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  1. 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

  2. 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

  3. 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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  4. 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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  5. 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

    Published on:

  6. 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

    Published on:

  7. 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

  8. 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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  9. 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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  10. 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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  11. 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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  12. 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:

  13. 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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  14. 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

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  15. 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

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  16. 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

  17. Content type: Research

    Antibiotic resistance and its rapid dissemination around the world threaten the efficacy of currently-used medical treatments and call for novel, innovative approaches to manage multi-drug resistant infections...

    Authors: Diogo Manuel Carvalho Leite, Xavier Brochet, Grégory Resch, Yok-Ai Que, Aitana Neves and Carlos Peña-Reyes

    Citation: BMC Bioinformatics 2018 19(Suppl 14):420

    Published on:

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

  18. 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

  19. 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

  20. 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

    The Correction to this article has been published in BMC Bioinformatics 2018 19:530

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. Content type: Research

    A significant number of adverse drug reactions is caused by unexpected Drug-drug interactions (DDIs). The identification of DDIs becomes crucial before the co-prescription of multiple drugs is made. Such a tas...

    Authors: Jian-Yu Shi, Hua Huang, Jia-Xin Li, Peng Lei, Yan-Ning Zhang, Kai Dong and Siu-Ming Yiu

    Citation: BMC Bioinformatics 2018 19(Suppl 14):411

    Published on:

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

  27. 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

  28. 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

  29. Content type: Methodology article

    Support vector machines (SVM) are a powerful tool to analyze data with a number of predictors approximately equal or larger than the number of observations. However, originally, application of SVM to analyze b...

    Authors: Hector Sanz, Clarissa Valim, Esteban Vegas, Josep M. Oller and Ferran Reverter

    Citation: BMC Bioinformatics 2018 19:432

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  30. Content type: Research article

    Because driver mutations provide selective advantage to the mutant clone, they tend to occur at a higher frequency in tumor samples compared to selectively neutral (passenger) mutations. However, mutation freq...

    Authors: Ivan P. Gorlov, Claudio W. Pikielny, Hildreth R. Frost, Stephanie C. Her, Michael D. Cole, Samuel D. Strohbehn, David Wallace-Bradley, Marek Kimmel, Olga Y. Gorlova and Christopher I. Amos

    Citation: BMC Bioinformatics 2018 19:430

    Published on:

  31. Content type: Research article

    High-throughput sequencing has rapidly become an essential part of precision cancer medicine. But validating results obtained from analyzing and interpreting genomic data remains a rate-limiting factor. The go...

    Authors: Xiaopeng Bian, Bin Zhu, Mingyi Wang, Ying Hu, Qingrong Chen, Cu Nguyen, Belynda Hicks and Daoud Meerzaman

    Citation: BMC Bioinformatics 2018 19:429

    Published on:

  32. Content type: Methodology article

    Image-based high-throughput screening (HTS) reveals a high level of heterogeneity in single cells and multiple cellular states may be observed within a single population. Currently available high-dimensional a...

    Authors: Yang Shen, Nard Kubben, Julián Candia, Alexandre V. Morozov, Tom Misteli and Wolfgang Losert

    Citation: BMC Bioinformatics 2018 19:427

    Published on:

  33. Content type: Methodology article

    Determining protein-protein interactions and their binding affinity are important in understanding cellular biological processes, discovery and design of novel therapeutics, protein engineering, and mutagenesi...

    Authors: Wajid Arshad Abbasi, Amina Asif, Asa Ben-Hur and Fayyaz ul Amir Afsar Minhas

    Citation: BMC Bioinformatics 2018 19:425

    Published on:

  34. Content type: Methodology article

    Somatic copy number alternation (SCNA) is a common feature of the cancer genome and is associated with cancer etiology and prognosis. The allele-specific SCNA analysis of a tumor sample aims to identify the al...

    Authors: Hyoyoung Choo-Wosoba, Paul S. Albert and Bin Zhu

    Citation: BMC Bioinformatics 2018 19:424

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  35. Content type: Research article

    RNA-Sequencing analysis methods are rapidly evolving, and the tool choice for each step of one common workflow, differential expression analysis, which includes read alignment, expression modeling, and differe...

    Authors: Alyssa Baccarella, Claire R. Williams, Jay Z. Parrish and Charles C. Kim

    Citation: BMC Bioinformatics 2018 19:423

    Published on:

  36. Content type: Software

    The discovery of functionally conserved proteins is a tough and important task in system biology. Global network alignment provides a systematic framework to search for these proteins from multiple protein-pro...

    Authors: Jialu Hu, Yiqun Gao, Junhao He, Yan Zheng and Xuequn Shang

    Citation: BMC Bioinformatics 2018 19:422

    Published on:

  37. Content type: Research article

    Towards discovering robust cancer biomarkers, it is imperative to unravel the cellular heterogeneity of patient samples and comprehend the interactions between cancer cells and the various cell types in the tu...

    Authors: Konstantina Dimitrakopoulou, Elisabeth Wik, Lars A. Akslen and Inge Jonassen

    Citation: BMC Bioinformatics 2018 19:408

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  38. Content type: Research article

    Long non-coding RNAs (lncRNAs) represent a novel class of non-coding RNAs having a crucial role in many biological processes. The identification of long non-coding homologs among different species is essential...

    Authors: Teresa M. R. Noviello, Antonella Di Liddo, Giovanna M. Ventola, Antonietta Spagnuolo, Salvatore D’Aniello, Michele Ceccarelli and Luigi Cerulo

    Citation: BMC Bioinformatics 2018 19:407

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  39. Content type: Methodology article

    Nowadays, according to valuable resources of high-quality genome sequences, reference-based assembly methods with high accuracy and efficiency are strongly required. Many different algorithms have been designe...

    Authors: Farzaneh Salari, Fatemeh Zare-Mirakabad, Mehdi Sadeghi and Hassan Rokni-Zadeh

    Citation: BMC Bioinformatics 2018 19:406

    Published on:

  40. Content type: Software

    Despite a wide adoption of English in science, a significant amount of biomedical data are produced in other languages, such as French. Yet a majority of natural language processing or semantic tools as well a...

    Authors: Andon Tchechmedjiev, Amine Abdaoui, Vincent Emonet, Stella Zevio and Clement Jonquet

    Citation: BMC Bioinformatics 2018 19:405

    Published on:

  41. Content type: Methodology article

    Gene set scoring provides a useful approach for quantifying concordance between sample transcriptomes and selected molecular signatures. Most methods use information from all samples to score an individual sam...

    Authors: Momeneh Foroutan, Dharmesh D. Bhuva, Ruqian Lyu, Kristy Horan, Joseph Cursons and Melissa J. Davis

    Citation: BMC Bioinformatics 2018 19:404

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  42. Content type: Software

    Systems biology takes a holistic approach by handling biomolecules and their interactions as big systems. Network based approach has emerged as a natural way to model these systems with the idea of representin...

    Authors: Erno Lindfors, Jesse C. J. van Dam, Carolyn Ming Chi Lam, Niels A. Zondervan, Vitor A. P. Martins dos Santos and Maria Suarez-Diez

    Citation: BMC Bioinformatics 2018 19:403

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