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  1. Content type: Methodology

    Molecular surveillance and outbreak investigation are important for elimination of hepatitis C virus (HCV) infection in the United States. A web-based system, Global Hepatitis Outbreak and Surveillance Technol...

    Authors: Seth Sims, Atkinson G. Longmire, David S. Campo, Sumathi Ramachandran, Magdalena Medrzycki, Lilia Ganova-Raeva, Yulin Lin, Amanda Sue, Hong Thai, Alexander Zelikovsky and Yury Khudyakov

    Citation: BMC Bioinformatics 2018 19(Suppl 11):358

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 11

  2. Content type: Methodology

    Due to recent advances in sequencing technologies, sequence-based analysis has been widely applied to detecting copy number variations (CNVs). There are several techniques for identifying CNVs using next gener...

    Authors: Fatima Zare, Abdelrahman Hosny and Sheida Nabavi

    Citation: BMC Bioinformatics 2018 19(Suppl 11):361

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 11

  3. Content type: Software

    Determining patterns of nucleotide and amino acid substitution is the first step during sequence evolution analysis. However, it is not easy to visualize the different phylogenetic signatures imprinted in alig...

    Authors: Kun Zhao, Elizabeth Henderson, Kelley Bullard, M. Steven Oberste, Cara C. Burns and Jaume Jorba

    Citation: BMC Bioinformatics 2018 19(Suppl 11):364

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 11

  4. Content type: Research

    Drug resistance in HIV is the major problem limiting effective antiviral therapy. Computational techniques for predicting drug resistance profiles from genomic data can accelerate the appropriate choice of the...

    Authors: Shrikant D. Pawar, Christopher Freas, Irene T. Weber and Robert W. Harrison

    Citation: BMC Bioinformatics 2018 19(Suppl 11):362

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 11

  5. Content type: Software

    The Epi-Info software suite, built and maintained by the Centers for Disease Control and Prevention (CDC), is widely used by epidemiologists and public health researchers to collect and analyze public health d...

    Authors: Blake Camp, Jaya Krishna Mandivarapu, Nagashayan Ramamurthy, James Wingo, Anu G. Bourgeois, Xiaojun Cao and Rajshekhar Sunderraman

    Citation: BMC Bioinformatics 2018 19(Suppl 11):359

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 11

  6. Content type: Software

    Reconstructing individual transmission events in an infectious disease outbreak can provide valuable information and help inform infection control policy. Recent years have seen considerable progress in the de...

    Authors: Finlay Campbell, Xavier Didelot, Rich Fitzjohn, Neil Ferguson, Anne Cori and Thibaut Jombart

    Citation: BMC Bioinformatics 2018 19(Suppl 11):363

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 11

  7. Content type: Methodology

    Many biological analysis tasks require extraction of families of genetically similar sequences from large datasets produced by Next-generation Sequencing (NGS). Such tasks include detection of viral transmissi...

    Authors: Viachaslau Tsyvina, David S. Campo, Seth Sims, Alex Zelikovsky, Yury Khudyakov and Pavel Skums

    Citation: BMC Bioinformatics 2018 19(Suppl 11):360

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 11

  8. Content type: Methodology article

    Ultra-deep next-generation sequencing of circulating tumor DNA (ctDNA) holds great promise as a tool for the early detection of cancer and for monitoring disease progression and therapeutic responses. However,...

    Authors: Shibing Deng, Maruja Lira, Donghui Huang, Kai Wang, Crystal Valdez, Jennifer Kinong, Paul A. Rejto, Jadwiga Bienkowska, James Hardwick and Tao Xie

    Citation: BMC Bioinformatics 2018 19:387

    Published on:

  9. Content type: Research article

    The consolidation of pathway databases, such as KEGG, Reactome and ConsensusPathDB, has generated widespread biological interest, however the issue of pathway redundancy impedes the use of these consolidated d...

    Authors: Ruth Alexandra Stoney, Jean-Marc Schwartz, David L Robertson and Goran Nenadic

    Citation: BMC Bioinformatics 2018 19:386

    Published on:

  11. Content type: Research article

    Connecting the dots between the protein sequence and its function is of fundamental interest for protein engineers. In-silico methods are useful in this quest especially when structural information is not avai...

    Authors: Frédéric Cadet, Nicolas Fontaine, Iyanar Vetrivel, Matthieu Ng Fuk Chong, Olivier Savriama, Xavier Cadet and Philippe Charton

    Citation: BMC Bioinformatics 2018 19:382

    Published on:

  12. Content type: Methodology article

    Targeted next-generation sequencing (NGS) is increasingly being adopted in clinical laboratories for genomic diagnostic tests.

    Authors: Yeeok Kang, Seong-Hyeuk Nam, Kyung Sun Park, Yoonjung Kim, Jong-Won Kim, Eunjung Lee, Jung Min Ko, Kyung-A Lee and Inho Park

    Citation: BMC Bioinformatics 2018 19:381

    Published on:

  13. Content type: Software

    High-throughput expression profiling experiments with ordered conditions (e.g. time-course or spatial-course) are becoming more common for studying detailed differentiation processes or spatial patterns. Ident...

    Authors: Rhonda Bacher, Ning Leng, Li-Fang Chu, Zijian Ni, James A. Thomson, Christina Kendziorski and Ron Stewart

    Citation: BMC Bioinformatics 2018 19:380

    Published on:

  14. Content type: Research article

    Since miRNAs can play important roles in different cancer types, how to discover cancer related miRNAs is an important issue. In general, the miRNAs with differential expression is the focus of attention. Howe...

    Authors: Cong Pian, Guangle Zhang, Sanling Wu and Fei Li

    Citation: BMC Bioinformatics 2018 19:379

    Published on:

  15. Content type: Research

    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):2299

    Published on:

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

  16. Content type: Research

    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):2300

    Published on:

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

  17. Content type: Research

    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):2298

    Published on:

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

  18. Content type: Software article

    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):2302

    Published on:

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

  19. Content type: Research

    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):2301

    Published on:

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

  20. Content type: Research

    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):2295

    Published on:

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

  21. Content type: Research

    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):2310

    Published on:

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

  22. Content type: Research

    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):2303

    Published on:

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

  23. Content type: Research

    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):2296

    Published on:

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

  24. Content type: Research article

    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

    Published on:

  26. Content type: Software

    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

    Published on:

  27. Content type: Research article

    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

    Published on:

  28. Content type: Research article

    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

    Published on:

  29. Content type: Software

    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

    Published on:

  30. Content type: Research article

    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

    Published on:

  32. Content type: Methodology article

    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

    Published on:

  33. Content type: Meeting report

    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

    Published on:

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

  34. Content type: Software

    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

    Published on:

  36. Content type: Methodology article

    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

    Published on:

  37. Content type: Software

    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

    Published on:

  39. Content type: Research article

    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

    Published on:

  40. Content type: Methodology article

    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

    Published on:

  41. Content type: Research article

    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

    Published on:

  42. Content type: Methodology article

    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

    Published on:

  44. Content type: Software

    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

    Published on:

  45. Content type: Research article

    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

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  46. Content type: Research article

    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

    Published on:

  47. Content type: Methodology article

    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

    Published on:

  48. Content type: Research article

    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

    Published on:

  49. Content type: Methodology article

    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

    Published on:

  50. Content type: Methodology article

    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

    Published on:

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