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  2. Whole-genome bisulfite sequencing currently provides the highest-precision view of the epigenome, with quantitative information about populations of cells down to single nucleotide resolution. Several studies ...

    Authors: Egor Dolzhenko and Andrew D Smith
    Citation: BMC Bioinformatics 2014 15:215
    Content type: Research article Published on:

  3. The life-science community faces a major challenge in handling “big data”, highlighting the need for high quality infrastructures capable of sharing and publishing research data. Data preservation, analysis, a...

    Authors: Daniel Arend, Matthias Lange, Jinbo Chen, Christian Colmsee, Steffen Flemming, Denny Hecht and Uwe Scholz
    Citation: BMC Bioinformatics 2014 15:214
    Content type: Software Published on:

  5. Chickpea (Cicer arietinum) is a widely grown legume crop in tropical, sub-tropical and temperate regions. Molecular breeding approaches seem to be essential for enhancing crop productivity in chickpea. Until rece...

    Authors: Dadakhalandar Doddamani, Mohan AVSK Katta, Aamir W Khan, Gaurav Agarwal, Trushar M Shah and Rajeev K Varshney
    Citation: BMC Bioinformatics 2014 15:212
    Content type: Database Published on:

  7. Despite increased investment in pharmaceutical research and development, fewer and fewer new drugs are entering the marketplace. This has prompted studies in repurposing existing drugs for use against diseases...

    Authors: Ruifeng Liu, Narender Singh, Gregory J Tawa, Anders Wallqvist and Jaques Reifman
    Citation: BMC Bioinformatics 2014 15:210
    Content type: Methodology article Published on:

  8. Differential gene expression patterns in cells of the mammalian brain result in the morphological, connectional, and functional diversity of cells. A wide variety of studies have shown that certain genes are e...

    Authors: Rongjian Li, Wenlu Zhang and Shuiwang Ji
    Citation: BMC Bioinformatics 2014 15:209
    Content type: Methodology article Published on:

  10. In quantitative proteomics, peptide mapping is a valuable approach to combine positional quantitative information with topographical and domain information of proteins. Quantitative proteomic analysis of cell ...

    Authors: Pavankumar Videm, Deepika Gunasekaran, Bernd Schröder, Bettina Mayer, Martin L Biniossek and Oliver Schilling
    Citation: BMC Bioinformatics 2014 15:207
    Content type: Software Published on:

  11. Parsimony and maximum likelihood methods of phylogenetic tree estimation and parsimony methods for genome rearrangements are central to the study of genome evolution yet to date they have largely been pursued ...

    Authors: Benedict Paten, Daniel R Zerbino, Glenn Hickey and David Haussler
    Citation: BMC Bioinformatics 2014 15:206
    Content type: Methodology article Published on:

  12. In many applications, a family of nucleotide or protein sequences classified into several subfamilies has to be modeled. Profile Hidden Markov Models (pHMMs) are widely used for this task, modeling each subfam...

    Authors: Ingo Bulla, Anne-Kathrin Schultz, Christophe Chesneau, Tanya Mark and Florin Serea
    Citation: BMC Bioinformatics 2014 15:205
    Content type: Research article Published on:

  14. Non-specific feature selection is a dimension reduction procedure performed prior to cluster analysis of high dimensional molecular data. Not all measured features are expected to show biological variation, so...

    Authors: Xinhui Wang, Peter W Laird, Toshinori Hinoue, Susan Groshen and Kimberly D Siegmund
    Citation: BMC Bioinformatics 2014 15:199
    Content type: Methodology article Published on:

  15. Detection of large genomic rearrangements, such as large indels, duplications or translocations is now commonly achieved by next generation sequencing (NGS) approaches. Recently, several tools have been develo...

    Authors: Delphine Naquin, Yves d’Aubenton-Carafa, Claude Thermes and Maud Silvain
    Citation: BMC Bioinformatics 2014 15:198
    Content type: Software Published on:

  16. The characterization of protein binding sites is a major challenge in computational biology. Proteins interact with a wide variety of molecules and understanding of such complex interactions is essential to ga...

    Authors: Saulo HP Oliveira, Felipe AN Ferraz, Rodrigo V Honorato, José Xavier-Neto, Tiago JP Sobreira and Paulo SL de Oliveira
    Citation: BMC Bioinformatics 2014 15:197
    Content type: Software Published on:

  17. Gut microbiome metagenomics has revealed many protein families and domains found largely or exclusively in that environment. Proteins containing the GxGYxYP domain are over-represented in the gut microbiota, a...

    Authors: Daniel J Rigden, Ruth Y Eberhardt, Harry J Gilbert, Qingping Xu, Yuanyuan Chang and Adam Godzik
    Citation: BMC Bioinformatics 2014 15:196
    Content type: Research article Published on:

  21. RNA interference (RNAi) is an effective and important tool used to study gene function. For large-scale screens, RNAi is used to systematically down-regulate genes of interest and analyze their roles in a biol...

    Authors: Bahar Yilmazel, Yanhui Hu, Frederic Sigoillot, Jennifer A Smith, Caroline E Shamu, Norbert Perrimon and Stephanie E Mohr
    Citation: BMC Bioinformatics 2014 15:192
    Content type: Software Published on:

  22. Meganucleases are important tools for genome engineering, providing an efficient way to generate DNA double-strand breaks at specific loci of interest. Numerous experimental efforts, ranging from in vivo selectio...

    Authors: Mikhail Zaslavskiy, Claudia Bertonati, Philippe Duchateau, Aymeric Duclert and George H Silva
    Citation: BMC Bioinformatics 2014 15:191
    Content type: Methodology article Published on:

  23. Data on single-nucleotide polymorphisms (SNPs) have been found to be useful in predicting phenotypes ranging from an individual’s class membership to his/her risk of developing a disease. In multi-class classi...

    Authors: Xinyu Liu, Yupeng Wang and TN Sriram
    Citation: BMC Bioinformatics 2014 15:190
    Content type: Methodology article Published on:

  24. Accurate computational identification of eukaryotic gene organization is a long-standing problem. Despite the fundamental importance of precise annotation of genes encoded in newly sequenced genomes, the accur...

    Authors: Osamu Gotoh, Mariko Morita and David R Nelson
    Citation: BMC Bioinformatics 2014 15:189
    Content type: Research article Published on:

  25. Transcriptome sequencing is a powerful tool for measuring gene expression, but as well as some other technologies, various artifacts and biases affect the quantification. In order to correct some of them, seve...

    Authors: Cyril Filloux, Meersseman Cédric, Philippe Romain, Forestier Lionel, Klopp Christophe, Rocha Dominique, Maftah Abderrahman and Petit Daniel
    Citation: BMC Bioinformatics 2014 15:188
    Content type: Research article Published on:

  27. Identification of protein complexes can help us get a better understanding of cellular mechanism. With the increasing availability of large-scale protein-protein interaction (PPI) data, numerous computational ...

    Authors: Xiao-Fei Zhang, Dao-Qing Dai, Le Ou-Yang and Hong Yan
    Citation: BMC Bioinformatics 2014 15:186
    Content type: Research article Published on:

  28. Erroneous patient birthdates are common in health databases. Detection of these errors usually involves manual verification, which can be resource intensive and impractical. By identifying a frequent manifesta...

    Authors: Wei Luo, Marcus Gallagher, Bill Loveday, Susan Ballantyne, Jason P Connor and Janet Wiles
    Citation: BMC Bioinformatics 2014 15:185
    Content type: Research article Published on:

  29. The high demanding computational requirements necessary to carry out protein motion simulations make it difficult to obtain information related to protein motion. On the one hand, molecular dynamics simulation...

    Authors: Mikel Diez, Víctor Petuya, Luis Alfonso Martínez-Cruz and Alfonso Hernández
    Citation: BMC Bioinformatics 2014 15:184
    Content type: Research article Published on:

  32. Various computer-based methods exist for the detection and quantification of protein spots in two dimensional gel electrophoresis images. Area-based methods are commonly used for spot quantification: an area i...

    Authors: Jan M Brauner, Teja W Groemer, Armin Stroebel, Simon Grosse-Holz, Timo Oberstein, Jens Wiltfang, Johannes Kornhuber and Juan Manuel Maler
    Citation: BMC Bioinformatics 2014 15:181
    Content type: Research article Published on:

  34. Understanding the molecular mechanisms involved in disease is critical for the development of more effective and individualized strategies for prevention and treatment. The amount of disease-related literature...

    Authors: Toshihide Ono and Satoru Kuhara
    Citation: BMC Bioinformatics 2014 15:179
    Content type: Research article Published on:

  35. The ability of science to produce experimental data has outpaced the ability to effectively visualize and integrate the data into a conceptual framework that can further higher order understanding. Multidimens...

    Authors: Marianna Budnikova, Jeffrey W Habig, Daniel Lobo, Nicolas Cornia, Michael Levin and Tim Andersen
    Citation: BMC Bioinformatics 2014 15:178
    Content type: Methodology article Published on:

  36. Networks of interacting genes and gene products mediate most cellular and developmental processes. High throughput screening methods combined with literature curation are identifying many of the protein-protei...

    Authors: Thilakam Murali, Svetlana Pacifico and Russell L Finley Jr
    Citation: BMC Bioinformatics 2014 15:177
    Content type: Research article Published on:

  37. Ongoing advancements in cloud computing provide novel opportunities in scientific computing, especially for distributed workflows. Modern web browsers can now be used as high-performance workstations for query...

    Authors: Sean R Wilkinson and Jonas S Almeida
    Citation: BMC Bioinformatics 2014 15:176
    Content type: Research article Published on:

  39. Gene expression in vertebrate cells may be controlled post-transcriptionally through regulatory elements in mRNAs. These are usually located in the untranslated regions (UTRs) of mRNA sequences, particularly t...

    Authors: Ambarish Biswas and Chris M Brown
    Citation: BMC Bioinformatics 2014 15:174
    Content type: Software Published on:

  40. Human disease often arises as a consequence of alterations in a set of associated genes rather than alterations to a set of unassociated individual genes. Most previous microarray-based meta-analyses identifie...

    Authors: Chun-Pei Cheng, Christopher DeBoever, Kelly A Frazer, Yu-Cheng Liu and Vincent S Tseng
    Citation: BMC Bioinformatics 2014 15:173
    Content type: Methodology article Published on:

  41. Identification of recombination events and which chromosomal segments contributed to an individual is useful for a number of applications in genomic analyses including haplotyping, imputation, signatures of se...

    Authors: Mohammad H Ferdosi, Brian P Kinghorn, Julius HJ van der Werf, Seung Hwan Lee and Cedric Gondro
    Citation: BMC Bioinformatics 2014 15:172
    Content type: Software Published on:

  42. Since proteins function by interacting with other molecules, analysis of protein-protein interactions is essential for comprehending biological processes. Whereas understanding of atomic interactions within a ...

    Authors: Reyhaneh Esmaielbeiki and Jean-Christophe Nebel
    Citation: BMC Bioinformatics 2014 15:171
    Content type: Research article Published on:

  43. The reproducibility of transcriptomic biomarkers across datasets remains poor, limiting clinical application. We and others have suggested that this is in-part caused by differential error-structure between da...

    Authors: Natalie S Fox, Maud HW Starmans, Syed Haider, Philippe Lambin and Paul C Boutros
    Citation: BMC Bioinformatics 2014 15:170
    Content type: Research article Published on:

  44. Retinal ganglion cell (RGC) loss is one of the earliest and most important cellular changes in glaucoma. The DARC (Detection of Apoptosing Retinal Cells) technology enables in vivo real-time non-invasive imaging ...

    Authors: Mukhtar Bizrah, Steve C Dakin, Li Guo, Farzana Rahman, Miles Parnell, Eduardo Normando, Shereen Nizari, Benjamin Davis, Ahmed Younis and M Francesca Cordeiro
    Citation: BMC Bioinformatics 2014 15:169
    Content type: Research article Published on:

  45. In vitro generated dose-response curves of human cancer cell lines are widely used to develop new therapeutics. The curves are summarised by simplified statistics that ignore the conventionally used dose-response...

    Authors: Steffen Falgreen, Maria Bach Laursen, Julie Støve Bødker, Malene Krag Kjeldsen, Alexander Schmitz, Mette Nyegaard, Hans Erik Johnsen, Karen Dybkær and Martin Bøgsted
    Citation: BMC Bioinformatics 2014 15:168
    Content type: Methodology article Published on:

  46. High-throughput Next-Generation Sequencing (NGS) techniques are advancing genomics and molecular biology research. This technology generates substantially large data which puts up a major challenge to the scie...

    Authors: Ranjan Kumar Maji, Arijita Sarkar, Sunirmal Khatua, Subhasis Dasgupta and Zhumur Ghosh
    Citation: BMC Bioinformatics 2014 15:167
    Content type: Methodology article Published on:

  47. Protein sequence similarities to any types of non-globular segments (coiled coils, low complexity regions, transmembrane regions, long loops, etc. where either positional sequence conservation is the result of...

    Authors: Wing-Cheong Wong, Sebastian Maurer-Stroh, Birgit Eisenhaber and Frank Eisenhaber
    Citation: BMC Bioinformatics 2014 15:166
    Content type: Methodology article Published on:

  50. Coronaviruses are the diverse group of RNA virus. From 1960, six strains of human coronaviruses have emerged that includes SARS-CoV and the recent infection by deadly MERS-CoV which is now going to cause anoth...

    Authors: Refat Sharmin and Abul Bashar Mir Md Khademul Islam
    Citation: BMC Bioinformatics 2014 15:161
    Content type: Research article Published on:

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