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  1. In the clinical practice, the objective quantification of histological results is essential not only to define objective and well-established protocols for diagnosis, treatment, and assessment, but also to ame...

    Authors: Elena Casiraghi, Veronica Huber, Marco Frasca, Mara Cossa, Matteo Tozzi, Licia Rivoltini, Biagio Eugenio Leone, Antonello Villa and Barbara Vergani
    Citation: BMC Bioinformatics 2018 19(Suppl 10):357
    Content type: Software article Published on:

    This article is part of a Supplement: Volume 19 Supplement 10

  2. R has become the de-facto reference analysis environment in Bioinformatics. Plenty of tools are available as packages that extend the R functionality, and many of them target the analysis of biological network...

    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(Suppl 10):356
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 10

    The Correction to this article has been published in BMC Bioinformatics 2018 19:456

  3. Statistical approaches to genetic sequences have revealed helpful to gain deeper insight into biological and structural functionalities, using ideas coming from information theory and stochastic modelling of s...

    Authors: Merlotti A., Faria do Valle I., Castellani G. and Remondini D.
    Citation: BMC Bioinformatics 2018 19(Suppl 10):355
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 10

  4. The high growth of Next Generation Sequencing data currently demands new knowledge extraction methods. In particular, the RNA sequencing gene expression experimental technique stands out for case-control studi...

    Authors: Emanuel Weitschek, Silvia Di Lauro, Eleonora Cappelli, Paola Bertolazzi and Giovanni Felici
    Citation: BMC Bioinformatics 2018 19(Suppl 10):354
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 10

  5. Several problems in network biology and medicine can be cast into a framework where entities are represented through partially labeled networks, and the aim is inferring the labels (usually binary) of the unla...

    Authors: Marco Frasca, Giuliano Grossi, Jessica Gliozzo, Marco Mesiti, Marco Notaro, Paolo Perlasca, Alessandro Petrini and Giorgio Valentini
    Citation: BMC Bioinformatics 2018 19(Suppl 10):353
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 10

  6. This preface introduces the content of the BioMed Central journal Supplement related to the 14th annual meeting of the Bioinformatics Italian Society, held in Cagliari, Italy, from the 5th to the 7th of July, ...

    Authors: Giuliano Armano, Giorgio Fotia and Andrea Manconi
    Citation: BMC Bioinformatics 2018 19(Suppl 10):352
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 10

  7. Nowadays, the increasing availability of omics data, due to both the advancements in the acquisition of molecular biology results and in systems biology simulation technologies, provides the bases for precisio...

    Authors: Marco Moscatelli, Andrea Manconi, Mauro Pessina, Giovanni Fellegara, Stefano Rampoldi, Luciano Milanesi, Andrea Casasco and Matteo Gnocchi
    Citation: BMC Bioinformatics 2018 19(Suppl 10):351
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 10

  8. High throughput technologies have provided the scientific community an unprecedented opportunity for large-scale analysis of genomes. Non-coding RNAs (ncRNAs), for a long time believed to be non-functional, ar...

    Authors: Vincenzo Bonnici, Giorgio De Caro, Giorgio Constantino, Sabino Liuni, Domenica D’Elia, Nicola Bombieri, Flavio Licciulli and Rosalba Giugno
    Citation: BMC Bioinformatics 2018 19(Suppl 10):350
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 10

  9. Reproducibility of a research is a key element in the modern science and it is mandatory for any industrial application. It represents the ability of replicating an experiment independently by the location and...

    Authors: Neha Kulkarni, Luca Alessandrì, Riccardo Panero, Maddalena Arigoni, Martina Olivero, Giulio Ferrero, Francesca Cordero, Marco Beccuti and Raffaele A. Calogero
    Citation: BMC Bioinformatics 2018 19(Suppl 10):349
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 10

  10. Relatively small changes to gene expression data dramatically affect co-expression networks inferred from that data which, in turn, can significantly alter the subsequent biological interpretation. This error ...

    Authors: Sean M Colby, Ryan S McClure, Christopher C Overall, Ryan S Renslow and Jason E McDermott
    Citation: BMC Bioinformatics 2018 19:376
    Content type: Research article Published on:

  11. Bayesian clustering algorithms, in particular those utilizing Dirichlet Processes (DP), return a sample of the posterior distribution of partitions of a set. However, in many applied cases a single clustering ...

    Authors: Thomas J. Glassen, Timo von Oertzen and Dmitry A. Konovalov
    Citation: BMC Bioinformatics 2018 19:375
    Content type: Research article Published on:

  12. Many algorithms and programs are available for phylogenetic reconstruction of families of proteins. Methods used widely at present use either a number of distance-based principles or character-based principles...

    Authors: Dmitry Penzar, Mikhail Krivozubov and Sergey Spirin
    Citation: BMC Bioinformatics 2018 19:374
    Content type: Software Published on:

  14. DNA inside eukaryotic cells wraps around histones to form the 11nm chromatin fiber that can further fold into higher-order DNA loops, which may depend on the binding of architectural factors. Predicting how th...

    Authors: Pau Farré, Alexandre Heurteau, Olivier Cuvier and Eldon Emberly
    Citation: BMC Bioinformatics 2018 19:372
    Content type: Research article Published on:

  15. With the exponential growth in available biomedical data, there is a need for data integration methods that can extract information about relationships between the data sets. However, these data sets might hav...

    Authors: Said el Bouhaddani, Hae-Won Uh, Geurt Jongbloed, Caroline Hayward, Lucija Klarić, Szymon M. Kiełbasa and Jeanine Houwing-Duistermaat
    Citation: BMC Bioinformatics 2018 19:371
    Content type: Software Published on:

  16. Identifying the interactions between proteins and long non-coding RNAs (lncRNAs) is of great importance to decipher the functional mechanisms of lncRNAs. However, current experimental techniques for detection ...

    Authors: Lei Deng, Junqiang Wang, Yun Xiao, Zixiang Wang and Hui Liu
    Citation: BMC Bioinformatics 2018 19:370
    Content type: Research article Published on:

  17. To integrate molecular features from multiple high-throughput platforms in prediction, a regression model that penalizes features from all platforms equally is commonly used. However, data from different platf...

    Authors: Jie Liu, Gangning Liang, Kimberly D Siegmund and Juan Pablo Lewinger
    Citation: BMC Bioinformatics 2018 19:369
    Content type: Methodology article Published on:

  19. This article describes the motivation, origin and evolution of the student symposia series organised by the ISCB Student Council. The meeting series started thirteen years ago in Madrid and has spread to four ...

    Authors: Mehedi Hassan, Aishwarya Alex Namasivayam, Dan DeBlasio, Nazeefa Fatima, Benjamin Siranosian, R. Gonzalo Parra, Bart Cuypers, Sayane Shome, Alexander Miguel Monzon, Julien Fumey and Farzana Rahman
    Citation: BMC Bioinformatics 2018 19(Suppl 12):347
    Content type: Meeting report Published on:

    This article is part of a Supplement: Volume 19 Supplement 12

  21. Mouse xenografts from (patient-derived) tumors (PDX) or tumor cell lines are widely used as models to study various biological and preclinical aspects of cancer. However, analyses of their RNA and DNA profiles...

    Authors: Roelof J. C. Kluin, Kristel Kemper, Thomas Kuilman, Julian R. de Ruiter, Vivek Iyer, Josep V. Forment, Paulien Cornelissen-Steijger, Iris de Rink, Petra ter Brugge, Ji-Ying Song, Sjoerd Klarenbeek, Ultan McDermott, Jos Jonkers, Arno Velds, David J. Adams, Daniel S. Peeper…
    Citation: BMC Bioinformatics 2018 19:366
    Content type: Software Published on:

  22. Automatic and reliable characterization of cells in cell cultures is key to several applications such as cancer research and drug discovery. Given the recent advances in light microscopy and the need for accur...

    Authors: Yousef Al-Kofahi, Alla Zaltsman, Robert Graves, Will Marshall and Mirabela Rusu
    Citation: BMC Bioinformatics 2018 19:365
    Content type: Methodology article Published on:

  23. Miniature inverted-repeat transposable elements (MITEs) are short, non-autonomous class II transposable elements present in a high number of conserved copies in eukaryote genomes. An accurate identification of...

    Authors: Juan Manuel Crescente, Diego Zavallo, Marcelo Helguera and Leonardo Sebastián Vanzetti
    Citation: BMC Bioinformatics 2018 19:348
    Content type: Software Published on:

  25. The Open Targets Platform integrates different data sources in order to facilitate identification of potential therapeutic drug targets to treat human diseases. It currently provides evidence for nearly 2.6 mi...

    Authors: Johannes M Freudenberg, Ian Dunham, Philippe Sanseau and Deepak K Rajpal
    Citation: BMC Bioinformatics 2018 19:345
    Content type: Research article Published on:

  26. Conventional methods of motor imagery brain computer interfaces (MI-BCIs) suffer from the limited number of samples and simplified features, so as to produce poor performances with spatial-frequency features a...

    Authors: Tian-jian Luo, Chang-le Zhou and Fei Chao
    Citation: BMC Bioinformatics 2018 19:344
    Content type: Research article Published on:

  27. Targeted amplicon sequencing of the 16S ribosomal RNA gene is one of the key tools for studying microbial diversity. The accuracy of this approach strongly depends on the choice of primer pairs and, in particu...

    Authors: Francesco Sambo, Francesca Finotello, Enrico Lavezzo, Giacomo Baruzzo, Giulia Masi, Elektra Peta, Marco Falda, Stefano Toppo, Luisa Barzon and Barbara Di Camillo
    Citation: BMC Bioinformatics 2018 19:343
    Content type: Methodology article Published on:

  29. Identification of homologous genes is fundamental to comparative genomics, functional genomics and phylogenomics. Extensive public homology databases are of great value for investigating homology but need to b...

    Authors: Siavash Sheikhizadeh Anari, Dick de Ridder, M. Eric Schranz and Sandra Smit
    Citation: BMC Bioinformatics 2018 19:340
    Content type: Methodology article Published on:

  30. Platform-specific error profiles necessitate confirmatory studies where predictions made on data generated using one technology are additionally verified by processing the same samples on an orthogonal technol...

    Authors: Christopher I Cooper, Delia Yao, Dorota H Sendorek, Takafumi N Yamaguchi, Christine P’ng, Kathleen E Houlahan, Cristian Caloian, Michael Fraser, Kyle Ellrott, Adam A Margolin, Robert G Bristow, Joshua M Stuart and Paul C Boutros
    Citation: BMC Bioinformatics 2018 19:339
    Content type: Software Published on:

  31. Eqolisins are rare acid proteases found in archaea, bacteria and fungi. Certain fungi secrete acids as part of their lifestyle and interestingly these also have many eqolisin paralogs, up to nine paralogs have...

    Authors: Nicolás Stocchi, María Victoria Revuelta, Priscila Ailín Lanza Castronuovo, D. Mariano A. Vera and Arjen ten Have
    Citation: BMC Bioinformatics 2018 19:338
    Content type: Research article Published on:

  32. With increasing interest in ab initio protein design, there is a desire to be able to fully explore the design space of insertions and deletions. Nature inserts and deletes residues to optimize energy and functio...

    Authors: William F. Hooper, Benjamin D. Walcott, Xing Wang and Christopher Bystroff
    Citation: BMC Bioinformatics 2018 19:337
    Content type: Methodology article Published on:

  33. Detection of highly divergent or yet unknown viruses from metagenomics sequencing datasets is a major bioinformatics challenge. When human samples are sequenced, a large proportion of assembled contigs are cla...

    Authors: Zurab Bzhalava, Ardi Tampuu, Piotr Bała, Raul Vicente and Joakim Dillner
    Citation: BMC Bioinformatics 2018 19:336
    Content type: Research article Published on:

  34. The development of a disease is a complex process that may result from joint effects of multiple genes. In this article, we propose the overlapping group screening (OGS) approach to determining active genes an...

    Authors: Jie-Huei Wang and Yi-Hau Chen
    Citation: BMC Bioinformatics 2018 19:335
    Content type: Methodology article Published on:

  35. The automated prediction of the enzymatic functions of uncharacterized proteins is a crucial topic in bioinformatics. Although several methods and tools have been proposed to classify enzymes, most of these st...

    Authors: Alperen Dalkiran, Ahmet Sureyya Rifaioglu, Maria Jesus Martin, Rengul Cetin-Atalay, Volkan Atalay and Tunca Doğan
    Citation: BMC Bioinformatics 2018 19:334
    Content type: Software Published on:

  36. Data-driven methods that automatically learn relations between attributes from given data are a popular tool for building mathematical models in computational biology. Since measurements are prone to errors, a...

    Authors: Lidija Magdevska, Miha Mraz, Nikolaj Zimic and Miha Moškon
    Citation: BMC Bioinformatics 2018 19:333
    Content type: Methodology article Published on:

  37. Protein complexes are one of the keys to deciphering the behavior of a cell system. During the past decade, most computational approaches used to identify protein complexes have been based on discovering dense...

    Authors: Xiaoxia Liu, Zhihao Yang, Shengtian Sang, Ziwei Zhou, Lei Wang, Yin Zhang, Hongfei Lin, Jian Wang and Bo Xu
    Citation: BMC Bioinformatics 2018 19:332
    Content type: Research article Published on:

  38. Sequence alignment is crucial in genomics studies. However, optimal multiple sequence alignment (MSA) is NP-hard. Thus, modern MSA methods employ progressive heuristics, breaking the problem into a series of p...

    Authors: Massimo Maiolo, Xiaolei Zhang, Manuel Gil and Maria Anisimova
    Citation: BMC Bioinformatics 2018 19:331
    Content type: Methodology article Published on:

  43. Spanins are phage lysis proteins required to disrupt the outer membrane. Phages employ either two-component spanins or unimolecular spanins in this final step of Gram-negative host lysis. Two-component spanins...

    Authors: Rohit Kongari, Manoj Rajaure, Jesse Cahill, Eric Rasche, Eleni Mijalis, Joel Berry and Ry Young
    Citation: BMC Bioinformatics 2018 19:326
    Content type: Research article Published on:

  44. Constraint-based metabolic flux analysis of knockout strategies is an efficient method to simulate the production of useful metabolites in microbes. Owing to the recent development of technologies for artifici...

    Authors: Takeyuki Tamura
    Citation: BMC Bioinformatics 2018 19:325
    Content type: Research article Published on:

  45. Conventional phylogenetic clustering approaches rely on arbitrary cutpoints applied a posteriori to phylogenetic estimates. Although in practice, Bayesian and bootstrap-based clustering tend to lead to similar...

    Authors: Luc Villandré, Aurélie Labbe, Bluma Brenner, Michel Roger and David A Stephens
    Citation: BMC Bioinformatics 2018 19:324
    Content type: Methodology article Published on:

  46. Procedures for controlling the false discovery rate (FDR) are widely applied as a solution to the multiple comparisons problem of high-dimensional statistics. Current FDR-controlling procedures require accurat...

    Authors: Matthew M. Parks, Benjamin J. Raphael and Charles E. Lawrence
    Citation: BMC Bioinformatics 2018 19:323
    Content type: Methodology article Published on:

  47. The inclusion of high-dimensional omics data in prediction models has become a well-studied topic in the last decades. Although most of these methods do not account for possibly different types of variables in...

    Authors: Simon Klau, Vindi Jurinovic, Roman Hornung, Tobias Herold and Anne-Laure Boulesteix
    Citation: BMC Bioinformatics 2018 19:322
    Content type: Methodology article Published on:

  49. Advancements in biophysical experimental techniques have pushed the limits in terms of the types of phenomena that can be characterized, the amount of data that can be produced and the resolution at which we c...

    Authors: Sandhya P. Tiwari, Florence Tama and Osamu Miyashita
    Citation: BMC Bioinformatics 2018 19:320
    Content type: Methodology article Published on:

  50. Transcription factor binding site (TFBS) loss, gain, and reshuffling within the sequence of a regulatory element could alter the function of that regulatory element. Some of the changes will be detrimental to ...

    Authors: Mario A. Flores and Ivan Ovcharenko
    Citation: BMC Bioinformatics 2018 19:316
    Content type: Research article Published on:

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