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  1. Although it is frequently observed that aligning short reads to genomes becomes harder if they contain complex repeat patterns, there has not been much effort to quantify the relationship between complexity of...

    Authors: Vinhthuy Phan, Shanshan Gao, Quang Tran and Nam S Vo
    Citation: BMC Bioinformatics 2015 16(Suppl 17):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 17

  2. Drug resistance is one of the most important causes for failure of anti-AIDS treatment. During therapy, multiple mutations accumulate in the HIV genome, eventually rendering the drugs ineffective in blocking r...

    Authors: Xiaxia Yu, Irene T Weber and Robert W Harrison
    Citation: BMC Bioinformatics 2015 16(Suppl 17):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 17

  7. The Pacific oyster, Crassostrea gigas, is one of the most important aquaculture shellfish resources worldwide. Important efforts have been undertaken towards a better knowledge of its genome and transcriptome, wh...

    Authors: Guillaume Riviere, Christophe Klopp, Nabihoudine Ibouniyamine, Arnaud Huvet, Pierre Boudry and Pascal Favrel
    Citation: BMC Bioinformatics 2015 16:401
    Content type: Database Published on:

  8. Transcription factors (TFs) are important regulatory proteins that govern transcriptional regulation. Today, it is known that in higher organisms different TFs have to cooperate rather than acting individually...

    Authors: Cornelia Meckbach, Rebecca Tacke, Xu Hua, Stephan Waack, Edgar Wingender and Mehmet Gültas
    Citation: BMC Bioinformatics 2015 16:400
    Content type: Methodology Article Published on:

  9. We describe a suite of tools and methods that form a core set of capabilities for researchers and clinical investigators to evaluate multiple analytical pipelines and quantify sensitivity and variability of th...

    Authors: Tahsin Kurc, Xin Qi, Daihou Wang, Fusheng Wang, George Teodoro, Lee Cooper, Michael Nalisnik, Lin Yang, Joel Saltz and David J. Foran
    Citation: BMC Bioinformatics 2015 16:399
    Content type: Research article Published on:

  10. The dimension and complexity of high-throughput gene expression data create many challenges for downstream analysis. Several approaches exist to reduce the number of variables with respect to small sample size...

    Authors: Behrouz Madahian, Sujoy Roy, Dale Bowman, Lih Y Deng and Ramin Homayouni
    Citation: BMC Bioinformatics 2015 16(Suppl 13):S13
    Content type: Proceedings Published on:

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

  11. Maize, a crop of global significance, is vulnerable to a variety of biotic stresses resulting in economic losses. Fusarium verticillioides (teleomorph Gibberella moniliformis) is one of the key fungal pathogens o...

    Authors: Mansuck Kim, Huan Zhang, Charles Woloshuk, Won-Bo Shim and Byung-Jun Yoon
    Citation: BMC Bioinformatics 2015 16(Suppl 13):S12
    Content type: Proceedings Published on:

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

  12. A wealth of protein interaction data has become available in recent years, creating an urgent need for powerful analysis techniques. In this context, the problem of finding biologically meaningful corresponden...

    Authors: Jakob Dohrmann, Juris Puchin and Rahul Singh
    Citation: BMC Bioinformatics 2015 16(Suppl 13):S11
    Content type: Proceedings Published on:

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

  13. Adapter trimming and removal of duplicate reads are common practices in next-generation sequencing pipelines. Sequencing reads ambiguously mapped to repetitive and low complexity regions can also be problemati...

    Authors: Mikhail G Dozmorov, Indra Adrianto, Cory B Giles, Edmund Glass, Stuart B Glenn, Courtney Montgomery, Kathy L Sivils, Lorin E Olson, Tomoaki Iwayama, Willard M Freeman, Christopher J Lessard and Jonathan D Wren
    Citation: BMC Bioinformatics 2015 16(Suppl 13):S10
    Content type: Proceedings Published on:

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

  14. As the major histocompatibility complex (MHC), human leukocyte antigens (HLAs) are one of the most polymorphic genes in humans. Patients carrying certain HLA alleles may develop adverse drug reactions (ADRs) a...

    Authors: Heng Luo, Hao Ye, Hui Wen Ng, Leming Shi, Weida Tong, William Mattes, Donna Mendrick and Huixiao Hong
    Citation: BMC Bioinformatics 2015 16(Suppl 13):S9
    Content type: Proceedings Published on:

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

  15. Topic modelling is an active research field in machine learning. While mainly used to build models from unstructured textual data, it offers an effective means of data mining where samples represent documents,...

    Authors: Weizhong Zhao, James J Chen, Roger Perkins, Zhichao Liu, Weigong Ge, Yijun Ding and Wen Zou
    Citation: BMC Bioinformatics 2015 16(Suppl 13):S8
    Content type: Proceedings Published on:

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

  16. It is understood that cancer is a clonal disease initiated by a single cell, and that metastasis, which is the spread of cancer from the primary site, is also initiated by a single cell. The seemingly natural ...

    Authors: Erich A Peterson, Michael A Bauer, Shweta S Chavan, Cody Ashby, Niels Weinhold, Christoph J Heuck, Gareth J Morgan and Donald J Johann
    Citation: BMC Bioinformatics 2015 16(Suppl 13):S7
    Content type: Proceedings Published on:

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

  17. Comprehensive capture of Adverse Events (AEs) is crucial for monitoring for side effects of a therapy while assessing efficacy. For cancer studies, the National Cancer Institute has developed the Common Termin...

    Authors: Alex Lencioni, Laura Hutchins, Sandy Annis, Wanchi Chen, Emre Ermisoglu, Zhidan Feng, Karen Mack, Kacie Simpson, Cheryl Lane and Umit Topaloglu
    Citation: BMC Bioinformatics 2015 16(Suppl 13):S6
    Content type: Proceedings Published on:

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

  18. Dermoscopy is a highly effective and noninvasive imaging technique used in diagnosis of melanoma and other pigmented skin lesions. Many aspects of the lesion under consideration are defined in relation to the ...

    Authors: James Lemon, Sinan Kockara, Tansel Halic and Mutlu Mete
    Citation: BMC Bioinformatics 2015 16(Suppl 13):S5
    Content type: Proceedings Published on:

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

  19. Drug repositioning is a cost-efficient and time-saving process to drug development compared to traditional techniques. A systematic method to drug repositioning is to identify candidate drug's gene expression ...

    Authors: Hui Huang, Thanh Nguyen, Sara Ibrahim, Sandeep Shantharam, Zongliang Yue and Jake Y Chen
    Citation: BMC Bioinformatics 2015 16(Suppl 13):S4
    Content type: Proceedings Published on:

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

  20. Most dynamical models for genomic networks are built upon two current methodologies, one process-based and the other based on Boolean-type networks. Both are problematic when it comes to experimental design pu...

    Authors: Daniel N Mohsenizadeh, Jianping Hua, Michael Bittner and Edward R Dougherty
    Citation: BMC Bioinformatics 2015 16(Suppl 13):S3
    Content type: Proceedings Published on:

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

  21. An accurate understanding of interactions among genes plays a major role in developing therapeutic intervention methods. Gene regulatory networks often contain a significant amount of uncertainty. The process ...

    Authors: Roozbeh Dehghannasiri, Byung-Jun Yoon and Edward R Dougherty
    Citation: BMC Bioinformatics 2015 16(Suppl 13):S2
    Content type: Proceedings Published on:

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

    The Erratum to this article has been published in BMC Bioinformatics 2015 16:410

  23. Identification of bacteria may be based on sequencing and molecular analysis of a specific locus such as 16S rRNA, or a set of loci such as in multilocus sequence typing. In the near future, healthcare institu...

    Authors: Dhany Saputra, Simon Rasmussen, Mette V. Larsen, Nizar Haddad, Maria Maddalena Sperotto, Frank M. Aarestrup, Ole Lund and Thomas Sicheritz-Pontén
    Citation: BMC Bioinformatics 2015 16:398
    Content type: Methodology Article Published on:

  24. Analysis of single cells in their native environment is a powerful method to address key questions in developmental systems biology. Confocal microscopy imaging of intact tissues, followed by automatic image s...

    Authors: Michael Chiang, Sam Hallman, Amanda Cinquin, Nabora Reyes de Mochel, Adrian Paz, Shimako Kawauchi, Anne L. Calof, Ken W. Cho, Charless C. Fowlkes and Olivier Cinquin
    Citation: BMC Bioinformatics 2015 16:397
    Content type: Methodology article Published on:

  25. In recent years, hyperspectral microscopy techniques such as infrared or Raman microscopy have been applied successfully for diagnostic purposes. In many of the corresponding studies, it is common practice to ...

    Authors: Chen Yang, Daniel Niedieker, Frederik Großerüschkamp, Melanie Horn, Andrea Tannapfel, Angela Kallenbach-Thieltges, Klaus Gerwert and Axel Mosig
    Citation: BMC Bioinformatics 2015 16:396
    Content type: Methodology Article Published on:

  26. Inferring gene regulatory network (GRN) has been an important topic in Bioinformatics. Many computational methods infer the GRN from high-throughput expression data. Due to the presence of time delays in the r...

    Authors: Leung-Yau Lo, Man-Leung Wong, Kin-Hong Lee and Kwong-Sak Leung
    Citation: BMC Bioinformatics 2015 16:395
    Content type: Research Article Published on:

  27. Available methods to simulate nucleotide or amino acid data typically use Markov models to simulate each position independently. These approaches are not appropriate to assess the performance of combinatorial ...

    Authors: Linda Dib, Xavier Meyer, Panu Artimo, Vassilios Ioannidis, Heinz Stockinger and Nicolas Salamin
    Citation: BMC Bioinformatics 2015 16:394
    Content type: Software Published on:

  28. The alignment of multiple protein sequences is one of the most commonly performed tasks in bioinformatics. In spite of considerable research and efforts that have been recently deployed for improving the perfo...

    Authors: Mufleh Al-Shatnawi, M. Omair Ahmad and M. N. S. Swamy
    Citation: BMC Bioinformatics 2015 16:393
    Content type: Research Article Published on:

  29. The number of γH2AX foci per nucleus is an accepted measure of the number of DNA double-strand breaks in single cells. One of the experimental techniques for γH2AX detection in cultured cells is immunofluoresc...

    Authors: Anastasiya Lapytsko, Gabriel Kollarovic, Lyubomira Ivanova, Maja Studencka and Jörg Schaber
    Citation: BMC Bioinformatics 2015 16:392
    Content type: Software Published on:

  30. Identification of one or several disease causing variant(s) from the large collection of variants present in an individual is often achieved by the sequential use of heuristic filters. The recent development o...

    Authors: Bart J. G. Broeckx, Frank Coopman, Geert Verhoeven, Tim Bosmans, Ingrid Gielen, Walter Dingemanse, Jimmy H. Saunders, Dieter Deforce and Filip Van Nieuwerburgh
    Citation: BMC Bioinformatics 2015 16:391
    Content type: Software Published on:

  32. Many functional RNA molecules fold into pseudoknot structures, which are often essential for the formation of an RNA’s 3D structure. Currently the design of RNA molecules, which fold into a specific structure ...

    Authors: Robert Kleinkauf, Torsten Houwaart, Rolf Backofen and Martin Mann
    Citation: BMC Bioinformatics 2015 16:389
    Content type: Software Published on:

  33. Plasma miRNAs have the potential as cancer biomarkers but no consolidated guidelines for data mining in this field are available. The purpose of the study was to apply a supervised data analysis strategy in a ...

    Authors: Elena Landoni, Rosalba Miceli, Maurizio Callari, Paola Tiberio, Valentina Appierto, Valentina Angeloni, Luigi Mariani and Maria Grazia Daidone
    Citation: BMC Bioinformatics 2015 16:388
    Content type: Research article Published on:

  34. For three decades, sequence logos are the de facto standard for the visualization of sequence motifs in biology and bioinformatics. Reasons for this success story are their simplicity and clarity. The number of i...

    Authors: Martin Nettling, Hendrik Treutler, Jan Grau, Jens Keilwagen, Stefan Posch and Ivo Grosse
    Citation: BMC Bioinformatics 2015 16:387
    Content type: Software Published on:

  35. Because of the short read length of high throughput sequencing data, assembly errors are introduced in genome assembly, which may have adverse impact to the downstream data analysis. Several tools have been de...

    Authors: Xiao Zhu, Henry C. M. Leung, Rongjie Wang, Francis Y. L. Chin, Siu Ming Yiu, Guangri Quan, Yajie Li, Rui Zhang, Qinghua Jiang, Bo Liu, Yucui Dong, Guohui Zhou and Yadong Wang
    Citation: BMC Bioinformatics 2015 16:386
    Content type: Research article Published on:

  37. Given a gene and a species tree, reconciliation methods attempt to retrieve the macro-evolutionary events that best explain the discrepancies between the two tree topologies. The DTL parsimonious approach sear...

    Authors: Thu-Hien To, Edwin Jacox, Vincent Ranwez and Celine Scornavacca
    Citation: BMC Bioinformatics 2015 16:384
    Content type: Research Article Published on:

  39. Single Nucleotide Polymorphisms (SNPs) are widely used molecular markers, and their use has increased massively since the inception of Next Generation Sequencing (NGS) technologies, which allow detection of la...

    Authors: Antonio Ribeiro, Agnieszka Golicz, Christine Anne Hackett, Iain Milne, Gordon Stephen, David Marshall, Andrew J. Flavell and Micha Bayer
    Citation: BMC Bioinformatics 2015 16:382
    Content type: Research Article Published on:

  40. Bacteriocins are peptide-derived molecules produced by bacteria, whose recently-discovered functions include virulence factors and signaling molecules as well as their better known roles as antibiotics. To dat...

    Authors: James T. Morton, Stefan D. Freed, Shaun W. Lee and Iddo Friedberg
    Citation: BMC Bioinformatics 2015 16:381
    Content type: Research Article Published on:

  41. Viruses are the most abundant and genetically diverse biological entities on earth, yet the repertoire of viral proteins remains poorly explored. As the number of sequenced virus genomes grows into the thousan...

    Authors: David M. Kristensen, Usman Saeed, Dmitrij Frishman and Eugene V. Koonin
    Citation: BMC Bioinformatics 2015 16:380
    Content type: Research article Published on:

  42. Next generation sequencing enables studying heterogeneous populations of viral infections. When the sequencing is done at high coverage depth (“deep sequencing”), low frequency variants can be detected. Here w...

    Authors: Koen Van der Borght, Kim Thys, Yves Wetzels, Lieven Clement, Bie Verbist, Joke Reumers, Herman van Vlijmen and Jeroen Aerssens
    Citation: BMC Bioinformatics 2015 16:379
    Content type: Methodology article Published on:

  43. Magnetic resonance spectroscopy provides metabolic information about living tissues in a non-invasive way. However, there are only few multi-centre clinical studies, mostly performed on a single scanner model ...

    Authors: Victor Mocioiu, Sandra Ortega-Martorell, Iván Olier, Michal Jablonski, Jana Starcukova, Paulo Lisboa, Carles Arús and Margarida Julià-Sapé
    Citation: BMC Bioinformatics 2015 16:378
    Content type: Software Published on:

  44. The detection of regulatory regions in candidate sequences is essential for the understanding of the regulation of a particular gene and the mechanisms involved. This paper proposes a novel methodology based o...

    Authors: Joan Maynou, Erola Pairó, Santiago Marco and Alexandre Perera
    Citation: BMC Bioinformatics 2015 16:377
    Content type: Methodology Article Published on:

  47. The explosion of NGS (Next Generation Sequencing) sequence data requires a huge effort in Bioinformatics methods and analyses. The creation of dedicated, robust and reliable pipelines able to handle dozens of ...

    Authors: Cécile Monat, Christine Tranchant-Dubreuil, Ayité Kougbeadjo, Cédric Farcy, Enrique Ortega-Abboud, Souhila Amanzougarene, Sébastien Ravel, Mawussé Agbessi, Julie Orjuela-Bouniol, Maryline Summo and François Sabot
    Citation: BMC Bioinformatics 2015 16:374
    Content type: SOFTWARE Published on:

  49. Genomic data production is at its highest level and continues to increase, making available novel primary data and existing public data to researchers for exploration. Here we explore the consequences of “batc...

    Authors: Andrew E. Jaffe, Thomas Hyde, Joel Kleinman, Daniel R. Weinbergern, Joshua G. Chenoweth, Ronald D. McKay, Jeffrey T. Leek and Carlo Colantuoni
    Citation: BMC Bioinformatics 2015 16:372
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Bioinformatics 2016 17:302

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