Affiliation: The Walter and Eliza Hall Institute of Medical Research
- An HMM model for coiled-coil domains and a comparison with PSSM-based predictionsMauro Delorenzi
Genetics and Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3050, Australia
Bioinformatics 18:617-25. 2002..The performance of the two approaches is tested for Coiled-Coil Domains (CCDs). The prediction of CCDs is used frequently, and its optimization seems worthwhile...
- A subset of Plasmodium falciparum SERA genes are expressed and appear to play an important role in the erythrocytic cycleSusanne K Miller
Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3050, Australia
J Biol Chem 277:47524-32. 2002..The inability to disrupt SERA4, -5, and -6 is consistent with their apparent dominant expression and implies an important role for these genes in maintenance of the erythrocytic cycle...
- Enzymic, phylogenetic, and structural characterization of the unusual papain-like protease domain of Plasmodium falciparum SERA5Anthony N Hodder
The Walter and Eliza Hall Institute of Medical Research, Melbourne, 1G Royal Parade, Parkville, Victoria 3050, Australia
J Biol Chem 278:48169-77. 2003..This study provides impetus for the examination of SERA5 as a target for antimalarial drug design...
- Genes for glycosylphosphatidylinositol toxin biosynthesis in Plasmodium falciparumMauro Delorenzi
The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3050, Australia
Infect Immun 70:4510-22. 2002..The biosynthetic pathway of the malaria parasite GPI offers potential targets for drug development and may be useful for studying parasite cell biology and the molecular basis for the pathophysiology of parasitic diseases...
- MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation dataChristoph D Schmid
Swiss Institute of Bioinformatics SIB, Lausanne, Switzerland
Nucleic Acids Res 35:W201-5. 2007..The program written in C++ can be freely downloaded from ftp://ftp.epd.unil.ch/pub/software/unix/madap. The MADAP web server can be accessed at http://www.isrec.isb-sib.ch/madap/...
- MAMOT: hidden Markov modeling toolFrederic Schutz
Swiss Institute of Bioinformatics and Bioinformatics Core Facility of the NCCR Molecular Oncology, CH 1015 Lausanne, Switzerland
Bioinformatics 24:1399-400. 2008..A wealth of useful features include the use of pseudocounts, state tying and fixing of selected parameters in learning, and the inclusion of prior probabilities in decoding...
- The serine repeat antigen (SERA) gene family phylogeny in Plasmodium: the impact of GC content and reconciliation of gene and species treesRichard Bourgon
Department of Statistics, University of California, Berkeley, USA
Mol Biol Evol 21:2161-71. 2004..Parsimony of reconciliation and a second criterion--implied mutational pattern at two key active sites in the SERA proteins-were also seen to be useful supplements to standard "bootstrap" analysis for inferred topologies...
- HTPSELEX--a database of high-throughput SELEX libraries for transcription factor binding sitesVidhya Jagannathan
Swiss Institute for Experimental Cancer Research and Swiss Institute of Bioinformatics, Ch des Boveresses 155, CH 1066 Epalinges, Switzerland
Nucleic Acids Res 34:D90-4. 2006..HTPSELEX is available from ftp://ftp.isrec.isb-sib.ch/pub/databases/htpselex/ and http://www.isrec.isb-sib.ch/htpselex...
- Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'Alexandre Kuhn
Swiss Institute of Bioinformatics SIB, CH 1015 Lausanne, Switzerland
BMC Bioinformatics 9:26. 2008..e. flat file databases. This common flat database format thus provides a simple and robust solution to flexibly integrate various sources of information and a basis for the combined analysis of heterogeneous gene expression profiles...
- An atlas of human gene expression from massively parallel signature sequencing (MPSS)C Victor Jongeneel
Office of Information Technology, Ludwig Institute for Cancer Research, and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
Genome Res 15:1007-14. 2005..The data are available on the Web at http://mpss.licr.org and http://sgb.lynxgen.com...