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  1. Computational modeling and simulation play an important role in analyzing the behavior of complex biological systems in response to the implantation of biomedical devices. Quantitative computational modeling d...

    Authors: Mingon Kang, Liping Tang and Jean Gao
    Citation: BMC Bioinformatics 2016 17:111
    Content type: Research Article Published on:

  2. To facilitate advances in personalized medicine, it is important to detect predictive, stable and interpretable biomarkers related with different clinical characteristics. These clinical characteristics may be...

    Authors: Meng-Yun Wu, Xiao-Fei Zhang, Dao-Qing Dai, Le Ou-Yang, Yuan Zhu and Hong Yan
    Citation: BMC Bioinformatics 2016 17:108
    Content type: Research Article Published on:

  3. The use of nanopore technologies is expected to spread in the future because they are portable and can sequence long fragments of DNA molecules without prior amplification. The first nanopore sequencer availab...

    Authors: Joaquin Tarraga, Asunción Gallego, Vicente Arnau, Ignacio Medina and Joaquin Dopazo
    Citation: BMC Bioinformatics 2016 17:107
    Content type: Software Published on:

  6. Often researchers are interested in comparing multiple experimental groups (e.g. tumor size) with a reference group (e.g. normal tissue) on the basis of thousands of features (e.g. genes) and determine if a di...

    Authors: Anjana Grandhi, Wenge Guo and Shyamal D. Peddada
    Citation: BMC Bioinformatics 2016 17:104
    Content type: Research Article Published on:

  7. High-throughput RNA-Sequencing (RNA-Seq) has become the preferred technique for studying gene expression differences between biological samples and for discovering novel isoforms, though the techniques to anal...

    Authors: Claire R. Williams, Alyssa Baccarella, Jay Z. Parrish and Charles C. Kim
    Citation: BMC Bioinformatics 2016 17:103
    Content type: Research article Published on:

  8. A1 Highlights from the eleventh ISCB Student Council Symposium 2015

    Authors: Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman, Griet Laenen, Sander Willems, Lieven Thorrez, Yves Moreau, Nagarajan Raju, Sonia Pankaj Chothani…
    Citation: BMC Bioinformatics 2016 17(Suppl 3):95
    Content type: Meeting Abstracts Published on:

    This article is part of a Supplement: Volume 17 Supplement 3

  10. Accurate detection of homologous relationships of biological sequences (DNA or amino acid) amongst organisms is an important and often difficult task that is essential to various evolutionary studies, ranging ...

    Authors: M. Stanley Fujimoto, Anton Suvorov, Nicholas O. Jensen, Mark J. Clement and Seth M. Bybee
    Citation: BMC Bioinformatics 2016 17:101
    Content type: Methodology article Published on:

  11. Protein complexes carry out nearly all signaling and functional processes within cells. The study of protein complexes is an effective strategy to analyze cellular functions and biological processes. With the ...

    Authors: Le Ou-Yang, Min Wu, Xiao-Fei Zhang, Dao-Qing Dai, Xiao-Li Li and Hong Yan
    Citation: BMC Bioinformatics 2016 17:100
    Content type: Research Article Published on:

  13. DNA methylation at a gene promoter region has the potential to regulate gene transcription. Patterns of methylation over multiple CpG sites in a region are often complex and cell type specific, with the region...

    Authors: Nicholas C. Wong, Bernard J. Pope, Ida L. Candiloro, Darren Korbie, Matt Trau, Stephen Q. Wong, Thomas Mikeska, Xinmin Zhang, Mark Pitman, Stefanie Eggers, Stephen R. Doyle and Alexander Dobrovic
    Citation: BMC Bioinformatics 2016 17:98
    Content type: Software Published on:

  15. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) experiments revolutionized genome-wide profiling of transcription factors and histone modifications. Although maturing sequencing technologies al...

    Authors: Qi Zhang, Xin Zeng, Sam Younkin, Trupti Kawli, Michael P. Snyder and Sündüz Keleş
    Citation: BMC Bioinformatics 2016 17:96
    Content type: Research Article Published on:

  16. Metagenomics is a genomics research discipline devoted to the study of microbial communities in environmental samples and human and animal organs and tissues. Sequenced metagenomic samples usually comprise rea...

    Authors: Minji Kim, Xiejia Zhang, Jonathan G. Ligo, Farzad Farnoud, Venugopal V. Veeravalli and Olgica Milenkovic
    Citation: BMC Bioinformatics 2016 17:94
    Content type: Methodology Article Published on:

  17. Genomics-based predictors of drug response have the potential to improve outcomes associated with cancer therapy. Osteosarcoma (OS), the most common primary bone cancer in dogs, is commonly treated with adjuva...

    Authors: Jared S. Fowles, Kristen C. Brown, Ann M. Hess, Dawn L. Duval and Daniel L. Gustafson
    Citation: BMC Bioinformatics 2016 17:93
    Content type: Research article Published on:

  19. The massive accumulation of protein sequences arising from the rapid development of high-throughput sequencing, coupled with automatic annotation, results in high levels of incorrect annotations. In this study...

    Authors: Ivan Vujaklija, Ana Bielen, Tina Paradžik, Siniša Biđin, Pavle Goldstein and Dušica Vujaklija
    Citation: BMC Bioinformatics 2016 17:91
    Content type: Methodology article Published on:

  20. The recent outbreak of Ebola has been cited as the largest in history. Despite this global health crisis, few drugs are available to efficiently treat Ebola infections. Drug repurposing provides a potentially ...

    Authors: Zheng Zhao, Che Martin, Raymond Fan, Philip E. Bourne and Lei Xie
    Citation: BMC Bioinformatics 2016 17:90
    Content type: Research article Published on:

  22. Robust methods for the segmentation and analysis of cells in 3D time sequences (3D+t) are critical for quantitative cell biology. While many automated methods for segmentation perform very well, few generalize...

    Authors: Diana L. Delibaltov, Utkarsh Gaur, Jennifer Kim, Matthew Kourakis, Erin Newman-Smith, William Smith, Samuel A. Belteton, Daniel B. Szymanski and B. S. Manjunath
    Citation: BMC Bioinformatics 2016 17:88
    Content type: Methodology Article Published on:

  23. Networks or graphs play an important role in the biological sciences. Protein interaction networks and metabolic networks support the understanding of basic cellular mechanisms. In the human brain, networks of...

    Authors: Klaus Hahn, Peter R. Massopust and Sergei Prigarin
    Citation: BMC Bioinformatics 2016 17:87
    Content type: Methodology Article Published on:

  24. Complex disease is largely determined by a number of biomolecules interwoven into networks, rather than a single biomolecule. A key but inadequately addressed issue is how to test possible differences of the n...

    Authors: Jiadong Ji, Zhongshang Yuan, Xiaoshuai Zhang and Fuzhong Xue
    Citation: BMC Bioinformatics 2016 17:86
    Content type: Methodology article Published on:

  25. The regulation of gene expression in eukaryotic cells is a complex process that involves epigenetic modifications and the interaction of DNA with multiple transcription factors. This process can be studied wit...

    Authors: Marcin Piechota, Michal Korostynski, Joanna Ficek, Andrzej Tomski and Ryszard Przewlocki
    Citation: BMC Bioinformatics 2016 17:85
    Content type: Software Published on:

  27. Phylogenetic analysis is now an important tool in the study of viral outbreaks. It can reconstruct epidemic history when surveillance epidemiology data are sparse, and can indicate transmission linkages among ...

    Authors: Simon Dellicour, Rebecca Rose and Oliver G. Pybus
    Citation: BMC Bioinformatics 2016 17:82
    Content type: Methodolgy article Published on:

  29. The increasing availability of resequencing data has led to a better understanding of the most important genes in cancer development. Nevertheless, the mutational landscape of many tumor types is heterogeneous...

    Authors: Giorgio E. M. Melloni, Stefano de Pretis, Laura Riva, Mattia Pelizzola, Arnaud Céol, Jole Costanza, Heiko Müller and Luca Zammataro
    Citation: BMC Bioinformatics 2016 17:80
    Content type: Software Published on:

  31. Repositioning approved drug and small molecules in novel therapeutic areas is of key interest to the pharmaceutical industry. A number of promising computational techniques have been developed to aid in reposi...

    Authors: Adam S. Brown, Sek Won Kong, Isaac S. Kohane and Chirag J. Patel
    Citation: BMC Bioinformatics 2016 17:78
    Content type: Methodology article Published on:

  32. It has been shown that a random-effects framework can be used to test the association between a gene’s expression level and the number of DNA copies of a set of genes. This gene-set modelling framework was lat...

    Authors: Renée X. Menezes, Leila Mohammadi, Jelle J. Goeman and Judith M. Boer
    Citation: BMC Bioinformatics 2016 17:77
    Content type: Methodology Article Published on:

  34. Increasing resistance to anti-tuberculosis drugs has driven the need for developing new drugs. Resources such as the tropical disease research (TDR) target database and AssessDrugTarget can help to prioritize ...

    Authors: Ruben Cloete, Ekow Oppon, Edwin Murungi, Wolf-Dieter Schubert and Alan Christoffels
    Citation: BMC Bioinformatics 2016 17:75
    Content type: Research article Published on:

  35. Gene set analysis (GSA) aims to evaluate the association between the expression of biological pathways, or a priori defined gene sets, and a particular phenotype. Numerous GSA methods have been proposed to ass...

    Authors: Huey-Miin Hsueh and Chen-An Tsai
    Citation: BMC Bioinformatics 2016 17:74
    Content type: Methodology Article Published on:

  36. Computer simulation is a resource which can be employed to identify optimal breeding strategies to effectively and efficiently achieve specific goals in developing improved cultivars. In some instances, it is ...

    Authors: Xiaochun Sun and Rita H. Mumm
    Citation: BMC Bioinformatics 2016 17:73
    Content type: Methodology article Published on:

  38. Malaria infection is still widespread in some parts of the world and threatens the lives of millions of people every year. Vaccines, especially oral vaccines are considered to be effective in reducing the burd...

    Authors: Shabnam Shamriz and Hamideh Ofoghi
    Citation: BMC Bioinformatics 2016 17:71
    Content type: Research article Published on:

  40. The intrinsic bendability of DNA plays an important role with relevance for myriad of essential cellular mechanisms. The flexibility of a DNA fragment can be experimentally and computationally examined by its ...

    Authors: Ludmil B. Alexandrov, Alan R. Bishop, Kim Ø. Rasmussen and Boian S. Alexandrov
    Citation: BMC Bioinformatics 2016 17:68
    Content type: Research article Published on:

  41. The sequencing of immunoglobulin (Ig) transcripts from single B cells yields essential information about Ig heavy:light chain pairing, which is lost in conventional bulk sequencing experiments. The previously ...

    Authors: Katharina Imkeller, Peter F. Arndt, Hedda Wardemann and Christian E. Busse
    Citation: BMC Bioinformatics 2016 17:67
    Content type: Software Published on:

  42. Many tools exist in the analysis of bacterial RNA sequencing (RNA-seq) transcriptional profiling experiments to identify differentially expressed genes between experimental conditions. Generally, the workflow ...

    Authors: Benjamin K. Johnson, Matthew B. Scholz, Tracy K. Teal and Robert B. Abramovitch
    Citation: BMC Bioinformatics 2016 17:66
    Content type: Software Published on:

  43. Modelling disease outbreaks often involves integrating the wealth of data that are gathered during modern outbreaks into complex mathematical or computational models of transmission. Incorporating these data i...

    Authors: Anthony O’Hare, Samantha J. Lycett, Thomas Doherty, Liliana C. M. Salvador and Rowland R. Kao
    Citation: BMC Bioinformatics 2016 17:65
    Content type: Software Published on:

  44. Dynamical models of gene regulatory networks (GRNs) are highly effective in describing complex biological phenomena and processes, such as cell differentiation and cancer development. Yet, the topological and ...

    Authors: Andrea Paroni, Alex Graudenzi, Giulio Caravagna, Chiara Damiani, Giancarlo Mauri and Marco Antoniotti
    Citation: BMC Bioinformatics 2016 17:64
    Content type: Software Published on:

  45. The impressively low cost and improved quality of genome sequencing provides to researchers of genetic diseases, such as cancer, a powerful tool to better understand the underlying genetic mechanisms of those ...

    Authors: Christos Kozanitis and David A. Patterson
    Citation: BMC Bioinformatics 2016 17:63
    Content type: Software Published on:

  47. The second Chargaff’s parity rule and its extensions are recognized as universal phenomena in DNA sequences. However, parity of the frequencies of reverse complementary oligonucleotides could be a mere consequ...

    Authors: Vera Afreixo, João M. O. S. Rodrigues, Carlos A. C. Bastos and Raquel M. Silva
    Citation: BMC Bioinformatics 2016 17:59
    Content type: Research Article Published on:

  48. Stored biological samples with pathology information and medical records are invaluable resources for translational medical research. However, RNAs extracted from the archived clinical tissues are often substa...

    Authors: Liguo Wang, Jinfu Nie, Hugues Sicotte, Ying Li, Jeanette E. Eckel-Passow, Surendra Dasari, Peter T. Vedell, Poulami Barman, Liewei Wang, Richard Weinshiboum, Jin Jen, Haojie Huang, Manish Kohli and Jean-Pierre A. Kocher
    Citation: BMC Bioinformatics 2016 17:58
    Content type: Methodology article Published on:

  49. Traditional Sanger sequencing has been used as a gold standard method for genetic testing in clinic to perform single gene test, which has been a cumbersome and expensive method to test several genes in hetero...

    Authors: Ram Vinay Pandey, Stephan Pabinger, Albert Kriegner and Andreas Weinhäusel
    Citation: BMC Bioinformatics 2016 17:56
    Content type: Software Published on:

  50. Success in genome-wide association studies and marker-assisted selection depends on good phenotypic and genotypic data. The more complete this data is, the more powerful will be the results of analysis. Nevert...

    Authors: A. Xavier, William M. Muir and Katy M. Rainey
    Citation: BMC Bioinformatics 2016 17:55
    Content type: Methodology article Published on:

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