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  1. Content type: Methodology

    Quorum sensing drives biofilm formation in bacteria in order to ensure that biofilm formation only occurs when colonies are of a sufficient size and density. This spatial behaviour is achieved by the broadcast...

    Authors: David Gilbert, Monika Heiner, Leila Ghanbar and Jacek Chodak

    Citation: BMC Bioinformatics 2019 20(Suppl 4):173

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

  2. Content type: Research

    In order to fully characterize the genome of an individual, the reconstruction of the two distinct copies of each chromosome, called haplotypes, is essential. The computational problem of inferring the full ha...

    Authors: Andrea Tangherloni, Simone Spolaor, Leonardo Rundo, Marco S. Nobile, Paolo Cazzaniga, Giancarlo Mauri, Pietro Liò, Ivan Merelli and Daniela Besozzi

    Citation: BMC Bioinformatics 2019 20(Suppl 4):172

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

  3. Content type: Research

    Next Generation Sequencing (NGS) experiments produce millions of short sequences that, mapped to a reference genome, provide biological insights at genomic, transcriptomic and epigenomic level. Typically the a...

    Authors: Mara Sangiovanni, Ilaria Granata, Amarinder Singh Thind and Mario Rosario Guarracino

    Citation: BMC Bioinformatics 2019 20(Suppl 4):168

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

  4. Content type: Research

    Obesity is a complex disorder associated with an increased risk of developing several comorbid chronic diseases, including postmenopausal breast cancer. Although many studies have investigated this issue, the ...

    Authors: Ilaria Granata, Enrico Troiano, Mara Sangiovanni and Mario Rosario Guarracino

    Citation: BMC Bioinformatics 2019 20(Suppl 4):162

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

  5. Content type: Methodology

    RNA secondary structure comparison is a fundamental task for several studies, among which are RNA structure prediction and evolution. The comparison can currently be done efficiently only for pseudoknot-free s...

    Authors: Michela Quadrini, Luca Tesei and Emanuela Merelli

    Citation: BMC Bioinformatics 2019 20(Suppl 4):161

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

  6. Content type: Research

    The somatic mutations found in a tumor have in most cases been caused by multiple mutational processes such as those related to extrinsic carcinogens like cigarette smoke, and those related to intrinsic proces...

    Authors: Sandra Krüger and Rosario M. Piro

    Citation: BMC Bioinformatics 2019 20(Suppl 4):152

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

  7. Content type: Software

    The analysis of gene expression levels is used in many clinical studies to know how patients evolve or to find new genetic biomarkers that could help in clinical decision making. However, the techniques and so...

    Authors: Ismael Navas-Delgado, José García-Nieto, Esteban López-Camacho, Maciej Rybinski, Rocio Lavado, Miguel Ángel Berciano Guerrero and José F. Aldana-Montes

    Citation: BMC Bioinformatics 2019 20(Suppl 4):150

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

  8. Content type: Research

    Bacterial surfaces are complex systems, constructed from membranes, peptidoglycan and, importantly, proteins. The proteins play crucial roles as critical regulators of how the bacterium interacts with and surv...

    Authors: Hamed Khakzad, Johan Malmström and Lars Malmström

    Citation: BMC Bioinformatics 2019 20(Suppl 4):141

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

  9. Content type: Research

    The interplay between metabolic processes and signalling pathways remains poorly understood. Global, detailed and comprehensive reconstructions of human metabolism and signalling pathways exist in the form of ...

    Authors: Nicolas Sompairac, Jennifer Modamio, Emmanuel Barillot, Ronan M. T. Fleming, Andrei Zinovyev and Inna Kuperstein

    Citation: BMC Bioinformatics 2019 20(Suppl 4):140

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

  10. Content type: Methodology

    Pharmacogenomics (PGx) studies how genomic variations impact variations in drug response phenotypes. Knowledge in pharmacogenomics is typically composed of units that have the form of ternary relationships gene v...

    Authors: Pierre Monnin, Joël Legrand, Graziella Husson, Patrice Ringot, Andon Tchechmedjiev, Clément Jonquet, Amedeo Napoli and Adrien Coulet

    Citation: BMC Bioinformatics 2019 20(Suppl 4):139

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

  11. Content type: Research

    Distributed approaches based on the MapReduce programming paradigm have started to be proposed in the Bioinformatics domain, due to the large amount of data produced by the next-generation sequencing technique...

    Authors: Umberto Ferraro Petrillo, Mara Sorella, Giuseppe Cattaneo, Raffaele Giancarlo and Simona E. Rombo

    Citation: BMC Bioinformatics 2019 20(Suppl 4):138

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

  12. Content type: Introduction

    The 17th International NETTAB workshop was held in Palermo, Italy, on October 16-18, 2017. The special topic for the meeting was “Methods, tools and platforms for Personalised Medicine in the Big Data Era”, bu...

    Authors: Paolo Romano, Arnaud Céol, Andreas Dräger, Antonino Fiannaca, Rosalba Giugno, Massimo La Rosa, Luciano Milanesi, Ulrich Pfeffer, Riccardo Rizzo, Soo-Yong Shin, Junfeng Xia and Alfonso Urso

    Citation: BMC Bioinformatics 2019 20(Suppl 4):125

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

  13. Content type: Software

    RNA editing is an important mechanism for gene expression in plants organelles. It alters the direct transfer of genetic information from DNA to proteins, due to the introduction of differences between RNAs an...

    Authors: Fabio Fassetti, Claudia Giallombardo, Ofelia Leone, Luigi Palopoli, Simona E. Rombo and Adolfo Saiardi

    Citation: BMC Bioinformatics 2019 20(Suppl 4):124

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

  14. Content type: Research

    MicroRNAs (miRNAs) are small non-coding RNA molecules mediating the translational repression and degradation of target mRNAs in the cell. Mature miRNAs are used as a template by the RNA-induced silencing compl...

    Authors: Giovanni Perconti, Patrizia Rubino, Flavia Contino, Serena Bivona, Giorgio Bertolazzi, Michele Tumminello, Salvatore Feo, Agata Giallongo and Claudia Coronnello

    Citation: BMC Bioinformatics 2019 20(Suppl 4):120

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

  15. Content type: Research

    The search for molecular biomarkers of early-onset colorectal cancer (CRC) is an important but still quite challenging and unsolved task. Detection of CpG methylation in human DNA obtained from blood or stool ...

    Authors: Alexander Kel, Ulyana Boyarskikh, Philip Stegmaier, Leonid S. Leskov, Andrey V. Sokolov, Ivan Yevshin, Nikita Mandrik, Daria Stelmashenko, Jeannette Koschmann, Olga Kel-Margoulis, Mathias Krull, Anna Martínez-Cardús, Sebastian Moran, Manel Esteller, Fedor Kolpakov, Maxim Filipenko…

    Citation: BMC Bioinformatics 2019 20(Suppl 4):119

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

  16. Content type: Methodology

    Amyotrophic lateral sclerosis (ALS) is an adult-onset neurodegenerative disease progressively affecting upper and lower motor neurons in the brain and spinal cord. Mean life expectancy is three to five years, ...

    Authors: Alessandro Zandonà, Rosario Vasta, Adriano Chiò and Barbara Di Camillo

    Citation: BMC Bioinformatics 2019 20(Suppl 4):118

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

  18. Content type: Methodology article

    The rapid increase in High-throughput sequencing of RNA (RNA-seq) has led to tremendous improvements in the detection and reconstruction of both expressed coding and non-coding RNA transcripts. Yet, the comple...

    Authors: Thomas Gatter and Peter F Stadler

    Citation: BMC Bioinformatics 2019 20:190

    Published on:

  20. Content type: Software

    The rapid growth of high-throughput sequencing-based microbiome profiling has yielded tremendous insights into human health and physiology. Data generated from high-throughput sequencing of 16S rRNA gene ampli...

    Authors: Nhan Thi Ho, Fan Li, Shuang Wang and Louise Kuhn

    Citation: BMC Bioinformatics 2019 20:188

    Published on:

  21. Content type: Research article

    Biological pathways represent chains of molecular interactions in biological systems that jointly form complex dynamic networks. The network structure changes from the significance of biological experiments an...

    Authors: Hsiang-Yun Wu, Martin Nöllenburg, Filipa L. Sousa and Ivan Viola

    Citation: BMC Bioinformatics 2019 20:187

    Published on:

  22. Content type: Research article

    Malaria is a major global health problem, with the Plasmodium falciparum protozoan parasite causing the most severe form of the disease. Prevalence of drug-resistant P. falciparum highlights the need to understan...

    Authors: Ana M. Untaroiu, Maureen A. Carey, Jennifer L. Guler and Jason A. Papin

    Citation: BMC Bioinformatics 2019 20:186

    Published on:

  23. Content type: Methodology article

    For many practical hypothesis testing (H-T) applications, the data are correlated and/or with heterogeneous variance structure. The regression t-test for weighted linear mixed-effects regression (LMER) is a legit...

    Authors: Yun Zhang, Gautam Bandyopadhyay, David J. Topham, Ann R. Falsey and Xing Qiu

    Citation: BMC Bioinformatics 2019 20:185

    Published on:

  24. Content type: Software

    Inexpensive high-throughput DNA sequencing has democratized access to genetic information for most organisms so that research utilizing a genome or transcriptome of an organism is not limited to model systems....

    Authors: Ousmane H. Cissé and Jason E. Stajich

    Citation: BMC Bioinformatics 2019 20:184

    Published on:

  25. Content type: Research article

    Neural network based embedding models are receiving significant attention in the field of natural language processing due to their capability to effectively capture semantic information representing words, sen...

    Authors: Kathrin Blagec, Hong Xu, Asan Agibetov and Matthias Samwald

    Citation: BMC Bioinformatics 2019 20:178

    Published on:

  28. Content type: Methodology article

    Establishment and maintenance of DNA methylation throughout the genome is an important epigenetic mechanism that regulates gene expression whose disruption has been implicated in human diseases like cancer. It...

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

    Citation: BMC Bioinformatics 2019 20:175

    Published on:

  29. Content type: Methodology article

    Identifying transcriptional enhancers and other cis-regulatory modules (CRMs) is an important goal of post-sequencing genome annotation. Computational approaches provide a useful complement to empirical methods f...

    Authors: Hasiba Asma and Marc S. Halfon

    Citation: BMC Bioinformatics 2019 20:174

    Published on:

  30. Content type: Software

    Molecular simulations are used to provide insight into protein structure and dynamics, and have the potential to provide important context when predicting the impact of sequence variation on protein function. ...

    Authors: Matthew D. McCoy, Vikram Shivakumar, Sridhar Nimmagadda, Mohsin Saleet Jafri and Subha Madhavan

    Citation: BMC Bioinformatics 2019 20:171

    Published on:

  32. Content type: Research article

    The detection of weak signals and selection of single particles from low-contrast micrographs of frozen hydrated biomolecules by cryo-electron microscopy (cryo-EM) represents a major practical bottleneck in cr...

    Authors: Wei Li Wang, Zhou Yu, Luis R. Castillo-Menendez, Joseph Sodroski and Youdong Mao

    Citation: BMC Bioinformatics 2019 20:169

    Published on:

  33. Content type: Methodology article

    Genome-wide prediction has become the method of choice in animal and plant breeding. Prediction of breeding values and phenotypes are routinely performed using large genomic data sets with number of markers on...

    Authors: Patrik Waldmann, Maja Ferenčaković, Gábor Mészáros, Negar Khayatzadeh, Ino Curik and Johann Sölkner

    Citation: BMC Bioinformatics 2019 20:167

    Published on:

  34. Content type: Methodology article

    The design of an experiment influences both what a researcher can measure, as well as how much confidence can be placed in the results. As such, it is vitally important that experimental design decisions do no...

    Authors: Daphne Ezer and Joseph Keir

    Citation: BMC Bioinformatics 2019 20:166

    Published on:

  35. Content type: Software

    Log-linear and multinomial modeling offer a flexible framework for genetic association analyses of offspring (child), parent-of-origin and maternal effects, based on genotype data from a variety of child-paren...

    Authors: Miriam Gjerdevik, Astanand Jugessur, Øystein A. Haaland, Julia Romanowska, Rolv T. Lie, Heather J. Cordell and Håkon K. Gjessing

    Citation: BMC Bioinformatics 2019 20:165

    Published on:

  36. Content type: Methodology article

    For large international research consortia, such as those funded by the European Union’s Horizon 2020 programme or the Innovative Medicines Initiative, good data coordination practices and tools are essential ...

    Authors: Wei Gu, Reha Yildirimman, Emmanuel Van der Stuyft, Denny Verbeeck, Sascha Herzinger, Venkata Satagopam, Adriano Barbosa-Silva, Reinhard Schneider, Bodo Lange, Hans Lehrach, Yike Guo, David Henderson and Anthony Rowe

    Citation: BMC Bioinformatics 2019 20:164

    Published on:

  37. Content type: Methodology article

    High-throughput techniques bring novel tools and also statistical challenges to genomic research. Identifying genes with differential expression between different species is an effective way to discover evolut...

    Authors: Yan Zhou, Jiadi Zhu, Tiejun Tong, Junhui Wang, Bingqing Lin and Jun Zhang

    Citation: BMC Bioinformatics 2019 20:163

    Published on:

  38. Content type: Software

    Bisulfite sequencing allows base-pair resolution profiling of DNA methylation and has recently been adapted for use in single-cells. Analyzing these data, including making comparisons with existing data, remai...

    Authors: Divy Kangeyan, Andrew Dunford, Sowmya Iyer, Chip Stewart, Megan Hanna, Gad Getz and Martin J. Aryee

    Citation: BMC Bioinformatics 2019 20:160

    Published on:

  39. Content type: Research

    The ab initio approaches to protein structure prediction usually employ the Monte Carlo technique to search the structural conformation that has the lowest energy. However, the widely-used energy functions are us...

    Authors: Chao Wang, Yi Wei, Haicang Zhang, Lupeng Kong, Shiwei Sun, Wei-Mou Zheng and Dongbo Bu

    Citation: BMC Bioinformatics 2019 20(Suppl 3):135

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 3

  40. Content type: Research

    In the field of drug repositioning, it is assumed that similar drugs may treat similar diseases, therefore many existing computational methods need to compute the similarities of drugs and diseases. However, t...

    Authors: Guangsheng Wu, Juan Liu and Xiang Yue

    Citation: BMC Bioinformatics 2019 20(Suppl 3):134

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 3

  41. Content type: Research

    The inference of splicing orthology relationships between gene transcripts is a basic step for the prediction of transcripts and the annotation of gene structures in genomes. The splicing structure of a sequen...

    Authors: Safa Jammali, Jean-David Aguilar, Esaie Kuitche and Aïda Ouangraoua

    Citation: BMC Bioinformatics 2019 20(Suppl 3):133

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 3

  42. Content type: Research

    Cryo-electron tomography (cryo-ET) enables the 3D visualization of cellular organization in near-native state which plays important roles in the field of structural cell biology. However, due to the low signal...

    Authors: Ran Li, Xiangrui Zeng, Stephanie E. Sigmund, Ruogu Lin, Bo Zhou, Chang Liu, Kaiwen Wang, Rui Jiang, Zachary Freyberg, Hairong Lv and Min Xu

    Citation: BMC Bioinformatics 2019 20(Suppl 3):132

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 3

  43. Content type: Research

    Detecting protein complex in protein-protein interaction (PPI) networks plays a significant part in bioinformatics field. It enables us to obtain the better understanding for the structures and characteristics...

    Authors: Xiujuan Lei, Ming Fang, Ling Guo and Fang-Xiang Wu

    Citation: BMC Bioinformatics 2019 20(Suppl 3):131

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 3

  44. Content type: Research

    Recently, next-generation sequencing techniques have been applied for the detection of RNA secondary structures, which is referred to as high-throughput RNA structural (HTS) analyses, and many different protoc...

    Authors: Risa Kawaguchi, Hisanori Kiryu, Junichi Iwakiri and Jun Sese

    Citation: BMC Bioinformatics 2019 20(Suppl 3):130

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 3

  45. Content type: Research

    Different types of viruses have different envelope proteins, and may have their shared or distinctive host-virus interactions which result in various post-infection effects in humans and animals. These effects...

    Authors: Quan Chen and Jun Zhu

    Citation: BMC Bioinformatics 2019 20(Suppl 3):129

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 3

  46. Content type: Research

    RNAs can interact and form complexes, which have various biological roles. The secondary structure prediction of those complexes is a first step towards the identification of their 3D structure. We propose an ...

    Authors: Audrey Legendre, Eric Angel and Fariza Tahi

    Citation: BMC Bioinformatics 2019 20(Suppl 3):128

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 3

  47. Content type: Research

    Super-enhancers or stretch enhancers are clusters of active enhancers that often coordinate cell-type specific gene regulation during development and differentiation. In addition, the enrichment of disease-ass...

    Authors: Jayoung Ryu, Hyunwoong Kim, Dongchan Yang, Andrew J. Lee and Inkyung Jung

    Citation: BMC Bioinformatics 2019 20(Suppl 3):127

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 3

  48. Content type: Research

    Mapping expression quantitative trait loci (eQTLs) has provided insight into gene regulation. Compared to cis-eQTLs, the regulatory mechanisms of trans-eQTLs are less known. Previous studies suggest that trans...

    Authors: Nayang Shan, Zuoheng Wang and Lin Hou

    Citation: BMC Bioinformatics 2019 20(Suppl 3):126

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 3

  49. Content type: Software

    Biological databases and repositories are incrementing in diversity and complexity over the years. This rapid expansion of current and new sources of biological knowledge raises serious problems of data access...

    Authors: Daniel Perez-Gil, Francisco J. Lopez, Joaquin Dopazo, Pablo Marin-Garcia, Augusto Rendon and Ignacio Medina

    Citation: BMC Bioinformatics 2019 20:159

    Published on:

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