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  1. Content type: Software

    Virus genome sequences, generated in ever-higher volumes, can provide new scientific insights and inform our responses to epidemics and outbreaks. To facilitate interpretation, such data must be organised and ...

    Authors: Joshua B. Singer, Emma C. Thomson, John McLauchlan, Joseph Hughes and Robert J. Gifford

    Citation: BMC Bioinformatics 2018 19:532

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  2. Content type: Methodology article

    Predicting prognosis in patients from large-scale genomic data is a fundamentally challenging problem in genomic medicine. However, the prognosis still remains poor in many diseases. The poor prognosis may be ...

    Authors: Jie Hao, Youngsoon Kim, Tae-Kyung Kim and Mingon Kang

    Citation: BMC Bioinformatics 2018 19:510

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  3. Content type: Research article

    Selection for feed efficiency is crucial for overall profitability and sustainability in dairy cattle production. Key regulator genes and genetic markers derived from co-expression networks underlying feed eff...

    Authors: S. M. Salleh, G. Mazzoni, P. Løvendahl and H. N. Kadarmideen

    Citation: BMC Bioinformatics 2018 19:513

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  4. Content type: Software

    Various algorithms have been developed to predict fetal trisomies using cell-free DNA in non-invasive prenatal testing (NIPT). As basis for prediction, a control group of non-trisomy samples is needed. Predict...

    Authors: Lennart F. Johansson, Hendrik A. de Weerd, Eddy N. de Boer, Freerk van Dijk, Gerard J. te Meerman, Rolf H. Sijmons, Birgit Sikkema-Raddatz and Morris A. Swertz

    Citation: BMC Bioinformatics 2018 19:531

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  5. Content type: Correction

    After publication of the original article [1], it was noticed that the dagger symbol indicating equal contribution wasn’t added next to the names of all authors.

    Authors: Paolo Boldi, Marco Frasca and Dario Malchiodi

    Citation: BMC Bioinformatics 2018 19:530

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    The original article was published in BMC Bioinformatics 2018 19:417

  6. Content type: Research article

    The current versions of reference genome assemblies still contain gaps represented by stretches of Ns. Since high throughput sequencing reads cannot be mapped to those gap regions, the regions are depleted of ...

    Authors: Diana Domanska, Chakravarthi Kanduri, Boris Simovski and Geir Kjetil Sandve

    Citation: BMC Bioinformatics 2018 19:481

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  7. Content type: Research article

    Sequence similarity networks are useful for classifying and characterizing biologically important proteins. Threshold-based approaches to similarity network construction using exact distance measures are prohi...

    Authors: Helen N. Catanese, Kelly A. Brayton and Assefaw H. Gebremedhin

    Citation: BMC Bioinformatics 2018 19:475

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  8. Content type: Software

    Targeted resequencing has become the most used and cost-effective approach for identifying causative mutations of Mendelian diseases both for diagnostics and research purposes. Due to very rapid technological ...

    Authors: F. Musacchia, A. Ciolfi, M. Mutarelli, A. Bruselles, R. Castello, M. Pinelli, S. Basu, S. Banfi, G. Casari, M. Tartaglia and V. Nigro

    Citation: BMC Bioinformatics 2018 19:477

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  9. Content type: Methodology article

    Unsupervised clustering represents one of the most widely applied methods in analysis of high-throughput ‘omics data. A variety of unsupervised model-based or parametric clustering methods and non-parametric c...

    Authors: Qian Li, Janelle R. Noel-MacDonnell, Devin C. Koestler, Ellen L. Goode and Brooke L. Fridley

    Citation: BMC Bioinformatics 2018 19:474

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  10. Content type: Methodology article

    Researchers typically sequence a given individual multiple times, either re-sequencing the same DNA sample (technical replication) or sequencing different DNA samples collected on the same individual (biologic...

    Authors: Ariel W. Chan, Amy L. Williams and Jean-Luc Jannink

    Citation: BMC Bioinformatics 2018 19:478

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  11. 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

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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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

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

  19. 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

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

  20. 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

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

  21. 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

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

  22. 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

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

  23. 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

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

  24. 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

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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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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  30. 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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  31. 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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  32. 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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  33. 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

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

  34. 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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  35. 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

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  36. 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

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  37. 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:

  38. 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

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  39. 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

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