves Semegni, Emil Pavlov Tanov, Adérito Luis Monjane, Gordon William Harkins, Arvind Varsani, Dionne Natalie Shepherd and Darren Patrick Martin.
    Evidence of pervasive biologically functional secondary-structures within the genomes of eukaryotic single-stranded DNA viruses.
    Virology. JVI.03031-13
    doi:10.1128/JVI.03031-13JVI.03031-13
  • Britt I. Drogemollera, Galen E.B. Wright, Dana J.H. Niehausb, Robin Emsleyb and Louise Warnicha.
    Next-generation sequencing of pharmacogenes: a critical analysis focusing on schizophrenia treatment.
    Pharmacogenetics and Genomics (December 2013) Volume 23 – Issue 12.

2012
  • Fisher R, van Zyl GU, Travers SA, Kosakovsky Pond SL, Engelbrech S, Murrell B, Scheffler K, Smith D. Deep sequencing reveals minor protease resistance mutations in patients failing a protease inhibitor regimen. J Virol. 2012 Jun;86(11):6231-7. Epub 2012 Mar 28.
  • Adam Dawe, Aleksandar Radovanovic, Mandeep Kaur, Sunil Sagar, Sundarararajan Seshadri, Ulf Schaefer, Allan Kamau, Alan Christoffels and Vladimir Bajic. DESTAF: A Database of Text-Mined Associations for Reproductive Toxins Potentially Affecting Human Fertility. Reproductive Toxicology 33 (2012) 99–105
  • Ishla Seager, Michael D. Leeson, Amelia C. Crampin,Dominic Mulawa,Neil French,Judith R. Glynn, Simon A.A. Travers, and Grace P. McCormack. HIV Type 1 Mutational Patterns in HIV Type 1 Subtype C-Infected Long-Term Survivors in Karonga District Malawi: Further Analysis and Correction. Aids Research and Human Retroviruses, Volume 28, Number 3, 2012. DOI: 10.1089/aid.2011.0168
  • Okpechi I, Swanepoel CR, Tiffin N, Duffield M, Rayner B. Clinicopathological insights into lupus nephritis in South Africans: A study of 251 patients. Lupus 2012, March 26, 2012.
  • M.V. Akinyi, C. Dandara, J. Gamieldien, J.M. Heckmann. Association of transforming growth factor beta-1 (TGFB1) regulatory region polymorphisms with myasthenia gravis-related ophthalmoparesis. Journal of Neuroimmunology 246 (2012) 96–99 doi:10.1016/j.jneuroim.2012.03.002
  • Saleema Crous, Ram K Shrestha, Simon A Travers.
    Appraising the performance of genotyping tools in the prediction of coreceptor tropism in HIV-1 subtype C viruses.
    BMC Infectious Diseases 2012, 12:203
    doi:10.1186/1471-2334-12-203
  • Rabhi I, Rabhi S, Ben-Othman R, Rasche A, Sysco Consortium (includes N Tiffin), et al. (2012). Transcriptomic Signature of Leishmania Infected Mice Macrophages: A Metabolic Point of View.
    PLoS Negl Trop Dis 6(8): e1763. doi:10.1371/journal.pntd.0001763
  • Simon A Travers
    Conservation, Compensation, and Evolution of N-Linked Glycans in the HIV-1 GroupMSubtypes and Circulating Recombinant Forms.
    International Scholarly Research Network, ISRN AIDS, Volume 2012, Article ID 823605
    doi:10.5402/2012/823605

2011
  • Vladimir Shulaev, Daniel J Sargent, Ross N Crowhurst, Todd C Mockler, Otto Folkerts, Arthur L Delcher, Pankaj Jaiswal, Keithanne Mockaotis, Aaron Liston, Shrinivasrao P Mane, Paul Burns, Thomas M Davis, Janet P Slovin, Nahla Bassil, Roger P Hellens, Clive Evans, Tim Harkins, Chinnappa Kodira, Brian Desany, Oswald R Crastam Roderick V Jensen, Andrew C Allan, Todd P Michael, Joao Carlos Setubal, Jean-Marc Celton, D Jasper G Rees, Kelly P Williams, Sarah H Holt, Juan Jairo Ruiz Rojas, Mithu Chatterjee, Bo Liu, Herman Silva, Lee Meisel, Avital Adato, Sergei A Filichkin, Michela Troggio, Roberto Viola, Tia-Lynn Ashman, Hao Wang, Palitha Dharmawardhana, Justin Elser, Rajani Raja, Henry D Priet, Douglas W Bruant Jr, Samuel E Fox, Scott A Givan, Larry J Wilhelm, Sushma Naithani, Alan Christoffels et al. The genome of woodland strawberry (Fragaria vesca). Nature Genetics. 2011. 43: 109-116. Doi:10.1038/ng.740
  • Samuel Kwofie, Ulf Schaefer, Vijayaraghava Sundararajan, Vladimir Bajic, Alan Christoffels. HCVpro: Hepatitis C virus protein interaction database (2011). Infection, Genetics and Evolution.
  • Vijay B Bansode, Simon A A Travers, Amelia C Crampin, Bagrey Ngwira, Neil French, Judith R Glynn and Grace P McCormack (2011) Reverse Transcriptase drug resistance mutations in HIV-1 Subtype C infected patients on ART in Karonga District, Malawi. AIDS Research and Therapy 8(38) doi:10.1186/1742-6405-8-38
  • Redmond N. E., Raleigh J, van Soest R.W.M., Kelly M., Travers S.A.A., Bradshaw B., Vartia S., McCormack G.P. (2011) Molecular Systematics of the Order Haplosclerida (Phylum Porifera) Employing Ribosomal (28S rRNA) and Mitochondrial (mtCOI, NAD1) Gene Sequence Data. Plos One. 6(9) e24344
  • Samuel K Kwofie, Aleksandar Radovanovic, Vijayaraghava S Sundararajan, Monique Maqungo, Alan Christoffels and Vladimir B Bajic. Dragon Exploratory System on Hepatitis C Virus (DESHCV). Infection, Genetics and Evolution. 2011. 11(4):734-9
  • Sarah Mwangi, Edwin Murungi, Mario Jonas and Alan Christoffels. Evolutionary Genomics of Glossina morsitans immune-related Serine proteases and Serine Protease inhibitors. Infection, Genetics and Evolution. 2011. 11(4): 740-745.
  • Seager I, Leeson MD, Crampin A, Mulawa D, French D, Glynn J, Travers S.A.A., McCormack GP. HIV-1 mutational patterns in HIV-1 subtype C infected long-term survivors in Karonga District Malawi: correction and further analysis. AIDS Research and Human Retroviruses, June 2011
  • Vijayaraghava Seshadri Sundararajan, Musa Nur Gabere, Ashley Pretorius, Saleem Adam, Alan Christoffels, Minna Lehvaslaiho, John A. C. Archer and Vladimir B. Bajic. DAMPD: a manually curated antimicrobial peptide database. Nucleic Acids Research, 2011 (1-5). doi:10.1093/nar/gkr1063
  • Niamh E. Redmond, Jean Raleigh, Rob W. M. van Soest, Michelle Kelly, Simon A. A. Travers, Brian Bradshaw, Salla Vartia, Kelly M. Stephens, Grace P. McCormack. Phylogenetic Relationships of the Marine Haplosclerida (Phylum Porifera) Employing Ribosomal (28S rRNA) and Mitochondrial (cox1, nad1) Gene Sequence Data. PLoS ONE. 2011. 6(9): e24344
  • 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. 2011 Sep 1;27(17):2443-5. Epub 2011 Jul 14.
  • Monjane AL, Harkins GW, Martin DP, Lemey P, Lefeuvre P, Shepherd DN, Oluwafemi S, Simuyandi M, Zinga I, Komba EK, Lakoutene DP, Mandakombo N, Mboukoulida J, Semballa S, Tagne A, Tiendrébéogo F, Erdmann JB, van Antwerpen T, Owor BE, Flett B, Ramusi M, Windram OP, Syed R, Lett JM, Briddon RW, Markham PG, Rybicki EP, Varsani A. Reconstructing the history of maize streak virus strain a dispersal to reveal diversification hot spots and its origin in southern Africa. Journal of Virology. 2011 Sep;85(18):9623-36. Epub 2011 Jun 29.
  • Lefeuvre P, Harkins GW, Lett JM, Briddon RW, Chase MW, Moury B, Martin DP. Evolutionary time-scale of the begomoviruses: evidence from integrated sequences in the Nicotiana genome. PLoS One. 2011;6(5):e19193. Epub 2011 May 16.
  • Tiffin, N. Conceptual thinking for prioritization of candidate disease genes. In Methods in Molecular

    Biology – In Silico Tools for Gene Discovery. Editors: Bing Yu; Marcus John Hinchcliffe. Publisher:

    Humana Press


2010
  • Meehan CJ, Hedge JA, Robertson DL, McCormack GP, Travers S. Emergence, dominance and possible decline of CXCR4 chemokine receptor usage during the course of HIV infection. J Med Virol. 82 (12): 2004-12.
  • Bansode V, Drebert ZJ, Travers SA, Banda E, Molesworth A, Crampin A, Ngwira B, French N, Glynn JR, McCormack GP. Drug resistance mutations in drug-naïve HIV type 1 subtype C-infected individuals from rural Malawi. AIDS Res Hum Retroviruses.
  • Tiffin N, Meintjes A, Ramesa R, Bajic VB, Rayner B. Computational Analysis of Candidate disease Genes and Variants for Salt-sensitive Hypertension in Indigenous Southern Africans. PloS One.2010 September 20;5(9):e12989
  • Okpechi I, Rayner BL, van der Merwe L, Mayosi BM, Adebowale A, Tiffin N, Ramesar R. Genetic variation at selected SNPs in the Leptin gene and association of Alleles with markers of kidney kidney disease in a Xhosa population of South Africa. PloS One 2010 Feb 5;5(2):e9086
  • Samuel K Kwofie, Aleksandar Radovanovic, Vijayaraghava S Sundararajan, Monique Maqungo, Alan Christoffels and Vladimir B Bajic. Hepatitis C Virus discovery database (HCVdd): Dragon Exploratory System on Hepatitis C Virus (DESHCV) 2010. Infection, Genetics and Evolution.
  • Sarah Mwangi, Edwin Murungi, Mario Jonas and Alan Christoffels (2010) Evolutionary Genomics of Glossina morsitans immune-related Serine proteases and Serine Protease inhibitors. Infection, Genetics and Evolution
  • Vladimir Shulaev, Daniel J Sargent, Ross N Crowhurst, Todd C Mockler, Otto Folkerts, Arthur L Delcher, Pankaj Jaiswal, Keithanne Mockaotis, Aaron Liston, Shrinivasrao P Mane, Paul Burns, Thomas M Davis, Janet P Slovin, Nahla Bassil, Roger P Hellens, Clive Evans, Tim Harkins, Chinnappa Kodira, Brian Desany, Oswald R Crastam Roderick V Jensen, Andrew C Allan, Todd P Michael, Joao Carlos Setubal, Jean-Marc Celton, D Jasper G Rees, Kelly P Williams, Sarah H Holt, Juan Jairo Ruiz Rojas, Mithu Chatterjee, Bo Liu, Herman Silva, Lee Meisel, Avital Adato, Sergei A Filichkin, Michela Troggio, Roberto Viola, Tia-Lynn Ashman, Hao Wang, Palitha Dharmawardhana, Justin Elser, Rajani Raja, Henry D Priet, Douglas W Bruant Jr, Samuel E Fox, Scott A Givan, Larry J Wilhelm, Sushma Naithani, Alan Christoffels et al (2010) The genome of woodland strawberry (Fragaria vesca). Nature Genetics. Doi:10.1038/ng.740
  • Jean-Marc Celton, Alan Christoffels, Daniel J Sargent, Xiangming X and David J.G Rees (2010) Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map. BMC Biology. 8:155-8
  • Monique Maqungo, Mandeep Kaur, Samuel K. Kwofie, Aleksandar Radovanovic, Ulf Schaefer, Sebastian Schmeier, Ekow Oppon, Alan Christoffels and Vladimir B. Bajic (2010). DDPC: Dragon Database of Genes associated with Prostate Cancer. Nucleic Acids Research; doi: 10.1093/nar/gkq849.
  • Rocca-Serra P, Brandizi M, Maguire E, Sklyar N, Taylor C, Begley K, Field D, Harris S, Hide W, Hofmann O, Neumann S, Sterk P, Tong W, Sansone SA. ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics. 26(18): 2354-6
  • Voight BF, Scott LJ, Steinthorsdottir V, Morris AP, Dina C, Welch RP, Zeggini E, Huth C, Aulchenko YS, Thorleifsson G, McCulloch LJ, Ferreira T, Grallert H, Amin N, Wu G, Willer CJ, Raychaudhuri S, McCarroll SA, Langenberg C, Hofmann OM, Dupuis J, Qi L, Segrè AV, van Hoek M, Navarro P, Ardlie K, Balkau B, Benediktsson R, Bennett AJ, Blagieva R, Boerwinkle E, Bonnycastle LL, Bengtsson Boström K, Bravenboer B, Bumpstead S, Burtt NP, Charpentier G, Chines PS, Cornelis M, Couper DJ, Crawford G, Doney AS, Elliott KS, Elliott AL, Erdos MR, Fox CS, Franklin CS, Ganser M, Gieger C, Grarup N, Green T, Griffin S, Groves CJ, Guiducci C, Hadjadj S, Hassanali N, Herder C, Isomaa B, Jackson AU, Johnson PR, Jørgensen T, Kao WH, Klopp N, Kong A, Kraft P, Kuusisto J, Lauritzen T, Li M, Lieverse A, Lindgren CM, Lyssenko V, Marre M, Meitinger T, Midthjell K, Morken MA, Narisu N, Nilsson P, Owen KR, Payne F, Perry JR, Petersen AK, Platou C, Proença C, Prokopenko I, Rathmann W, Rayner NW, Robertson NR, Rocheleau G, Roden M, Sampson MJ, Saxena R, Shields BM, Shrader P, Sigurdsson G, Sparsø T, Strassburger K, Stringham HM, Sun Q, Swift AJ, Thorand B, Tichet J, Tuomi T, van Dam RM, van Haeften TW, van Herpt T, van Vliet-Ostaptchouk JV, Walters GB, Weedon MN, Wijmenga C, Witteman J, Bergman RN, Cauchi S, Collins FS, Gloyn AL, Gyllensten U, Hansen T, Hide WA, Hitman GA, Hofman A, Hunter DJ, Hveem K, Laakso M, Mohlke KL, Morris AD, Palmer CN, Pramstaller PP, Rudan I, Sijbrands E, Stein LD, Tuomilehto J, Uitterlinden A, Walker M, Wareham NJ, Watanabe RM, Abecasis GR, Boehm BO, Campbell H, Daly MJ, Hattersley AT, Hu FB, Meigs JB, Pankow JS, Pedersen O, Wichmann HE, Barroso I, Florez JC, Frayling TM, Groop L, Sladek R, Thorsteinsdottir U, Wilson JF, Illig T, Froguel P, van Duijn CM, Stefansson K, Altshuler D, Boehnke M, McCarthy MI; MAGIC investigators; GIANT Consortium. Twelve Type 2 diabetes susceptibility loci identified through large-scale association analysis. Nature Genetics. 42 (7): 579-89.
  • Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kamburov A, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, MacPherson CR, Ogawa C, Radovanovic A, Schwartz A, Teasdale RD, Tegnér J, Lenhard B, Teichmann SA, Arakawa T, Ninomiya N, Murakami K, Tagami M, Fukuda S, Imamura K, Kai C, Ishihara R, Kitazume Y, Kawai J, Hume DA, Ideker T, Hayashizaki Y. An atlas of combinatorial transcriptional regulation in mouse and man. Cell. 140 (5): 744-52
  • Gichora NN, Fatumo SA, Ngara MV, Chelbat N, Ramdayal K, Opap KB, Siwo GH, Adebiyi MO, El Gonnouni A, Zofou D, Maurady AA, Adebiyi EF, de Villiers EP, Masiga DK, Bizzaro JW, Suravajhala P, Ommeh SC, Hide W. Ten simple rules for organizing a virtual conference—anywhere. PLoS Comput Biol. 6(2):e1000650.
  • Lefeuvre P, Martin DP, Harkins GW, Lemey P, Gray AJA, Meredith S, Lakay F, Monjane A, Lett J, Varsani A, Heydarnejad J. The Spread of Tomato Yellow Leaf Curl Virus from the Middle East to the World. PLoS pathogens 6(10):e1001164

2009
  • Dalai SC, de Oliveira T, Harkins GW, Kassaye SG, Lint J, Manasa J, Johnston E, Katzenstein D, Evolution and molecular epidemiology of subtype C HIV-1 in Zimbabwe, AIDS. 2009 Nov 27;23(18):2523-32
  • Hofmann O, Caballero OL, Stevenson BJ, Chen YT, Cohen T, Chua R, Maher CA, Panji S, Schaefer U, Kruger A, Lehvaslaiho M, Carninci P, Hayashizaki Y, Jongeneel CV, Simpson AJG, Old LJ, Hide W, Genome-wide analysis of cancer/testis gene expression, Proceedings of the National Academy of Sciences of the United States of America, In Press.
  • Quantitating the multiplicity of infection with HIV-1 subtype C, M-R Abrahams, JA Anderson, EE Giorgi, C Seoighe, K Mlisana, L-H Ping, GS Athreya, F Treurnicht, B Keele, N Wood, J Gonzalez-Salazar, J Passmore, L Roberts, T Bhattacharya, H. Chu, I Hoffman, S Galvin, C Mapanje, P Kazembe, R Thebus, S Fiscus, W Hide, MS Cohen, S Abdool Karim, BF Haynes, GM Shaw, BH Hahn, BT Korber, R Swanstrom, C Williamson, for the CAPRISA Acute Infection Study Team and the Center for HIV-AIDS Vaccine Immunology Consortium. Journal of Virology. In press.

2008
  • Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS, Balgley MB, Bantscheff M, Bennett KL Björling E, Blagoev B, Bose R, Bahmachari SK, Burlingame AS, Bustelo XR, Cagney G, Cantin GT, Cardasis HL, Celis JE, Chaerkady R, Chu F, Cole PA, Costello CE, Cotter RJ, Crockett D, DeLany JP, De Marzo AM, DeSouza LV, Deutsch EW, Dransfield E, Drewes G, Droit A, Dunn MJ, Elenitoba-Johnson K, Ewing RM, Van Eyk J, Faca V, Falkner J, Fang X Fenselau C, Figeys D, Gagné P, Gelfi C, Gevaert K, Gimble JM, Gnad F, Goel R, Gromov P, Hanash SM, Hancock WS, Harsha HC, Hart G, Hays F, He F, Hebbar P, Helsens K, Hermeking H, Hide WA, Hjernø K, Hochstrasser DF, Hofmann O, Horn DM, Hruban RH, Ibarrola N, James P, Jensen ON, Jensen PH, Jung P, Kandasamy K, Kheterpal I, Kikuno RF, Korf U, Körner R, Kuster B, Kwon MS, Lee HJ, Lee YJ, Lefevre M, Lehvaslaiho M, Lescuyer P, Levander F, Lim MS, Löbke C, Loo JA, Mann M, Martens L, Martinez-Heredia J, McComb M, McRedmond J, Mehrle A, Menon R, Miller CA, Mischak H, Mohan SS, Mohmood R, Molina H, Moran MF, Morgan JD, Moritz R, Morzel M, Muddiman DC, Nalli A, Navarro JD, Neubert TA, Ohara O, Oliva R, Omenn GS, Oyama M, Paik YK, Pennington K, Pepperkok R, Periaswamy B, Petricoin EF, Poirier GG, Prasad TS, Purvine SO, Rahiman BA, Ramachandran P, Ramachandra YL, Rice RH, Rick J, Ronnholm RH, Salonen J, Sanchez JC, Sayd T, Seshi B, Shankari K, Sheng SJ, Shetty V, Shivakumar K, Simpson RJ, Sirdeshmukh R, Siu KW, Smith JC, Smith RD, States DJ, Sugano S, Sullivan M, Superti-Furga G, Takatalo M, Thongboonkerd V, Trinidad JC, Uhlen M, Vandekerckhove J, Vasilescu J, Veenstra TD, Vidal-Taboada JM, Vihinen M, Wait R, Wang X, Wiemann S, Wu B, Xu T, Yates JR, Zhong J, Zhou M, Zhu Y, Zurbig P, Pandey A. Human Proteinpedia enables sharing of human protein data, Nature Biotechnology, 2008 Feb;26(2):164-7
  • Sagar S, Kaur M, Dawe A, Seshadri SV, Christoffels A, Schaefer U, Radovanovic A, Bajic VB, DDESC: Dragon Database for Exploration of Sodium Channels in Human, BMC Genomics, 9:622, 2008 (IF=4.18)
  • Thompson CL, Pathak S, Jeromin A, Ng L, MacPherson C, Mortrud M, Cusick A, Riley Z, Sunkin SM, Bernard A, Puchalski R, Gage FH, Jones AR, Bajic VB, Hawrylycz MJ, Lein ES. Genomic Anatomy of the Hippocampus, Neuron, 60(6):1010-1021, 2008 (IF=13.4)
  • Meier S, Gehring C, MacPherson CR, Kaur M, Maqungo M, Reuben S, Muyanga S, Shih MD, Wei FJ, Wanchana S, Mauleon R, Radovanovic A, Bruskiewich R, Tanaka T, Mohanty B, Itoh T, Wing R, Gojobori T, Sasaki T, Swarup S, Hsing YI, Bajic VB, The promoter signatures in rice LEA genes can be used to build a co-expressing LEA gene network, RICE, 2008, 1(2): 177
  • Rajini Sreenivasan, Minnie Cai, Richard Bartfai, Xingang Wang, Alan Christoffels and Laszlo Orban (2008). Transcriptomic analyses reveal novel genes with sexually dimorphic expression in the zebrafish gonad and brain. PloSONE 3(3) e1791.
  • Hazelhurst S, Hide W, Liptak Z, Nogueira R, Starfield R. An overview of the wcd EST Clustering Tool, Bioinformatics. 2008 Jul 1;24(13):1542-6. Epub 2008 May 14
  • Douglas Howe, Maria Costanzo, Petra Fey, Takashi Gojobori, Linda Hannick, Winston Hide, David P. Hill, Renate Kania, Mary Schaeffer, Susan St. Pierre, Simon Twigger, Owen White, Seung Yon Rhee. The Future of Biocuration, Nature. 2008 Sep 4;455(7209):47-50.
  • Gautier Koscielny, Vincent Le Texier, Chellappa Gopalakrishnan, Vasudev Kumanduri, Jean-Jack Riethoven, Francesco Nardone, Eleanor Stanley, Christine Fallsehr, Oliver Hofmann, Meelis Kull, Eoghan Harrington, Stéphanie Boué, Eduardo Eyras, Mireya Plass, Fabrice Lopez, William Ritchie, Virginie Moucadel, Takeshi Ara, Heike Pospisil, Alexander Herrmann, Jens G. Reich, Roderic Guigó, Peer Bork, Magnus von Knebel Doeberitz, Jaak Vilo, Winston Hide, Rolf Apweiler, Thangavel Alphonse Thanaraj, Daniel Gautheret. ASTD: the Alternative Splicing and Transcript Diversity Database, Genomics. 2008 Dec 3. [Epub ahead of print]
  • Kaur M, Schmeier S, MacPherson CR, Hofmann O, Hide WA, Taylor S, Willcox N, Bajic VB, Prioritizing genes of potential relevance to diseases affected by sex hormones: An example of Myasthenia Gravis, BMC Genomics, 2008, 13;9(1):481. [Epub ahead of print] (IF=4.18)
  • Kaur M, Radovanovic A, Essack M, Schaefer U, Maqungo M, Kibler T, Schmeier S, Christoffels A, Narasimhan K, Choolani M, Bajic VB, Database for exploration of functional context of genes implicated in ovarian cancer, Nucleic Acids Research, 2008 Sep 12. [Epub ahead of print] (IF=6.954)
  • Meier S, Bastian R, Donaldson L, Murray S, Bajic VB, Gehring C, Co-expression and Promoter Content Analyses Assign a Role in Biotic and Abiotic Stress Responses to Plant Natriuretic Peptides, BMC Plant Biology, 2008 Feb 29;8:24 (IF=3.44)

2007
  • Lombard Z, Tiffin N, Hofmann O, Bajic VB, Hide W, Ramsay M. Computational selection and prioritization of candidate genes for Fetal Alcohol Syndrome, BMC Genomics, 2007. 8(1): 389.
  • Hannah MF, Bajic VB, Klein SL, Sex differences in the recognition of and innate antiviral responses to Seoul virus in Norway rats, Brain, Behavior, and Immunity, 2008 May;22(4):503-16. Epub 2007 Nov 28. (IF=3.757)
  • Christoffels, A (2007). Dealing with duplicated geomes in teleosts. In: Acquaculture Genome technologies. 511-524. Editor: Zhanjiang Liu. Blackwell Publishers, UK. ISBN 9780813802039.
  • Bartfai R., Wang X, Sreenivasan R, Cai M, Srinivasan H, Hossain MS, Komen J, Christoffels A and Orban L. (2007) Cyprinid gonad differentiation: A comparative genomics study. Aquaculture. 272: S244-S245. Elsevier Science, Netherlands. ISSN 0044-8486.
  • Seoighe C, Ketwaroo F, Pillay V, Scheffler K, Wood N, Duffet R, Zvelebil M, Martinson N, McIntyre J, Morris L, Hide, W, A Model of Directional Selection Applied to the Evolution of Drug Resistance in HIV-1, Mol Biol Evol, doi: 10.1093/molbev/msm021 . 2007. 24(4): 1025-1031
  • Schwegmann A, Guler R, Cutler AJ, Arendse B, Horsnell WGC, Flemming A, Kottmann AH, Ryan G, Hide W, Leitges M, Seoighe C, Brombacher F, Protein kinase C-delta is essential for optimal macrophage-mediated phagosomal containment of Listeria monocytogenes, Proceedings of the National Academy of Sciences of the United States of America, 2007. 104(41): 16251-16256.
  • Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, Sanbonmatsu R, Shiba R, Suzuki M, Takabayashi K, Takahashi A, Tamura T, Tanaka M, Tanaka S, Todokoro F, Yamaguchi K, Yamamoto N, Okido T, Mashima J, Hashizume A, Jin L, Lee KB, Lin YC, Nozaki A, Sakai K, Tada M, Miyazaki S, Makino T, Ohyanagi H, Osato N, Tanaka N, Suzuki Y, Ikeo K, Saitou N, Sugawara H, O’Donovan C, Kulikova T, Whitfield E, Halligan B, Shimoyama M, Twigger S, Yura K, Kimura K, Yasuda T, Nishikawa T, Akiyama Y, Motono C, Mukai Y, Nagasaki H, Suwa M, Horton P, Kikuno R, Ohara O, Lancet D, Eveno E, Graudens E, Imbeaud S, Debily MA, Hayashizaki Y, Amid C, Han M, Osanger A, Endo T, Thomas MA, Hirakawa M, Makalowski W, Nakao M, Kim NS, Yoo HS, De Souza SJ, Bonaldo M, Niimura Y, Kuryshev V, Schupp I, Wiemann S, Bellgard M, Shionyu M, Jia L, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Zhang Q, Go M, Minoshima S, Ohtsubo M, Hanada K, Tonellato P, Isogai T, Zhang J, Lenhard B, Kim S, Chen Z, Hinz U, Estreicher A, Nakai K, Makalowska I, Hide W, Tiffin N, Wilming L, Chakraborty R, Soares M, Chiusano ML, Suzuki Y, Auffray C, Yamaguchi-Kabata Y, Itoh T, Hishiki T, Fukuchi S, Nishikawa K, Sugano S, Nomura N, Tateno Y, Imanishi T, and Gojobori, The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts, Nucleic Acids Research, 2007. 10.1093/nar/gkm999 Database issue.
  • Kruger A, Hofmann O, Carninci P, Hayashizaki Y, Hide W, Simplified ontologies allowing comparison of developmental mammalian gene expression.Genome Biology, 2007, 8:R229.

2006
  • Bajic VB, Brent MR, Brown RH, Frankish A, Harrow J, Ohler U, Solovyev VV, Tan SL.: Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment. Genome Biol. 2006;7 Suppl 1:S3.1-13. Epub 2006 Aug 7. Review.
  • Guigo R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, Hubbard T, Lewis SE, Reese MG: EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol. 2006;7 Suppl 1:S2.1-31. Epub 2006 Aug 7. Review.
  • Nilsson R, Bajic VB, Suzuki H, di Bernardo D, Bjorkegren J, Katayama S, Reid JF, Sweet MJ, Gariboldi M, Carninci P, Hayashizaki Y, Hume DA, Tegner J, Ravasi T.: Transcriptional network dynamics in macrophage activation. Genomics. 2006 Aug;88(2):133-42. Epub 2006 May 12.
  • A Christoffels, R Bartfai, H Srinivasan, H Komen and L Orban (2006). Comparative genomics in cyprinids: Common carp ESTs help the annotation of the zebrafish genome. BMC Bioinformatics 7 Suppl 5:S2.
  • A Christoffels, Sydney Brenner and Byrappa Venkatesh (2006). Tetraodon genome analysis provides further evidence for whole-genome duplication in the ray-finned fish lineage. Comparative Biochemistry and Physiology Part D. 13-19.
  • Bajic VB, Tan SL, Christoffels A, Schonbach C, Lipovich L, Yang L, Hofmann O, Kruger A, Hide W, Kai C, Kawai J, Hume DA, Carninci P, Hayashizaki Y.: Mice and men: their promoter properties. PLoS Genet. 2006 Apr;2(4):e54. Epub 2006 Apr 28.
  • Tiffin N, Adie E, Turner F, Brunner HG, van Driel MA, Oti M, Lopez-Bigas N, Ouzounis C, Perez-Iratxeta C, Andrade-Navarro MA, Adeyemo A, Patti ME, Semple CA, Hide W, Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes. Nucleic Acids Res. 2006 Jun 6;34(10):3067-81. Print 2006.
  • Mehrle A, Rosenfelder H, Schupp I, del Val C, Arlt D, Hahne F, Bechtel S, Simpson J, Hofmann O, Hide W, Glatting KH, Huber W, Pepperkok R, Poustka A, Wiemann S.: The LIFEdb database in 2006. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D415-8.
  • Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schonbach C, Sekiguchi K, Semple CA, Seno S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishio T, Okada M, Plessy C, Shibata K, Shiraki T, Suzuki S, Tagami M, Waki K, Watahiki A, Okamura-Oho Y, Suzuki H, Kawai J, Hayashizaki Y; FANTOM Consortium; RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group).: The transcriptional landscape of the mammalian genome. Science. 2005 Sep 2;309(5740):1559-63. Erratum in: Science. 2006 Mar 24;311(5768):1713.

2005
  • Ptitsyn A, Hide W, CLU: a new algorithm for EST clustering, BMC Bioinformatics, 2005 Jul 15;6 Suppl 2:S3.
  • Tiffin N, Kelso JF, Powell AR, Pan H, Bajic VB, Hide WA, Integration of text- and data-mining using ontologies successfully selects disease gene candidates, Nucleic Acids Res, 2005, Mar 14;33(5):1544-52. Print 2005.
  • Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schonbach C, Sekiguchi K, Semple CA, Seno S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishio T, Okada M, Plessy C, Shibata K, Shiraki T, Suzuki S, Tagami M, Waki K, Watahiki A, Okamura-Oho Y, Suzuki H, Kawai J, Hayashizaki Y; FANTOM Consortium; RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group), The transcriptional landscape of the mammalian genome, Science, 309: 1559-1563, 02 Sept. 2005
  • Nicki Tiffin, Janet F. Kelso, Alan R. Powell, Hong Pan, Vladimir B. Bajic and Winston A. Hide, Integration of text- and data-mining using ontologies successfully selects disease gene candidates, Nucleic Acids Research, 2005 33(5):1544-1552
  • Winston Hide, EST Clustering: A short tutorial, 2005
  • A case for Glossina genome project. Serap Aksoy, Matt Berriman, Neil Hall, Masahira Hattori, Winston Hide, Michael J. Lehane. Trends in Parasitology 2005
  • The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms. Tanino M, Debily MA, Tamura T, Hishiki T, Ogasawara O, Murakawa K, Kawamoto S, Itoh K, Watanabe S, de Souza SJ, Imbeaud S, Graudens E, Eveno E, Hilton P, Sudo Y, Kelso J, Ikeo K, Imanishi T, Gojobori T, Auffray C, Hide W, Okubo K, Nucleic Acids Research, 2005 1(33): Database Issue 567-572
  • VB Bajic, M Veronika, PS Veladandi, A Meka, M-W Heng, K Rajaraman, H Pan, S Swarup, DPBE: A Text-mining Tool for Integrating Associations between Genetic and Biochemical Entities with Genome Annotation and Biochemical Terms Lists, Plant Physiology, 138 (4), 1914-1925, 2005
  • R Chowdhary, R. Ayesha Ali, W Albig, D Doenecke and VB Bajic, Promoter modeling: The case study of mammalian histone promoters, Bioinformatics, Mar 15; 21(11):2623-2628, 2005
  • N Tiffin, JF Kelso, AR Powell, H Pan, VB Bajic, WA Hide, Integration of Text- and Data-Mining Using Ontologies Successfully Selects Disease Gene Candidates, Nucleic Acids Research, 33(5):1544-1552, 2005
  • B Mohanty, SPT Krishnan, S Swarup, VB Bajic, Detection and Preliminary Analysis of Motifs in Promoters of Anaerobically Induced Genes of Different Plant Species, Ann Bot-London, Jul 18; 96(4):669-81, 2005
  • L Yang, E Huang, VB Bajic, Some implementation issues of heuristic methods for motif extraction from DNA sequences, Int.J.Comp.Syst.Signals, 6(2):3-12, 2005
  • VB Bajic, TW Tan (Eds.), Information Processing and Living Systems, World Scientific, 800 pages, 2005
  • H Pan, L Zuo, K Rajaraman, Z Zhang, V Choudhary, B Mohanty, SL Tan, S.P.T. Krishnan, PS Veladandi, A Meka, WK Choy, S Swarup, VB Bajic, Extracting information for meaningful function inference through text-mining, Chapter in Discovering Biomolecular Mechanism with Computational Biology (F Eisenhaber, Ed.), Landes Bioscience, 2005
  • VB Bajic, T Werner, Promoter Prediction, Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Part 4. Bioinformatics, 4.2. Gene Finding and Gene Structure, John Wiley & Sons, Ltd., DOI: 7:2881-2886, 2005
  • TW Tan, KH Choo, JC Tong, MT Tammi, VB Bajic, Biological Databases and Web Services: Metrics for Quality, Chapter 16 in Information Processing and Living Systems, World Scientific, 771-777, 2005
  • K Rajaraman, L Zuo, V Choudhary, Z Zhang, VB Bajic, H Pan, T-S Sim, S Swarup, Overview of text-mining in life sciences, Chapter 9 in Information Processing and Living Systems, World Scientific, 687-694, 2005
  • E Huang, L Yang, R Chowdhary, A Kassim, VB Bajic, An algorithm for ab initio DNA motif detection, Chapter 4 in Information Processing and Living Systems, World Scientific, 611-614, 2005
  • SL Tan, V Choudhary, A Christoffels, B Venkatesh, VB Bajic, Comparison of core promoters in Fugu rubripes and human (Keynote lecture), (Eds. Y-P P Chen and L Wong) in Proc. of the 3rd Asia-Pacific Bioinformatics Conference (APBC05), Imperial College Press, 379, 2005

2004

2003

2002

2001

2000
  • Malaria and the Developing Worlds of Genome Bioinformatics. W Hide, Science Scope, 1 May 2000.
  • Prevalence of small inversions in yeast gene order volution. Seoighe C, Federspiel N, Jones T, Hansen N, Bivolarovic V, Surzycki R, Tamse R, Komp C, Huizar L, Davis RW, Scherer S, Tait E, Shaw DJ, Harris D, Murphy L, Oliver K, Taylor K, Rajandream MA, Barrell BG, Wolfe KH. Proceedings of the National Acadamy of Science of the United States of America. 19 Dec 2000. 97(26): 14433-14437.
  • High Frequency of Inversions during Eukaryote Gene Order Evolution in Comparative Genomics. McLysaght, A., Seoighe, C. and Wolfe, KH. Eds. D. Sankoff and J.H. Nadeau. 2000. Kluyver Academic Publishers pp 47-58.
  • A Career in Bioinformatics. J Kelso. SA Society of Biochemists and Molecular Biologists. January 2000; 3 (2).
  • P Tabakov, VB Bajic, Genetic Algorithms and extraction of rules for detection of short DNA motifs, International Journal of Computers, Systems and Signals, (Special issue: Knowledge discovery from structured and unstructured data), 1(1):106-117, 2000.
  • Z Ma, A Jutan, VB Bajic, Nonlinear self-tuning controller for plants with Hammerstein type model and application to a pressure tank system, International Journal of Computers, Systems and Signals, (Special issue: Computer-based control systems), 1(2):221-230, 2000.
  • Z Ma, A Jutan, VB Bajic, Adaptive control of a nonlinear pressure tank using gray box modelling with neural networks, Journal of Applied Computer Science, 8(2):45-63, 2000
  • X Li, VB Bajic, D. Sha, X Wang, Neural network control with fuzzy-logic compensation, Journal of Applied Computer Science, (Special issue: Selected Applications of Artificial Intelligence), 8(2):121-127, 2000.
  • VB Bajic, Stability problems of fuzzy-descriptor systems, Facta Universitatis, Series: Mechanics, Automatic Control and Robotics, Invited paper, 2(10):1403-1413, 2000.
  • VB Bajic, D. Sha, X Li, AI-based discrete sliding-mode control for real-time implementation, International Journal of Computers, Systems and Signals (Special issue: Computer-based control systems), 1(2):196-213, 2000.
  • D Sha, VB Bajic, X Li, X Wang, Real-time experiments with discrete sliding-mode control enhanced by AI components, Journal of Applied Computer Science (Special issue: Selected Applications of Artificial Intelligence), 8(2): 99-117, 2000.
  • VB Bajic, Comparing the success of different prediction software in sequence analysis: A review, Briefings in Bioinformatics, 1(3):214-228, 2000.
  • S. Human, VB Bajic, Modelling Ultraviolet Irradiance in South Africa, Radiation Protection Dosimetry, 91(1-3):181-183, 2000.
  • D Sha, VB Bajic, Robust Discrete Adaptive I/O Based Sliding Mode Controller, International Journal of Systems Science, 31(12):1601-1614, 2000
  • KJ Duffy, VB Bajic, BR Page, Analysis and Dynamics of an Elephant-Tree Ecosystem having Abundant and Rare Tree Species, Systems Analysis Modelling Simulations, 38:663-676, 2000
  • VB Bajic, Neural network clustering of DNA data for improved PWM determination, Journal of Applied Computer Science, 8(1):49-61, 2000.
  • Z Ma, VB Bajic, Adaptive Controller for a Class of Systems with Saturation Nonlinearity, Systems Analysis Modelling Simulation, 37(1):1-14, 2000.
  • VB Bajic, IV Bajic, Neural network system for promoter recognition (20 pages), Chapter 14 in Future Directions for Intelligent Systems and Information Science (Nik Kasabov, Ed.), 288-305, Physica-Verlag, New York, 2000.

1999
  • D Sha, VB Bajic, Adaptive on-line ANN learning algorithm and application to identification of non-linear systems, Informatica: An International Journal of Computing and Informatics, 23(4):251-259, 1999.
  • D Sha, VB Bajic, On-line adaptive learning rate BP algorithm for MLP and application to an identification problem, Journal of Applied Computer Science, 7(2):67-82, 1999.
  • KJ Duffy, BR Page, JH Swart, VB Bajic, Realistic Parameter Assessment for a Well Known Elephant-Tree Ecosystem Model Reveals that Limit Cycles are Unlikely, Ecological Modelling, 121:115-125, 1999
  • Z Ma, VB Bajic, DWC Ho, Neural Network based Adaptive Internal Model Control for Nonlinear Plants, Journal of Applied Computer Science, 7(1):63-78, 1999.
  • VB Bajic, D Sha, Eds, Development and Practice of Artificial Intelligence Techniques, ISBN 0-620-24836-X, IAAMSAD, Durban, South Africa, 1999
  • VB Bajic, IV Bajic, Neural networks in promoter recognition, in Development and Practice of Artificial Intelligence Techniques (V B Bajic, D Sha, Editors), pp. 20-24, IAAMSAD, South Africa, 1999 – (also Plenary lecture at the International Conference on Artificial Intelligence – ICAI’99, 24-26 September 1999).

1998

1997

1994

1992

1991
  • Is the guinea pig a rodent? Graur, D., W. Hide and W-H. Li. Nature 1991 351(6328): 649-652.
  • Structure and evolution of the apolipoprotein and lipase gene families. Chan, L., W.A. Hide, Y-W Yang and W-H Li. Cellular and Molecular Biology of Atherosclerosis. 1991 A.M. Gotto Jr. Ed. Springer-Verlag (London).