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  1. Population genetics and association studies usually rely on a set of known variable sites that are then genotyped in subsequent samples, because it is easier to genotype than to discover the variation. This is...

    Authors: José Ignacio Lucas-Lledó, David Vicente-Salvador, Cristina Aguado and Mario Cáceres
    Citation: BMC Bioinformatics 2014 15:163
    Content type: Software Published on:

  2. To leverage the potential of multi-omics studies, exploratory data analysis methods that provide systematic integration and comparison of multiple layers of omics information are required. We describe multiple...

    Authors: Chen Meng, Bernhard Kuster, Aedín C Culhane and Amin Moghaddas Gholami
    Citation: BMC Bioinformatics 2014 15:162
    Content type: Methodology article Published on:

  3. Our environment is composed of biological components of varying magnitude. The relationships between the different biological elements can be represented as a biological network. The process of mating in S. cerev...

    Authors: Abhishek Majumdar, Stephen D Scott, Jitender S Deogun and Steven Harris
    Citation: BMC Bioinformatics 2014 15(Suppl 7):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 7

  4. Since the advent of next-generation sequencing many previously untestable hypotheses have been realized. Next-generation sequencing has been used for a wide range of studies in diverse fields such as populatio...

    Authors: Mark TW Ebbert, Mark E Wadsworth, Kevin L Boehme, Kaitlyn L Hoyt, Aaron R Sharp, Brendan D O'Fallon, John SK Kauwe and Perry G Ridge
    Citation: BMC Bioinformatics 2014 15(Suppl 7):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 7

  5. The expansion of polyglutamine (poly-Q) repeats in several unrelated proteins is associated with at least ten neurodegenerative diseases. The length of the poly-Q regions plays an important role in the progres...

    Authors: Jingran Wen, Daniel R Scoles and Julio C Facelli
    Citation: BMC Bioinformatics 2014 15(Suppl 7):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 7

  6. Biological networks connect genes, gene products to one another. A network of co-regulated genes may form gene clusters that can encode proteins and take part in common biological processes. A gene co-expressi...

    Authors: Swarup Roy, Dhruba K Bhattacharyya and Jugal K Kalita
    Citation: BMC Bioinformatics 2014 15(Suppl 7):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 7

  7. For decades, mass spectrometry data has been analyzed to investigate a wide array of research interests, including disease diagnostics, biological and chemical theory, genomics, and drug development. Progress ...

    Authors: Rob Smith, Andrew D Mathis, Dan Ventura and John T Prince
    Citation: BMC Bioinformatics 2014 15(Suppl 7):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 7

  8. Population stratification is a key concern for genetic association analyses. In addition, extreme homogeneity of ethnic origins of a population can make it difficult to interpret how genetic associations in th...

    Authors: Aaron R Sharp, Perry G Ridge, Matthew H Bailey, Kevin L Boehme, Maria C Norton, JoAnn T Tschanz, Ronald G Munger, Christopher D Corcoran and John SK Kauwe
    Citation: BMC Bioinformatics 2014 15(Suppl 7):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 7

  9. Cellular differentiation during development is controlled by gene regulatory networks (GRNs). This complex process is always subject to gene expression noise. There is evidence suggesting that commonly seen pa...

    Authors: Ahmadreza Ghaffarizadeh, Nicholas S Flann and Gregory J Podgorski
    Citation: BMC Bioinformatics 2014 15(Suppl 7):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 7

  10. The mitochondria are essential organelles and are the location of cellular respiration, which is responsible for the majority of ATP production. Each cell contains multiple mitochondria, and each mitochondrion...

    Authors: Perry G Ridge, Taylor J Maxwell, Spencer J Foutz, Matthew H Bailey, Christopher D Corcoran, JoAnn T Tschanz, Maria C Norton, Ronald G Munger, Elizabeth O'Brien, Richard A Kerber, Richard M Cawthon and John SK Kauwe
    Citation: BMC Bioinformatics 2014 15(Suppl 7):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 7

  11. Inference of gene regulatory networks (GRNs) from gene microarray expression data is of great interest and remains a challenging task in systems biology. Despite many efforts to develop efficient computational...

    Authors: Jung Hun Oh and Joseph O Deasy
    Citation: BMC Bioinformatics 2014 15(Suppl 7):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 7

  12. Currently available microRNA (miRNA) target prediction algorithms require the presence of a conserved seed match to the 5' end of the miRNA and limit the target sites to the 3' untranslated regions of mRNAs. H...

    Authors: Wenlong Xu, Anthony San Lucas, Zixing Wang and Yin Liu
    Citation: BMC Bioinformatics 2014 15(Suppl 7):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 7

  13. Error correction is an important step in increasing the quality of next-generation sequencing data for downstream analysis and use. Polymorphic datasets are a challenge for many bioinformatic software packages...

    Authors: M Stanley Fujimoto, Paul M Bodily, Nozomu Okuda, Mark J Clement and Quinn Snell
    Citation: BMC Bioinformatics 2014 15(Suppl 7):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 7

  14. Interactions between the epigenome and structural genomic variation are potentially bi-directional. In one direction, structural variants may cause epigenomic changes in cis. In the other direction, specific loca...

    Authors: Cristian Coarfa, Christina Stewart Pichot, Andrew Jackson, Arpit Tandon, Viren Amin, Sriram Raghuraman, Sameer Paithankar, Adrian V Lee, Sean E McGuire and Aleksandar Milosavljevic
    Citation: BMC Bioinformatics 2014 15(Suppl 7):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 7

  15. Drug discovery, disease detection, and personalized medicine are fast-growing areas of genomic research. With the advancement of next-generation sequencing techniques, researchers can obtain an abundance of da...

    Authors: Nathan L Clement, Lee P Thompson and Daniel P Miranker
    Citation: BMC Bioinformatics 2014 15(Suppl 7):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 7

  18. SNP genotyping microarrays have revolutionized the study of complex disease. The current range of commercially available genotyping products contain extensive catalogues of low frequency and rare variants. Exi...

    Authors: Ruijie Liu, Zhiyin Dai, Meredith Yeager, Rafael A Irizarry and Matthew E Ritchie
    Citation: BMC Bioinformatics 2014 15:158
    Content type: Methodology article Published on:

  19. Several methods are available for the detection of covarying positions from a multiple sequence alignment (MSA). If the MSA contains a large number of sequences, information about the proximities between resid...

    Authors: Greg W Clark, Sharon H Ackerman, Elisabeth R Tillier and Domenico L Gatti
    Citation: BMC Bioinformatics 2014 15:157
    Content type: Methodology article Published on:

  20. The locations of the TM segments inside the membrane proteins are the consequence of a cascade of several events: the localizing of the nascent chain to the membrane, its insertion through the translocon, and ...

    Authors: Dominique Tessier, Sami Laroum, Béatrice Duval, Emma M Rath, W Bret Church and Jin-Kao Hao
    Citation: BMC Bioinformatics 2014 15:156
    Content type: Research article Published on:

  21. The Gene Ontology project integrates data about the function of gene products across a diverse range of organisms, allowing the transfer of knowledge from model organisms to humans, and enabling computational ...

    Authors: Rachael P Huntley, Midori A Harris, Yasmin Alam-Faruque, Judith A Blake, Seth Carbon, Heiko Dietze, Emily C Dimmer, Rebecca E Foulger, David P Hill, Varsha K Khodiyar, Antonia Lock, Jane Lomax, Ruth C Lovering, Prudence Mutowo-Meullenet, Tony Sawford, Kimberly Van Auken…
    Citation: BMC Bioinformatics 2014 15:155
    Content type: Methodology article Published on:

  22. Accurate somatic mutation-calling is essential for insightful mutation analyses in cancer studies. Several mutation-callers are publicly available and more are likely to appear. Nonetheless, mutation-calling i...

    Authors: Su Yeon Kim, Laurent Jacob and Terence P Speed
    Citation: BMC Bioinformatics 2014 15:154
    Content type: Research article Published on:

  23. Many variable selection techniques have been proposed for the clustering of gene expression data. While these methods tend to filter out irrelevant genes and identify informative genes that contribute to a clu...

    Authors: Zixing Wang, F Anthony San Lucas, Peng Qiu and Yin Liu
    Citation: BMC Bioinformatics 2014 15:153
    Content type: Research article Published on:

  24. Genome-wide association studies (GWAS) have successfully identified a large number of single nucleotide polymorphisms (SNPs) that are associated with a wide range of human diseases. However, many of these dise...

    Authors: Shangwei Ning, Zuxianglan Zhao, Jingrun Ye, Peng Wang, Hui Zhi, Ronghong Li, Tingting Wang and Xia Li
    Citation: BMC Bioinformatics 2014 15:152
    Content type: Database Published on:

  31. Inferring operon maps is crucial to understanding the regulatory networks of prokaryotic genomes. Recently, RNA-seq based transcriptome studies revealed that in many bacterial species the operon structure vary...

    Authors: Vittorio Fortino, Olli-Pekka Smolander, Petri Auvinen, Roberto Tagliaferri and Dario Greco
    Citation: BMC Bioinformatics 2014 15:145
    Content type: Research article Published on:

  32. Cap analysis of gene expression (CAGE) is a sequencing based technology to capture the 5’ ends of RNAs in a biological sample. After mapping, a CAGE peak on the genome indicates the position of an active trans...

    Authors: Akira Hasegawa, Carsten Daub, Piero Carninci, Yoshihide Hayashizaki and Timo Lassmann
    Citation: BMC Bioinformatics 2014 15:144
    Content type: Software Published on:

  34. Antibiotics are the widely prescribed drugs for children and most likely to be related with adverse reactions. Record on adverse reactions and allergies from antibiotics considerably affect the prescription ch...

    Authors: Pinar Yildirim, Ljiljana Majnarić, Ozgur Ilyas Ekmekci and Andreas Holzinger
    Citation: BMC Bioinformatics 2014 15(Suppl 6):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 6

  35. Cancer is a complex disease that has proven to be difficult to understand on the single-gene level. For this reason a functional elucidation needs to take interactions among genes on a systems-level into accou...

    Authors: Frank Emmert-Streib, Ricardo de Matos Simoes, Galina Glazko, Simon McDade, Benjamin Haibe-Kains, Andreas Holzinger, Matthias Dehmer and Frederick Charles Campbell
    Citation: BMC Bioinformatics 2014 15(Suppl 6):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 6

  36. This paper presents multilevel data glyphs optimized for the interactive knowledge discovery and visualization of large biomedical data sets. Data glyphs are three- dimensional objects defined by multiple leve...

    Authors: Heimo Müller, Robert Reihs, Kurt Zatloukal and Andreas Holzinger
    Citation: BMC Bioinformatics 2014 15(Suppl 6):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 6

  37. Cluster analysis is widely used to discover patterns in multi-dimensional data. Clustered heatmaps are the standard technique for visualizing one-way and two-way clustering results. In clustered heatmaps, rows...

    Authors: Marc Streit, Samuel Gratzl, Michael Gillhofer, Andreas Mayr, Andreas Mitterecker and Sepp Hochreiter
    Citation: BMC Bioinformatics 2014 15(Suppl 6):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 6

  38. Patterns of disease incidence can identify new risk factors for the disease or provide insight into the etiology. For example, allergies and infectious diseases have been shown to follow periodic temporal patt...

    Authors: Rachel D Melamed, Hossein Khiabanian and Raul Rabadan
    Citation: BMC Bioinformatics 2014 15(Suppl 6):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 6

  39. Heart rate variability is the variation of the time interval between consecutive heartbeats. Entropy is a commonly used tool to describe the regularity of data sets. Entropy functions are defined using multipl...

    Authors: Christopher C Mayer, Martin Bachler, Matthias Hörtenhuber, Christof Stocker, Andreas Holzinger and Siegfried Wassertheurer
    Citation: BMC Bioinformatics 2014 15(Suppl 6):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 6

  40. Finding an efficient method to solve the parameter estimation problem (inverse problem) for nonlinear biochemical dynamical systems could help promote the functional understanding at the system level for signa...

    Authors: Jun Sun, Vasile Palade, Yujie Cai, Wei Fang and Xiaojun Wu
    Citation: BMC Bioinformatics 2014 15(Suppl 6):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 6

  42. Because of its important effects, as an epigenetic factor, on gene expression and disease development, DNA methylation has drawn much attention from researchers. Detecting differentially methylated loci is an ...

    Authors: Zhongxue Chen, Hanwen Huang and Qingzhong Liu
    Citation: BMC Bioinformatics 2014 15:142
    Content type: Methodology article Published on:

  43. Array based methylation profiling is a cost-effective solution to study the association between genome methylation and human disease & development. Available tools to analyze the Illumina Infinium HumanMethyla...

    Authors: Martin A Rijlaarsdam, Yvonne G van der Zwan, Lambert CJ Dorssers and Leendert HJ Looijenga
    Citation: BMC Bioinformatics 2014 15:141
    Content type: Software Published on:

  45. The use of classification algorithms is becoming increasingly important for the field of computational biology. However, not only the quality of the classification, but also its biological interpretation is im...

    Authors: Susanne Bornelöv, Simon Marillet and Jan Komorowski
    Citation: BMC Bioinformatics 2014 15:139
    Content type: Methodology article Published on:

  47. DNA microarrays are potentially powerful technology for improving diagnostic classification, treatment selection, and prognostic assessment. The use of this technology to predict cancer outcome has a history o...

    Authors: Minta Thomas, Kris De Brabanter and Bart De Moor
    Citation: BMC Bioinformatics 2014 15:137
    Content type: Methodology article Published on:

  48. Optimization is the key to solving many problems in computational biology. Global optimization methods, which provide a robust methodology, and metaheuristics in particular have proven to be the most efficient...

    Authors: Jose A Egea, David Henriques, Thomas Cokelaer, Alejandro F Villaverde, Aidan MacNamara, Diana-Patricia Danciu, Julio R Banga and Julio Saez-Rodriguez
    Citation: BMC Bioinformatics 2014 15:136
    Content type: Software Published on:

  50. Over the last 20 years in biotechnology, the production of recombinant proteins has been a crucial bioprocess in both biopharmaceutical and research arena in terms of human health, scientific impact and econom...

    Authors: Narjeskhatoon Habibi, Siti Z Mohd Hashim, Alireza Norouzi and Mohammed Razip Samian
    Citation: BMC Bioinformatics 2014 15:134
    Content type: Research article Published on:

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