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BMC Bioinformatics publishes selected research, proceedings and collections of thematic reviews as supplements. All articles published in supplements are subject to peer review and are free to access online. The journal also publishes supplements containing meeting abstracts.

Volume 14 Supplement 2

Selected articles from the Eleventh Asia Pacific Bioinformatics Conference (APBC 2013): Bioinformatics

Proceedings

The Eleventh Asia Pacific Bioinformatics Conference (APBC 2013)

Vancouver, Canada

21-24 January 2013

Edited by Cenk Sahinalp and Steven Jones

Publication of this supplement was funded by the authors.

| Conference website

Shape and secondary structure prediction for ncRNAs including pseudoknots based on linear SVM

Rujira Achawanantakun, Yanni Sun BMC Bioinformatics 2013, 14(Suppl 2):S1 (21 January 2013)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

CoNVEX: copy number variation estimation in exome sequencing data using HMM

Kaushalya C Amarasinghe, Jason Li, Saman K Halgamuge BMC Bioinformatics 2013, 14(Suppl 2):S2 (21 January 2013)

Abstract | Full text | PDF | PubMed

Widespread evidence of viral miRNAs targeting host pathways

Joseph W Carl, Joanne Trgovcich, Sridhar Hannenhalli BMC Bioinformatics 2013, 14(Suppl 2):S3 (21 January 2013)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs

Tzu-Hao Chang, Hsi-Yuan Huang, Justin Hsu, Shun-Long Weng, Jorng-Tzong Horng, Hsien-Da Huang BMC Bioinformatics 2013, 14(Suppl 2):S4 (21 January 2013)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

iStable: off-the-shelf predictor integration for predicting protein stability changes

Chi-Wei Chen, Jerome Lin, Yen-Wei Chu BMC Bioinformatics 2013, 14(Suppl 2):S5 (21 January 2013)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

Sequence-only evolutionary and predicted structural features for the prediction of stability changes in protein mutants

Lukas Folkman, Bela Stantic, Abdul Sattar BMC Bioinformatics 2013, 14(Suppl 2):S6 (21 January 2013)

Abstract | Full text | PDF | PubMed

Discovery and analysis of consistent active sub-networks in cancers

Raj K Gaire, Lorey Smith, Patrick Humbert, James Bailey, Peter J Stuckey, Izhak Haviv BMC Bioinformatics 2013, 14(Suppl 2):S7 (21 January 2013)

Abstract | Full text | PDF | PubMed

Building Markov state models with solvent dynamics

Chen Gu, Huang-Wei Chang, Lutz Maibaum, Vijay S Pande, Gunnar E Carlsson, Leonidas J Guibas BMC Bioinformatics 2013, 14(Suppl 2):S8 (21 January 2013)

Abstract | Full text | PDF | PubMed

A multispecies polyadenylation site model

Eric S Ho, Samuel I Gunderson, Siobain Duffy BMC Bioinformatics 2013, 14(Suppl 2):S9 (21 January 2013)

Abstract | Full text | PDF | PubMed

Prediction of B-cell epitopes using evolutionary information and propensity scales

Scott Lin, Cheng-Wei Cheng, Emily Su BMC Bioinformatics 2013, 14(Suppl 2):S10 (21 January 2013)

Abstract | Full text | PDF

Inferring homologous protein-protein interactions through pair position specific scoring matrix

Chun-Yu Lin, Yung-Chiang Chen, Yu-Shu Lo, Jinn-Moon Yang BMC Bioinformatics 2013, 14(Suppl 2):S11 (21 January 2013)

Abstract | Full text | PDF | PubMed

Reconstruction of phyletic trees by global alignment of multiple metabolic networks

Cheng-Yu Ma, Shu-Hsi Lin, Chi-Ching Lee, Chuan Yi Tang, Bonnie Berger, Chung-Shou Liao BMC Bioinformatics 2013, 14(Suppl 2):S12 (21 January 2013)

Abstract | Full text | PDF | PubMed

Prediction of peptides binding to MHC class I and II alleles by temporal motif mining

Cem Meydan, Hasan H Otu, Osman Sezerman BMC Bioinformatics 2013, 14(Suppl 2):S13 (21 January 2013)

Abstract | Full text | PDF | PubMed

A model of the circadian clock in the cyanobacterium Cyanothece sp. ATCC 51142

Nguyen Vinh, Madhu Chetty, Ross Coppel, Sandeep Gaudana, Pramod P Wangikar BMC Bioinformatics 2013, 14(Suppl 2):S14 (21 January 2013)

Abstract | Full text | PDF | PubMed

Identifying cross-category relations in gene ontology and constructing genome-specific term association networks

Jiajie Peng, Jin Chen, Yadong Wang BMC Bioinformatics 2013, 14(Suppl 2):S15 (21 January 2013)

Abstract | Full text | PDF | PubMed

Spiral search: a hydrophobic-core directed local search for simplified PSP on 3D FCC lattice

Mahmood A Rashid, MA Hakim Newton, Md Tamjidul Hoque, Swakkhar Shatabda, Duc Pham, Abdul Sattar BMC Bioinformatics 2013, 14(Suppl 2):S16 (21 January 2013)

Abstract | Full text | PDF | PubMed

Adaptive bi-level programming for optimal gene knockouts for targeted overproduction under phenotypic constraints

Shaogang Ren, Bo Zeng, Xiaoning Qian BMC Bioinformatics 2013, 14(Suppl 2):S17 (21 January 2013)

Abstract | Full text | PDF | PubMed

A practical O(n log² n) time algorithm for computing the triplet distance on binary trees

Andreas Sand, Gerth Brodal, Rolf Fagerberg, Christian NS Pedersen, Thomas Mailund BMC Bioinformatics 2013, 14(Suppl 2):S18 (21 January 2013)

Abstract | Full text | PDF | PubMed

The road not taken: retreat and diverge in local search for simplified protein structure prediction

Swakkhar Shatabda, MA Hakim Newton, Mahmood A Rashid, Duc Pham, Abdul Sattar BMC Bioinformatics 2013, 14(Suppl 2):S19 (21 January 2013)

Abstract | Full text | PDF | PubMed

Protein disulfide topology determination through the fusion of mass spectrometric analysis and sequence-based prediction using Dempster-Shafer theory

Rahul Singh, William Murad BMC Bioinformatics 2013, 14(Suppl 2):S20 (21 January 2013)

Abstract | Full text | PDF | PubMed