InCoB celebrates its tenth anniversary as first joint conference with ISCB-Asia
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InCoB celebrates its tenth anniversary as firstjoint conference with ISCB-AsiaChristian Schnbach1*, Tin Wee Tan2, Janet Kelso3, Burkhard Rost4, Sheila Nathan5,6, Shoba Ranganathan7,2
From Asia Pacific Bioinformatics Network (APBioNet) Tenth International Conference on Bioinformatics FirstISCB Asia Joint Conference 2011 (InCoB/ISCB-Asia 2011)Kuala Lumpur, Malaysia. 30 November - 2 December 2011
In 2009 the International Society for Computational Biology (ISCB) started to roll out regional bioinformaticsconferences in Africa, Latin America and Asia. The open and competitive bid for the first meeting in Asia (ISCB-Asia) was awarded to Asia-Pacific Bioinformatics Network (APBioNet) which has been running the InternationalConference on Bioinformatics (InCoB) in the Asia-Pacific region since 2002. InCoB/ISCB-Asia 2011 is held fromNovember 30 to December 2, 2011 in Kuala Lumpur, Malaysia. Of 104 manuscripts submitted to BMC Genomicsand BMC Bioinformatics conference supplements, 49 (47.1%) were accepted. The strong showing of Asia amongsubmissions (82.7%) and acceptances (81.6%) signals the success of this tenth InCoB anniversary meeting, andbodes well for the future of ISCB-Asia.
IntroductionThe tenth InCoB (International Conference on Bioinfor-matics), an official conference of the Asia-Pacific Bioin-formatics Network (APBioNet) , was held in KualaLumpur, Malaysia as a joint conference with the ISCB-Asia meeting of the International Society for Computa-tional Biology (ISCB) . InCoB/ISCB-Asia 2011 is theresult of ISCBs mission to host meetings in locationsthat are not well served by the worlds largest bioinfor-matics conference ISMB (International Conference onIntelligent Systems for Molecular Biology). Owing to thesuccess of previous InCoB conferences [3,4], and asISCBs first regional affiliate, APBioNet was selected toco-organize the first ISCB-Asia conference.
Manuscript submission and reviewWe offered authors three tracks to submit manuscriptsfor potential publication in the supplement issues ofBMC Bioinformatics or BMC Genomics (BMC track)and Immunome Research (IR) . Of 110 submitted
manuscripts from 19 countries 104 were designated forthe BMC track. Immunome Research received threesubmissions. Shorter manuscripts representing researchin progress were also sought for Bioinformation (BI),which received three submissions. Most manuscriptsreceived three reviews from the 76 member strong Pro-gram Committee, supported by 39 additional reviewers(Additional File 1). The first round of reviews resultedin the provisional acceptance of 32 (30.8%) manuscripts,with minor revisions. The authors of 28 manuscripts,including three that were transferred by the ProgramCommittee Co-chairs to BI and IR tracks, had toaddress major concerns raised by the reviewers. After asecond round of review, 26 (25%) manuscripts were pro-visionally accepted pending minor revisions. A statisticsof submissions and final acceptances by countries isshown in Additional File 2. The manuscript revision andre-review policy of InCoB/ISCB-Asia 2011 resulted in amore than twofold greater acceptance rate compared toISMB/ECCB 2011  which considers only manuscriptsrequiring minor revisions.The 25 articles selected for this issue represent a
cross-section of scientific and technological innovationsaccelerating bioinformatics in the areas of databases,software tools, RNomics, next-generation sequencing,
* Correspondence: email@example.comDepartment of Bioscience and Bioinformatics, Graduate School of ComputerScience and Systems Engineering, Kyushu Institute of Technology, Fukuoka820-8502, JapanFull list of author information is available at the end of the article
Schnbach et al. BMC Genomics 2011, 12(Suppl 3):S1http://www.biomedcentral.com/1471-2164/12/S3/S1
2011 Schnbach et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the CreativeCommons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, andreproduction in any medium, provided the original work is properly cited.
sequence analysis, evolution, proteome analysis anddisease informatics. The remaining 24 accepted BMCarticles are published as a BMC Bioinformatics supple-ment .
Biological databases and software toolsPapers presenting a wide variety of databases and soft-ware tools were accepted [8-12]. Particular focus areasinclude the development of software for the alignmentof apicomplexan sequences  which have an unusualsequence composition, software for the identification ofgene regulatory modules from microarray data , andsoftware for the identification of taxonomic identityfrom metagenomic samples . Liverome  andDetoxiprot  represent databases for collecting andsharing of network modules enriched in liver cancer-pathways as well as enzymes, substrates, inducers andinhibitors of detoxification.
RNomics and next-generation sequencingFour papers make use of next-generation sequencing(NGS) [13-16] to address a range of challenges from theidentification of the taxonomic origin of organismsequences in metagenomic studies  to the identifica-tion of unique and novel genes in metatranscriptomicdata [14,15].Fast-growing trees from plantations are used in pulp
and fiber production. Lignin, an essential component ofthe tree structure, is undesired in this process. Ong andWickneswari  applied NGS to profile the expressionof Acacia mangium small RNAs in secondary xylemsamples of varying lignin content. The obtained smallRNA profiles, which include 82 novel miRNAs mayopen venues to silence monolignol biosynthesis-asso-ciated genes without compromising the fitness of thetree.Secretory proteins are important players in host-
pathogen interactions. Existing prediction tools do notsupport the identification of secretory protein candidatesfrom NGS data, thus hampering the identification ofnon-classical secreted protein candidates. Garg and Ran-ganathan  developed an assembly protocol for NGS-derived sequence data to cluster, translate and homologysearch an in-house dataset of experimentally determinedparasitic helminth excretory/secretory proteins. Anotheraspect of the cellular secretome is exosomes or vesiclesused in intracellular communication and transport ofcellular components such as RNA. Since exosomescould be used as vectors for therapeutic drug delivery, itis of interest to identify motifs involved in targetingRNA for secretion. Bagatov and colleagues  deter-mined ab initio various short linear motifs that are spe-cific for certain exosome-enriched RNAs.
Evolution and sequence analysisThe growing number of complete genome drafts andprotein sequence data allows to re-visit questions on theorigin of vertebrate promoters, evolutionary conservationof enzymes, as well as the generation of functional diver-sity through gene duplication and alternative splicing.Profiling of ascidian promoters revealed a primordial ver-tebrate promoter type that appears to be partially methy-lated with a high but limited extent of CpG scores and G+C content . Phylogenetic profiles of rate-limitingenzymes with inhibiting relations showed higher conser-vation across human, rat, mouse, budding yeast and E.coli than common enzymes . Chen et al.  ana-lysed the relationship between the two mechanisms usingprotein sequence and paralog information of sevenorganisms ranging from human to C. elegans. The resultsindicate a duplication age-dependent relationship ofalternative splicing and an evolutionary constraint amongduplicates. Alternative splicing was more frequentlyobserved among ancient than recent duplicates.The increasing scale and speed of whole-genome
sequencing requires faster and high-accuracy genomemapping methods. A new method that utilizes perfectHamming Code with a hash table significantly reducesthe number of hash keys required for searching genomepositions . The Universal Automatic SNP Identifica-tion System (UASIS) , cross-references SNP identi-fiers of various databases to bridge potential SNPnomenclature ambiguities and to promote compliancewith Human Genome Variation Society guidelines.
Proteome analysisKnowledge of protein-protein interaction (PPI) dataquality and their limitations is critical for interpretingresults and essential for using them as a reference set.Zhou and Wong  found that M. tuberculosis H37Rvbacterial two-hybrid (B2H) data seemed to containnumerous false positives and false negatives, while theH37Rv STRING predicted PPIs included many none-direct interactions. Yet, stringently predicted H37RvSTRING PPI data appeared to be suitable as a referencefor analysing functional associations rather than physicalinteractions. To understand the behaviour of proteins inPPI networks, PPIs are often correlated with geneexpression parameters. The correlation of high-confi-dence human PPIs derived from the HitPredict databasewith gene expression stability improved the classificationof transient obligatory hubs and revealed functionallydistinct, previously unknown type of hubs .All protein domains common to mouse-infecting
viruses and mice were analyzed and published as Mus-Virus database and tool . Biochemical and functionalinterpretations of the shared domains indicated that the
Schnbach et al. BMC Genomics 2011, 12(Suppl 3):S1http://www.biomedcentral.com/1471-2164/12/S3/S1
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analysed viruses prefer to acquire genes of the innateimmune response pathways. Granzymes are serine pro-teases that are implicated in the pathogenesis of severalchronic inflammatory and cardiovascular disorders. Weeet al.  implemented a webserver to predict thepotential granzyme B degradome using support vectormachine classifiers derived from experim