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  1. Content type: Software

    Targeted PCR amplicon sequencing (TAS) techniques provide a sensitive, scalable, and cost-effective way to query and identify closely related bacterial species and strains. Typically, this is accomplished by t...

    Authors: Tara N. Furstenau, Jill H. Cocking, Jason W. Sahl and Viacheslav Y. Fofanov

    Citation: BMC Bioinformatics 2018 19:222

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  2. Content type: Methodology article

    Discovering over-represented approximate motifs in DNA sequences is an essential part of bioinformatics. This topic has been studied extensively because of the increasing number of potential applications. Howe...

    Authors: Chadi Saad, Laurent Noé, Hugues Richard, Julie Leclerc, Marie-Pierre Buisine, Hélène Touzet and Martin Figeac

    Citation: BMC Bioinformatics 2018 19:223

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  3. Content type: Methodology article

    The single cell RNA sequencing (scRNA-seq) technique begin a new era by allowing the observation of gene expression at the single cell level. However, there is also a large amount of technical and biological n...

    Authors: Wuming Gong, Il-Youp Kwak, Pruthvi Pota, Naoko Koyano-Nakagawa and Daniel J. Garry

    Citation: BMC Bioinformatics 2018 19:220

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  4. Content type: Research article

    The heterogeneity of cells across tissue types represents a major challenge for studying biological mechanisms as well as for therapeutic targeting of distinct tissues. Computational prediction of tissue-speci...

    Authors: Ankit Jambusaria, Jeff Klomp, Zhigang Hong, Shahin Rafii, Yang Dai, Asrar B. Malik and Jalees Rehman

    Citation: BMC Bioinformatics 2018 19:217

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  5. Content type: Methodology article

    Discovery of mutated driver genes is one of the primary objective for studying tumorigenesis. To discover some relatively low frequently mutated driver genes from somatic mutation data, many existing methods i...

    Authors: Jianing Xi, Minghui Wang and Ao Li

    Citation: BMC Bioinformatics 2018 19:214

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  6. Content type: Software

    Advances in sequencing technologies have facilitated large-scale comparative genomics based on whole genome sequencing. Constructing and investigating conserved genomic regions among multiple species (called s...

    Authors: Jongin Lee, Daehwan Lee, Mikang Sim, Daehong Kwon, Juyeon Kim, Younhee Ko and Jaebum Kim

    Citation: BMC Bioinformatics 2018 19:216

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  7. Content type: Research article

    Identifying protein functional sites (PFSs) and, particularly, the physicochemical interactions at these sites is critical to understanding protein functions and the biochemical reactions involved. Several kno...

    Authors: Min Han, Yifan Song, Jiaqiang Qian and Dengming Ming

    Citation: BMC Bioinformatics 2018 19:204

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  8. Content type: Research article

    Core collections provide genebank curators and plant breeders a way to reduce size of their collections and populations, while minimizing impact on genetic diversity and allele frequency. Many methods have bee...

    Authors: Herman De Beukelaer, Guy F Davenport and Veerle Fack

    Citation: BMC Bioinformatics 2018 19:203

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  9. Content type: Research article

    Three dimensional (3D) genome spatial organization is critical for numerous cellular functions, including transcription, while certain conformation-driven structural alterations are frequently oncogenic. Genom...

    Authors: Mark R. Segal and Henrik L. Bengtsson

    Citation: BMC Bioinformatics 2018 19:196

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  10. Content type: Research article

    Predicting a list of plant taxa most likely to be observed at a given geographical location and time is useful for many scenarios in biodiversity informatics. Since efficient plant species identification is im...

    Authors: Hans Christian Wittich, Marco Seeland, Jana Wäldchen, Michael Rzanny and Patrick Mäder

    Citation: BMC Bioinformatics 2018 19:190

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  11. Content type: Methodology article

    Genome annotation is of key importance in many research questions. The identification of protein-coding genes is often based on transcriptome sequencing data, ab-initio or homology-based prediction. Recently, it ...

    Authors: Jens Keilwagen, Frank Hartung, Michael Paulini, Sven O. Twardziok and Jan Grau

    Citation: BMC Bioinformatics 2018 19:189

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  12. Content type: Methodology article

    To ensure cancer patients are stratified towards treatments that are optimally beneficial, it is a priority to define robust molecular subtypes using clustering methods applied to high-dimensional biological d...

    Authors: Katherine Eason, Gift Nyamundanda and Anguraj Sadanandam

    Citation: BMC Bioinformatics 2018 19:182

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  13. Content type: Software

    A quantitative trait locus (QTL) is a genomic region that correlates with a phenotype. Most of the experimental information about QTL mapping studies is described in tables of scientific publications. Traditio...

    Authors: Gurnoor Singh, Arnold Kuzniar, Erik M. van Mulligen, Anand Gavai, Christian W. Bachem, Richard G.F. Visser and Richard Finkers

    Citation: BMC Bioinformatics 2018 19:183

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