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  1. Content type: Research

    Sequencing highly-variable 16S regions is a common and often effective approach to the study of microbial communities, and next-generation sequencing (NGS) technologies provide abundant quantities of data for ...

    Authors: Timothy Chappell, Shlomo Geva, James M. Hogan, Flavia Huygens, Irani U. Rathnayake, Stephen Rudd, Wayne Kelly and Dimitri Perrin

    Citation: BMC Bioinformatics 2018 19(Suppl 20):509

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 20

  2. Content type: Research

    With applications in cancer, drug metabolism, and disease etiology, understanding structural variation in the human genome is critical in advancing the thrusts of individualized medicine. However, structural v...

    Authors: Zachary Stephens, Chen Wang, Ravishankar K. Iyer and Jean-Pierre Kocher

    Citation: BMC Bioinformatics 2018 19(Suppl 20):508

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 20

  3. Content type: Research

    The traditional methods of visualizing high-dimensional data objects in low-dimensional metric spaces are subject to the basic limitations of metric space. These limitations result in multidimensional scaling ...

    Authors: Xianchao Zhu, Xianjun Shen, Xingpeng Jiang, Kaiping Wei, Tingting He, Yuanyuan Ma, Jiaqi Liu and Xiaohua Hu

    Citation: BMC Bioinformatics 2018 19(Suppl 20):505

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 20

  4. Content type: Research

    Bacterial small non-coding RNAs (sRNAs) have emerged as important elements in diverse physiological processes, including growth, development, cell proliferation, differentiation, metabolic reactions and carbon...

    Authors: Guifeng Tang, Jingwen Shi, Wenjian Wu, Xiang Yue and Wen Zhang

    Citation: BMC Bioinformatics 2018 19(Suppl 20):503

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 20

  5. Content type: Research

    Biomedical semantic indexing is important for information retrieval and many other research fields in bioinformatics. It annotates biomedical citations with Medical Subject Headings. In face of unbalanced cate...

    Authors: Yongping Du, Yunpeng Pan, Chencheng Wang and Junzhong Ji

    Citation: BMC Bioinformatics 2018 19(Suppl 20):502

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 20

  6. Content type: Methodology

    Current multi-petaflop supercomputers are powerful systems, but present challenges when faced with problems requiring large machine learning workflows. Complex algorithms running at system scale, often with di...

    Authors: Justin M. Wozniak, Rajeev Jain, Prasanna Balaprakash, Jonathan Ozik, Nicholson T. Collier, John Bauer, Fangfang Xia, Thomas Brettin, Rick Stevens, Jamaludin Mohd-Yusof, Cristina Garcia Cardona, Brian Van Essen and Matthew Baughman

    Citation: BMC Bioinformatics 2018 19(Suppl 18):491

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 18

  7. Content type: Research

    Real-time analysis of patient data during medical procedures can provide vital diagnostic feedback that significantly improves chances of success. With sensors becoming increasingly fast, frameworks such as De...

    Authors: Ahmed Sanaullah, Chen Yang, Yuri Alexeev, Kazutomo Yoshii and Martin C. Herbordt

    Citation: BMC Bioinformatics 2018 19(Suppl 18):490

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 18

  8. Content type: Research

    Deep Learning (DL) has advanced the state-of-the-art capabilities in bioinformatics applications which has resulted in trends of increasingly sophisticated and computationally demanding models trained by large...

    Authors: John X. Qiu, Hong-Jun Yoon, Kshitij Srivastava, Thomas P. Watson, J. Blair Christian, Arvind Ramanathan, Xiao C. Wu, Paul A. Fearn and Georgia D. Tourassi

    Citation: BMC Bioinformatics 2018 19(Suppl 18):488

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 18

  9. Content type: Research

    The National Cancer Institute drug pair screening effort against 60 well-characterized human tumor cell lines (NCI-60) presents an unprecedented resource for modeling combinational drug activity.

    Authors: Fangfang Xia, Maulik Shukla, Thomas Brettin, Cristina Garcia-Cardona, Judith Cohn, Jonathan E. Allen, Sergei Maslov, Susan L. Holbeck, James H. Doroshow, Yvonne A. Evrard, Eric A. Stahlberg and Rick L. Stevens

    Citation: BMC Bioinformatics 2018 19(Suppl 18):486

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 18

  10. Content type: Research

    We examine the problem of clustering biomolecular simulations using deep learning techniques. Since biomolecular simulation datasets are inherently high dimensional, it is often necessary to build low dimensio...

    Authors: Debsindhu Bhowmik, Shang Gao, Michael T. Young and Arvind Ramanathan

    Citation: BMC Bioinformatics 2018 19(Suppl 18):484

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 18

  11. Content type: Methodology

    Cancer is a complex, multiscale dynamical system, with interactions between tumor cells and non-cancerous host systems. Therapies act on this combined cancer-host system, sometimes with unexpected results. Sys...

    Authors: Jonathan Ozik, Nicholson Collier, Justin M. Wozniak, Charles Macal, Chase Cockrell, Samuel H. Friedman, Ahmadreza Ghaffarizadeh, Randy Heiland, Gary An and Paul Macklin

    Citation: BMC Bioinformatics 2018 19(Suppl 18):483

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 18

  12. Content type: Research

    Resistance to chemotherapy and molecularly targeted therapies is a major factor in limiting the effectiveness of cancer treatment. In many cases, resistance can be linked to genetic changes in target proteins,...

    Authors: Jumana Dakka, Matteo Turilli, David W. Wright, Stefan J. Zasada, Vivek Balasubramanian, Shunzhou Wan, Peter V. Coveney and Shantenu Jha

    Citation: BMC Bioinformatics 2018 19(Suppl 18):482

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 18

  13. Content type: Research article

    The deployment of Genome-wide association studies (GWASs) requires genomic information of a large population to produce reliable results. This raises significant privacy concerns, making people hesitate to con...

    Authors: Charlotte Bonte, Eleftheria Makri, Amin Ardeshirdavani, Jaak Simm, Yves Moreau and Frederik Vercauteren

    Citation: BMC Bioinformatics 2018 19:537

    Published on:

  14. Content type: Research article

    Identifying protein complexes from protein-protein interaction (PPI) network is one of the most important tasks in proteomics. Existing computational methods try to incorporate a variety of biological evidence...

    Authors: Bo Xu, Kun Li, Wei Zheng, Xiaoxia Liu, Yijia Zhang, Zhehuan Zhao and Zengyou He

    Citation: BMC Bioinformatics 2018 19:535

    Published on:

  15. 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

    Published on:

  16. 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

    Published on:

  17. 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

    Published on:

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

  18. 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

    Published on:

  19. 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

    Published on:

  20. 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

    Published on:

  21. 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

    Published on:

  22. 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

    Published on:

  23. 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

    Published on:

  24. 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

    Published on:

  25. 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:

  26. 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

    Published on:

  27. 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

    Published on:

  28. 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

    Published on:

  29. 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

    Published on:

  30. 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

    Published on:

  31. 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

    Published on:

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

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