SABioinf 2007: List of all papers and posters

Invited Lectures

• Tandem repeats analysis Eric Rivals
• Cyprinid Genomics: A GMOD-based framework for cross-species integration of transcripts into closely-related genomes Alan Christoffels
• Male mutation bias and X chromosome inactivation in the age of genomics Kateryna Makova
• The Neanderthal Genome Project: Bioinformatics challenges Janet Kelso
• Dual Coding in Eukaryotic Genomes Defies Statistical Odds Anton Nekrutenko

Reviewed Papers and Presentations

Full research papers

1. A two-phase approach for detecting recombination in nucleotide sequences C.X. Chan, R. Beiko, and M.A. Ragan
2. Identification of orphan environmental sequences by relative abundance of oligonucleotides O. Reva
3. On the Detection of Recombination in Minisatellite Data E. Adebiyi and E. Rivals

   Short papers and works-in-progress

4. Using a Tuple Space Web Service for Parallel Processing in Bioinformatics B. Mueller, L. Schule, G. Wells
5. Low-resolution structural genomics by structure prediction and filtering of decoys using sparse experimental data J. M. Bujnicki
6. Progress towards Determining the Structure of \emph {Plasmodium falciparum Pyridoxal Kinase \"O. Tastan Bishop, G. Wells, F. Joubert, C. Wrenger, R. D. Walter and A.I. Louw
7. Learning a Subclass of Tree Adjoining Grammars S. Al Seesi, S. Rajasekaran, R. Ammar
8. Knowledge Driven User Interfaces for Complex Biological Queries K. O'Neill, A. Garcia-Castro and D. Jacobson
9. MScanner: A tool to expand a corpus of Medline citations G.L. Poulter, C. Seoighe, D.L. Rubin, R.B. Altman
10. Mitochondrial DNA shows three cryptic populations of Campbell's and Lowe's monkeys (\emph {Cercopithecus campbelli, Waterhouse, 1838) in C\^ote d'Ivoire S. Gonedel\'e Bi, A. Sangare, E. N'Goran, D. Zinner, H. Siedel, L. Vigilant, C. Boesch
11. In-silico Modelling of \emph {Helicoverpa armigera Aminopeptidase-N receptor C.V.S. Siva Prasad and A. Singh
12. ISR-mediated gene expression provides insight into the molecular regulation of systemic plant protection by non-pathogenic bacteria S. Muyanga, S. Meier, C. Gehring and V. Bajic
13. A Computational Approach to Candidate Gene Prioritisation Using Data-Mining and Clinically-Informed Binary Filtering Z. Lombard, M. Ramsay, and W. Hide

    Reviewed Presentations

14. Development of a web toolkit for the biological interpretation of microarray gene clusters P.J. Law, C. Claudel-Renard, F. Joubert, D. K. Berger and A.I. Louw
15. A model of directional selection applied to the evolution of drug resistance in HIV-1 C. Seoighe, K. Scheffler, V. Pillay, L. Morris and W. Hide
16. CTL response to HIV-1 subtype C is poorly predicted by epitope motifs N. Ngandu, C. Seoighe, H. Bredell, C. Williamson, C.M. Gray and the HIVNET028 Study Team
17. An Efficient Algorithm for Oligonucleotides Selection in a Large EST Database E. Adebiyi
18. What do haplotype inferral programs tell us? An investigation of the human haptoglobin locus Tracy McLellan, Lindiwe Skhosana and Steven Hecht Orzack
19. Comparison of Developmental Mammalian Gene Expression Using Simplified Ontologies A. Kruger, O. Hofmann and W. Hide
20. Standards in alternative splicing O. Hofmann, C. Iseli, C. Mungall, M. Sammeth, E. Eyras, S. Lewis, and W. Hide
21. Molecular Library Building through a Markush-like Molecular Enumeration Technique W. Cochrane and F. Joubert
22. Integration of HIV clinical and molecular data using Open Source genome managements tools H. Lehvaslaiho, A. Dawe, A. Kamau, R. Van Rooyen, A. Boardman, Alan Powell And Winston Hide
23. Extracting value from single-read sequence data G. Koning, S. Hazelhurst, M. Jonas, A. Murray, J. Grzymski, C. Maher, D. Cowan And W. Hide
24. Elucidation of Sulfadoxine Resistance with Structural Models of the Bifunctional \emph {Plasmodium falciparum Dihydropterin Pyrophosphokinase Dihydropteroate Synthase T. De Beer, A.I. Louw, and F. Joubert
25. Application of a Robust Method to Reevaluate Evidence for Positive Selection in HIV Coding Sequences N. Wood, K. Scheffler and C. Seoighe
26. Identification of allele-specific mRNA transcripts through an integrative analysis of genomic and EST data V. Nembaware, B. Lupindo, K. Scheffler AND Cathal Seoighe

Posters

1. Identification of a new arenavirus in Hylomyscus Simus in C\^ote D'Ivoire D. N'Golo Coulibaly, C. Akoua Koffi, S.K. Kouassi, B. Becker-Ziaja, B. Allali, B. Liedigk, E. Ekaza, M. Dosso, E. Fichet-Calvet, J. ter Meulen and S. G\"unther
2. Protein Analysis Made Easy T. de Beer and F. Joubert
3. Exploring unusual regulatory behaviour in a simple metabolic pathway using {PySCeS B.G. Olivier, J.M. Rohwer and J.-H.S. Hofmeyr
4. Comparative genome analysis of pathogenic and non-pathogenic African Swine Fever Virus genomes E.P. de Villiers, C. Gallardo, E. Blanco, A. Llorente, F. Kamanu and R. Bishop
5. Prevalence of SNPs at exon-intron junctions of alternatively spliced genes B. Lupindo AND C. Seoighe
6. Microarray Analysis For Human Malaria Parasite Plasmodium Falciparum Using K-Means Clustering Computational Approaches V. Osamor and E. Adebiyi
7. Prediction of Nuclear Hormone Response Elements A. Reba\"\i
8. Comparative sequence analysis of microbial genomes to identify potential virulence genes in Mycobacterium tuberculosis G. Jamieson, H. Rabiu, V. Vuppu, and N. Mulder
9. The elucidation of host responses to South African cassava mosaic virus using cDNA microarrays F. van Schalk and M.E.C. Rey
10. Providing python bindings for the SUNDIALS suite of dynamic system solvers using ctypes J. Dominy, J. Rohwer and J.-H.S. Hofmeyr
11. Use of oligonucleotide frequencies to derive signatures for prokaryotic genomes C.F. Davenport, O. Reva and B. Tuemmler
12. An Easy On The Eye Whole Genome Browser H. Ganesan, A. Rakitianskaia and O. Reva
13. In Silico Identification of Possible Leishmanial Secretory Proteins with Sequence-Specific Nucleic Acid Binding Competency K.F. Kinyua
14. Detecting Recombination within large groups of sequences using an FPGA L. Thomson
15. The Crystal Structure of a Mutant Nitrile Hydratase S. Kwofie, P. Kowlessur, A.O. Bishop, T. Tsekoa, S. Muhammed, T. Sewell and D. Cowan
16. A generic rate equation for catalysed, template-directed polymerisation reactions for use in computational systems biology O.P. Gqwaka, J.M. Rohwer and J.-H.S. Hofmeyr
17. Homology modelling of human protein cathepsin A. R. Reja and G.K. Maheshwari
18. CAGED: Chromosomal Arrangement of Gene Expression Data S. Somers, C. Gehring, C. Seoighe
19. Mechanistic insight into the working of spermidine synthase of \emph {Plasmodium falciparum from a homology model P.B. Burger, L.-M. Birkholtz, F. Joubert, N. Haider, R.D. Walter and A.I. Louw
20. Plant-scale structural model of carbon fixation and sucrose accumulation in sugarcane K.L. Meyer, L. Uys and J.M. Rohwer
21. Modelling sucrose accumulation in maturing sugarcane L. Uys and J. Rohwer
22. A structural bioinformatics approach to \emph {Theileria parva genome annotation T. Shah, E. de Villiers, V. Nene, M. Gardner, R. Bishop
23. d¹ EST clustering D. Kennedy
24. Understanding the control and regulation of the mammalian cell cycle R. Conradie and J.L. Snoep
25. Oscillatory behaviour and synchronisation in a detailed model of yeast glycolysis F.B. du Preez and J.L. Snoep
26. A sequence-centric biological workbench as part of a bioinformatics information management system C.A. Hefer and F. Joubert
27. Review of the implementation of codon usage bias in software utilised in the design of functional synthetic protein coding regions J.S. Baxter, G.L. Blatch, G. J\"ager
28. Identification and characterisation of potential duplicate genes in \emph {Mycobacterium tuberculosis through comparative genomic studies V. Vuppu and N. Mulder
29. Annotation of a cDNA Microarray using SSHscreen and MADIBA software D. Berger and N. Coetzer
30. The JWS Online Project C. van Gend and J. Snoep
31. Symbolic Control Analysis of Cellular Systems T.J. Akhurst, J.-H.S. Hofmeyr and J.M. Rohwer
32. Clustering Expressed Sequenced Tags using a Tree-Structured Index Algorithm B. Kumwenda
33. A Graph-relational Integrated Database of Human and Mouse Omics data J. Gamieldien, D. Otgaar, N. Southgate, D.A. Jacobson
34. Digr: A web interface for mining Digrabase graph databases K. O'Neill, H. Murrell, D.A. Jacobson
35. BISI: an integrative, extensible and minable database of South African wildlife and indigenous livestock biomaterial information A. Maclear, D. Otgaar, J. Gamieldien, P. Bartels, A. Kotze, D. Jacobson
36. BLAST on Virtual Clusters, Affordable High Performance Computing I. Scheepers, D.A. Jacobson
37. Vector Graphics to improve Blast graphic representations R. Jimenez, H. Murrell, D. Jacobson
38. DigraBase --- A Multigraph-based Data Store for Integrating Biological Data D. Otgaar, J. Gamieldien, F. Martinez, B.Nortier, D. Jacobson
39. BioFrame --- A Java-based Software Development framework for Bioinformatics F. Martinez, J. Gamieldien, D. Otgaar, D. Jacobson
40. Large-scale design of primers for genes from atypical plants. I. Riani, Y. Trifa, K.W. Berendzen and A. BenKahla
41. Global analysis of Leishmania genes expression using SAGE libraries}. S. Smandi, F. Guerfali, D. Laouini, K. Dellagi and A. Benkahla