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  1. 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

  2. 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

  3. 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

  4. 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

  5. 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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  6. 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

  7. 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

  8. 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

  9. 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

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  10. 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

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  11. 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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  12. 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

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  13. 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

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  14. 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

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  15. 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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  16. 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

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  17. 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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  18. 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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  19. 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

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  20. 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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  21. 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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  22. 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

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  23. Content type: Research article

    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

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  24. Content type: Database

    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

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  25. Content type: Software

    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

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  26. Content type: Methodology article

    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

    Published on:

  27. Content type: Research article

    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

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  28. Content type: Software

    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

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  29. Content type: Software

    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

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  30. Content type: Methodology article

    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

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  31. Content type: Methodology article

    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

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  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

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  40. 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:

  41. 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

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  42. 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

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  43. 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:

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