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  1. Content type: Research

    Two important challenges in the analysis of molecular biology information are data (multi-omic information) integration and the detection of patterns across large scale molecular networks and sequences. They a...

    Authors: Francesco Bardozzo, Pietro Lió and Roberto Tagliaferri

    Citation: BMC Bioinformatics 2018 19(Suppl 7):194

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 7

  2. Content type: Research

    A huge and continuous increase in the number of completely sequenced chloroplast genomes, available for evolutionary and functional studies in plants, has been observed during the past years. Consequently, it ...

    Authors: Régis Garnier, Christophe Guyeux, Jean-François Couchot, Michel Salomon, Bashar Al-Nuaimi and Bassam AlKindy

    Citation: BMC Bioinformatics 2018 19(Suppl 7):218

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 7

  3. Content type: Methodology article

    Current high-throughput sequencing platforms provide capacity to sequence multiple samples in parallel. Different samples are labeled by attaching a short sample specific nucleotide sequence, barcode, to each ...

    Authors: Panu Somervuo, Patrik Koskinen, Peng Mei, Liisa Holm, Petri Auvinen and Lars Paulin

    Citation: BMC Bioinformatics 2018 19:257

    Published on:

  4. Content type: Correction

    Following publication of the original article [1], the authors reported that Figs. 1 and 3 were interchanged. The original article has been corrected.

    Authors: Maxwell Shapiro, Stephen Meier and Thomas MacCarthy

    Citation: BMC Bioinformatics 2018 19:256

    Published on:

    The original article was published in BMC Bioinformatics 2018 19:163

  5. Content type: Research Article

    Gene expression in plant chloroplasts and mitochondria is affected by RNA editing. Numerous C-to-U conversions, accompanied by reverse U-to-C exchanges in some plant clades, alter the genetic information encod...

    Authors: Henning Lenz, Anke Hein and Volker Knoop

    Citation: BMC Bioinformatics 2018 19:255

    Published on:

  6. Content type: Methodology article

    Haplotype assembly is the process of assigning the different alleles of the variants covered by mapped sequencing reads to the two haplotypes of the genome of a human individual. Long reads, which are nowadays...

    Authors: Stefano Beretta, Murray D. Patterson, Simone Zaccaria, Gianluca Della Vedova and Paola Bonizzoni

    Citation: BMC Bioinformatics 2018 19:252

    Published on:

  7. Content type: Software

    Computation of reaction similarity is a pre-requisite for several bioinformatics applications including enzyme identification for specific biochemical reactions, enzyme classification and mining for specific i...

    Authors: Tadi Venkata Sivakumar, Anirban Bhaduri, Rajasekhara Reddy Duvvuru Muni, Jin Hwan Park and Tae Yong Kim

    Citation: BMC Bioinformatics 2018 19:254

    Published on:

  8. Content type: Correction

    Following publication of the original article [1], the authors reported that there was an error in the spelling of the name of one of the authors.

    Authors: Makbule Gulcin Ozsoy, Tansel Özyer, Faruk Polat and Reda Alhajj

    Citation: BMC Bioinformatics 2018 19:250

    Published on:

    The original article was published in BMC Bioinformatics 2018 19:136

  9. Content type: Database

    For automated reading of scientific publications to extract useful information about molecular mechanisms it is critical that genes, proteins and other entities be correctly associated with uniform identifiers...

    Authors: John A. Bachman, Benjamin M. Gyori and Peter K. Sorger

    Citation: BMC Bioinformatics 2018 19:248

    Published on:

  10. Content type: Research article

    Circadian rhythms comprise oscillating molecular interactions, the disruption of the homeostasis of which would cause various disorders. To understand this phenomenon systematically, an accurate technique to i...

    Authors: Hitoshi Iuchi, Masahiro Sugimoto and Masaru Tomita

    Citation: BMC Bioinformatics 2018 19:249

    Published on:

  11. Content type: Software

    GenoGAM (Genome-wide generalized additive models) is a powerful statistical modeling tool for the analysis of ChIP-Seq data with flexible factorial design experiments. However large runtime and memory requirem...

    Authors: Georg Stricker, Mathilde Galinier and Julien Gagneur

    Citation: BMC Bioinformatics 2018 19:247

    Published on:

  12. Content type: Software

    Bacterial pan-genomes, comprised of conserved and variable genes across multiple sequenced bacterial genomes, allow for identification of genomic regions that are phylogenetically discriminating or functionall...

    Authors: Thomas H. Clarke, Lauren M. Brinkac, Jason M. Inman, Granger Sutton and Derrick E. Fouts

    Citation: BMC Bioinformatics 2018 19:246

    Published on:

  13. Content type: Software

    The advent of next-generation sequencing (NGS) has made whole-genome sequencing of cohorts of individuals a reality. Primary datasets of raw or aligned reads of this sort can get very large. For scientific que...

    Authors: Kristiina Ausmees, Aji John, Salman Z. Toor, Andreas Hellander and Carl Nettelblad

    Citation: BMC Bioinformatics 2018 19:240

    Published on:

  14. Content type: Software

    High-throughput bioinformatics analyses of next generation sequencing (NGS) data often require challenging pipeline optimization. The key problem is choosing appropriate tools and selecting the best parameters...

    Authors: Nikola Tom, Ondrej Tom, Jitka Malcikova, Sarka Pavlova, Blanka Kubesova, Tobias Rausch, Miroslav Kolarik, Vladimir Benes, Vojtech Bystry and Sarka Pospisilova

    Citation: BMC Bioinformatics 2018 19:243

    Published on:

  15. Content type: Research article

    The Top Scoring Pair (TSP) classifier, based on the concept of relative ranking reversals in the expressions of pairs of genes, has been proposed as a simple, accurate, and easily interpretable decision rule f...

    Authors: Dimitri Kagaris, Alireza Khamesipour and Constantin T. Yiannoutsos

    Citation: BMC Bioinformatics 2018 19:244

    Published on:

  16. Content type: Methodology article

    Asthma and allergies prevalence increased in recent decades, being a serious global health problem. They are complex diseases with strong contextual influence, so that the use of advanced machine learning tool...

    Authors: Rafael V. Veiga, Helio J. C. Barbosa, Heder S. Bernardino, João M. Freitas, Caroline A. Feitosa, Sheila M. A. Matos, Neuza M. Alcântara-Neves and Maurício L. Barreto

    Citation: BMC Bioinformatics 2018 19:245

    Published on:

  17. Content type: Research article

    Lysine succinylation is a new kind of post-translational modification which plays a key role in protein conformation regulation and cellular function control. To understand the mechanism of succinylation profo...

    Authors: Qiao Ning, Xiaosa Zhao, Lingling Bao, Zhiqiang Ma and Xiaowei Zhao

    Citation: BMC Bioinformatics 2018 19:237

    Published on:

  18. Content type: Research article

    The adaptive immune response intrinsically depends on hypervariable human leukocyte antigen (HLA) genes. Concomitantly, correct HLA phenotyping is crucial for successful donor-patient matching in organ transpl...

    Authors: Maria Luisa Matey-Hernandez, Søren Brunak and Jose M. G. Izarzugaza

    Citation: BMC Bioinformatics 2018 19:239

    Published on:

  19. Content type: Methodology article

    Current normalization methods for RNA-sequencing data allow either for intersample comparison to identify differentially expressed (DE) genes or for intrasample comparison for the discovery and validation of g...

    Authors: Marcel Smid, Robert R. J. Coebergh van den Braak, Harmen J. G. van de Werken, Job van Riet, Anne van Galen, Vanja de Weerd, Michelle van der Vlugt-Daane, Sandra I. Bril, Zarina S. Lalmahomed, Wigard P. Kloosterman, Saskia M. Wilting, John A. Foekens, Jan N. M. IJzermans, John W. M. Martens and Anieta M. Sieuwerts

    Citation: BMC Bioinformatics 2018 19:236

    Published on:

Page 2 of 356

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