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BMC Bioinformatics


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  1. Content type: Software

    Large image datasets acquired on automated microscopes typically have some fraction of low quality, out-of-focus images, despite the use of hardware autofocus systems. Identification of these images using auto...

    Authors: Samuel J. Yang, Marc Berndl, D. Michael Ando, Mariya Barch, Arunachalam Narayanaswamy, Eric Christiansen, Stephan Hoyer, Chris Roat, Jane Hung, Curtis T. Rueden, Asim Shankar, Steven Finkbeiner and Philip Nelson

    Citation: BMC Bioinformatics 2018 19:77

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  2. Content type: Methodology Article

    Expression quantitative trait loci (eQTL) analysis identifies genetic markers associated with the expression of a gene. Most existing eQTL analyses and methods investigate association in a single, readily avai...

    Authors: Gen Li, Dereje Jima, Fred A. Wright and Andrew B. Nobel

    Citation: BMC Bioinformatics 2018 19:95

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  3. Content type: Software

    With the recent proliferation of single-cell RNA-Seq experiments, several methods have been developed for unsupervised analysis of the resulting datasets. These methods often rely on unintuitive hyperparameter...

    Authors: Jesse M. Zhang, Jue Fan, H. Christina Fan, David Rosenfeld and David N. Tse

    Citation: BMC Bioinformatics 2018 19:93

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  4. Content type: Research Article

    Various indexing techniques have been applied by next generation sequencing read mapping tools. The choice of a particular data structure is a trade-off between memory consumption, mapping throughput, and cons...

    Authors: Haowen Zhang, Yuandong Chan, Kaichao Fan, Bertil Schmidt and Weiguo Liu

    Citation: BMC Bioinformatics 2018 19:92

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  5. Content type: Software

    The biomedical literature continues to grow at a rapid pace, making the challenge of knowledge retrieval and extraction ever greater. Tools that provide a means to search and mine the full text of literature t...

    Authors: H.-M. Müller, K. M. Van Auken, Y. Li and P. W. Sternberg

    Citation: BMC Bioinformatics 2018 19:94

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  6. Content type: Research

    System toxicology aims at understanding the mechanisms used by biological systems to respond to toxicants. Such understanding can be leveraged to assess the risk of chemicals, drugs, and consumer products in l...

    Authors: Maurizio Giordano, Kumar Parijat Tripathi and Mario Rosario Guarracino

    Citation: BMC Bioinformatics 2018 19(Suppl 2):48

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    This article is part of a Supplement: Volume 19 Supplement 2

  7. Content type: Research

    During the last years, several approaches were applied on biomedical data to detect disease specific proteins and genes in order to better target drugs. It was shown that statistical and machine learning based...

    Authors: Lokmane Chebouba, Bertrand Miannay, Dalila Boughaci and Carito Guziolowski

    Citation: BMC Bioinformatics 2018 19(Suppl 2):59

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    This article is part of a Supplement: Volume 19 Supplement 2

  8. Content type: Research

    The endomembrane system, known as secretory pathway, is responsible for the synthesis and transport of protein molecules in cells. Therefore, genes involved in the secretory pathway are essential for the cellu...

    Authors: Kumar Parijat Tripathi, Marina Piccirillo and Mario Rosario Guarracino

    Citation: BMC Bioinformatics 2018 19(Suppl 2):58

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    This article is part of a Supplement: Volume 19 Supplement 2

  9. Content type: Research

    Convolutional Neural Networks can be effectively used only when data are endowed with an intrinsic concept of neighbourhood in the input space, as is the case of pixels in images. We introduce here Ph-CNN, a n...

    Authors: Diego Fioravanti, Ylenia Giarratano, Valerio Maggio, Claudio Agostinelli, Marco Chierici, Giuseppe Jurman and Cesare Furlanello

    Citation: BMC Bioinformatics 2018 19(Suppl 2):49

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    This article is part of a Supplement: Volume 19 Supplement 2

  10. Content type: Research Article

    Non-small cell lung cancer (NSCLC) with activating EGFR mutations, especially exon 19 deletions and the L858R point mutation, is particularly responsive to gefitinib and erlotinib. However, the sensitivity var...

    Authors: Bin Zou, Victor H. F. Lee and Hong Yan

    Citation: BMC Bioinformatics 2018 19:88

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  11. Content type: Methodology Article

    DNA methylation is a stable form of epigenetic memory used by cells to control gene expression. Whole genome bisulfite sequencing (WGBS) has emerged as a gold-standard experimental technique for studying DNA m...

    Authors: Garrett Jenkinson, Jordi Abante, Andrew P. Feinberg and John Goutsias

    Citation: BMC Bioinformatics 2018 19:87

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  12. Content type: Research Article

    Systematic analysis of a parasite interactome is a key approach to understand different biological processes. It makes possible to elucidate disease mechanisms, to predict protein functions and to select promi...

    Authors: Crhisllane Rafaele dos Santos Vasconcelos, Túlio de Lima Campos and Antonio Mauro Rezende

    Citation: BMC Bioinformatics 2018 19:85

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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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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

    Social Media Impact
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