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  1. Sequencing datasets consist of a finite number of reads which map to specific regions of a reference genome. Most effort in modeling these datasets focuses on the detection of univariate differentially express...

    Authors: Jason M Knight, Ivan Ivanov and Edward R Dougherty
    Citation: BMC Bioinformatics 2014 15:401
    Content type: Research Article Published on:

  3. Network-based approaches for the analysis of large-scale genomics data have become well established. Biological networks provide a knowledge scaffold against which the patterns and dynamics of ‘omics’ data can be...

    Authors: Aravind Venkatesan, Sushil Tripathi, Alejandro Sanz de Galdeano, Ward Blondé, Astrid Lægreid, Vladimir Mironov and Martin Kuiper
    Citation: BMC Bioinformatics 2014 15:386
    Content type: Research article Published on:

  4. Our knowledge of global protein-protein interaction (PPI) networks in complex organisms such as humans is hindered by technical limitations of current methods.

    Authors: Andrew Schoenrock, Bahram Samanfar, Sylvain Pitre, Mohsen Hooshyar, Ke Jin, Charles A Phillips, Hui Wang, Sadhna Phanse, Katayoun Omidi, Yuan Gui, Md Alamgir, Alex Wong, Fredrik Barrenäs, Mohan Babu, Mikael Benson, Michael A Langston…
    Citation: BMC Bioinformatics 2014 15:383
    Content type: Research article Published on:

  5. Metabolomics is one of most recent omics technologies. It has been applied on fields such as food science, nutrition, drug discovery and systems biology. For this, gas chromatography-mass spectrometry (GC-MS) ...

    Authors: Raphael BM Aggio, Arno Mayor, Sophie Reade, Chris SJ Probert and Katya Ruggiero
    Citation: BMC Bioinformatics 2014 15:374
    Content type: Software Published on:

  6. 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:

    This article is part of a Supplement: Volume 15 Supplement 16

  7. 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:

    This article is part of a Supplement: Volume 15 Supplement 16

  8. 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:

    This article is part of a Supplement: Volume 15 Supplement 16

  9. 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:

    This article is part of a Supplement: Volume 15 Supplement 16

  10. 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:

    This article is part of a Supplement: Volume 15 Supplement 16

  11. 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:

    This article is part of a Supplement: Volume 15 Supplement 16

  12. 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:

    This article is part of a Supplement: Volume 15 Supplement 16

  13. 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:

    This article is part of a Supplement: Volume 15 Supplement 16

  14. 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:

    This article is part of a Supplement: Volume 15 Supplement 16

  15. 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:

    This article is part of a Supplement: Volume 15 Supplement 16

  16. 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:

    This article is part of a Supplement: Volume 15 Supplement 16

  17. 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:

    This article is part of a Supplement: Volume 15 Supplement 16

  18. 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:

    This article is part of a Supplement: Volume 15 Supplement 16

  19. 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:

    This article is part of a Supplement: Volume 15 Supplement 16

  20. 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:

    This article is part of a Supplement: Volume 15 Supplement 16

  21. 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:

    This article is part of a Supplement: Volume 15 Supplement 16

  22. 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:

    This article is part of a Supplement: Volume 15 Supplement 16

  24. Applying machine learning methods on microarray gene expression profiles for disease classification problems is a popular method to derive biomarkers, i.e. sets of genes that can predict disease state or outco...

    Authors: Lingjian Yang, Chrysanthi Ainali, Sophia Tsoka and Lazaros G Papageorgiou
    Citation: BMC Bioinformatics 2014 15:390
    Content type: Research article Published on:

  25. Within many research areas, such as transcriptomics, the millions of short DNA fragments (reads) produced by current sequencing platforms need to be assembled into transcript sequences before they can be utili...

    Authors: John Archer, Gareth Whiteley, Nicholas R Casewell, Robert A Harrison and Simon C Wagstaff
    Citation: BMC Bioinformatics 2014 15:389
    Content type: Software Published on:

  26. The exponential growth of next-generation sequencing (NGS) derived DNA data poses great challenges to data storage and transmission. Although many compression algorithms have been proposed for DNA reads in NGS...

    Authors: Jiarui Zhou, Zhen Ji, Zexuan Zhu and Shan He
    Citation: BMC Bioinformatics 2014 15(Suppl 15):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 15

  27. Identifying protein-protein interactions (PPIs) is essential for elucidating protein functions and understanding the molecular mechanisms inside the cell. However, the experimental methods for detecting PPIs a...

    Authors: Zhu-Hong You, Lin Zhu, Chun-Hou Zheng, Hong-Jie Yu, Su-Ping Deng and Zhen Ji
    Citation: BMC Bioinformatics 2014 15(Suppl 15):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 15

  28. To infer gene regulatory networks from time series gene profiles, two important tasks that are related to biological systems must be undertaken. One task is to determine a valid network structure that has topo...

    Authors: Yu-Ting Hsiao and Wei-Po Lee
    Citation: BMC Bioinformatics 2014 15(Suppl 15):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 15

  29. Expressed sequences (e.g. ESTs) are a strong source of evidence to improve gene structures and predict reliable alternative splicing events. When a genome assembly is available, ESTs are suitable to generate g...

    Authors: Vitoantonio Bevilacqua, Nicola Pietroleonardo, Ely Ignazio Giannino, Fabio Stroppa, Domenico Simone, Graziano Pesole and Ernesto Picardi
    Citation: BMC Bioinformatics 2014 15(Suppl 15):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 15

  30. Measuring protein structural similarity attempts to establish a relationship of equivalence between polymer structures based on their conformations. In several recent studies, researchers have explored protein...

    Authors: Sheng-Lung Peng and Yu-Wei Tsay
    Citation: BMC Bioinformatics 2014 15(Suppl 15):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 15

  31. Interaction of proteins with other molecules plays an important role in many biological activities. As many structures of protein-DNA complexes and protein-RNA complexes have been determined in the past years,...

    Authors: Byungkyu Park, Hyungchan Kim and Kyungsook Han
    Citation: BMC Bioinformatics 2014 15(Suppl 15):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 15

  32. Protein-ligand binding is important for some proteins to perform their functions. Protein-ligand binding sites are the residues of proteins that physically bind to ligands. Despite of the recent advances in co...

    Authors: Peng Chen, Jianhua Z Huang and Xin Gao
    Citation: BMC Bioinformatics 2014 15(Suppl 15):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 15

  33. Differential coexpression analysis usually requires the definition of 'distance' or 'similarity' between measured datasets. Until now, the most common choice is Pearson correlation coefficient. However, Pearso...

    Authors: Chun-Hou Zheng, Lin Yuan, Wen Sha and Zhan-Li Sun
    Citation: BMC Bioinformatics 2014 15(Suppl 15):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 15

  34. Previous studies have demonstrated that machine learning based molecular cancer classification using gene expression profiling (GEP) data is promising for the clinic diagnosis and treatment of cancer. Novel cl...

    Authors: Shu-Lin Wang, Liuchao Sun and Jianwen Fang
    Citation: BMC Bioinformatics 2014 15(Suppl 15):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 15

  35. Protein folding structure prediction is one of the most challenging problems in the bioinformatics domain. Because of the complexity of the realistic protein structure, the simplified structure model and the c...

    Authors: Xiaoli Lin, Xiaolong Zhang and Fengli zhou
    Citation: BMC Bioinformatics 2014 15(Suppl 15):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 15

  36. Predication of gene regularity network (GRN) from expression data is a challenging task. There are many methods that have been developed to address this challenge ranging from supervised to unsupervised method...

    Authors: Zeeshan Gillani, Muhammad Sajid Hamid Akash, MD Matiur Rahaman and Ming Chen
    Citation: BMC Bioinformatics 2014 15:395
    Content type: Research article Published on:

  37. The invasion of red blood cells (RBCs) by malarial parasites is an essential step in the life cycle of Plasmodium falciparum. Human-parasite surface protein interactions play a critical role in this process. Alth...

    Authors: Xuewu Liu, Yuxiao Huang, Jiao Liang, Shuai Zhang, Yinghui Li, Jun Wang, Yan Shen, Zhikai Xu and Ya Zhao
    Citation: BMC Bioinformatics 2014 15:393
    Content type: Research article Published on:

  38. The identification of new diagnostic or prognostic biomarkers is one of the main aims of clinical cancer research. Technologies like mass spectrometry are commonly being used in proteomic research. Mass spectr...

    Authors: Caroline Truntzer, Elise Mostacci, Aline Jeannin, Jean-Michel Petit, Patrick Ducoroy and Hervé Cardot
    Citation: BMC Bioinformatics 2014 15:385
    Content type: Research Article Published on:

  39. In order to extract meaningful information from electronic medical records, such as signs and symptoms, diagnoses, and treatments, it is important to take into account the contextual properties of the identifi...

    Authors: Zubair Afzal, Ewoud Pons, Ning Kang, Miriam CJM Sturkenboom, Martijn J Schuemie and Jan A Kors
    Citation: BMC Bioinformatics 2014 15:373
    Content type: Research article Published on:

  40. Increasing number of eQTL (Expression Quantitative Trait Loci) datasets facilitate genetics and systems biology research. Meta-analysis tools are in need to jointly analyze datasets of same or similar issue ty...

    Authors: Antonio Fabio Di Narzo, Haoxiang Cheng, Jianwei Lu and Ke Hao
    Citation: BMC Bioinformatics 2014 15:392
    Content type: Software Published on:

  45. Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools ...

    Authors: Steffen Möller, Enis Afgan, Michael Banck, Raoul JP Bonnal, Timothy Booth, John Chilton, Peter JA Cock, Markus Gumbel, Nomi Harris, Richard Holland, Matúš Kalaš, László Kaján, Eri Kibukawa, David R Powel, Pjotr Prins, Jacqueline Quinn…
    Citation: BMC Bioinformatics 2014 15(Suppl 14):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 14

  46. Text mining services are rapidly becoming a crucial component of various knowledge management pipelines, for example in the process of database curation, or for exploration and enrichment of biomedical data wi...

    Authors: Fabio Rinaldi, Simon Clematide, Hernani Marques, Tilia Ellendorff, Martin Romacker and Raul Rodriguez-Esteban
    Citation: BMC Bioinformatics 2014 15(Suppl 14):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 14

  47. Reporting and sharing experimental metadata- such as the experimental design, characteristics of the samples, and procedures applied, along with the analysis results, in a standardised manner ensures that data...

    Authors: Alejandra González-Beltrán, Eamonn Maguire, Susanna-Assunta Sansone and Philippe Rocca-Serra
    Citation: BMC Bioinformatics 2014 15(Suppl 14):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 14

  48. Life-science laboratories make increasing use of Next Generation Sequencing (NGS) for studying bio-macromolecules and their interactions. Array-based methods for measuring gene expression or protein-DNA intera...

    Authors: Francesco Venco, Yuriy Vaskin, Arnaud Ceol and Heiko Muller
    Citation: BMC Bioinformatics 2014 15(Suppl 14):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 14

  49. Computing semantic relatedness between textual labels representing biological and medical concepts is a crucial task in many automated knowledge extraction and processing applications relevant to the biomedica...

    Authors: Maciej Rybinski and José Francisco Aldana-Montes
    Citation: BMC Bioinformatics 2014 15(Suppl 14):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 14

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