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BMC Bioinformatics


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  1. Content type: Research Article

    Integration of transcriptomic and metabolomic data improves functional interpretation of disease-related metabolomic phenotypes, and facilitates discovery of putative metabolite biomarkers and gene targets. Fo...

    Authors: Jalal K. Siddiqui, Elizabeth Baskin, Mingrui Liu, Carmen Z. Cantemir-Stone, Bofei Zhang, Russell Bonneville, Joseph P. McElroy, Kevin R. Coombes and Ewy A. Mathé

    Citation: BMC Bioinformatics 2018 19:81

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  2. Content type: Methodology Article

    The nearest neighbor model and associated dynamic programming algorithms allow for the efficient estimation of the RNA secondary structure Boltzmann ensemble. However because a given RNA secondary structure on...

    Authors: Luan Lin, Wilson H. McKerrow, Bryce Richards, Chukiat Phonsom and Charles E. Lawrence

    Citation: BMC Bioinformatics 2018 19:82

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  3. Content type: Methodology Article

    Clustering of protein sequences is of key importance in predicting the structure and function of newly sequenced proteins and is also of use for their annotation. With the advent of multiple high-throughput se...

    Authors: Armen Abnousi, Shira L. Broschat and Ananth Kalyanaraman

    Citation: BMC Bioinformatics 2018 19:83

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  4. Content type: Software

    Drawing integrated conclusions from diverse source data requires synthesis across multiple types of information. The ToxPi (Toxicological Prioritization Index) is an analytical framework that was developed to ...

    Authors: Skylar W. Marvel, Kimberly To, Fabian A. Grimm, Fred A. Wright, Ivan Rusyn and David M. Reif

    Citation: BMC Bioinformatics 2018 19:80

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  5. Content type: Research Article

    When many (up to millions) of statistical tests are conducted in discovery set analyses such as genome-wide association studies (GWAS), approaches controlling family-wise error rate (FWER) or false discovery r...

    Authors: Regina Brinster, Anna Köttgen, Bamidele O. Tayo, Martin Schumacher and Peggy Sekula

    Citation: BMC Bioinformatics 2018 19:78

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  6. Content type: Software

    Automated bioinformatics workflows are more robust, easier to maintain, and results more reproducible when built with command-line utilities than with custom-coded scripts. Command-line utilities further benef...

    Authors: Yözen Hernández, Rocky Bernstein, Pedro Pagan, Levy Vargas, William McCaig, Girish Ramrattan, Saymon Akther, Amanda Larracuente, Lia Di, Filipe G. Vieira and Wei-Gang Qiu

    Citation: BMC Bioinformatics 2018 19:76

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  7. Content type: Methodology Article

    In the field of biomarker validation with mass spectrometry, controlling the technical variability is a critical issue. In selected reaction monitoring (SRM) measurements, this issue provides the opportunity o...

    Authors: Amna Klich, Catherine Mercier, Laurent Gerfault, Pierre Grangeat, Corinne Beaulieu, Elodie Degout-Charmette, Tanguy Fortin, Pierre Mahé, Jean-François Giovannelli, Jean-Philippe Charrier, Audrey Giremus, Delphine Maucort-Boulch and Pascal Roy

    Citation: BMC Bioinformatics 2018 19:73

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  8. Content type: Methodology Article

    The application of high-throughput sequencing in a broad range of quantitative genomic assays (e.g., DNA-seq, ChIP-seq) has created a high demand for the analysis of large-scale read-count data. Typically, the...

    Authors: WeiBo Wang, Wei Sun, Wei Wang and Jin Szatkiewicz

    Citation: BMC Bioinformatics 2018 19:74

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  9. Content type: Methodology Article

    Crm1-dependent Nuclear Export Signals (NESs) are clusters of alternating hydrophobic and non-hydrophobic amino acid residues between 10 to 15 amino acids in length. NESs were largely thought to follow simple c...

    Authors: Muluye E. Liku, Elizabeth-Ann Legere and Alan M. Moses

    Citation: BMC Bioinformatics 2018 19:65

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  10. Content type: Research Article

    Pathological angiogenesis has been identified in many malignancies as a potential prognostic factor and target for therapy. In most cases, angiogenic analysis is based on the measurement of microvessel density...

    Authors: Faliu Yi, Lin Yang, Shidan Wang, Lei Guo, Chenglong Huang, Yang Xie and Guanghua Xiao

    Citation: BMC Bioinformatics 2018 19:64

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  11. Content type: Software

    Fungi have diverse biotechnological applications in, among others, agriculture, bioenergy generation, or remediation of polluted soil and water. In this context, culture media based on color change in response...

    Authors: César Domínguez, Jónathan Heras, Eloy Mata and Vico Pascual

    Citation: BMC Bioinformatics 2018 19:66

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  12. Content type: Software

    Quantitative trait locus (QTL) mapping in genetic data often involves analysis of correlated observations, which need to be accounted for to avoid false association signals. This is commonly performed by model...

    Authors: Andrey Ziyatdinov, Miquel Vázquez-Santiago, Helena Brunel, Angel Martinez-Perez, Hugues Aschard and Jose Manuel Soria

    Citation: BMC Bioinformatics 2018 19:68

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  13. Content type: Research Article

    Protein crystal structures are potentially over-interpreted since they are routinely refined without any restraint on the upper limit of atomic B-factors. Consequently, some of their atoms, undetected in the e...

    Authors: Oliviero Carugo

    Citation: BMC Bioinformatics 2018 19:61

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  14. Content type: Software

    Prioritization of sequence variants for diagnosis and discovery of Mendelian diseases is challenging, especially in large collections of whole genome sequences (WGS). Fast, scalable solutions are needed for di...

    Authors: Steven Flygare, Edgar Javier Hernandez, Lon Phan, Barry Moore, Man Li, Anthony Fejes, Hao Hu, Karen Eilbeck, Chad Huff, Lynn Jorde, Martin G. Reese and Mark Yandell

    Citation: BMC Bioinformatics 2018 19:57

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  15. Content type: Software

    The analysis of modular gene co-expression networks is a well-established method commonly used for discovering the systems-level functionality of genes. In addition, these studies provide a basis for the disco...

    Authors: Pedro S. T. Russo, Gustavo R. Ferreira, Lucas E. Cardozo, Matheus C. Bürger, Raul Arias-Carrasco, Sandra R. Maruyama, Thiago D. C. Hirata, Diógenes S. Lima, Fernando M. Passos, Kiyoshi F. Fukutani, Melissa Lever, João S. Silva, Vinicius Maracaja-Coutinho and Helder I. Nakaya

    Citation: BMC Bioinformatics 2018 19:56

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  16. Content type: Research

    LncRNAs are long regulatory non-coding RNAs, some of which are arguably predicted to have coding potential. Despite coding potential classifiers that utilize ribosome profiling data successfully detected activ...

    Authors: Seo-Won Choi and Jin-Wu Nam

    Citation: BMC Bioinformatics 2018 19(Suppl 1):41

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    This article is part of a Supplement: Volume 19 Supplement 1

  17. Content type: Research

    It is known that functional RNAs often switch their functions by forming different secondary structures. Popular tools for RNA secondary structures prediction, however, predict the single ‘best’ structures, an...

    Authors: Taichi Hagio, Shun Sakuraba, Junichi Iwakiri, Ryota Mori and Kiyoshi Asai

    Citation: BMC Bioinformatics 2018 19(Suppl 1):38

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    This article is part of a Supplement: Volume 19 Supplement 1

  18. Content type: Research

    DNA damage causes aging, cancer, and other serious diseases. The comet assay can detect multiple types of DNA lesions with high sensitivity, and it has been widely applied. Although comet assay platforms have ...

    Authors: Taehoon Lee, Sungmin Lee, Woo Young Sim, Yu Mi Jung, Sunmi Han, Joong-Ho Won, Hyeyoung Min and Sungroh Yoon

    Citation: BMC Bioinformatics 2018 19(Suppl 1):44

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    This article is part of a Supplement: Volume 19 Supplement 1

  19. Content type: Research

    Since many proteins become functional only after they interact with their partner proteins and form protein complexes, it is essential to identify the sets of proteins that form complexes. Therefore, several c...

    Authors: Peiying Ruan, Morihiro Hayashida, Tatsuya Akutsu and Jean-Philippe Vert

    Citation: BMC Bioinformatics 2018 19(Suppl 1):39

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    This article is part of a Supplement: Volume 19 Supplement 1

  20. Content type: Methodology

    The read length of single-molecule DNA sequencers is reaching 1 Mb. Popular alignment software tools widely used for analyzing such long reads often take advantage of single-instruction multiple-data (SIMD) op...

    Authors: Hajime Suzuki and Masahiro Kasahara

    Citation: BMC Bioinformatics 2018 19(Suppl 1):45

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    This article is part of a Supplement: Volume 19 Supplement 1

  21. Content type: Methodology

    Bioinformatics research for finding biological mechanisms can be done by analysis of transcriptome data with pathway based interpretation. Therefore, researchers have tried to develop tools to analyze transcri...

    Authors: Inyoung Kim, Saemi Choi and Sun Kim

    Citation: BMC Bioinformatics 2018 19(Suppl 1):42

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 1

  22. Content type: Methodology

    While next-generation sequencing (NGS) costs have fallen in recent years, the cost and complexity of computation remain substantial obstacles to the use of NGS in bio-medical care and genomic research. The rap...

    Authors: GunHwan Ko, Pan-Gyu Kim, Jongcheol Yoon, Gukhee Han, Seong-Jin Park, Wangho Song and Byungwook Lee

    Citation: BMC Bioinformatics 2018 19(Suppl 1):43

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 1

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2016 Journal Metrics

  • Citation Impact
    2.448 - 2-year Impact Factor
    3.450 - 5-year Impact Factor
    0.946 - Source Normalized Impact per Paper (SNIP)
    1.467 - SCImago Journal Rank (SJR)

    1405 Usage Factor

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