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  1. Content type: Research article

    Count data generated by next-generation sequencing assays do not measure absolute transcript abundances. Instead, the data are constrained to an arbitrary “library size” by the sequencing depth of the assay, a...

    Authors: Thomas P. Quinn, Tamsyn M. Crowley and Mark F. Richardson

    Citation: BMC Bioinformatics 2018 19:274

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  2. Content type: Software

    Transfer of genetic material from microbes or viruses into the host genome is known as horizontal gene transfer (HGT). The integration of viruses into the human genome is associated with multiple cancers, and ...

    Authors: Saurabh Baheti, Xiaojia Tang, Daniel R. O’Brien, Nicholas Chia, Lewis R. Roberts, Heidi Nelson, Judy C. Boughey, Liewei Wang, Matthew P. Goetz, Jean-Pierre A. Kocher and Krishna R. Kalari

    Citation: BMC Bioinformatics 2018 19:271

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  3. Content type: Methodology article

    Tandem repeats comprise significant proportion of the human genome including coding and regulatory regions. They are highly prone to repeat number variation and nucleotide mutation due to their repetitive and ...

    Authors: Devika Ganesamoorthy, Minh Duc Cao, Tania Duarte, Wenhan Chen and Lachlan Coin

    Citation: BMC Bioinformatics 2018 19:267

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  4. Content type: Software

    Public biomedical data repositories often provide web-based interfaces to collect experimental metadata. However, these interfaces typically reflect the ad hoc metadata specification practices of the associate...

    Authors: Syed Ahmad Chan Bukhari, Marcos Martínez-Romero, Martin J. O’ Connor, Attila L. Egyedi, Debra Willrett, John Graybeal, Mark A. Musen, Kei-Hoi Cheung and Steven H. Kleinstein

    Citation: BMC Bioinformatics 2018 19:268

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  5. Content type: Research article

    There are different and complicated associations between genes and diseases. Finding the causal associations between genes and specific diseases is still challenging. In this work we present a method to predic...

    Authors: Ryohei Eguchi, Mohammand Bozlul Karim, Pingzhao Hu, Tetsuo Sato, Naoaki Ono, Shigehiko Kanaya and Md. Altaf-Ul-Amin

    Citation: BMC Bioinformatics 2018 19:264

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  6. Content type: Methodology article

    Detection of genomic inversions remains challenging. Many existing methods primarily target inzversions with a non repetitive breakpoint, leaving inverted repeat (IR) mediated non-allelic homologous recombinat...

    Authors: Haojing Shao, Devika Ganesamoorthy, Tania Duarte, Minh Duc Cao, Clive J. Hoggart and Lachlan J. M. Coin

    Citation: BMC Bioinformatics 2018 19:261

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  7. Content type: Methodology article

    The locations and shapes of synapses are important in reconstructing connectomes and analyzing synaptic plasticity. However, current synapse detection and segmentation methods are still not adequate for accura...

    Authors: Chi Xiao, Weifu Li, Hao Deng, Xi Chen, Yang Yang, Qiwei Xie and Hua Han

    Citation: BMC Bioinformatics 2018 19:263

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  8. Content type: Software

    Methylated RNA immunoprecipitation sequencing (MeRIP-seq or m6A-seq) has been extensively used for profiling transcriptome-wide distribution of RNA N6-Methyl-Adnosine methylation. However, due to the intrinsic pr...

    Authors: Teng Zhang, Shao-Wu Zhang, Lin Zhang and Jia Meng

    Citation: BMC Bioinformatics 2018 19:260

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  9. Content type: Methodology article

    Combining genomic data sets from multiple studies is advantageous to increase statistical power in studies where logistical considerations restrict sample size or require the sequential generation of data. How...

    Authors: Yuqing Zhang, David F. Jenkins, Solaiappan Manimaran and W. Evan Johnson

    Citation: BMC Bioinformatics 2018 19:262

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  10. 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

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

  11. 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

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

  12. Content type: Software

    Network controllability focuses on discovering combinations of external interventions that can drive a biological system to a desired configuration. In practice, this approach translates into finding a combine...

    Authors: Krishna Kanhaiya, Vladimir Rogojin, Keivan Kazemi, Eugen Czeizler and Ion Petre

    Citation: BMC Bioinformatics 2018 19(Suppl 7):185

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

  13. Content type: Research

    Determining the value of kinetic constants for a metabolic system in the exact physiological conditions is an extremely hard task. However, this kind of information is of pivotal relevance to effectively simul...

    Authors: Riccardo Colombo, Chiara Damiani, David Gilbert, Monika Heiner, Giancarlo Mauri and Dario Pescini

    Citation: BMC Bioinformatics 2018 19(Suppl 7):251

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

  14. Content type: Research

    De novo assembly of RNA-seq data allows the study of transcriptome in absence of a reference genome either if data is obtained from a single organism or from a mixed sample as in metatranscriptomics studies. G...

    Authors: Igor Saggese, Elisa Bona, Max Conway, Francesco Favero, Marco Ladetto, Pietro Liò, Giovanni Manzini and Flavio Mignone

    Citation: BMC Bioinformatics 2018 19(Suppl 7):184

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

  15. Content type: Research

    The analysis of tissue-specific protein interaction networks and their functional enrichment in pathological and normal tissues provides insights on the etiology of diseases. The Pan-cancer proteomic project, ...

    Authors: Davide S. Sardina, Giovanni Micale, Alfredo Ferro, Alfredo Pulvirenti and Rosalba Giugno

    Citation: BMC Bioinformatics 2018 19(Suppl 7):188

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

  16. Content type: Research

    The aim of this article is to analyze the effect on biochemical recurrence and on overall survival of removing an extensive number of pelvic lymph nodes during prostate cancer surgery. The lack of evidence fro...

    Authors: Chiara Gigliarano, Alessandro Nonis, Alberto Briganti, Marco Bonetti and Clelia Di Serio

    Citation: BMC Bioinformatics 2018 19(Suppl 7):200

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

  17. Content type: Research

    With ever increasing accessibility to high throughput technologies, more complex treatment structures can be assessed in a variety of ’omics applications. This adds an extra layer of complexity to the analysis...

    Authors: Kirsty L. Hassall and Andrew Mead

    Citation: BMC Bioinformatics 2018 19(Suppl 7):199

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

  18. Content type: Research

    Recent advances in data analysis methods based on principles of Mendelian Randomisation, such as Egger regression and the weighted median estimator, add to the researcher’s ability to infer cause-effect links ...

    Authors: Susana Conde, Xiaoguang Xu, Hui Guo, Markus Perola, Teresa Fazia, Luisa Bernardinelli and Carlo Berzuini

    Citation: BMC Bioinformatics 2018 19(Suppl 7):195

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

  19. Content type: Research

    An open challenge in translational bioinformatics is the analysis of sequenced metagenomes from various environmental samples. Of course, several studies demonstrated the 16S ribosomal RNA could be considered ...

    Authors: Antonino Fiannaca, Laura La Paglia, Massimo La Rosa, Giosue’ Lo Bosco, Giovanni Renda, Riccardo Rizzo, Salvatore Gaglio and Alfonso Urso

    Citation: BMC Bioinformatics 2018 19(Suppl 7):198

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

  20. Content type: Research

    In exploring the time course of a disease to support or generate biological hypotheses, the shape of the hazard function provides relevant information. For long follow-ups the shape of hazard function may be c...

    Authors: Marco Fornili, Patrizia Boracchi, Federico Ambrogi and Elia Biganzoli

    Citation: BMC Bioinformatics 2018 19(Suppl 7):186

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

  21. 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

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  22. 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

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

  23. 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

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  24. 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

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  25. 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

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  26. 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

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

  27. 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

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  28. 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

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  29. 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

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  30. 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

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  31. 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

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  32. 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

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  33. 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

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  34. 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

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  35. 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

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  36. 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

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  37. 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

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    2.213 - 2-year Impact Factor
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