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  1. Multivariate approaches have been successfully applied to genome wide association studies. Recently, a Partial Least Squares (PLS) based approach was introduced for mapping yeast genotype-phenotype relations, ...

    Authors: Tahir Mehmood, Jonas Warringer, Lars Snipen and Solve Sæbø
    Citation: BMC Bioinformatics 2012 13:327
    Content type: Research article Published on:

  2. High throughput ’omics’ experiments are usually designed to compare changes observed between different conditions (or interventions) and to identify biomarkers capable of characterizing each condition. We cons...

    Authors: Benoit Liquet, Kim-Anh Lê Cao, Hakim Hocini and Rodolphe Thiébaut
    Citation: BMC Bioinformatics 2012 13:325
    Content type: Methodology article Published on:

  3. For shotgun mass spectrometry based proteomics the most computationally expensive step is in matching the spectra against an increasingly large database of sequences and their post-translational modifications ...

    Authors: Steven Lewis, Attila Csordas, Sarah Killcoyne, Henning Hermjakob, Michael R Hoopmann, Robert L Moritz, Eric W Deutsch and John Boyle
    Citation: BMC Bioinformatics 2012 13:324
    Content type: Software Published on:

  5. MicroRNAs (miRNAs) are important regulators of gene expression encoded by a variety of organisms, including viruses. Although the function of most of the viral miRNAs is currently unknown, there is evidence th...

    Authors: Isana Veksler-Lublinsky, Yonat Shemer-Avni, Eti Meiri, Zvi Bentwich, Klara Kedem and Michal Ziv-Ukelson
    Citation: BMC Bioinformatics 2012 13:322
    Content type: Research article Published on:

  6. Methods of weakening and attenuating pathogens’ abilities to infect and propagate in a host, thus allowing the natural immune system to more easily decimate invaders, have gained attention as alternatives to b...

    Authors: Eithon Cadag, Peter Tarczy-Hornoch and Peter J Myler
    Citation: BMC Bioinformatics 2012 13:321
    Content type: Methodology article Published on:

  7. It is desirable in genomic studies to select biomarkers that differentiate between normal and diseased populations based on related data sets from different platforms, including microarray expression and prote...

    Authors: Shicheng Wu, Yawen Xu, Zeny Feng, Xiaojian Yang, Xiaogang Wang and Xin Gao
    Citation: BMC Bioinformatics 2012 13:320
    Content type: Methodology article Published on:

  8. Genome-wide association studies (GWAS) using single nucleotide polymorphism (SNP) markers generate large quantities of tests results. Global and local graphical viewing of the test results is an effective appr...

    Authors: Shengwen Wang, Daniel Dvorkin and Yang Da
    Citation: BMC Bioinformatics 2012 13:319
    Content type: Software Published on:

  10. Discovery of functionally significant short, statistically overrepresented subsequence patterns (motifs) in a set of sequences is a challenging problem in bioinformatics. Oftentimes, not all sequences in the s...

    Authors: Phillip Seitzer, Elizabeth G Wilbanks, David J Larsen and Marc T Facciotti
    Citation: BMC Bioinformatics 2012 13:317
    Content type: Research article Published on:

  14. Epitope identification is an essential step toward synthetic vaccine development since epitopes play an important role in activating immune response. Classical experimental approaches are laborious and time-co...

    Authors: Thammakorn Saethang, Osamu Hirose, Ingorn Kimkong, Vu Anh Tran, Xuan Tho Dang, Lan Anh T Nguyen, Tu Kien T Le, Mamoru Kubo, Yoichi Yamada and Kenji Satou
    Citation: BMC Bioinformatics 2012 13:313
    Content type: Research article Published on:

  15. Sampling core subsets from genetic resources while maintaining as much as possible the genetic diversity of the original collection is an important but computationally complex task for gene bank managers. The ...

    Authors: Herman De Beukelaer, Petr Smýkal, Guy F Davenport and Veerle Fack
    Citation: BMC Bioinformatics 2012 13:312
    Content type: Research article Published on:

  16. MicroRNAs (miRNAs) are noncoding RNAs that direct post-transcriptional regulation of protein coding genes. Recent studies have shown miRNAs are important for controlling many biological processes, including ne...

    Authors: Susan C Tilton, Tamara L Tal, Sheena M Scroggins, Jill A Franzosa, Elena S Peterson, Robert L Tanguay and Katrina M Waters
    Citation: BMC Bioinformatics 2012 13:311
    Content type: Software Published on:

  17. This paper addresses the prediction of the free energy of binding of a drug candidate with enzyme InhA associated with Mycobacterium tuberculosis. This problem is found within rational drug design, where interact...

    Authors: Rodrigo C Barros, Ana T Winck, Karina S Machado, Márcio P Basgalupp, André CPLF de Carvalho, Duncan D Ruiz and Osmar Norberto de Souza
    Citation: BMC Bioinformatics 2012 13:310
    Content type: Research article Published on:

  18. Epitope prediction using computational methods represents one of the most promising approaches to vaccine development. Reduction of time, cost, and the availability of completely sequenced genomes are key poin...

    Authors: Daniela M Resende, Antônio M Rezende, Nesley JD Oliveira, Izabella CA Batista, Rodrigo Corrêa-Oliveira, Alexandre B Reis and Jeronimo C Ruiz
    Citation: BMC Bioinformatics 2012 13:309
    Content type: Research article Published on:

  19. Spectral counting methods provide an easy means of identifying proteins with differing abundances between complex mixtures using shotgun proteomics data. The crux spectral-counts command, implemented as part of t...

    Authors: Sean McIlwain, Michael Mathews, Michael S Bereman, Edwin W Rubel, Michael J MacCoss and William Stafford Noble
    Citation: BMC Bioinformatics 2012 13:308
    Content type: Software Published on:

  20. Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the ...

    Authors: Jim Jing-Yan Wang, Halima Bensmail and Xin Gao
    Citation: BMC Bioinformatics 2012 13:307
    Content type: Methodology article Published on:

  22. DNA capture technologies combined with high-throughput sequencing now enable cost-effective, deep-coverage, targeted sequencing of complete exomes. This is well suited for SNP discovery and genotyping. However...

    Authors: Jiantao Wu, Krzysztof R Grzeda, Chip Stewart, Fabian Grubert, Alexander E Urban, Michael P Snyder and Gabor T Marth
    Citation: BMC Bioinformatics 2012 13:305
    Content type: Methodology article Published on:

  23. Current research has shown that major difficulties in event extraction for the biomedical domain are traceable to coreference. Therefore, coreference resolution is believed to be useful for improving event ext...

    Authors: Ngan Nguyen, Jin-Dong Kim, Makoto Miwa, Takuya Matsuzaki and Junichi Tsujii
    Citation: BMC Bioinformatics 2012 13:304
    Content type: Research article Published on:

  24. 454 pyrosequencing is a commonly used massively parallel DNA sequencing technology with a wide variety of application fields such as epigenetics, metagenomics and transcriptomics. A well-known problem of this ...

    Authors: Kristof De Beuf, Joachim De Schrijver, Olivier Thas, Wim Van Criekinge, Rafael A Irizarry and Lieven Clement
    Citation: BMC Bioinformatics 2012 13:303
    Content type: Methodology article Published on:

  26. Analyzing regions of the genome where genetic variation is free from the confounding effects of natural selection is essential for many population genetic studies. Several recent studies in humans have stresse...

    Authors: Leonardo Arbiza, Elaine Zhong and Alon Keinan
    Citation: BMC Bioinformatics 2012 13:301
    Content type: Software Published on:

  27. Time-course gene expression data such as yeast cell cycle data may be periodically expressed. To cluster such data, currently used Fourier series approximations of periodic gene expressions have been found not...

    Authors: Kui Wang, Shu Kay Ng and Geoffrey J McLachlan
    Citation: BMC Bioinformatics 2012 13:300
    Content type: Methodology article Published on:

  28. Evolution of splice sites is a well-known phenomenon that results in transcript diversity during human evolution. Many novel splice sites are derived from repetitive elements and may not contribute to protein ...

    Authors: Dong Seon Kim and Yoonsoo Hahn
    Citation: BMC Bioinformatics 2012 13:299
    Content type: Research article Published on:

  29. Even though the classification of cancer tissue samples based on gene expression data has advanced considerably in recent years, it faces great challenges to improve accuracy. One of the challenges is to estab...

    Authors: Hongyan Zhang, Haiyan Wang, Zhijun Dai, Ming-shun Chen and Zheming Yuan
    Citation: BMC Bioinformatics 2012 13:298
    Content type: Methodology article Published on:

  30. Despite significant advancement in alignment algorithms, the exponential growth of nucleotide sequencing throughput threatens to outpace bioinformatic analysis. Computation may become the bottleneck of genome ...

    Authors: Brendan A Veeneman, Matthew K Iyer and Arul M Chinnaiyan
    Citation: BMC Bioinformatics 2012 13:297
    Content type: Software Published on:

  31. Fluorescence loss in photobleaching (FLIP) is a widely used imaging technique, which provides information about protein dynamics in various cellular regions. In FLIP, a small cellular region is repeatedly illu...

    Authors: Daniel Wüstner, Lukasz M Solanko, Frederik W Lund, Daniel Sage, Hans J Schroll and Michael A Lomholt
    Citation: BMC Bioinformatics 2012 13:296
    Content type: Methodology article Published on:

  32. Metabolic flux analysis has become an established method in systems biology and functional genomics. The most common approach for determining intracellular metabolic fluxes is to utilize mass spectrometry in c...

    Authors: C Hart Poskar, Jan Huege, Christian Krach, Mathias Franke, Yair Shachar-Hill and Björn H Junker
    Citation: BMC Bioinformatics 2012 13:295
    Content type: Software Published on:

  33. Previous studies have noted that drug targets appear to be associated with higher-degree or higher-centrality proteins in interaction networks. These studies explicitly or tacitly make choices of different sou...

    Authors: Antonio Mora and Ian M Donaldson
    Citation: BMC Bioinformatics 2012 13:294
    Content type: Research article Published on:

  34. The inference of homologies among DNA sequences, that is, positions in multiple genomes that share a common evolutionary origin, is a crucial, yet difficult task facing biologists. Its computational counterpar...

    Authors: Andrés Varón and Ward C Wheeler
    Citation: BMC Bioinformatics 2012 13:293
    Content type: Research article Published on:

  36. The robust identification of isotope patterns originating from peptides being analyzed through mass spectrometry (MS) is often significantly hampered by noise artifacts and the interference of overlapping patt...

    Authors: Martin Slawski, Rene Hussong, Andreas Tholey, Thomas Jakoby, Barbara Gregorius, Andreas Hildebrandt and Matthias Hein
    Citation: BMC Bioinformatics 2012 13:291
    Content type: Methodology article Published on:

  38. Computational models of protein structures were proved to be useful as search models in Molecular Replacement (MR), a common method to solve the phase problem faced by macromolecular crystallography. The succe...

    Authors: Marcin Pawlowski and Janusz M Bujnicki
    Citation: BMC Bioinformatics 2012 13:289
    Content type: Research article Published on:

  39. Protein inference from peptide identifications in shotgun proteomics must deal with ambiguities that arise due to the presence of peptides shared between different proteins, which is common in higher eukaryote...

    Authors: Gorka Prieto, Kerman Aloria, Nerea Osinalde, Asier Fullaondo, Jesus M Arizmendi and Rune Matthiesen
    Citation: BMC Bioinformatics 2012 13:288
    Content type: Software Published on:

  41. As it is the case with any OMICs technology, the value of proteomics data is defined by the degree of its functional interpretation in the context of phenotype. Functional analysis of proteomics profiles is in...

    Authors: Marina Bessarabova, Alexander Ishkin, Lellean JeBailey, Tatiana Nikolskaya and Yuri Nikolsky
    Citation: BMC Bioinformatics 2012 13(Suppl 16):S13
    Content type: Review Published on:

    This article is part of a Supplement: Volume 13 Supplement 16

  42. Quantitative proteomics now provides abundance ratios for thousands of proteins upon perturbations. These need to be functionally interpreted and correlated to other types of quantitative genome-wide data such...

    Authors: Juergen Cox and Matthias Mann
    Citation: BMC Bioinformatics 2012 13(Suppl 16):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 16

  43. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) imaging mass spectrometry, also called MALDI-imaging, is a label-free bioanalytical technique used for spatially-resolved chemical analysi...

    Authors: Theodore Alexandrov
    Citation: BMC Bioinformatics 2012 13(Suppl 16):S11
    Content type: Review Published on:

    This article is part of a Supplement: Volume 13 Supplement 16

  44. Data visualization plays a critical role in interpreting experimental results of proteomic experiments. Heat maps are particularly useful for this task, as they allow us to find quantitative patterns across pr...

    Authors: Melissa Key
    Citation: BMC Bioinformatics 2012 13(Suppl 16):S10
    Content type: Review Published on:

    This article is part of a Supplement: Volume 13 Supplement 16

  46. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) is widely used for quantitative proteomic investigations. The typical output of such studies is a list of identified and quantified peptid...

    Authors: Timothy Clough, Safia Thaminy, Susanne Ragg, Ruedi Aebersold and Olga Vitek
    Citation: BMC Bioinformatics 2012 13(Suppl 16):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 16

  47. Shotgun proteomics has recently emerged as a powerful approach to characterizing proteomes in biological samples. Its overall objective is to identify the form and quantity of each protein in a high-throughput...

    Authors: Yong Fuga Li and Predrag Radivojac
    Citation: BMC Bioinformatics 2012 13(Suppl 16):S4
    Content type: Review Published on:

    This article is part of a Supplement: Volume 13 Supplement 16

  48. Peptides are routinely identified from mass spectrometry-based proteomics experiments by matching observed spectra to peptides derived from protein databases. The error rates of these identifications can be es...

    Authors: Viktor Granholm, William Stafford Noble and Lukas Käll
    Citation: BMC Bioinformatics 2012 13(Suppl 16):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 16

  49. Automated database search engines are one of the fundamental engines of high-throughput proteomics enabling daily identifications of hundreds of thousands of peptides and proteins from tandem mass (MS/MS) spec...

    Authors: Kyowon Jeong, Sangtae Kim and Nuno Bandeira
    Citation: BMC Bioinformatics 2012 13(Suppl 16):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 16

  50. PeptideProphet is a post-processing algorithm designed to evaluate the confidence in identifications of MS/MS spectra returned by a database search. In this manuscript we describe the "what and how" of Peptide...

    Authors: Kelvin Ma, Olga Vitek and Alexey I Nesvizhskii
    Citation: BMC Bioinformatics 2012 13(Suppl 16):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 13 Supplement 16

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