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Results and data

This section incorporates novel results, useful tools, and methods using bioinformatics in new ways, including but not limited to: biological conclusions that are only supported by bioinformatics analyses.

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  1. Content type: Methodology article

    Finding epistatic interactions in large association studies like genome-wide association studies (GWAS) with the nowadays-available large volume of genomic data is a challenging and largely unsolved issue. Few...

    Authors: Sinan Abo Alchamlat and Frédéric Farnir

    Citation: BMC Bioinformatics 2017 18:184

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  2. Content type: Methodology article

    Many computational approaches have been used for target prediction, including machine learning, reverse docking, bioactivity spectra analysis, and chemical similarity searching. Recent studies have suggested t...

    Authors: Tao Huang, Hong Mi, Cheng-yuan Lin, Ling Zhao, Linda L. D. Zhong, Feng-bin Liu, Ge Zhang, Ai-ping Lu and Zhao-xiang Bian

    Citation: BMC Bioinformatics 2017 18:165

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  3. Content type: Software

    The lipid scrambling activity of protein extracts and purified scramblases is typically measured using a fluorescence-based assay. While the assay has yielded insight into the scramblase activity in crude memb...

    Authors: Richard J. Cotton, Birgit Ploier, Michael A. Goren, Anant K. Menon and Johannes Graumann

    Citation: BMC Bioinformatics 2017 18:146

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  4. Content type: Software

    The Stochastic Process Model (SPM) represents a general framework for modeling the joint evolution of repeatedly measured variables and time-to-event outcomes observed in longitudinal studies, i.e., SPM relate...

    Authors: Ilya Y. Zhbannikov, Konstantin Arbeev, Igor Akushevich, Eric Stallard and Anatoliy I. Yashin

    Citation: BMC Bioinformatics 2017 18:125

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  5. Content type: Methodology article

    Intra-sample cellular heterogeneity presents numerous challenges to the identification of biomarkers in large Epigenome-Wide Association Studies (EWAS). While a number of reference-based deconvolution algorith...

    Authors: Andrew E. Teschendorff, Charles E. Breeze, Shijie C. Zheng and Stephan Beck

    Citation: BMC Bioinformatics 2017 18:105

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  6. Content type: Research Article

    Loss-of-function phenotypes are widely used to infer gene function using the principle that similar phenotypes are indicative of similar functions. However, converting phenotypic to functional annotations requ...

    Authors: Beatriz Serrano-Solano, Antonio Díaz Ramos, Jean-Karim Hériché and Juan A. G. Ranea

    Citation: BMC Bioinformatics 2017 18:96

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    The Erratum to this article has been published in BMC Bioinformatics 2017 18:194

  7. Content type: Software

    MCMC-based methods are important for Bayesian inference of phylogeny and related parameters. Although being computationally expensive, MCMC yields estimates of posterior distributions that are useful for estim...

    Authors: Raja H. Ali, Mikael Bark, Jorge Miró, Sayyed A. Muhammad, Joel Sjöstrand, Syed M. Zubair, Raja M. Abbas and Lars Arvestad

    Citation: BMC Bioinformatics 2017 18:97

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  8. Content type: Methodology article

    Tracing stable isotopes, such as 13C using various mass spectrometry (MS) methods provides a valuable information necessary for the study of biochemical processes in cells. However, extracting such information re...

    Authors: Vitaly A. Selivanov, Adrián Benito, Anibal Miranda, Esther Aguilar, Ibrahim Halil Polat, Josep J. Centelles, Anusha Jayaraman, Paul W. N. Lee, Silvia Marin and Marta Cascante

    Citation: BMC Bioinformatics 2017 18:88

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  9. Content type: Methodology article

    ERp is a variable selection and classification method for metabolomics data. ERp uses minimized classification error rates, based on data from a control and experimental group, to test the null hypothesis of n...

    Authors: Mari van Reenen, Johan A. Westerhuis, Carolus J. Reinecke and J Hendrik Venter

    Citation: BMC Bioinformatics 2017 18:83

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  10. Content type: Software

    Proton magnetic resonance spectroscopy is a non-invasive measurement technique which provides information about concentrations of up to 20 metabolites participating in intracellular biochemical processes. In o...

    Authors: Michał Jabłoński, Jana Starčuková and Zenon Starčuk Jr.

    Citation: BMC Bioinformatics 2017 18:56

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  11. Content type: Research Article

    Biclustering techniques are capable of simultaneously clustering rows and columns of a data matrix. These techniques became very popular for the analysis of gene expression data, since a gene can take part of ...

    Authors: Victor A. Padilha and Ricardo J. G. B. Campello

    Citation: BMC Bioinformatics 2017 18:55

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  12. Content type: Database

    Many eukaryotic RNAs have been considered non-coding as they only contain short open reading frames (sORFs). However, there is increasing evidence for the translation of these sORFs into bioactive peptides wit...

    Authors: Rashmi R. Hazarika, Barbara De Coninck, Lidia R. Yamamoto, Laura R. Martin, Bruno P. A. Cammue and Vera van Noort

    Citation: BMC Bioinformatics 2017 18:37

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  13. Content type: Software

    Reduction in the cost of genomic assays has generated large amounts of biomedical-related data. As a result, current studies perform multiple experiments in the same subjects. While Bioconductor’s methods and ...

    Authors: Carles Hernandez-Ferrer, Carlos Ruiz-Arenas, Alba Beltran-Gomila and Juan R. González

    Citation: BMC Bioinformatics 2017 18:36

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  14. Content type: Research Article

    The manual diagnosis of neurodegenerative disorders such as Alzheimer’s disease (AD) and related Dementias has been a challenge. Currently, these disorders are diagnosed using specific clinical diagnostic crit...

    Authors: Sylvester O. Orimaye, Jojo S-M. Wong, Karen J. Golden, Chee P. Wong and Ireneous N. Soyiri

    Citation: BMC Bioinformatics 2017 18:34

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  15. Content type: Research article

    The current state-of-the-art in cancer diagnosis and treatment is not ideal; diagnostic tests are accurate but invasive, and treatments are “one-size fits-all” instead of being personalized. Recently, miRNA’s ...

    Authors: Nikhil Cheerla and Olivier Gevaert

    Citation: BMC Bioinformatics 2017 18:32

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  16. Content type: Software

    Genome-wide association studies (GWAS) of single nucleotide polymorphisms (SNPs) have been successful in identifying loci contributing genetic effects to a wide range of complex human diseases and quantitative...

    Authors: Reedik Mägi, Yury V. Suleimanov, Geraldine M. Clarke, Marika Kaakinen, Krista Fischer, Inga Prokopenko and Andrew P. Morris

    Citation: BMC Bioinformatics 2017 18:25

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  17. Content type: Methodology article

    Compound selectivity is an important issue when developing a new drug. In many instances, a lack of selectivity can translate to increased toxicity. Protein kinases are particularly concerned with this issue b...

    Authors: Nicolas Bosc, Christophe Meyer and Pascal Bonnet

    Citation: BMC Bioinformatics 2017 18:17

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  18. Content type: Methodology Article

    Epistasis marker effect models incorporating products of marker values as predictor variables in a linear regression approach (extended GBLUP, EGBLUP) have been assessed as potentially beneficial for genomic p...

    Authors: Johannes W. R. Martini, Ning Gao, Diercles F. Cardoso, Valentin Wimmer, Malena Erbe, Rodolfo J. C. Cantet and Henner Simianer

    Citation: BMC Bioinformatics 2017 18:3

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  19. Content type: Software

    Data extraction and integration methods are becoming essential to effectively access and take advantage of the huge amounts of heterogeneous genomics and clinical data increasingly available. In this work, we ...

    Authors: Fabio Cumbo, Giulia Fiscon, Stefano Ceri, Marco Masseroli and Emanuel Weitschek

    Citation: BMC Bioinformatics 2017 18:6

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  20. Content type: Software

    Next-generation sequencing (NGS) technologies have accelerated considerably the investigation into the composition of genomes and their functions. Genotyping-by-sequencing (GBS) is a genotyping approach that m...

    Authors: Davoud Torkamaneh, Jérôme Laroche, Maxime Bastien, Amina Abed and François Belzile

    Citation: BMC Bioinformatics 2017 18:5

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  21. Content type: Research Article

    Biological systems and processes are highly dynamic. To gain insights into their functioning time-resolved measurements are necessary. Time-resolved gene expression data captures temporal behaviour of the gene...

    Authors: Svetlana Bulashevska, Colin Priest, Daniel Speicher, Jörg Zimmermann, Frank Westermann and Armin B. Cremers

    Citation: BMC Bioinformatics 2016 17:532

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  22. Content type: Methodology article

    The binary similarity and dissimilarity measures have critical roles in the processing of data consisting of binary vectors in various fields including bioinformatics and chemometrics. These metrics express th...

    Authors: Sony Hartono Wijaya, Farit Mochamad Afendi, Irmanida Batubara, Latifah K. Darusman, Md Altaf-Ul-Amin and Shigehiko Kanaya

    Citation: BMC Bioinformatics 2016 17:520

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  23. Content type: Software

    Recent advances in next-generation sequencing have revolutionized genomic research. 16S rRNA amplicon sequencing using paired-end sequencing on the MiSeq platform from Illumina, Inc., is being used to characte...

    Authors: Hardik I. Parikh, Vishal N. Koparde, Steven P. Bradley, Gregory A. Buck and Nihar U. Sheth

    Citation: BMC Bioinformatics 2016 17:491

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  24. Content type: Research article

    Biological macromolecules (DNA, RNA and proteins) are capable of processing physical or chemical inputs to generate outputs that parallel conventional Boolean logical operators. However, the design of function...

    Authors: Yiling Lee, Rozieffa Roslan, Shariza Azizan, Mohd Firdaus-Raih and Effirul I. Ramlan

    Citation: BMC Bioinformatics 2016 17:438

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  25. Content type: Methodology Article

    In omics data integration studies, it is common, for a variety of reasons, for some individuals to not be present in all data tables. Missing row values are challenging to deal with because most statistical me...

    Authors: Valentin Voillet, Philippe Besse, Laurence Liaubet, Magali San Cristobal and Ignacio González

    Citation: BMC Bioinformatics 2016 17:402

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  26. Content type: Research article

    DNA methylation plays a key role in developmental processes, which is reflected in changing methylation patterns at specific CpG sites over the lifetime of an individual. The underlying mechanisms are complex ...

    Authors: Behrooz Torabi Moghadam, Michal Dabrowski, Bozena Kaminska, Manfred G. Grabherr and Jan Komorowski

    Citation: BMC Bioinformatics 2016 17:393

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  27. Content type: Research Article

    Proliferation and expansion of security risks necessitates new measures to ensure authenticity and validation of GMOs. Watermarking and other cryptographic methods are available which conceal and recover the o...

    Authors: Siguna Mueller, Farhad Jafari and Don Roth

    Citation: BMC Bioinformatics 2016 17:389

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  28. Content type: Software

    Clustering is a widely used collection of unsupervised learning techniques for identifying natural classes within a data set. It is often used in bioinformatics to infer population substructure. Genomic data a...

    Authors: Bertrand S. Clarke, Saeid Amiri and Jennifer L. Clarke

    Citation: BMC Bioinformatics 2016 17:380

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  29. Content type: Methodology Article

    Hierarchical Multi-Label Classification is a classification task where the classes to be predicted are hierarchically organized. Each instance can be assigned to classes belonging to more than one path in the ...

    Authors: Ricardo Cerri, Rodrigo C. Barros, André C. P. L. F. de Carvalho and Yaochu Jin

    Citation: BMC Bioinformatics 2016 17:373

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  30. Content type: Software

    Pathogen metadata includes information about where and when a pathogen was collected and the type of environment it came from. Along with genomic nucleotide sequence data, this metadata is growing rapidly and ...

    Authors: Wenling E. Chang, Matthew W. Peterson, Christopher D. Garay and Tonia Korves

    Citation: BMC Bioinformatics 2016 17:379

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  31. Content type: Software

    Uncovering how phenotypic diversity arises and is maintained in nature has long been a major interest of evolutionary biologists. Recent advances in genome sequencing technologies have remarkably increased the...

    Authors: Emanuel Maldonado, Daniela Almeida, Tibisay Escalona, Imran Khan, Vitor Vasconcelos and Agostinho Antunes

    Citation: BMC Bioinformatics 2016 17:354

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  32. Content type: Methodology article

    The Random Forest (RF) algorithm for supervised machine learning is an ensemble learning method widely used in science and many other fields. Its popularity has been increasing, but relatively few studies addr...

    Authors: Barbara F.F. Huang and Paul C. Boutros

    Citation: BMC Bioinformatics 2016 17:331

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  33. Content type: Research Article

    High-throughput technology allows for genome-wide measurements at different molecular levels for the same patient, e.g. single nucleotide polymorphisms (SNPs) and gene expression. Correspondingly, it might be ...

    Authors: Stefanie Hieke, Axel Benner, Richard F. Schlenl, Martin Schumacher, Lars Bullinger and Harald Binder

    Citation: BMC Bioinformatics 2016 17:327

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  34. Content type: Research article

    Cellular respiration is a catabolic pathway for producing adenosine triphosphate (ATP) and is the most efficient process through which cells harvest energy from consumed food. When cells undergo cellular respi...

    Authors: Nguyen-Quoc-Khanh Le and Yu-Yen Ou

    Citation: BMC Bioinformatics 2016 17:298

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  35. Content type: Database

    Intronless genes are a significant characteristic of prokaryotes. Systematic identification and annotation are primary and crucial steps for determining the functions of intronless genes and understanding thei...

    Authors: Hanwei Yan, Xiaogang Dai, Kai Feng, Qiuyue Ma and Tongming Yin

    Citation: BMC Bioinformatics 2016 17:289

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  36. Content type: Methodology Article

    When constructing new biomarker or gene signature scores for time-to-event outcomes, the underlying aims are to develop a discrimination model that helps to predict whether patients have a poor or good prognos...

    Authors: Andreas Mayr, Benjamin Hofner and Matthias Schmid

    Citation: BMC Bioinformatics 2016 17:288

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2017 Journal Metrics

  • Citation Impact
    2.213 - 2-year Impact Factor
    3.114 - 5-year Impact Factor
    0.878 - Source Normalized Impact per Paper (SNIP)
    1.479 - SCImago Journal Rank (SJR)


    Social Media Impact
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