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  1. Content type: Research article

    Sequence logo plots have become a standard graphical tool for visualizing sequence motifs in DNA, RNA or protein sequences. However standard logo plots primarily highlight enrichment of symbols, and may fail t...

    Authors: Kushal K. Dey, Dongyue Xie and Matthew Stephens

    Citation: BMC Bioinformatics 2018 19:473

    Published on:

  2. Content type: Research article

    Parkinson’s Disease (PD) is a chronic neurodegenerative disease associated with motor problems such as gait impairment. Different systems based on 3D cameras, accelerometers or gyroscopes have been used in rel...

    Authors: Lacramioara Dranca, Lopez de Abetxuko Ruiz de Mendarozketa, Alfredo Goñi, Arantza Illarramendi, Irene Navalpotro Gomez, Manuel Delgado Alvarado and María Cruz Rodríguez-Oroz

    Citation: BMC Bioinformatics 2018 19:471

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  3. Content type: Software

    Biological interpretation of gene/protein lists resulting from -omics experiments can be a complex task. A common approach consists of reviewing Gene Ontology (GO) annotations for entries in such lists and sea...

    Authors: Mikhail Pomaznoy, Brendan Ha and Bjoern Peters

    Citation: BMC Bioinformatics 2018 19:470

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  4. Content type: Research article

    Antimicrobial peptides attract considerable interest as novel agents to combat infections. Their long-time potency across bacteria, viruses and fungi as part of diverse innate immune systems offers a solution ...

    Authors: Kyle Boone, Kyle Camarda, Paulette Spencer and Candan Tamerler

    Citation: BMC Bioinformatics 2018 19:469

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  5. Content type: Research article

    Biological regulatory networks, representing the interactions between genes and their products, control almost every biological activity in the cell. Shortest path search is critical to apprehend the structure...

    Authors: Yuanfang Ren, Ahmet Ay and Tamer Kahveci

    Citation: BMC Bioinformatics 2018 19:465

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  6. Content type: Methodology article

    The use of whole genome sequence has increased recently with rapid progression of next-generation sequencing (NGS) technologies. However, storing raw sequence reads to perform large-scale genome analysis pose ...

    Authors: Peter Sona, Jong Hui Hong, Sunho Lee, Byong Joon Kim, Woon-Young Hong, Jongcheol Jung, Han-Na Kim, Hyung-Lae Kim, David Christopher, Laurent Herviou, Young Hwan Im, Kwee-Yum Lee, Tae Soon Kim and Jongsun Jung

    Citation: BMC Bioinformatics 2018 19:462

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  7. Content type: Research article

    Growing concern about the emergence of antibiotic resistance is compelling the pharmaceutical industry to search for new antimicrobial agents. The availability of genome sequences has enabled the development o...

    Authors: Shirley Fritz, Andriamiharimamy Rajaonison, Olivier Chabrol, Didier Raoult, Jean-Marc Rolain and Vicky Merhej

    Citation: BMC Bioinformatics 2018 19:463

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  8. Content type: Research

    It is well-known that glioblastoma contains self-renewing, stem-like subpopulation with the ability to sustain tumor growth. These cells – called cancer stem-like cells – share certain phenotypic characteristi...

    Authors: Giulia Fiscon, Federica Conte and Paola Paci

    Citation: BMC Bioinformatics 2018 19(Suppl 15):436

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 15

  9. Content type: Research

    Spaced-seeds, i.e. patterns in which some fixed positions are allowed to be wild-cards, play a crucial role in several bioinformatics applications involving substrings counting and indexing, by often providing...

    Authors: Samuele Girotto, Matteo Comin and Cinzia Pizzi

    Citation: BMC Bioinformatics 2018 19(Suppl 15):441

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 15

  10. Content type: Research

    Pan-genome approaches afford the discovery of homology relations in a set of genomes, by determining how some gene families are distributed among a given set of genomes. The retrieval of a complete gene distri...

    Authors: Vincenzo Bonnici, Rosalba Giugno and Vincenzo Manca

    Citation: BMC Bioinformatics 2018 19(Suppl 15):437

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 15

  11. Content type: Research

    “Omics” approaches may provide useful information for a deeper understanding of speciation events, diversification and function innovation. This can be achieved by investigating the molecular similarities at s...

    Authors: Luca Ambrosino, Valentino Ruggieri, Hamed Bostan, Marco Miralto, Nicola Vitulo, Mohamed Zouine, Amalia Barone, Mondher Bouzayen, Luigi Frusciante, Mario Pezzotti, Giorgio Valle and Maria Luisa Chiusano

    Citation: BMC Bioinformatics 2018 19(Suppl 15):435

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 15

  12. Content type: Methodology

    Inflammation is a core element of many different, systemic and chronic diseases that usually involve an important autoimmune component. The clinical phase of inflammatory diseases is often the culmination of a...

    Authors: Hui Xiao, Krzysztof Bartoszek and Pietro Lio’

    Citation: BMC Bioinformatics 2018 19(Suppl 15):439

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 15

  13. Content type: Research

    Study of macromolecular assemblies is fundamental to understand functions in cells. X-ray crystallography is the most common technique to solve their 3D structure at atomic resolution. In a crystal, however, b...

    Authors: Katarina Elez, Alexandre M. J. J. Bonvin and Anna Vangone

    Citation: BMC Bioinformatics 2018 19(Suppl 15):438

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 15

  14. Content type: Software

    Microbes are essentail components of all ecosystems because they drive many biochemical processes and act as primary producers. In freshwater ecosystems, the biodiversity in and the composition of microbial co...

    Authors: Theodor Sperlea, Stefan Füser, Jens Boenigk and Dominik Heider

    Citation: BMC Bioinformatics 2018 19(Suppl 15):440

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 15

  15. Content type: Software

    Environmental metagenomics is a challenging approach that is exponentially spreading in the scientific community to investigate taxonomic diversity and possible functions of the biological components. The mass...

    Authors: M. Tangherlini, M. Miralto, C. Colantuono, M. Sangiovanni, A. Dell’ Anno, C. Corinaldesi, R. Danovaro and M. L. Chiusano

    Citation: BMC Bioinformatics 2018 19(Suppl 15):443

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 15

  16. Content type: Research

    Severity gradation of missense mutations is a big challenge for exome annotation. Predictors of deleteriousness that are most frequently used to filter variants found by next generation sequencing, produce qua...

    Authors: Chiara Cimmaruta, Valentina Citro, Giuseppina Andreotti, Ludovica Liguori, Maria Vittoria Cubellis and Bruno Hay Mele

    Citation: BMC Bioinformatics 2018 19(Suppl 15):433

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 15

  17. Content type: Research

    microRNAs act as regulators of gene expression interacting with their gene targets. Current bioinformatics services, such as databases of validated miRNA-target interactions and prediction tools, usually provi...

    Authors: Antonino Fiannaca, Massimo La Rosa, Laura La Paglia and Alfonso Urso

    Citation: BMC Bioinformatics 2018 19(Suppl 15):434

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 15

  18. Content type: Research

    The study of cell metabolism is becoming central in several fields such as biotechnology, evolution/adaptation and human disease investigations. Here we present CiliateGEM, the first metabolic network reconstr...

    Authors: Alessio Mancini, Filmon Eyassu, Maxwell Conway, Annalisa Occhipinti, Pietro Liò, Claudio Angione and Sandra Pucciarelli

    Citation: BMC Bioinformatics 2018 19(Suppl 15):442

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 15

  19. Content type: Research article

    Benchmark datasets are essential for both method development and performance assessment. These datasets have numerous requirements, representativeness being one. In the case of variant tolerance/pathogenicity ...

    Authors: Gerard C. P. Schaafsma and Mauno Vihinen

    Citation: BMC Bioinformatics 2018 19:461

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  20. Content type: Software

    The Pan-African bioinformatics network, H3ABioNet, comprises 27 research institutions in 17 African countries. H3ABioNet is part of the Human Health and Heredity in Africa program (H3Africa), an African-led re...

    Authors: Shakuntala Baichoo, Yassine Souilmi, Sumir Panji, Gerrit Botha, Ayton Meintjes, Scott Hazelhurst, Hocine Bendou, Eugene de Beste, Phelelani T. Mpangase, Oussema Souiai, Mustafa Alghali, Long Yi, Brian D. O’Connor, Michael Crusoe, Don Armstrong, Shaun Aron…

    Citation: BMC Bioinformatics 2018 19:457

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  21. Content type: Methodology article

    Genome-Wide Association Studies (GWAS) seek to identify causal genomic variants associated with rare human diseases. The classical statistical approach for detecting these variants is based on univariate hypot...

    Authors: Florent Guinot, Marie Szafranski, Christophe Ambroise and Franck Samson

    Citation: BMC Bioinformatics 2018 19:459

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  22. Content type: Software

    Network medicine aims to map molecular perturbations of any given diseases onto complex networks with functional interdependencies that underlie a pathological phenotype. Furthermore, investigating the time di...

    Authors: Ruoting Yang, Daniel Watson, Joshua Williams, Raina Kumar, Ross Campbell, Uma Mudunuri, Rasha Hammamieh and Marti Jett

    Citation: BMC Bioinformatics 2018 19:458

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  23. Content type: Correction

    After publication of this supplement article [1], it was brought to our attention that reference 10 and reference 12 in the article are incorrect.

    Authors: Vincenzo Bonnici, Federico Busato, Stefano Aldegheri, Murodzhon Akhmedov, Luciano Cascione, Alberto Arribas Carmena, Francesco Bertoni, Nicola Bombieri, Ivo Kwee and Rosalba Giugno

    Citation: BMC Bioinformatics 2018 19:456

    Published on:

    The original article was published in BMC Bioinformatics 2018 19:356

  24. Content type: Methodology article

    Large-scale pairwise drug combination analysis has lately gained momentum in drug discovery and development projects, mainly due to the employment of advanced experimental-computational pipelines. This is fort...

    Authors: Efthymia Chantzi, Malin Jarvius, Mia Niklasson, Anna Segerman and Mats G. Gustafsson

    Citation: BMC Bioinformatics 2018 19:453

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  25. Content type: Software

    The response of many biomedical systems can be modelled using a linear combination of damped exponential functions. The approximation parameters, based on equally spaced samples, can be obtained using Prony’s ...

    Authors: A. Fernández Rodríguez, L. de Santiago Rodrigo, E. López Guillén, J. M. Rodríguez Ascariz, J. M. Miguel Jiménez and Luciano Boquete

    Citation: BMC Bioinformatics 2018 19:451

    Published on:

  26. Content type: Software

    Imaging is one of the major biomedical technologies to investigate the status of a living object. But the biomedical image based data mining problem requires extensive knowledge across multiple disciplinaries,...

    Authors: Ruochi Zhang, Ruixue Zhao, Xinyang Zhao, Di Wu, Weiwei Zheng, Xin Feng and Fengfeng Zhou

    Citation: BMC Bioinformatics 2018 19:452

    Published on:

  27. Content type: Software

    Testing the dependence of two variables is one of the fundamental tasks in statistics. In this work, we developed an open-source R package (knnAUC) for detecting nonlinear dependence between one continuous var...

    Authors: Yi Li, Xiaoyu Liu, Yanyun Ma, Yi Wang, Weichen Zhou, Meng Hao, Zhenghong Yuan, Jie Liu, Momiao Xiong, Yin Yao Shugart, Jiucun Wang and Li Jin

    Citation: BMC Bioinformatics 2018 19:448

    Published on:

  28. Content type: Software

    Visualization plays an important role in epidemic time series analysis and forecasting. Viewing time series data plotted on a graph can help researchers identify anomalies and unexpected trends that could be o...

    Authors: Swapna Thorve, Mandy L. Wilson, Bryan L. Lewis, Samarth Swarup, Anil Kumar S. Vullikanti and Madhav V. Marathe

    Citation: BMC Bioinformatics 2018 19:449

    Published on:

  29. Content type: Software

    Primer design is a crucial step in establishing specific and sensitive qPCR assays. Even though numerous tools for primer design exist, the majority of resulting assays still requires extensive testing and opt...

    Authors: Florian Burger, Michele Angioni, Gianluca Russo, Martina Schad and Jim Kallarackal

    Citation: BMC Bioinformatics 2018 19:447

    Published on:

  30. Content type: Methodology article

    Despite the successful mapping of genes involved in the determinism of numerous traits, a large part of the genetic variation remains unexplained. A possible explanation is that the simple models used in many ...

    Authors: Sinan Abo Alchamlat and Frédéric Farnir

    Citation: BMC Bioinformatics 2018 19:445

    Published on:

  31. Content type: Research

    The potential for astrocyte participation in central nervous system recovery is highlighted by in vitro experiments demonstrating their capacity to transdifferentiate into neurons. Understanding astrocyte plas...

    Authors: V. Bleu Knight and Elba E. Serrano

    Citation: BMC Bioinformatics 2018 19(Suppl 14):412

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 14

  32. Content type: Research

    The advances in high-throughput sequencing technologies are allowing more and more de novo assembling of transcriptomes from many new organisms. Some degree of automation and evaluation is required to warrant ...

    Authors: Pedro Seoane, Marina Espigares, Rosario Carmona, Álvaro Polonio, Julia Quintana, Enrico Cretazzo, Josefina Bota, Alejandro Pérez-García, Juan de Dios Alché, Luis Gómez and M. Gonzalo Claros

    Citation: BMC Bioinformatics 2018 19(Suppl 14):416

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 14

  33. Content type: Methodology article

    While the reconstruction of transcripts from a sample of RNA-Seq data is a computationally expensive and complicated task, the detection of splicing events from RNA-Seq data and a gene annotation is computatio...

    Authors: Luca Denti, Raffaella Rizzi, Stefano Beretta, Gianluca Della Vedova, Marco Previtali and Paola Bonizzoni

    Citation: BMC Bioinformatics 2018 19:444

    Published on:

  34. Content type: Research

    Transcription regulation is a major controller of gene expression dynamics during development and disease, where transcription factors (TFs) modulate expression of genes through direct or indirect DNA interact...

    Authors: Guillaume Devailly and Anagha Joshi

    Citation: BMC Bioinformatics 2018 19(Suppl 14):409

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 14

  35. Content type: Research

    The prediction of calmodulin-binding (CaM-binding) proteins plays a very important role in the fields of biology and biochemistry, because the calmodulin protein binds and regulates a multitude of protein targ...

    Authors: Yixun Li, Mina Maleki, Nicholas J. Carruthers, Paul M. Stemmer, Alioune Ngom and Luis Rueda

    Citation: BMC Bioinformatics 2018 19(Suppl 14):410

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 14

  36. Content type: Research

    Ebola still remains as one of the most problematic infectious diseases in Africa with a high rate of mortality. Although this disease has been known for an almost half-century, there are no vaccines and drugs ...

    Authors: Mochammad Arfin Fardiansyah Nasution, Erwin Prasetya Toepak, Ahmad Husein Alkaff and Usman Sumo Friend Tambunan

    Citation: BMC Bioinformatics 2018 19(Suppl 14):419

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 14

  37. Content type: Methodology

    Although the etiology of chronic lymphocytic leukemia (CLL), the most common type of adult leukemia, is still unclear, strong evidence implicates antigen involvement in disease ontogeny and evolution. Primary ...

    Authors: Eleftheria Polychronidou, Ilias Kalamaras, Andreas Agathangelidis, Lesley-Ann Sutton, Xiao-Jie Yan, Vasilis Bikos, Anna Vardi, Konstantinos Mochament, Nicholas Chiorazzi, Chrysoula Belessi, Richard Rosenquist, Paolo Ghia, Kostas Stamatopoulos, Panayiotis Vlamos, Anna Chailyan, Nanna Overby…

    Citation: BMC Bioinformatics 2018 19(Suppl 14):414

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 14

  38. Content type: Research

    Ageing can be classified in two different ways, chronological ageing and biological ageing. While chronological age is a measure of the time that has passed since birth, biological (also known as transcriptomi...

    Authors: Elisabeth Yaneske and Claudio Angione

    Citation: BMC Bioinformatics 2018 19(Suppl 14):415

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 14

  39. Content type: Research

    We present a performance per watt analysis of CUDAlign 4.0, a parallel strategy to obtain the optimal pairwise alignment of huge DNA sequences in multi-GPU platforms using the exact Smith-Waterman method.

    Authors: Jesús Pérez-Serrano, Edans Sandes, Alba Cristina Magalhaes Alves de Melo and Manuel Ujaldón

    Citation: BMC Bioinformatics 2018 19(Suppl 14):421

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 14

  40. Content type: Research

    Supervised machine learning methods when applied to the problem of automated protein-function prediction (AFP) require the availability of both positive examples (i.e., proteins which are known to possess a given...

    Authors: Paolo Boldi, Marco Frasca and Dario Malchiodi

    Citation: BMC Bioinformatics 2018 19(Suppl 14):417

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 14

  41. Content type: Research

    Nucleosomes are DNA-histone complex, each wrapping about 150 pairs of double-stranded DNA. Their function is fundamental for one of the primary functions of Chromatin i.e. packing the DNA into the nucleus of t...

    Authors: Mattia Di Gangi, Giosuè Lo Bosco and Riccardo Rizzo

    Citation: BMC Bioinformatics 2018 19(Suppl 14):418

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 14

  42. Content type: Research

    Families of related proteins and their different functions may be described systematically using common classifications and ontologies such as Pfam and GO (Gene Ontology), for example. However, many proteins c...

    Authors: Seyed Ziaeddin Alborzi, David W. Ritchie and Marie-Dominique Devignes

    Citation: BMC Bioinformatics 2018 19(Suppl 14):413

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 14

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