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  1. 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
    Content type: Methodology article Published on:

  2. 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
    Content type: Research Published on:

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

  3. 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
    Content type: Research Published on:

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

  4. 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
    Content type: Research Published on:

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

  5. 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
    Content type: Research Published on:

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

  6. 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
    Content type: Research Published on:

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

  7. 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
    Content type: Research Published on:

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

  8. 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
    Content type: Methodology article Published on:

  10. 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
    Content type: Research article Published on:

  11. 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
    Content type: Research article Published on:

  13. 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
    Content type: Methodology article Published on:

  14. 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
    Content type: Methodology article Published on:

  15. 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
    Content type: Methodology article Published on:

  16. 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
    Content type: Research article Published on:

  17. 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
    Content type: Software Published on:

  18. 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
    Content type: Research article Published on:

  19. 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
    Content type: Research article Published on:

  20. 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
    Content type: Methodology article Published on:

  21. 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
    Content type: Software Published on:

  22. 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
    Content type: Methodology article Published on:

  23. 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
    Content type: Software Published on:

  25. The development of clinical -omic biomarkers for predicting patient prognosis has mostly focused on multi-gene models. However, several studies have described significant weaknesses of multi-gene biomarkers. I...

    Authors: Michal R. Grzadkowski, Dorota H. Sendorek, Christine P’ng, Vincent Huang and Paul C. Boutros
    Citation: BMC Bioinformatics 2018 19:400
    Content type: Research article Published on:

  27. Genotyping-by-sequencing (GBS) has been used broadly in genetic studies for several species, especially those with agricultural importance. However, its use is still limited in autopolyploid species because ge...

    Authors: Guilherme S. Pereira, Antonio Augusto F. Garcia and Gabriel R. A. Margarido
    Citation: BMC Bioinformatics 2018 19:398
    Content type: Software Published on:

  28. Influenza A Virus (IAV) causes respiratory disease in swine and is a zoonotic pathogen. Uncontrolled IAV in swine herds not only affects animal health, it also impacts production through increased costs associ...

    Authors: Michael A Zeller, Tavis K Anderson, Rasna W Walia, Amy L Vincent and Phillip C Gauger
    Citation: BMC Bioinformatics 2018 19:397
    Content type: Database Published on:

  29. Using knowledge-based interpretation to analyze omics data can not only obtain essential information regarding various biological processes, but also reflect the current physiological status of cells and tissu...

    Authors: Shenghui Liu, Chunrui Xu, Yusen Zhang, Jiaguo Liu, Bin Yu, Xiaoping Liu and Matthias Dehmer
    Citation: BMC Bioinformatics 2018 19:396
    Content type: Research article Published on:

  31. Comprehensive analyzing multi-omics biological data in different conditions is important for understanding biological mechanism in system level. Multiple or multi-layer network model gives us a new insight int...

    Authors: Peizhuo Wang, Lin Gao, Yuxuan Hu and Feng Li
    Citation: BMC Bioinformatics 2018 19:394
    Content type: Methodology article Published on:

  32. Genome sequencing yields the sequence of many short snippets of DNA (reads) from a genome. Genome assembly attempts to reconstruct the original genome from which these reads were derived. This task is difficul...

    Authors: Shaun D. Jackman, Lauren Coombe, Justin Chu, Rene L. Warren, Benjamin P. Vandervalk, Sarah Yeo, Zhuyi Xue, Hamid Mohamadi, Joerg Bohlmann, Steven J.M. Jones and Inanc Birol
    Citation: BMC Bioinformatics 2018 19:393
    Content type: Software Published on:

  33. Network analyses, such as of gene co-expression networks, metabolic networks and ecological networks have become a central approach for the systems-level study of biological data. Several software packages exi...

    Authors: Deisy Morselli Gysi, Andre Voigt, Tiago de Miranda Fragoso, Eivind Almaas and Katja Nowick
    Citation: BMC Bioinformatics 2018 19:392
    Content type: Software Published on:

  35. The Ageing Factor Database AgeFactDB contains a large number of lifespan observations for ageing-related factors like genes, chemical compounds, and other factors such as dietary restriction in different organ...

    Authors: Rolf Hühne, Viktor Kessler, Axel Fürstberger, Silke Kühlwein, Matthias Platzer, Jürgen Sühnel, Ludwig Lausser and Hans A. Kestler
    Citation: BMC Bioinformatics 2018 19:390
    Content type: Methodology article Published on:

  36. Pooling techniques, where multiple sub-samples are mixed in a single sample, are widely used to take full advantage of high-throughput DNA sequencing. Recently, Ranjard et al. (PLoS ONE 13:0195090, 2018) propo...

    Authors: Thomas K. F. Wong, Louis Ranjard, Yu Lin and Allen G. Rodrigo
    Citation: BMC Bioinformatics 2018 19:389
    Content type: Methodology article Published on:

  37. 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
    Content type: Software Published on:

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

  38. 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
    Content type: Software Published on:

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

  39. 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
    Content type: Research Published on:

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

  40. 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
    Content type: Methodology Published on:

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

  41. 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
    Content type: Methodology Published on:

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

  42. 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
    Content type: Software Published on:

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

  43. 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
    Content type: Methodology Published on:

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

  44. 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
    Content type: Methodology article Published on:

  45. 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
    Content type: Research article Published on:

  47. 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
    Content type: Research article Published on:

  48. 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
    Content type: Methodology article Published on:

  49. 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
    Content type: Software Published on:

  50. 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
    Content type: Research article Published on:

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