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  1. Detecting and visualizing nonlinear interaction effects of single nucleotide polymorphisms (SNPs) or epistatic interactions are important topics in bioinformatics since they play an important role in unravelin...

    Authors: Junliang Shang, Yingxia Sun, Jin-Xing Liu, Junfeng Xia, Junying Zhang and Chun-Hou Zheng
    Citation: BMC Bioinformatics 2016 17:214
    Content type: Methodology article Published on:

  2. Next-generation sequencing (NGS) technologies have provided researchers with vast possibilities in various biological and biomedical research areas. Efficient data mining strategies are in high demand for larg...

    Authors: Weizhong Zhao, James J. Chen, Roger Perkins, Yuping Wang, Zhichao Liu, Huixiao Hong, Weida Tong and Wen Zou
    Citation: BMC Bioinformatics 2016 17:213
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Bioinformatics 2016 17:301

  3. The underlying molecular processes representing stress responses to low-dose ionising radiation (LDIR) in mammals are just beginning to be understood. In particular, LDIR effects on the brain and their possibl...

    Authors: Christos Karapiperis, Stefan J. Kempf, Roel Quintens, Omid Azimzadeh, Victoria Linares Vidal, Simonetta Pazzaglia, Dimitry Bazyka, Pier G. Mastroberardino, Zacharias G. Scouras, Soile Tapio, Mohammed Abderrafi Benotmane and Christos A. Ouzounis
    Citation: BMC Bioinformatics 2016 17:212
    Content type: Database Published on:

  4. Gene expression connectivity mapping has gained much popularity recently with a number of successful applications in biomedical research testifying its utility and promise. Previously methodological research i...

    Authors: Qing Wen, Chang-Sik Kim, Peter W. Hamilton and Shu-Dong Zhang
    Citation: BMC Bioinformatics 2016 17:211
    Content type: Methodology Article Published on:

  5. MicroRNAs (miRNAs) impact various biological processes within animals and plants. They complementarily bind target mRNAs, effecting a post-transcriptional negative regulation on mRNA level. The investigation o...

    Authors: Julia Bayer, Carsten Kuenne, Jens Preussner and Mario Looso
    Citation: BMC Bioinformatics 2016 17:210
    Content type: Software Published on:

  6. Genomics and proteomics are nowadays the dominant techniques for novel biomarker discovery. However, histopathology images contain a wealth of information related to the tumor histology, morphology and tumor-h...

    Authors: Vlad Popovici, Eva Budinská, Lenka Čápková, Daniel Schwarz, Ladislav Dušek, Josef Feit and Rolf Jaggi
    Citation: BMC Bioinformatics 2016 17:209
    Content type: Research Article Published on:

  11. The targeting of disease-related proteins is important for drug discovery, and yet target-based discovery has not been fruitful. Contextualizing overall biological processes is critical to formulating successf...

    Authors: Naiem T. Issa, Jordan Kruger, Henri Wathieu, Rajarajan Raja, Stephen W. Byers and Sivanesan Dakshanamurthy
    Citation: BMC Bioinformatics 2016 17:202
    Content type: Research article Published on:

  13. Non-negative linear combinations of elementary flux modes (EMs) describe all feasible reaction flux distributions for a given metabolic network under the quasi steady state assumption. However, only a small su...

    Authors: Moritz von Stosch, Cristiana Rodrigues de Azevedo, Mauro Luis, Sebastiao Feyo de Azevedo and Rui Oliveira
    Citation: BMC Bioinformatics 2016 17:200
    Content type: Methodology article Published on:

  14. TopHat is a popular spliced junction mapper for RNA sequencing data, and writes files in the BAM format – the binary version of the Sequence Alignment/Map (SAM) format. BAM is the standard exchange format for ...

    Authors: Christian Brueffer and Lao H. Saal
    Citation: BMC Bioinformatics 2016 17:199
    Content type: Software Published on:

  15. Gene expression connectivity mapping has proven to be a powerful and flexible tool for research. Its application has been shown in a broad range of research topics, most commonly as a means of identifying pote...

    Authors: Paul G. O’Reilly, Qing Wen, Peter Bankhead, Philip D. Dunne, Darragh G. McArt, Suzanne McPherson, Peter W. Hamilton, Ken I. Mills and Shu-Dong Zhang
    Citation: BMC Bioinformatics 2016 17:198
    Content type: Software Published on:

  16. Single particle tracking (SPT) is nowadays one of the most popular technique to probe spatio-temporal dynamics of proteins diffusing within the plasma membrane. Indeed membrane components of eukaryotic cells a...

    Authors: Patrice Dosset, Patrice Rassam, Laurent Fernandez, Cedric Espenel, Eric Rubinstein, Emmanuel Margeat and Pierre-Emmanuel Milhiet
    Citation: BMC Bioinformatics 2016 17:197
    Content type: Research article Published on:

  17. Endocytosis is regarded as a mechanism of attenuating the epidermal growth factor receptor (EGFR) signaling and of receptor degradation. There is increasing evidence becoming available showing that breast canc...

    Authors: Lu Cao, Marjo de Graauw, Kuan Yan, Leah Winkel and Fons J. Verbeek
    Citation: BMC Bioinformatics 2016 17:196
    Content type: Methodology Article Published on:

  18. G-DOC Plus is a data integration and bioinformatics platform that uses cloud computing and other advanced computational tools to handle a variety of biomedical BIG DATA including gene expression arrays, NGS and m...

    Authors: Krithika Bhuvaneshwar, Anas Belouali, Varun Singh, Robert M. Johnson, Lei Song, Adil Alaoui, Michael A. Harris, Robert Clarke, Louis M. Weiner, Yuriy Gusev and Subha Madhavan
    Citation: BMC Bioinformatics 2016 17:193
    Content type: Software Published on:

  19. The development of high-throughput sequencing technologies has revolutionized the field of microbial ecology via the sequencing of phylogenetic marker genes (e.g. 16S rRNA gene amplicon sequencing). Denoising,...

    Authors: Mohamed Mysara, Natalie Leys, Jeroen Raes and Pieter Monsieurs
    Citation: BMC Bioinformatics 2016 17:192
    Content type: Research article Published on:

  20. MicroRNAs (miRNAs) are small ~22 nucleotide non-coding RNAs that function as post-transcriptional regulators of messenger RNA (mRNA) through base-pairing to 6–8 nucleotide long target sites, usually located wi...

    Authors: Bridget C. Ryan, Torben S. Werner, Perry L. Howard and Robert L. Chow
    Citation: BMC Bioinformatics 2016 17:190
    Content type: Software Published on:

  22. Detection of tandem duplication within coding exons, referred to as internal tandem duplication (ITD), remains challenging due to inefficiencies in alignment of ITD-containing reads to the reference genome. Th...

    Authors: Navin Rustagi, Oliver A Hampton, Jie Li, Liu Xi, Richard A. Gibbs, Sharon E. Plon, Marek Kimmel and David A. Wheeler
    Citation: BMC Bioinformatics 2016 17:188
    Content type: Methodology article Published on:

  23. We have previously presented a formal language for describing population dynamics based on environment-dependent Stochastic Tree Grammars (eSTG). The language captures in broad terms the effect of the changing...

    Authors: Adam Spiro and Ehud Shapiro
    Citation: BMC Bioinformatics 2016 17:187
    Content type: Software Published on:

    The Erratum to this article has been published in BMC Bioinformatics 2016 17:303

  24. Recently, high-throughput experimental techniques have generated a large amount of protein-protein interaction (PPI) data which can construct large complex PPI networks for numerous organisms. System biology a...

    Authors: Yijia Zhang, Hongfei Lin, Zhihao Yang and Jian Wang
    Citation: BMC Bioinformatics 2016 17:186
    Content type: Research article Published on:

  25. Network visualization and analysis tools aid in better understanding of complex biological systems. Furthermore, to understand the differences in behaviour of system(s) under various environmental conditions (...

    Authors: Bhusan K. Kuntal, Anirban Dutta and Sharmila S. Mande
    Citation: BMC Bioinformatics 2016 17:185
    Content type: Software Published on:

    The Correction to this article has been published in BMC Bioinformatics 2019 20:600

  26. Proteins are the important molecules which participate in virtually every aspect of cellular function within an organism in pairs. Although high-throughput technologies have generated considerable protein-prot...

    Authors: Yu-An Huang, Zhu-Hong You, Xing Chen, Keith Chan and Xin Luo
    Citation: BMC Bioinformatics 2016 17:184
    Content type: Research article Published on:

  27. Cell culture on printed micropatterns slides combined with automated fluorescent microscopy allows for extraction of tens of thousands of videos of small isolated growing cell clusters. The analysis of such la...

    Authors: Yingbo Li, France Rose, Florencia di Pietro, Xavier Morin and Auguste Genovesio
    Citation: BMC Bioinformatics 2016 17:183
    Content type: Methodology Article Published on:

  29. There is growing evidence that DNA methylation alterations may contribute to carcinogenesis. Recent data also suggest that DNA methylation field defects in normal pre-neoplastic tissue represent infrequent sto...

    Authors: Andrew E. Teschendorff, Allison Jones and Martin Widschwendter
    Citation: BMC Bioinformatics 2016 17:178
    Content type: Research article Published on:

  31. Amplicon pyrosequencing targets a known genetic region and thus inherently produces reads highly anticipated to have certain features, such as conserved nucleotide sequence, and in the case of protein coding D...

    Authors: Thomas S. Rask, Bent Petersen, Donald S. Chen, Karen P. Day and Anders Gorm Pedersen
    Citation: BMC Bioinformatics 2016 17:176
    Content type: Methodology article Published on:

  33. The immune system is multifaceted, structured by diverse components that interconnect using multilayered dynamic cellular processes. Genomic technologies provide a means for investigating, at the molecular lev...

    Authors: Hong Liu, Jessica Liu, Michelle Toups, Timothy Soos and Christopher Arendt
    Citation: BMC Bioinformatics 2016 17:171
    Content type: Research article Published on:

  34. The nature of somatic mutations observed in human tumors at single gene or genome-wide levels can reveal information on past carcinogenic exposures and mutational processes contributing to tumor development. W...

    Authors: Maude Ardin, Vincent Cahais, Xavier Castells, Liacine Bouaoun, Graham Byrnes, Zdenko Herceg, Jiri Zavadil and Magali Olivier
    Citation: BMC Bioinformatics 2016 17:170
    Content type: Software Published on:

  36. The α + β barrel superfamily of the ferredoxin-like fold consists of a functionally diverse group of evolutionarily related proteins. The barrel architecture of these proteins is formed by either homo-/hetero-...

    Authors: Giriraj Acharya, Gurmeet Kaur and Srikrishna Subramanian
    Citation: BMC Bioinformatics 2016 17:168
    Content type: Research article Published on:

  37. MicroRNAs (miRNAs) are about 22 nucleotides, non-coding RNAs that affect various cellular functions, and play a regulatory role in different organisms including human. Until now, more than 2500 mature miRNAs i...

    Authors: Emily Chia-Yu Su, Yu-Sing Chen, Yun-Cheng Tien, Jeff Liu, Bing-Ching Ho, Sung-Liang Yu and Sher Singh
    Citation: BMC Bioinformatics 2016 17:167
    Content type: Software Published on:

  38. Many popular dengue forecasting techniques have been used by several researchers to extrapolate dengue incidence rates, including the K-H model, support vector machines (SVM), and artificial neural networks (A...

    Authors: Padet Siriyasatien, Atchara Phumee, Phatsavee Ongruk, Katechan Jampachaisri and Kraisak Kesorn
    Citation: BMC Bioinformatics 2016 17:166
    Content type: Research article Published on:

  39. Previously, we described ROVER, a DNA variant caller which identifies genetic variants from PCR-targeted massively parallel sequencing (MPS) datasets generated by the Hi-Plex protocol. ROVER permits stringent ...

    Authors: Daniel J. Park, Roger Li, Edmund Lau, Peter Georgeson, Tú Nguyen-Dumont and Bernard J. Pope
    Citation: BMC Bioinformatics 2016 17:165
    Content type: Software Published on:

  41. Entity coreference is common in biomedical literature and it can affect text understanding systems that rely on accurate identification of named entities, such as relation extraction and automatic summarizatio...

    Authors: Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman and Thomas C. Rindflesch
    Citation: BMC Bioinformatics 2016 17:163
    Content type: Research Article Published on:

  43. The importance of the material properties of membranes for diverse cellular processes is well established. Notably, the elastic properties of the membrane, which depend on its composition, can directly influen...

    Authors: Niklaus Johner, Daniel Harries and George Khelashvili
    Citation: BMC Bioinformatics 2016 17:161
    Content type: Software Published on:

    The Erratum to this article has been published in BMC Bioinformatics 2016 17:236

  45. Accurate adjustment for the amplification efficiency (AE) is an important part of real-time quantitative polymerase chain reaction (qPCR) experiments. The most commonly used correction strategy is to estimate ...

    Authors: Anders E. Bilgrau, Steffen Falgreen, Anders Petersen, Malene K. Kjeldsen, Julie S. Bødker, Hans E. Johnsen, Karen Dybkær and Martin Bøgsted
    Citation: BMC Bioinformatics 2016 17:159
    Content type: Methodology Article Published on:

  46. Existing feature selection methods typically do not consider prior knowledge in the form of structural relationships among features. In this study, the features are structured based on prior knowledge into gro...

    Authors: Mohamed F. Ghalwash, Xi Hang Cao, Ivan Stojkovic and Zoran Obradovic
    Citation: BMC Bioinformatics 2016 17:158
    Content type: Methodology Article Published on:

  47. Biological research increasingly relies on network models to study complex phenomena. Signal Transduction Pathways are molecular circuits that model how cells receive, process, and respond to information from ...

    Authors: Gianfranco Politano, Francesca Orso, Monica Raimo, Alfredo Benso, Alessandro Savino, Daniela Taverna and Stefano Di Carlo
    Citation: BMC Bioinformatics 2016 17:157
    Content type: Software Published on:

  48. Compound Heterozygosity (CH) in classical genetics is the presence of two different recessive mutations at a particular gene locus. A relaxed form of CH alleles may account for an essential proportion of the m...

    Authors: Kaiyin Zhong, Lennart C. Karssen, Manfred Kayser and Fan Liu
    Citation: BMC Bioinformatics 2016 17:156
    Content type: Software Published on:

  49. Understanding the interactions between antibodies and the linear epitopes that they recognize is an important task in the study of immunological diseases. We present a novel computational method for the design...

    Authors: Rob Patro, Raquel Norel, Robert J. Prill, Julio Saez-Rodriguez, Peter Lorenz, Felix Steinbeck, Bjoern Ziems, Mitja Luštrek, Nicola Barbarini, Alessandra Tiengo, Riccardo Bellazzi, Hans-Jürgen Thiesen, Gustavo Stolovitzky and Carl Kingsford
    Citation: BMC Bioinformatics 2016 17:155
    Content type: Research Article Published on:

  50. Interoperability between formats is a recurring problem in systems biology research. Many tools have been developed to convert computational models from one format to another. However, they have been developed...

    Authors: Nicolas Rodriguez, Jean-Baptiste Pettit, Piero Dalle Pezze, Lu Li, Arnaud Henry, Martijn P. van Iersel, Gael Jalowicki, Martina Kutmon, Kedar N. Natarajan, David Tolnay, Melanie I. Stefan, Chris T. Evelo and Nicolas Le Novère
    Citation: BMC Bioinformatics 2016 17:154
    Content type: Software Published on:

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