Volume 15 Supplement 16

Thirteenth International Conference on Bioinformatics (InCoB2014): Bioinformatics

Research

Edited by Shoba Ranganathan, Christian Schönbach and Tin Wee Tan

This collection of articles has not been sponsored. Information about the source of funding for publication charges can be found in the individual articles. Articles are based on presentations made at the Thirteenth International Conference on Bioinformatics (InCob2014) of the Asia Pacific Bioinformatics Network (APBioNet). The peer review process was overseen by the Supplement Editors in accordance with BioMed Central's peer review guidelines for supplements. The Supplement Editors declare that they have no competing interests.

Asia Pacific Bioinformatics Network (APBioNet) Thirteenth International Conference on Bioinformatics (InCoB2014). Go to conference site.

Sydney, Australia31 July - 2 August 2014

Related articles have been published in supplements to BMC Genomics, BMC Medical Genomics and BMC Systems Biology.

Characterization and identification of protein O-GlcNAcylation sites with substrate specificity

Protein O-GlcNAcylation, involving the attachment of single N-acetylglucosamine (GlcNAc) to the hydroxyl group of serine or threonine residues. Elucidation of O-GlcNAcylation sites on proteins is required in orde...

Authors: Hsin-Yi Wu, Cheng-Tsung Lu, Hui-Ju Kao, Yi-Ju Chen, Yu-Ju Chen and Tzong-Yi Lee

Citation: BMC Bioinformatics 2014 15(Suppl 16):S1

Content type: Research Published on: 8 December 2014
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An integrative model of multi-organ drug-induced toxicity prediction using gene-expression data

In practice, some drugs produce a number of negative biological effects that can mitigate their effectiveness as a remedy. To address this issue, several studies have been performed for the prediction of drug-...

Authors: Jinwoo Kim and Miyoung Shin

Citation: BMC Bioinformatics 2014 15(Suppl 16):S2

Content type: Research Published on: 8 December 2014
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Use B-factor related features for accurate classification between protein binding interfaces and crystal packing contacts

Distinction between true protein interactions and crystal packing contacts is important for structural bioinformatics studies to respond to the need of accurate classification of the rapidly increasing protein...

Authors: Qian Liu, Zhenhua Li and Jinyan Li

Citation: BMC Bioinformatics 2014 15(Suppl 16):S3

Content type: Research Published on: 8 December 2014
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SCMHBP: prediction and analysis of heme binding proteins using propensity scores of dipeptides

Heme binding proteins (HBPs) are metalloproteins that contain a heme ligand (an iron-porphyrin complex) as the prosthetic group. Several computational methods have been proposed to predict heme binding residue...

Authors: Yi-Fan Liou, Phasit Charoenkwan, Yerukala Sathipati Srinivasulu, Tamara Vasylenko, Shih-Chung Lai, Hua-Chin Lee, Yi-Hsiung Chen, Hui-Ling Huang and Shinn-Ying Ho

Citation: BMC Bioinformatics 2014 15(Suppl 16):S4

Content type: Research Published on: 8 December 2014
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Combining spatial and chemical information for clustering pharmacophores

A pharmacophore model consists of a group of chemical features arranged in three-dimensional space that can be used to represent the biological activities of the described molecules. Clustering of molecular in...

Authors: Lingxiao Zhou, Renate Griffith and Bruno Gaeta

Citation: BMC Bioinformatics 2014 15(Suppl 16):S5

Content type: Research Published on: 8 December 2014
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FMAj: a tool for high content analysis of muscle dynamics in Drosophila metamorphosis

During metamorphosis in Drosophila melanogaster, larval muscles undergo two different developmental fates; one population is removed by cell death, while the other persistent subset undergoes morphological remode...

Authors: Yadav Kuleesha, Wee Choo Puah, Feng Lin and Martin Wasser

Citation: BMC Bioinformatics 2014 15(Suppl 16):S6

Content type: Research Published on: 8 December 2014
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Bhageerath-H: A homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins

The advent of human genome sequencing project has led to a spurt in the number of protein sequences in the databanks. Success of structure based drug discovery severely hinges on the availability of structures...

Authors: B Jayaram, Priyanka Dhingra, Avinash Mishra, Rahul Kaushik, Goutam Mukherjee, Ankita Singh and Shashank Shekhar

Citation: BMC Bioinformatics 2014 15(Suppl 16):S7

Content type: Research Published on: 8 December 2014
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Protein inter-domain linker prediction using Random Forest and amino acid physiochemical properties

Protein chains are generally long and consist of multiple domains. Domains are distinct structural units of a protein that can evolve and function independently. The accurate prediction of protein domain linke...

Authors: Maad Shatnawi, Nazar Zaki and Paul D Yoo

Citation: BMC Bioinformatics 2014 15(Suppl 16):S8

Content type: Research Published on: 8 December 2014
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IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking

Protein-protein docking is an in silico method to predict the formation of protein complexes. Due to limited computational resources, the protein-protein docking approach has been developed under the assumption o...

Authors: Chinh Tran-To Su, Thuy-Diem Nguyen, Jie Zheng and Chee-Keong Kwoh

Citation: BMC Bioinformatics 2014 15(Suppl 16):S9

Content type: Research Published on: 8 December 2014
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iPhos: a toolkit to streamline the alkaline phosphatase-assisted comprehensive LC-MS phosphoproteome investigation

Comprehensive characterization of the phosphoproteome in living cells is critical in signal transduction research. But the low abundance of phosphopeptides among the total proteome in cells remains an obstacle...

Authors: Tzu-Hsien Yang, Hong-Tsun Chang, Eric SL Hsiao, Juo-Ling Sun, Chung-Ching Wang, Hsin-Yi Wu, Pao-Chi Liao and Wei-Sheng Wu

Citation: BMC Bioinformatics 2014 15(Suppl 16):S10

Content type: Research Published on: 8 December 2014
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Genetic algorithm with logistic regression for prediction of progression to Alzheimer's disease

Assessment of risk and early diagnosis of Alzheimer's disease (AD) is a key to its prevention or slowing the progression of the disease. Previous research on risk factors for AD typically utilizes statistical ...

Authors: Piers Johnson, Luke Vandewater, William Wilson, Paul Maruff, Greg Savage, Petra Graham, Lance S Macaulay, Kathryn A Ellis, Cassandra Szoeke, Ralph N Martins, Christopher C Rowe, Colin L Masters, David Ames and Ping Zhang

Citation: BMC Bioinformatics 2014 15(Suppl 16):S11

Content type: Research Published on: 8 December 2014
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Improving protein fold recognition using the amalgamation of evolutionary-based and structural based information

Deciphering three dimensional structure of a protein sequence is a challenging task in biological science. Protein fold recognition and protein secondary structure prediction are transitional steps in identify...

Authors: Kuldip K Paliwal, Alok Sharma, James Lyons and Abdollah Dehzangi

Citation: BMC Bioinformatics 2014 15(Suppl 16):S12

Content type: Research Published on: 8 December 2014
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Computational identification of novel natural inhibitors of glucagon receptor for checking type II diabetes mellitus

Interaction of the small peptide hormone glucagon with glucagon receptor (GCGR) stimulates the release of glucose from the hepatic cells during fasting; hence GCGR performs a significant function in glucose ho...

Authors: Sonam Grover, Jaspreet Kaur Dhanjal, Sukriti Goyal, Abhinav Grover and Durai Sundar

Citation: BMC Bioinformatics 2014 15(Suppl 16):S13

Content type: Research Published on: 8 December 2014
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Introducing TreeCollapse: a novel greedy algorithm to solve the cophylogeny reconstruction problem

Cophylogeny mapping is used to uncover deep coevolutionary associations between two or more phylogenetic histories at a macro coevolutionary scale. As cophylogeny mapping is NP-Hard, this technique relies heav...

Authors: Benjamin Drinkwater and Michael A Charleston

Citation: BMC Bioinformatics 2014 15(Suppl 16):S14

Content type: Research Published on: 8 December 2014
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Verification and validation of bioinformatics software without a gold standard: a case study of BWA and Bowtie

Bioinformatics software quality assurance is essential in genomic medicine. Systematic verification and validation of bioinformatics software is difficult because it is often not possible to obtain a realistic...

Authors: Eleni Giannoulatou, Shin-Ho Park, David T Humphreys and Joshua WK Ho

Citation: BMC Bioinformatics 2014 15(Suppl 16):S15

Content type: Research Published on: 8 December 2014
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Supervised prediction of drug-induced nephrotoxicity based on interleukin-6 and -8 expression levels

Drug-induced nephrotoxicity causes acute kidney injury and chronic kidney diseases, and is a major reason for late-stage failures in the clinical trials of new drugs. Therefore, early, pre-clinical prediction ...

Authors: Ran Su, Yao Li, Daniele Zink and Lit-Hsin Loo

Citation: BMC Bioinformatics 2014 15(Suppl 16):S16

Content type: Research Published on: 8 December 2014
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InCoB2014: bioinformatics to tackle the data to knowledge challenge

Since 2006, the International Conference on Bioinformatics (InCoB) has been publishing selected papers in BMC Bioinformatics. Papers within the scope of the journal from the 13th InCoB July 31-2 August, 2014 i...

Authors: Shoba Ranganathan, Tin Wee Tan and Christian Schönbach

Citation: BMC Bioinformatics 2014 15(Suppl 16):I1

Content type: Introduction Published on: 8 December 2014
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Thirteenth International Conference on Bioinformatics (InCoB2014): Bioinformatics

Research

Characterization and identification of protein O-GlcNAcylation sites with substrate specificity

An integrative model of multi-organ drug-induced toxicity prediction using gene-expression data

Use B-factor related features for accurate classification between protein binding interfaces and crystal packing contacts

SCMHBP: prediction and analysis of heme binding proteins using propensity scores of dipeptides

Combining spatial and chemical information for clustering pharmacophores

FMAj: a tool for high content analysis of muscle dynamics in Drosophila metamorphosis

Bhageerath-H: A homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins

Protein inter-domain linker prediction using Random Forest and amino acid physiochemical properties

IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking

iPhos: a toolkit to streamline the alkaline phosphatase-assisted comprehensive LC-MS phosphoproteome investigation

Genetic algorithm with logistic regression for prediction of progression to Alzheimer's disease

Improving protein fold recognition using the amalgamation of evolutionary-based and structural based information

Computational identification of novel natural inhibitors of glucagon receptor for checking type II diabetes mellitus

Introducing TreeCollapse: a novel greedy algorithm to solve the cophylogeny reconstruction problem

Verification and validation of bioinformatics software without a gold standard: a case study of BWA and Bowtie

Supervised prediction of drug-induced nephrotoxicity based on interleukin-6 and -8 expression levels

InCoB2014: bioinformatics to tackle the data to knowledge challenge

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