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  1. One of the most important application spectrums of transcriptomic data is cancer phenotype classification. Many characteristics of transcriptomic data, such as redundant features and technical artifacts, make ...

    Authors: Askar Obulkasim, Maarten Fornerod, Michel C. Zwaan, Dirk Reinhardt and Marry M. van den Heuvel-Eibrink
    Citation: BMC Bioinformatics 2015 16:305
    Content type: Research Article Published on:

  2. Next-generation sequencing (NGS) technologies have become much more efficient, allowing whole human genomes to be sequenced faster and cheaper than ever before. However, processing the raw sequence reads assoc...

    Authors: Kristopher A. Standish, Tristan M. Carland, Glenn K. Lockwood, Wayne Pfeiffer, Mahidhar Tatineni, C Chris Huang, Sarah Lamberth, Yauheniya Cherkas, Carrie Brodmerkel, Ed Jaeger, Lance Smith, Gunaretnam Rajagopal, Mark E. Curran and Nicholas J. Schork
    Citation: BMC Bioinformatics 2015 16:304
    Content type: Methodology Article Published on:

  3. Codon usage plays a crucial role when recombinant proteins are expressed in different organisms. This is especially the case if the codon usage frequency of the organism of origin and the target host organism ...

    Authors: Edward Daniel, Goodluck U. Onwukwe, Rik K. Wierenga, Susan E. Quaggin, Seppo J. Vainio and Mirja Krause
    Citation: BMC Bioinformatics 2015 16:303
    Content type: Software Published on:

  4. Studies regarding coxsackievirus (CV) tend to focus on epidemic outbreaks, an imbalanced topology is considered to be an indication of acute infection with partial cross-immunity. In enteroviruses, a clear und...

    Authors: Hui-Wen Huang, Yao-Shen Chen, Jeff Yi-Fu Chen, Po-Liang Lu, Yung-Cheng Lin, Bao-Chen Chen, Li-Chiu Chou, Chu-Feng Wang, Hui-Ju Su, Yi-Chien Huang, Yong-Ying Shi, Hsiu-Lin Chen, Bintou Sanno-Duanda, Tsi-Shu Huang, Kuei-Hsiang Lin, Yu-Chang Tyan…
    Citation: BMC Bioinformatics 2015 16:302
    Content type: Research article Published on:

  5. Local trend (i.e. shape) analysis of time series data reveals co-changing patterns in dynamics of biological systems. However, slow permutation procedures to evaluate the statistical significance of local tren...

    Authors: Li C. Xia, Dongmei Ai, Jacob A. Cram, Xiaoyi Liang, Jed A. Fuhrman and Fengzhu Sun
    Citation: BMC Bioinformatics 2015 16:301
    Content type: Methodology Article Published on:

  6. In clinical research prediction models are used to accurately predict the outcome of the patients based on some of their characteristics. For high-dimensional prediction models (the number of variables greatly...

    Authors: Rok Blagus and Lara Lusa
    Citation: BMC Bioinformatics 2015 16:300
    Content type: Research Article Published on:

  7. In most sequenced organisms the number of known regulatory genes (e.g., transcription factors (TFs)) vastly exceeds the number of experimentally-verified regulons that could be associated with them. At present...

    Authors: Abdulkadir Elmas, Xiaodong Wang and Michael S. Samoilov
    Citation: BMC Bioinformatics 2015 16:299
    Content type: Methodology Article Published on:

  8. Technological advances have enabled the analysis of very small amounts of DNA in forensic cases. However, the DNA profiles from such evidence are frequently incomplete and can contain contributions from multip...

    Authors: Keith Inman, Norah Rudin, Ken Cheng, Chris Robinson, Adam Kirschner, Luke Inman-Semerau and Kirk E. Lohmueller
    Citation: BMC Bioinformatics 2015 16:298
    Content type: Software Published on:

  9. Two component systems (TCS) are signalling complexes manifested by a histidine kinase (receptor) and a response regulator (effector). They are the most abundant signalling pathways in prokaryotes and control a...

    Authors: Altan Kara, Martin Vickers, Martin Swain, David E. Whitworth and Narcis Fernandez-Fuentes
    Citation: BMC Bioinformatics 2015 16:297
    Content type: Methodology article Published on:

  11. Third generation sequencing methods, like SMRT (Single Molecule, Real-Time) sequencing developed by Pacific Biosciences, offer much longer read length in comparison to Next Generation Sequencing (NGS) methods....

    Authors: Kai Bernd Stadermann, Bernd Weisshaar and Daniela Holtgräwe
    Citation: BMC Bioinformatics 2015 16:295
    Content type: Methodology article Published on:

  13. This work seeks to develop a methodology for identifying reliable biomarkers of disease activity, progression and outcome through the identification of significant associations between high-throughput flow cyt...

    Authors: Hongtai Huang, Andrea Fava, Tara Guhr, Raffaello Cimbro, Antony Rosen, Francesco Boin and Hugh Ellis
    Citation: BMC Bioinformatics 2015 16:293
    Content type: Methodology article Published on:

  16. T cell epitope prediction tools and associated vaccine design algorithms have accelerated the development of vaccines for humans. Predictive tools for swine and other food animals are not as well developed, pr...

    Authors: Andres H. Gutiérrez, William D. Martin, Chris Bailey-Kellogg, Frances Terry, Leonard Moise and Anne S. De Groot
    Citation: BMC Bioinformatics 2015 16:290
    Content type: Research article Published on:

  17. This study addresses a recurrent biological problem, that is to define a formal clustering structure for a set of tissues on the basis of the relative abundance of multiple alternatively spliced isoforms mRNAs...

    Authors: Michele Pelosi, Marco Alfò, Francesca Martella, Elisa Pappalardo and Antonio Musarò
    Citation: BMC Bioinformatics 2015 16:289
    Content type: Methodology article Published on:

  18. Data volumes generated by next-generation sequencing (NGS) technologies is now a major concern for both data storage and transmission. This triggered the need for more efficient methods than general purpose co...

    Authors: Gaëtan Benoit, Claire Lemaitre, Dominique Lavenier, Erwan Drezen, Thibault Dayris, Raluca Uricaru and Guillaume Rizk
    Citation: BMC Bioinformatics 2015 16:288
    Content type: Research Article Published on:

  19. During the last decade, many scientific works have concerned the possible use of miRNA levels as diagnostic and prognostic tools for different kinds of cancer. The development of reliable classifiers requires ...

    Authors: Leonardo Ricci, Valerio Del Vescovo, Chiara Cantaloni, Margherita Grasso, Mattia Barbareschi and Michela Alessandra Denti
    Citation: BMC Bioinformatics 2015 16:287
    Content type: Methodology Article Published on:

  23. The inference of complex networks from data is a challenging problem in biological sciences, as well as in a wide range of disciplines such as chemistry, technology, economics, or sociology. The quantity and q...

    Authors: Abel Folch-Fortuny, Alejandro F. Villaverde, Alberto Ferrer and Julio R. Banga
    Citation: BMC Bioinformatics 2015 16:283
    Content type: Methodology Article Published on:

  25. The sequencing depth provided by high-throughput sequencing technologies has allowed a rise in the number of de novo sequenced genomes that could potentially be closed without further sequencing. However, genome ...

    Authors: Gregory K. Farrant, Mark Hoebeke, Frédéric Partensky, Gwendoline Andres, Erwan Corre and Laurence Garczarek
    Citation: BMC Bioinformatics 2015 16:281
    Content type: Methodology article Published on:

  27. Transcription factors (TFs) act downstream of the major signalling pathways functioning as master regulators of cell fate. Their activity is tightly regulated at the transcriptional, post-transcriptional and p...

    Authors: Gennaro Gambardella, Ivana Peluso, Sandro Montefusco, Mukesh Bansal, Diego L. Medina, Neil Lawrence and Diego di Bernardo
    Citation: BMC Bioinformatics 2015 16:279
    Content type: Methodology article Published on:

  28. RNA-seq has been widely used for genome-wide expression profiling. RNA-seq data typically consists of tens of millions of short sequenced reads from different transcripts. However, due to sequence similarity a...

    Authors: Soohyun Lee, Chae Hwa Seo, Burak Han Alver, Sanghyuk Lee and Peter J. Park
    Citation: BMC Bioinformatics 2015 16:278
    Content type: Research article Published on:

  29. The study of nuclear architecture using Chromosome Conformation Capture (3C) technologies is a novel frontier in biology. With further reduction in sequencing costs, the potential of Hi-C in describing nuclear...

    Authors: Marc W. Schmid, Stefan Grob and Ueli Grossniklaus
    Citation: BMC Bioinformatics 2015 16:277
    Content type: Software Published on:

  30. The function of RNA is strongly dependent on its structure, so an appropriate recognition of this structure, on every level of organization, is of great importance. One particular concern is the assessment of ...

    Authors: Agnieszka Rybarczyk, Natalia Szostak, Maciej Antczak, Tomasz Zok, Mariusz Popenda, Ryszard Adamiak, Jacek Blazewicz and Marta Szachniuk
    Citation: BMC Bioinformatics 2015 16:276
    Content type: Methodology article Published on:

  31. Gene ontology (GO) enrichment is commonly used for inferring biological meaning from systems biology experiments. However, determining differential GO and pathway enrichment between DNA-binding experiments or ...

    Authors: Ashley J. Waardenberg, Samuel D. Bassett, Romaric Bouveret and Richard P. Harvey
    Citation: BMC Bioinformatics 2015 16:275
    Content type: Software Published on:

    The Erratum to this article has been published in BMC Bioinformatics 2016 17:179

  34. Gene set analysis (GSA) of gene expression data can be highly powerful when the biological signal is weak compared to other sources of variability in the data. However, many gene set analysis approaches utiliz...

    Authors: Jacob A. Turner, Christopher R. Bolen and Derek M. Blankenship
    Citation: BMC Bioinformatics 2015 16:272
    Content type: Methodology Article Published on:

  36. DNA fingerprinting is a technique for comparing DNA patterns that has applications in a wide variety of contexts. Several commercial and freely-available tools can be used to analyze DNA fingerprint gel images...

    Authors: Jónathan Heras, César Domínguez, Eloy Mata, Vico Pascual, Carmen Lozano, Carmen Torres and Myriam Zarazaga
    Citation: BMC Bioinformatics 2015 16:270
    Content type: Software Published on:

  37. Multiple sequence alignments (MSA) are widely used in sequence analysis for a variety of tasks. Outlier sequences can make downstream analyses unreliable or make the alignments less accurate while they are bei...

    Authors: Peter Jehl, Fabian Sievers and Desmond G. Higgins
    Citation: BMC Bioinformatics 2015 16:269
    Content type: Research Article Published on:

  38. When biomolecules physically interact, natural selection operates on them jointly. Contacting positions in protein and RNA structures exhibit correlated patterns of sequence evolution due to constraints impose...

    Authors: Aram Avila-Herrera and Katherine S. Pollard
    Citation: BMC Bioinformatics 2015 16:268
    Content type: Research Published on:

  39. The identification of protein functional modules would be a great aid in furthering our knowledge of the principles of cellular organization. Most existing algorithms for identifying protein functional modules...

    Authors: Xianjun Shen, Li Yi, Yang Yi, Jincai Yang, Tingting He and Xiaohua Hu
    Citation: BMC Bioinformatics 2015 16(Suppl 12):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 12

  40. Recent quality control of complex mixtures, including herbal medicines, is not limited to chemical chromatographic definition of one or two selected compounds; multivariate linear regression methods with dimen...

    Authors: Hao Chen, Josiah Poon, Simon K Poon, Lizhi Cui, Kei Fan and Daniel Man-yuen Sze
    Citation: BMC Bioinformatics 2015 16(Suppl 12):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 12

  41. Revealing protein complexes are important for understanding principles of cellular organization and function. High-throughput experimental techniques have produced a large amount of protein interactions, which...

    Authors: Feng Ying Yu, Zhi Hao Yang, Xiao Hua Hu, Yuan Yuan Sun, Hong Fei Lin and Jian Wang
    Citation: BMC Bioinformatics 2015 16(Suppl 12):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 12

  42. Computational modeling techniques are playing increasingly important roles in advancing a systems-level mechanistic understanding of biological processes. Computer simulations guide and underpin experimental a...

    Authors: Yongguo Mei, Vida Abedi, Adria Carbo, Xiaoying Zhang, Pinyi Lu, Casandra Philipson, Raquel Hontecillas, Stefan Hoops, Nathan Liles and Josep Bassaganya-Riera
    Citation: BMC Bioinformatics 2015 16(Suppl 12):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 12

  43. It has become a very important and full of challenge task to predict bacterial protein subcellular locations using computational methods. Although there exist a lot of prediction methods for bacterial proteins...

    Authors: Xiao Wang, Jun Zhang and Guo-Zheng Li
    Citation: BMC Bioinformatics 2015 16(Suppl 12):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 12

  44. Biological pathways are descriptive diagrams of biological processes widely used for functional analysis of differentially expressed genes or proteins. Primary data analysis, such as quality control, normalisa...

    Authors: Anwesha Bohler, Lars M. T. Eijssen, Martijn P. van Iersel, Christ Leemans, Egon L. Willighagen, Martina Kutmon, Magali Jaillard and Chris T. Evelo
    Citation: BMC Bioinformatics 2015 16:267
    Content type: Software Published on:

  45. Membrane proteins represent over 25 % of human protein genes and account for more than 60 % of drug targets due to their accessibility from the extracellular environment. The increasing number of available cry...

    Authors: Marc Perea, Ivar Lugtenburg, Eduardo Mayol, Arnau Cordomí, Xavier Deupí, Leonardo Pardo and Mireia Olivella
    Citation: BMC Bioinformatics 2015 16:266
    Content type: Database Published on:

  46. Scoring DNA sequences against Position Weight Matrices (PWMs) is a widely adopted method to identify putative transcription factor binding sites. While common bioinformatics tools produce scores that can refle...

    Authors: Xiaoyan Ma, Daphne Ezer, Carmen Navarro and Boris Adryan
    Citation: BMC Bioinformatics 2015 16:265
    Content type: Research Article Published on:

  47. In many domains, scientists build complex simulators of natural phenomena that encode their hypotheses about the underlying processes. These simulators can be deterministic or stochastic, fast or slow, constra...

    Authors: Edward Meeds, Michael Chiang, Mary Lee, Olivier Cinquin, John Lowengrub and Max Welling
    Citation: BMC Bioinformatics 2015 16:264
    Content type: Methodology Article Published on:

  48. Multiple high-throughput molecular profiling by omics technologies can be collected for the same individuals. Combining these data, rather than exploiting them separately, can significantly increase the power ...

    Authors: Angela Serra, Michele Fratello, Vittorio Fortino, Giancarlo Raiconi, Roberto Tagliaferri and Dario Greco
    Citation: BMC Bioinformatics 2015 16:261
    Content type: Research Article Published on:

  49. Gas chromatography coupled with mass spectrometry (GC-MS) is one of the technologies widely used for qualitative and quantitative analysis of small molecules. In particular, GC coupled to single quadrupole MS ...

    Authors: Mohammad R. Nezami Ranjbar, Cristina Di Poto, Yue Wang and Habtom W. Ressom
    Citation: BMC Bioinformatics 2015 16:259
    Content type: Software Published on:

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