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  1. Modeling of microbial metabolism is a topic of growing importance in biotechnology. Mathematical modeling helps provide a mechanistic understanding for the studied process, separating the main drivers from the...

    Authors: Garrett W. Birkel, Amit Ghosh, Vinay S. Kumar, Daniel Weaver, David Ando, Tyler W. H. Backman, Adam P. Arkin, Jay D. Keasling and Héctor García Martín
    Citation: BMC Bioinformatics 2017 18:205
    Content type: Software Published on:

    The Erratum to this article has been published in BMC Bioinformatics 2017 18:219

  4. A comprehensive map of the human-M. tuberculosis (MTB) protein interactome would help fill the gaps in our understanding of the disease, and computational prediction can aid and complement experimental studies to...

    Authors: Gaurang Mahajan and Shekhar C. Mande
    Citation: BMC Bioinformatics 2017 18:201
    Content type: Research article Published on:

  5. Systematic, standardized and in-depth phenotyping and data analyses of rodent behaviour empowers gene-function studies, drug testing and therapy design. However, no data repositories are currently available fo...

    Authors: Bastijn Koopmans, August B. Smit, Matthijs Verhage and Maarten Loos
    Citation: BMC Bioinformatics 2017 18:200
    Content type: Database Published on:

  6. Factor graphs provide a flexible and general framework for specifying probability distributions. They can capture a range of popular and recent models for analysis of both genomics data as well as data from ot...

    Authors: Tobias Madsen, Asger Hobolth, Jens Ledet Jensen and Jakob Skou Pedersen
    Citation: BMC Bioinformatics 2017 18:199
    Content type: Methodology Article Published on:

  8. Understanding the working mechanism of the brain is one of the grandest challenges for modern science. Toward this end, the BigNeuron project was launched to gather a worldwide community to establish a big dat...

    Authors: Zhijiang Wan, Yishan He, Ming Hao, Jian Yang and Ning Zhong
    Citation: BMC Bioinformatics 2017 18:197
    Content type: Methodology article Published on:

  10. The canonical code, although prevailing in complex genomes, is not universal. It was shown the canonical genetic code superior robustness compared to random codes, but it is not clearly determined how it evolv...

    Authors: José Santos and Ángel Monteagudo
    Citation: BMC Bioinformatics 2017 18:195
    Content type: Research Article Published on:

  12. MicroRNAs always function cooperatively in their regulation of gene expression. Dysfunctions of these co-functional microRNAs can play significant roles in disease development. We are interested in those multi...

    Authors: Hui Peng, Chaowang Lan, Yi Zheng, Gyorgy Hutvagner, Dacheng Tao and Jinyan Li
    Citation: BMC Bioinformatics 2017 18:193
    Content type: Research Article Published on:

  13. Population structure inference using the software STRUCTURE has become an integral part of population genetic studies covering a broad spectrum of taxa including humans. The ever-expanding size of genetic data...

    Authors: Vikram E. Chhatre and Kevin J. Emerson
    Citation: BMC Bioinformatics 2017 18:192
    Content type: Software Published on:

  14. Genome-wide assisted selection is a critical tool for the genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fittin...

    Authors: Alencar Xavier, Shizhong Xu, William Muir and Katy Martin Rainey
    Citation: BMC Bioinformatics 2017 18:191
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Bioinformatics 2017 18:222

  15. Insecticide resistance is a major challenge for the control program of insect pests in the fields of crop protection, human and animal health etc. Resistance to different insecticides is conferred by the prote...

    Authors: Prabina Kumar Meher, Tanmaya Kumar Sahu, Anjali Banchariya and Atmakuri Ramakrishna Rao
    Citation: BMC Bioinformatics 2017 18:190
    Content type: Research article Published on:

  16. In recent years, the microscopy technology for imaging cells has developed greatly and rapidly. The accompanying requirements for automatic segmentation and quantification of the imaged cells are becoming more...

    Authors: Zhenzhou Wang and Haixing Li
    Citation: BMC Bioinformatics 2017 18:189
    Content type: Research article Published on:

  17. Bacterial sRNA-mediated regulatory networks has been introduced as a powerful way to analyze the fast rewiring capabilities of a bacteria in response to changing environmental conditions. The identification of...

    Authors: Romain Bourqui, Isabelle Dutour, Jonathan Dubois, William Benchimol and Patricia Thébault
    Citation: BMC Bioinformatics 2017 18:188
    Content type: Software Published on:

  18. The unveiling of long non-coding RNAs as important gene regulators in many biological contexts has increased the demand for efficient and robust computational methods to identify novel long non-coding RNAs fro...

    Authors: Giovanna M. M. Ventola, Teresa M. R. Noviello, Salvatore D’Aniello, Antonietta Spagnuolo, Michele Ceccarelli and Luigi Cerulo
    Citation: BMC Bioinformatics 2017 18:187
    Content type: Research Article Published on:

  21. In recent years long non coding RNAs (lncRNAs) have been the subject of increasing interest. Thanks to many recent functional studies, the existence of a large class of lncRNAs with potential regulatory functi...

    Authors: Umberto Perron, Paolo Provero and Ivan Molineris
    Citation: BMC Bioinformatics 2017 18(Suppl 5):144
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 5

  22. Methods for inference and comparison of biological networks are emerging as powerful tools for the identification of groups of tightly connected genes whose activity may be altered during disease progression o...

    Authors: Francesca Mulas, Amy Li, David H. Sherr and Stefano Monti
    Citation: BMC Bioinformatics 2017 18(Suppl 5):130
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 5

  23. NGS technology represents a powerful alternative to the standard Sanger sequencing in the context of clinical setting. The proprietary software that are generally used for variant calling often depend on prese...

    Authors: Simona De Summa, Giovanni Malerba, Rosamaria Pinto, Antonio Mori, Vladan Mijatovic and Stefania Tommasi
    Citation: BMC Bioinformatics 2017 18(Suppl 5):119
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 5

  24. The statistical evaluation of pathway enrichment, i.e. of gene profiles' confluence to the pathway level, allows exploring molecular landscapes using functionally annotated gene sets. However, pathway scores c...

    Authors: Ashwini Jeggari and Andrey Alexeyenko
    Citation: BMC Bioinformatics 2017 18(Suppl 5):118
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 5

  25. One goal of structural biology is to understand how a protein’s 3-dimensional conformation determines its capacity to interact with potential ligands. In the case of small chemical ligands, deconstructing a st...

    Authors: Raquel Dias and Bryan Kolaczkowski
    Citation: BMC Bioinformatics 2017 18(Suppl 5):102
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 5

  26. The 15th International NETTAB workshop and the 11th Integrative Bioinformatics Symposium were held together in Bari, on October 14–16, 2016, as Joint NETTAB/IB 2015 Meeting. A special topic for the meeting was “B...

    Authors: Paolo Romano, Ralf Hofestädt, Matthias Lange and Domenica D’Elia
    Citation: BMC Bioinformatics 2017 18(Suppl 5):101
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 18 Supplement 5

  28. Time-Frequency (TF) analysis has been extensively used for the analysis of non-stationary numeric signals in the past decade. At the same time, recent studies have statistically confirmed the non-stationarity ...

    Authors: Hamed Hassani Saadi, Reza Sameni and Amin Zollanvari
    Citation: BMC Bioinformatics 2017 18(Suppl 4):154
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 4

  29. Analysis of integrated genome-scale networks is a challenging problem due to heterogeneity of high-throughput data. There are several topological measures, such as graphlet counts, for characterization of biol...

    Authors: Arzu Burcak Sonmez and Tolga Can
    Citation: BMC Bioinformatics 2017 18(Suppl 4):135
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 4

  30. Prostate cancer is one of the most prevalent cancers in males in the United States and amongst the leading causes of cancer related deaths. A particularly virulent form of this disease is castration-resistant ...

    Authors: Osama Ali Arshad and Aniruddha Datta
    Citation: BMC Bioinformatics 2017 18(Suppl 4):134
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 4

  31. Deconvolution is a mathematical process of resolving an observed function into its constituent elements. In the field of biomedical research, deconvolution analysis is applied to obtain single cell-type or tis...

    Authors: Haijing Jin, Ying-Wooi Wan and Zhandong Liu
    Citation: BMC Bioinformatics 2017 18(Suppl 4):117
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 4

  32. Design of personalized targeted therapies involve modeling of patient sensitivity to various drugs and drug combinations. Majority of studies evaluate the sensitivity of tumor cells to targeted drugs without m...

    Authors: Kevin Matlock, Noah Berlow, Charles Keller and Ranadip Pal
    Citation: BMC Bioinformatics 2017 18(Suppl 4):116
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 4

  33. Finding epistatic interactions in large association studies like genome-wide association studies (GWAS) with the nowadays-available large volume of genomic data is a challenging and largely unsolved issue. Few...

    Authors: Sinan Abo Alchamlat and Frédéric Farnir
    Citation: BMC Bioinformatics 2017 18:184
    Content type: Methodology article Published on:

  35. Characterization of mature protein N-termini by large scale proteomics is challenging. This is especially true for proteins undergoing cleavage of transit peptides when they are targeted to specific organelles...

    Authors: Willy Vincent Bienvenut, Jean-Pierre Scarpelli, Johan Dumestier, Thierry Meinnel and Carmela Giglione
    Citation: BMC Bioinformatics 2017 18:182
    Content type: Methodology article Published on:

  37. Genome-wide miRNA expression data can be used to study miRNA dysregulation comprehensively. Although many open-source tools for microRNA (miRNA)-seq data analyses are available, challenges remain in accurate m...

    Authors: Shanrong Zhao, William Gordon, Sarah Du, Chi Zhang, Wen He, Li Xi, Sachin Mathur, Michael Agostino, Theresa Paradis, David von Schack, Michael Vincent and Baohong Zhang
    Citation: BMC Bioinformatics 2017 18:180
    Content type: Software Published on:

  38. The rapid progress of high-throughput DNA sequencing techniques has dramatically reduced the costs of whole genome sequencing, which leads to revolutionary advances in gene industry. The explosively increasing...

    Authors: Zhi-An Huang, Zhenkun Wen, Qingjin Deng, Ying Chu, Yiwen Sun and Zexuan Zhu
    Citation: BMC Bioinformatics 2017 18:179
    Content type: Software Published on:

  39. Using phylogenomic analysis tools for tracking pathogens has become standard practice in academia, public health agencies, and large industries. Using the same raw read genomic data as input, there are several...

    Authors: Emily Jane McTavish, James Pettengill, Steven Davis, Hugh Rand, Errol Strain, Marc Allard and Ruth E. Timme
    Citation: BMC Bioinformatics 2017 18:178
    Content type: Software Published on:

  40. The number of genomics and proteomics experiments is growing rapidly, producing an ever-increasing amount of data that are awaiting functional interpretation. A number of function prediction algorithms were de...

    Authors: Qing Wei, Ishita K. Khan, Ziyun Ding, Satwica Yerneni and Daisuke Kihara
    Citation: BMC Bioinformatics 2017 18:177
    Content type: Software Published on:

  41. Manual assessment and evaluation of fluorescent micrograph cell experiments is time-consuming and tedious. Automated segmentation pipelines can ensure efficient and reproducible evaluation and analysis with co...

    Authors: Veit Wiesmann, Matthias Bergler, Ralf Palmisano, Martin Prinzen, Daniela Franz and Thomas Wittenberg
    Citation: BMC Bioinformatics 2017 18:176
    Content type: Research Article Published on:

  43. Phenotypic studies in Triticeae have shown that low temperature-induced protective mechanisms are developmentally regulated and involve dynamic acclimation processes. Understanding these mechanisms is importan...

    Authors: Alain B. Tchagang, François Fauteux, Dan Tulpan and Youlian Pan
    Citation: BMC Bioinformatics 2017 18:174
    Content type: Research article Published on:

  44. The current gold standard in dimension reduction methods for high-throughput genotype data is the Principle Component Analysis (PCA). The presence of PCA is so dominant, that other methods usually cannot be fo...

    Authors: Daniel Fischer, Mervi Honkatukia, Maria Tuiskula-Haavisto, Klaus Nordhausen, David Cavero, Rudolf Preisinger and Johanna Vilkki
    Citation: BMC Bioinformatics 2017 18:173
    Content type: Methodology Article Published on:

  45. Taxonomic classification based on the 16S rRNA gene sequence is important for the profiling of microbial communities. In addition to giving the best possible accuracy, it is also important to quantify uncertai...

    Authors: Kristian Hovde Liland, Hilde Vinje and Lars Snipen
    Citation: BMC Bioinformatics 2017 18:172
    Content type: Software Published on:

  46. Protein-protein interactions (PPIs) can offer compelling evidence for protein function, especially when viewed in the context of proteome-wide interactomes. Bacteria have been popular subjects of interactome s...

    Authors: J. Harry Caufield, Christopher Wimble, Semarjit Shary, Stefan Wuchty and Peter Uetz
    Citation: BMC Bioinformatics 2017 18:171
    Content type: Research article Published on:

  47. Some applications, especially those clinical applications requiring high accuracy of sequencing data, usually have to face the troubles caused by unavoidable sequencing errors. Several tools have been proposed...

    Authors: Shifu Chen, Tanxiao Huang, Yanqing Zhou, Yue Han, Mingyan Xu and Jia Gu
    Citation: BMC Bioinformatics 2017 18(Suppl 3):80
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 3

  48. Residues in a protein might be buried inside or exposed to the solvent surrounding the protein. The buried residues usually form hydrophobic cores to maintain the structural integrity of proteins while the exp...

    Authors: Hai’e Gong, Haicang Zhang, Jianwei Zhu, Chao Wang, Shiwei Sun, Wei-Mou Zheng and Dongbo Bu
    Citation: BMC Bioinformatics 2017 18(Suppl 3):70
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 3

  50. Structural variations (SVs) are wide-spread in human genomes and may have important implications in disease-related and evolutionary studies. High-throughput sequencing (HTS) has become a major platform for SV...

    Authors: Yuchao Xia, Yun Liu, Minghua Deng and Ruibin Xi
    Citation: BMC Bioinformatics 2017 18(Suppl 3):53
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 3

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