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  1. Clustering of protein sequences is of key importance in predicting the structure and function of newly sequenced proteins and is also of use for their annotation. With the advent of multiple high-throughput se...

    Authors: Armen Abnousi, Shira L. Broschat and Ananth Kalyanaraman
    Citation: BMC Bioinformatics 2018 19:83
    Content type: Methodology Article Published on:

  2. The nearest neighbor model and associated dynamic programming algorithms allow for the efficient estimation of the RNA secondary structure Boltzmann ensemble. However because a given RNA secondary structure on...

    Authors: Luan Lin, Wilson H. McKerrow, Bryce Richards, Chukiat Phonsom and Charles E. Lawrence
    Citation: BMC Bioinformatics 2018 19:82
    Content type: Methodology Article Published on:

  3. Integration of transcriptomic and metabolomic data improves functional interpretation of disease-related metabolomic phenotypes, and facilitates discovery of putative metabolite biomarkers and gene targets. Fo...

    Authors: Jalal K. Siddiqui, Elizabeth Baskin, Mingrui Liu, Carmen Z. Cantemir-Stone, Bofei Zhang, Russell Bonneville, Joseph P. McElroy, Kevin R. Coombes and Ewy A. Mathé
    Citation: BMC Bioinformatics 2018 19:81
    Content type: Research Article Published on:

  4. When many (up to millions) of statistical tests are conducted in discovery set analyses such as genome-wide association studies (GWAS), approaches controlling family-wise error rate (FWER) or false discovery r...

    Authors: Regina Brinster, Anna Köttgen, Bamidele O. Tayo, Martin Schumacher and Peggy Sekula
    Citation: BMC Bioinformatics 2018 19:78
    Content type: Research Article Published on:

  5. Automated bioinformatics workflows are more robust, easier to maintain, and results more reproducible when built with command-line utilities than with custom-coded scripts. Command-line utilities further benef...

    Authors: Yözen Hernández, Rocky Bernstein, Pedro Pagan, Levy Vargas, William McCaig, Girish Ramrattan, Saymon Akther, Amanda Larracuente, Lia Di, Filipe G. Vieira and Wei-Gang Qiu
    Citation: BMC Bioinformatics 2018 19:76
    Content type: Software Published on:

  6. The application of high-throughput sequencing in a broad range of quantitative genomic assays (e.g., DNA-seq, ChIP-seq) has created a high demand for the analysis of large-scale read-count data. Typically, the...

    Authors: WeiBo Wang, Wei Sun, Wei Wang and Jin Szatkiewicz
    Citation: BMC Bioinformatics 2018 19:74
    Content type: Methodology Article Published on:

  7. In the field of biomarker validation with mass spectrometry, controlling the technical variability is a critical issue. In selected reaction monitoring (SRM) measurements, this issue provides the opportunity o...

    Authors: Amna Klich, Catherine Mercier, Laurent Gerfault, Pierre Grangeat, Corinne Beaulieu, Elodie Degout-Charmette, Tanguy Fortin, Pierre Mahé, Jean-François Giovannelli, Jean-Philippe Charrier, Audrey Giremus, Delphine Maucort-Boulch and Pascal Roy
    Citation: BMC Bioinformatics 2018 19:73
    Content type: Methodology Article Published on:

  8. Quantitative trait locus (QTL) mapping in genetic data often involves analysis of correlated observations, which need to be accounted for to avoid false association signals. This is commonly performed by model...

    Authors: Andrey Ziyatdinov, Miquel Vázquez-Santiago, Helena Brunel, Angel Martinez-Perez, Hugues Aschard and Jose Manuel Soria
    Citation: BMC Bioinformatics 2018 19:68
    Content type: Software Published on:

  10. Fungi have diverse biotechnological applications in, among others, agriculture, bioenergy generation, or remediation of polluted soil and water. In this context, culture media based on color change in response...

    Authors: César Domínguez, Jónathan Heras, Eloy Mata and Vico Pascual
    Citation: BMC Bioinformatics 2018 19:66
    Content type: Software Published on:

  11. Crm1-dependent Nuclear Export Signals (NESs) are clusters of alternating hydrophobic and non-hydrophobic amino acid residues between 10 to 15 amino acids in length. NESs were largely thought to follow simple c...

    Authors: Muluye E. Liku, Elizabeth-Ann Legere and Alan M. Moses
    Citation: BMC Bioinformatics 2018 19:65
    Content type: Methodology Article Published on:

  12. Pathological angiogenesis has been identified in many malignancies as a potential prognostic factor and target for therapy. In most cases, angiogenic analysis is based on the measurement of microvessel density...

    Authors: Faliu Yi, Lin Yang, Shidan Wang, Lei Guo, Chenglong Huang, Yang Xie and Guanghua Xiao
    Citation: BMC Bioinformatics 2018 19:64
    Content type: Research Article Published on:

  13. Protein crystal structures are potentially over-interpreted since they are routinely refined without any restraint on the upper limit of atomic B-factors. Consequently, some of their atoms, undetected in the e...

    Authors: Oliviero Carugo
    Citation: BMC Bioinformatics 2018 19:61
    Content type: Research Article Published on:

  14. Prioritization of sequence variants for diagnosis and discovery of Mendelian diseases is challenging, especially in large collections of whole genome sequences (WGS). Fast, scalable solutions are needed for di...

    Authors: Steven Flygare, Edgar Javier Hernandez, Lon Phan, Barry Moore, Man Li, Anthony Fejes, Hao Hu, Karen Eilbeck, Chad Huff, Lynn Jorde, Martin G. Reese and Mark Yandell
    Citation: BMC Bioinformatics 2018 19:57
    Content type: Software Published on:

  15. The analysis of modular gene co-expression networks is a well-established method commonly used for discovering the systems-level functionality of genes. In addition, these studies provide a basis for the disco...

    Authors: Pedro S. T. Russo, Gustavo R. Ferreira, Lucas E. Cardozo, Matheus C. Bürger, Raul Arias-Carrasco, Sandra R. Maruyama, Thiago D. C. Hirata, Diógenes S. Lima, Fernando M. Passos, Kiyoshi F. Fukutani, Melissa Lever, João S. Silva, Vinicius Maracaja-Coutinho and Helder I. Nakaya
    Citation: BMC Bioinformatics 2018 19:56
    Content type: Software Published on:

  16. The haplotype assembly problem for diploid is to find a pair of haplotypes from a given set of aligned Single Nucleotide Polymorphism (SNP) fragments (reads). It has many applications in association studies, d...

    Authors: Maryam Etemadi, Mehri Bagherian, Zhi-Zhong Chen and Lusheng Wang
    Citation: BMC Bioinformatics 2018 19(Suppl 1):52
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 19 Supplement 1

  17. The read length of single-molecule DNA sequencers is reaching 1 Mb. Popular alignment software tools widely used for analyzing such long reads often take advantage of single-instruction multiple-data (SIMD) op...

    Authors: Hajime Suzuki and Masahiro Kasahara
    Citation: BMC Bioinformatics 2018 19(Suppl 1):45
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 19 Supplement 1

  18. DNA damage causes aging, cancer, and other serious diseases. The comet assay can detect multiple types of DNA lesions with high sensitivity, and it has been widely applied. Although comet assay platforms have ...

    Authors: Taehoon Lee, Sungmin Lee, Woo Young Sim, Yu Mi Jung, Sunmi Han, Joong-Ho Won, Hyeyoung Min and Sungroh Yoon
    Citation: BMC Bioinformatics 2018 19(Suppl 1):44
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 1

    The Correction to this article has been published in BMC Bioinformatics 2018 19:170

  19. While next-generation sequencing (NGS) costs have fallen in recent years, the cost and complexity of computation remain substantial obstacles to the use of NGS in bio-medical care and genomic research. The rap...

    Authors: GunHwan Ko, Pan-Gyu Kim, Jongcheol Yoon, Gukhee Han, Seong-Jin Park, Wangho Song and Byungwook Lee
    Citation: BMC Bioinformatics 2018 19(Suppl 1):43
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 19 Supplement 1

  20. Bioinformatics research for finding biological mechanisms can be done by analysis of transcriptome data with pathway based interpretation. Therefore, researchers have tried to develop tools to analyze transcri...

    Authors: Inyoung Kim, Saemi Choi and Sun Kim
    Citation: BMC Bioinformatics 2018 19(Suppl 1):42
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 19 Supplement 1

  21. LncRNAs are long regulatory non-coding RNAs, some of which are arguably predicted to have coding potential. Despite coding potential classifiers that utilize ribosome profiling data successfully detected activ...

    Authors: Seo-Won Choi and Jin-Wu Nam
    Citation: BMC Bioinformatics 2018 19(Suppl 1):41
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 1

  23. Since many proteins become functional only after they interact with their partner proteins and form protein complexes, it is essential to identify the sets of proteins that form complexes. Therefore, several c...

    Authors: Peiying Ruan, Morihiro Hayashida, Tatsuya Akutsu and Jean-Philippe Vert
    Citation: BMC Bioinformatics 2018 19(Suppl 1):39
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 1

  24. It is known that functional RNAs often switch their functions by forming different secondary structures. Popular tools for RNA secondary structures prediction, however, predict the single ‘best’ structures, an...

    Authors: Taichi Hagio, Shun Sakuraba, Junichi Iwakiri, Ryota Mori and Kiyoshi Asai
    Citation: BMC Bioinformatics 2018 19(Suppl 1):38
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 1

  25. The function of many noncoding RNAs (ncRNAs) depend upon their secondary structures. Over the last decades, several methodologies have been developed to predict such structures or to use them to functionally a...

    Authors: Raúl Arias-Carrasco, Yessenia Vásquez-Morán, Helder I. Nakaya and Vinicius Maracaja-Coutinho
    Citation: BMC Bioinformatics 2018 19:55
    Content type: Software Published on:

  26. Small RNA molecules play important roles in many biological processes and their dysregulation or dysfunction can cause disease. The current method of choice for genome-wide sRNA expression profiling is deep se...

    Authors: Raza-Ur Rahman, Abhivyakti Gautam, Jörn Bethune, Abdul Sattar, Maksims Fiosins, Daniel Sumner Magruder, Vincenzo Capece, Orr Shomroni and Stefan Bonn
    Citation: BMC Bioinformatics 2018 19:54
    Content type: Software Published on:

  28. The ease at which influenza virus sequence data can be used to estimate antigenic relationships between strains and the existence of databases containing sequence data for hundreds of thousands influenza strai...

    Authors: Christopher S. Anderson, Patrick R. McCall, Harry A. Stern, Hongmei Yang and David J. Topham
    Citation: BMC Bioinformatics 2018 19:51
    Content type: Research Article Published on:

  29. Long read sequencing is changing the landscape of genomic research, especially de novo assembly. Despite the high error rate inherent to long read technologies, increased read lengths dramatically improve the con...

    Authors: Jeremy R. Wang, James Holt, Leonard McMillan and Corbin D. Jones
    Citation: BMC Bioinformatics 2018 19:50
    Content type: Methodology Article Published on:

  30. Prioritizing disease genes is trying to identify potential disease causing genes for a given phenotype, which can be applied to reveal the inherited basis of human diseases and facilitate drug development. Our...

    Authors: Yaogong Zhang, Jiahui Liu, Xiaohu Liu, Xin Fan, Yuxiang Hong, Yuan Wang, YaLou Huang and MaoQiang Xie
    Citation: BMC Bioinformatics 2018 19:47
    Content type: Methodology Article Published on:

  31. The advent of modern high-throughput genetics continually broadens the gap between the rising volume of sequencing data, and the tools required to process them. The need to pinpoint a small subset of functiona...

    Authors: Monika Mozere, Mehmet Tekman, Jameela Kari, Detlef Bockenhauer, Robert Kleta and Horia Stanescu
    Citation: BMC Bioinformatics 2018 19:46
    Content type: Software Published on:

  33. Over the last few decades, computational genomics has tremendously contributed to decipher biology from genome sequences and related data. Considerable effort has been devoted to the prediction of transcriptio...

    Authors: Marco Di Salvo, Eva Pinatel, Adelfia Talà, Marco Fondi, Clelia Peano and Pietro Alifano
    Citation: BMC Bioinformatics 2018 19:36
    Content type: Software Published on:

  35. Consumers increasingly use online resources for their health information needs. While current search engines can address these needs to some extent, they generally do not take into account that most health inf...

    Authors: Halil Kilicoglu, Asma Ben Abacha, Yassine Mrabet, Sonya E. Shooshan, Laritza Rodriguez, Kate Masterton and Dina Demner-Fushman
    Citation: BMC Bioinformatics 2018 19:34
    Content type: Research Article Published on:

  37. Genomic islands play an important role in microbial genome evolution, providing a mechanism for strains to adapt to new ecological conditions. A variety of computational methods, both genome-composition based ...

    Authors: Eliot C. Bush, Anne E. Clark, Carissa A. DeRanek, Alexander Eng, Juliet Forman, Kevin Heath, Alexander B. Lee, Daniel M. Stoebel, Zunyan Wang, Matthew Wilber and Helen Wu
    Citation: BMC Bioinformatics 2018 19:32
    Content type: Software Published on:

  38. Identification of differentially methylated regions (DMRs) is the initial step towards the study of DNA methylation-mediated gene regulation. Previous approaches to call DMRs suffer from false prediction, use ...

    Authors: David E. Condon, Phu V. Tran, Yu-Chin Lien, Jonathan Schug, Michael K. Georgieff, Rebecca A. Simmons and Kyoung-Jae Won
    Citation: BMC Bioinformatics 2018 19:31
    Content type: Software Published on:

  39. Application Programming Interfaces (APIs) are now widely used to distribute biological data. And many popular biological APIs developed by many different research teams have adopted Javascript Object Notation ...

    Authors: Jiwen Xin, Cyrus Afrasiabi, Sebastien Lelong, Julee Adesara, Ginger Tsueng, Andrew I. Su and Chunlei Wu
    Citation: BMC Bioinformatics 2018 19:30
    Content type: Research Article Published on:

  40. Protein structure can be described by backbone torsion angles: rotational angles about the N-Cα bond (φ) and the Cα-C bond (ψ) or the angle between Cαi-1-Cαi-Cαi + 1 (θ) and the rotational angle about the Cαi-Cαi...

    Authors: Jianzhao Gao, Yuedong Yang and Yaoqi Zhou
    Citation: BMC Bioinformatics 2018 19:29
    Content type: Research Article Published on:

  41. The clinical sequencing of cancer genomes to personalize therapy is becoming routine across the world. However, concerns over patient re-identification from these data lead to questions about how tightly acces...

    Authors: Dorota H. Sendorek, Cristian Caloian, Kyle Ellrott, J. Christopher Bare, Takafumi N. Yamaguchi, Adam D. Ewing, Kathleen E. Houlahan, Thea C. Norman, Adam A. Margolin, Joshua M. Stuart and Paul C. Boutros
    Citation: BMC Bioinformatics 2018 19:28
    Content type: Research Article Published on:

  42. Biocatalysis in organic solvents is nowadays a common practice with a large potential in Biotechnology. Several studies report that proteins which are co-crystallized or soaked in organic solvents preserve the...

    Authors: Ana Julia Velez Rueda, Alexander Miguel Monzon, Sebastián M. Ardanaz, Luis E. Iglesias and Gustavo Parisi
    Citation: BMC Bioinformatics 2018 19:27
    Content type: Research Article Published on:

  44. GenIO is a novel web-server, designed to assist clinical genomics researchers and medical doctors in the diagnostic process of rare genetic diseases. The tool identifies the most probable variants causing a ra...

    Authors: Daniel Koile, Marta Cordoba, Maximiliano de Sousa Serro, Marcelo Andres Kauffman and Patricio Yankilevich
    Citation: BMC Bioinformatics 2018 19:25
    Content type: Software Published on:

  45. Protein or nucleic acid sequences contain a multitude of associated annotations representing continuous sequence elements (CSEs). Comparing these CSEs is needed, whenever we want to match identical annotations...

    Authors: Roman Prytuliak, Friedhelm Pfeiffer and Bianca Hermine Habermann
    Citation: BMC Bioinformatics 2018 19:24
    Content type: Methodology Article Published on:

  46. The uncovering of genes linked to human diseases is a pressing challenge in molecular biology and precision medicine. This task is often hindered by the large number of candidate genes and by the heterogeneity...

    Authors: Guido Zampieri, Dinh Van Tran, Michele Donini, Nicolò Navarin, Fabio Aiolli, Alessandro Sperduti and Giorgio Valle
    Citation: BMC Bioinformatics 2018 19:23
    Content type: Research Article Published on:

  48. Molecular biomarkers that can predict drug efficacy in cancer patients are crucial components for the advancement of precision medicine. However, identifying these molecular biomarkers remains a laborious and ...

    Authors: Kyubum Lee, Byounggun Kim, Yonghwa Choi, Sunkyu Kim, Wonho Shin, Sunwon Lee, Sungjoon Park, Seongsoon Kim, Aik Choon Tan and Jaewoo Kang
    Citation: BMC Bioinformatics 2018 19:21
    Content type: Research Article Published on:

  50. Feature selection is commonly employed for identifying collectively-predictive biomarkers and biosignatures; it facilitates the construction of small statistical models that are easier to verify, visualize, an...

    Authors: Michail Tsagris, Vincenzo Lagani and Ioannis Tsamardinos
    Citation: BMC Bioinformatics 2018 19:17
    Content type: Research Article Published on:

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