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  1. 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

    Published on:

  2. 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

    Published on:

  3. 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

    Published on:

  4. 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

    Published on:

  5. 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

    Published on:

  6. 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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  7. 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

    Published on:

  8. 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

  9. 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

  10. 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

    Published on:

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

  11. 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

    Published on:

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

  12. 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

    Published on:

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

  13. 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

    Published on:

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

  14. 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

    Published on:

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

  15. 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

    Published on:

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

  16. 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

    Published on:

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

  17. 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

    Published on:

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

  18. 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

    Published on:

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

  19. 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:

Page 1 of 356

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