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  1. Classifying cancers by gene selection is among the most important and challenging procedures in biomedicine. A major challenge is to design an effective method that eliminates irrelevant, redundant, or noisy g...

    Authors: Xiaoping Cheng, Hongmin Cai, Yue Zhang, Bo Xu and Weifeng Su
    Citation: BMC Bioinformatics 2015 16:219
    Content type: Methodology Article Published on:

  2. Clustering protein sequences according to inferred homology is a fundamental step in the analysis of many large data sets. Since the publication of the Markov Clustering (MCL) algorithm in 2002, it has been th...

    Authors: Theodore R. Gibbons, Stephen M. Mount, Endymion D. Cooper and Charles F. Delwiche
    Citation: BMC Bioinformatics 2015 16:218
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Bioinformatics 2015 16:274

  5. The concept of Petri nets (PN) is widely used in systems biology and allows modeling of complex biochemical systems like metabolic systems, signal transduction pathways, and gene expression networks. In partic...

    Authors: Pavel Balazki, Klaus Lindauer, Jens Einloft, Jörg Ackermann and Ina Koch
    Citation: BMC Bioinformatics 2015 16:215
    Content type: Software Published on:

    The Erratum to this article has been published in BMC Bioinformatics 2015 16:371

  6. Despite ongoing reduction in genotyping costs, genomic studies involving large numbers of species with low economic value (such as Black Tiger prawns) remain cost prohibitive. In this scenario DNA pooling is a...

    Authors: Andrew D Hellicar, Ashfaqur Rahman, Daniel V Smith and John M Henshall
    Citation: BMC Bioinformatics 2015 16:214
    Content type: Methodology Article Published on:

  8. Analyzing the integration profile of retroviral vectors is a vital step in determining their potential genotoxic effects and developing safer vectors for therapeutic use. Identifying retroviral vector integrat...

    Authors: Jonah D. Hocum, Logan R. Battrell, Ryan Maynard, Jennifer E. Adair, Brian C. Beard, David J. Rawlings, Hans-Peter Kiem, Daniel G. Miller and Grant D. Trobridge
    Citation: BMC Bioinformatics 2015 16:212
    Content type: Software Published on:

  9. Long et al. (BMC Bioinformatics 2014, 15(1):278) describe a “discrepancy” in using UniFrac to assess statistical significance of community differences. Specifically, they find that weighted UniFrac results differ...

    Authors: Catherine A. Lozupone and Rob Knight
    Citation: BMC Bioinformatics 2015 16:211
    Content type: Research Published on:

  10. Numerous organisms have evolved a wide range of toxic peptides for self-defense and predation. Their effective interstitial and macro-environmental use requires energetic and structural stability. One successf...

    Authors: S. M. Ashiqul Islam, Tanvir Sajed, Christopher Michel Kearney and Erich J Baker
    Citation: BMC Bioinformatics 2015 16:210
    Content type: Methodology article Published on:

  11. The increasing abundance of neuromorphological data provides both the opportunity and the challenge to compare massive numbers of neurons from a wide diversity of sources efficiently and effectively. We implem...

    Authors: Todd A Gillette, Parsa Hosseini and Giorgio A Ascoli
    Citation: BMC Bioinformatics 2015 16:209
    Content type: Research article Published on:

  12. RNA sequencing (RNA-Seq) allows an unbiased survey of the entire transcriptome in a high-throughput manner. A major application of RNA-Seq is to detect differential isoform expression across experimental condi...

    Authors: Cheng Jia, Weihua Guan, Amy Yang, Rui Xiao, W. H. Wilson Tang, Christine S. Moravec, Kenneth B. Margulies, Thomas P. Cappola, Chun Li and Mingyao Li
    Citation: BMC Bioinformatics 2015 16:208
    Content type: Methodology article Published on:

  13. The analysis of correlations of amino acid occurrences in globular domains has led to the development of statistical tools that can identify native contacts – portions of the chains that come to close distance...

    Authors: Rocío Espada, R Gonzalo Parra, Thierry Mora, Aleksandra M Walczak and Diego U Ferreiro
    Citation: BMC Bioinformatics 2015 16:207
    Content type: Research Article Published on:

  14. Protein sequence alignments and database search methods use standard scoring matrices calculated from amino acid substitution frequencies in general sets of proteins. These general-purpose matrices are not opt...

    Authors: Santiago Rios, Marta F. Fernandez, Gianluigi Caltabiano, Mercedes Campillo, Leonardo Pardo and Angel Gonzalez
    Citation: BMC Bioinformatics 2015 16:206
    Content type: Research article Published on:

  16. The number and size of tree topologies that are being compared by phylogenetic systematists is increasing due to technological advancements in high-throughput DNA sequencing. However, we still lack tools to fa...

    Authors: Denis Jacob Machado
    Citation: BMC Bioinformatics 2015 16:204
    Content type: Software Published on:

  17. Substantial advances in microbiology, molecular evolution and biodiversity have been carried out in recent years thanks to Metagenomics, which allows to unveil the composition and functions of mixed microbial ...

    Authors: Bruno Fosso, Monica Santamaria, Marinella Marzano, Daniel Alonso-Alemany, Gabriel Valiente, Giacinto Donvito, Alfonso Monaco, Pasquale Notarangelo and Graziano Pesole
    Citation: BMC Bioinformatics 2015 16:203
    Content type: Methodology Published on:

  18. Infection with feline immunodeficiency virus (FIV) causes an immunosuppressive disease whose consequences are less severe if cats are co-infected with an attenuated FIV strain (PLV). We use virus diversity mea...

    Authors: Yang Liu, Francesca Chiaromonte, Howard Ross, Raunaq Malhotra, Daniel Elleder and Mary Poss
    Citation: BMC Bioinformatics 2015 16:202
    Content type: Research article Published on:

  20. Exploratory analysis of multi-dimensional high-throughput datasets, such as microarray gene expression time series, may be instrumental in understanding the genetic programs underlying numerous biological proc...

    Authors: Anirban Bhar, Martin Haubrock, Anirban Mukhopadhyay and Edgar Wingender
    Citation: BMC Bioinformatics 2015 16:200
    Content type: Research Article Published on:

  21. Huge amounts of electronic biomedical documents, such as molecular biology reports or genomic papers are generated daily. Nowadays, these documents are mainly available in the form of unstructured free texts, ...

    Authors: Xiao Liu, Antoine Bordes and Yves Grandvalet
    Citation: BMC Bioinformatics 2015 16(Suppl 10):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 10

  22. Biomedical event extraction has been a major focus of biomedical natural language processing (BioNLP) research since the first BioNLP shared task was held in 2009. Accordingly, a large number of event extracti...

    Authors: Makoto Miwa and Sophia Ananiadou
    Citation: BMC Bioinformatics 2015 16(Suppl 10):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 10

  23. The acquisition of knowledge about relations between bacteria and their locations (habitats and geographical locations) in short texts about bacteria, as defined in the BioNLP-ST 2013 Bacteria Biotope task, de...

    Authors: Thomas Lavergne, Cyril Grouin and Pierre Zweigenbaum
    Citation: BMC Bioinformatics 2015 16(Suppl 10):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 10

  24. Information regarding bacteria biotopes is important for several research areas including health sciences, microbiology, and food processing and preservation. One of the challenges for scientists in these doma...

    Authors: İlknur Karadeniz and Arzucan Özgür
    Citation: BMC Bioinformatics 2015 16(Suppl 10):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 10

  25. The BioNLP Gene Regulation Task has attracted a diverse collection of submissions showcasing state-of-the-art systems. However, a principal challenge remains in obtaining a significant amount of recall. We arg...

    Authors: Thomas Provoost and Marie-Francine Moens
    Citation: BMC Bioinformatics 2015 16(Suppl 10):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 10

  26. The third edition of the BioNLP Shared Task was held with the grand theme "knowledge base construction (KB)". The Genia Event (GE) task was re-designed and implemented in light of this theme. For its final rep...

    Authors: Jin-Dong Kim, Jung-jae Kim, Xu Han and Dietrich Rebholz-Schuhmann
    Citation: BMC Bioinformatics 2015 16(Suppl 10):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 10

  27. Since their introduction in 2009, the BioNLP Shared Task events have been instrumental in advancing the development of methods and resources for the automatic extraction of information from the biomedical lite...

    Authors: Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Andrew Rowley, Hong-Woo Chun, Sung-Jae Jung, Sung-Pil Choi, Jun'ichi Tsujii and Sophia Ananiadou
    Citation: BMC Bioinformatics 2015 16(Suppl 10):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 10

  28. We present the two Bacteria Track tasks of BioNLP 2013 Shared Task (ST): Gene Regulation Network (GRN) and Bacteria Biotope (BB). These tasks were previously introduced in the 2011 BioNLP-ST Bacteria Track as Bac...

    Authors: Robert Bossy, Wiktoria Golik, Zorana Ratkovic, Dialekti Valsamou, Philippe Bessières and Claire Nédellec
    Citation: BMC Bioinformatics 2015 16(Suppl 10):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 10

  29. Class prediction models have been shown to have varying performances in clinical gene expression datasets. Previous evaluation studies, mostly done in the field of cancer, showed that the accuracy of class pre...

    Authors: Putri W. Novianti, Victor L. Jong, Kit C. B. Roes and Marinus J. C. Eijkemans
    Citation: BMC Bioinformatics 2015 16:199
    Content type: Research article Published on:

  30. The rapid pace of bioscience research makes it very challenging to track relevant articles in one’s area of interest. MEDLINE, a primary source for biomedical literature, offers access to more than 20 million ...

    Authors: Padmini Srinivasan, Xiao-Ning Zhang, Roxane Bouten and Caren Chang
    Citation: BMC Bioinformatics 2015 16:198
    Content type: Research article Published on:

  31. The universal qPCR data exchange file format RDML is today well accepted by the scientific community, part of the MIQE guidelines and implemented in many qPCR instruments. With the increased use of RDML new ch...

    Authors: Jan M. Ruijter, Steve Lefever, Jasper Anckaert, Jan Hellemans, Michael W. Pfaffl, Vladimir Benes, Stephen A. Bustin, Jo Vandesompele and Andreas Untergasser
    Citation: BMC Bioinformatics 2015 16:197
    Content type: Software Published on:

  32. We consider data from a time course microarray experiment that was conducted on grapevines over the development cycle of the grape berries at two different vineyards in South Australia. Although the underlying...

    Authors: Sean Robinson, Garique Glonek, Inge Koch, Mark Thomas and Christopher Davies
    Citation: BMC Bioinformatics 2015 16:196
    Content type: Research Article Published on:

  34. One aspect in which RNA sequencing is more valuable than microarray-based methods is the ability to examine the allelic imbalance of the expression of a gene. This process is often a complex task that entails ...

    Authors: Jesper R. Gådin, Ferdinand M. van’t Hooft, Per Eriksson and Lasse Folkersen
    Citation: BMC Bioinformatics 2015 16:194
    Content type: Software Published on:

  35. Improvements in sequencing technology now allow easy acquisition of large datasets; however, analyzing these data for phylogenetics can be challenging. We have developed a novel method to rapidly obtain homolo...

    Authors: Rachel S. Schwartz, Kelly M. Harkins, Anne C. Stone and Reed A. Cartwright
    Citation: BMC Bioinformatics 2015 16:193
    Content type: Methodology Article Published on:

  36. As the next-generation sequencing (NGS) technologies producing hundreds of millions of reads every day, a tremendous computational challenge is to map NGS reads to a given reference genome efficiently. However...

    Authors: Haoyu Cheng, Huaipan Jiang, Jiaoyun Yang, Yun Xu and Yi Shang
    Citation: BMC Bioinformatics 2015 16:192
    Content type: Methodology Article Published on:

  39. Imaging and image analysis advances are yielding increasingly complete and complicated records of cellular events in tissues and whole embryos. The ability to follow hundreds to thousands of cells at the indiv...

    Authors: Anthony Santella, Raúl Catena, Ismar Kovacevic, Pavak Shah, Zidong Yu, Javier Marquina-Solis, Abhishek Kumar, Yicong Wu, James Schaff, Daniel Colón-Ramos, Hari Shroff, William A. Mohler and Zhirong Bao
    Citation: BMC Bioinformatics 2015 16:189
    Content type: Software Published on:

  40. The exponential growth of next generation sequencing (NGS) data has posed big challenges to data storage, management and archive. Data compression is one of the effective solutions, where reference-based compr...

    Authors: Yongpeng Zhang, Linsen Li, Yanli Yang, Xiao Yang, Shan He and Zexuan Zhu
    Citation: BMC Bioinformatics 2015 16:188
    Content type: Methodology article Published on:

  41. Due to the large amount of data produced by advanced microscopy, automated image analysis is crucial in modern biology. Most applications require reliable cell nuclei segmentation. However, in many biological ...

    Authors: B. Mathew, A. Schmitz, S. Muñoz-Descalzo, N. Ansari, F. Pampaloni, E.H.K. Stelzer and S.C. Fischer
    Citation: BMC Bioinformatics 2015 16:187
    Content type: Methodology article Published on:

  42. People with an autistic spectrum disorder (ASD) display a variety of characteristic behavioral traits, including impaired social interaction, communication difficulties and repetitive behavior. This complex ne...

    Authors: Sejal Patel, Paola Roncaglia and Ruth C. Lovering
    Citation: BMC Bioinformatics 2015 16:186
    Content type: Methodology article Published on:

  43. Advances in the next generation sequencing technology has accelerated the pace of individualized medicine (IM), which aims to incorporate genetic/genomic information into medicine. One immediate need in interp...

    Authors: Komandur Elayavilli Ravikumar, Kavishwar B. Wagholikar, Dingcheng Li, Jean-Pierre Kocher and Hongfang Liu
    Citation: BMC Bioinformatics 2015 16:185
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Bioinformatics 2016 17:162

  44. Collective analysis of the increasingly emerging gene expression datasets are required. The recently proposed binarisation of consensus partition matrices (Bi-CoPaM) method can combine clustering results from mul...

    Authors: Basel Abu-Jamous, Rui Fa, David J. Roberts and Asoke K. Nandi
    Citation: BMC Bioinformatics 2015 16:184
    Content type: Methodology article Published on:

  45. Infectious disease modeling and computational power have evolved such that large-scale agent-based models (ABMs) have become feasible. However, the increasing hardware complexity requires adapted software desi...

    Authors: Lander Willem, Sean Stijven, Engelbert Tijskens, Philippe Beutels, Niel Hens and Jan Broeckhove
    Citation: BMC Bioinformatics 2015 16:183
    Content type: Methodology Article Published on:

  46. Mathematical and computational modelling of biochemical systems has seen a lot of effort devoted to the definition and implementation of high-performance mechanistic simulation frameworks. Within these framewo...

    Authors: Giulio Caravagna, Luca De Sano and Marco Antoniotti
    Citation: BMC Bioinformatics 2015 16(Suppl 9):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 9

  47. The understanding of mechanisms and functions of microRNAs (miRNAs) is fundamental for the study of many biological processes and for the elucidation of the pathogenesis of many human diseases. Technological a...

    Authors: Gianvito Pio, Michelangelo Ceci, Donato Malerba and Domenica D'Elia
    Citation: BMC Bioinformatics 2015 16(Suppl 9):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 9

  48. Many biological laboratories that deal with genomic samples are facing the problem of sample tracking, both for pure laboratory management and for efficiency. Our laboratory exploits PCR techniques and Next Ge...

    Authors: Andrea Calabria, Giulio Spinozzi, Fabrizio Benedicenti, Erika Tenderini and Eugenio Montini
    Citation: BMC Bioinformatics 2015 16(Suppl 9):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 9

  49. Tumour markers are standard tools for the differential diagnosis of cancer. However, the occurrence of nonspecific symptoms and different malignancies involving the same cancer site may lead to a high proporti...

    Authors: Stefano Parodi, Rosa Filiberti, Paola Marroni, Roberta Libener, Giovanni Paolo Ivaldi, Michele Mussap, Enrico Ferrari, Chiara Manneschi, Erika Montani and Marco Muselli
    Citation: BMC Bioinformatics 2015 16(Suppl 9):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 9

  50. This Preface introduces the content of the BioMed Central journal Supplements related to BITS2014 meeting, held in Rome, Italy, from the 26th to the 28th of February, 2014.

    Authors: Angelo Facchiano, Claudia Angelini, Roberta Bosotti, Alessandro Guffanti, Anna Marabotti, Roberto Marangoni, Stefano Pascarella, Paolo Romano, Andreas Zanzoni and Manuela Helmer-Citterich
    Citation: BMC Bioinformatics 2015 16(Suppl 9):S1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 16 Supplement 9

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