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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. Phenome-wide association studies (PheWAS) are a high-throughput approach to evaluate comprehensive associations between genetic variants and a wide range of phenotypic measures. PheWAS has varying sample sizes...

    Authors: Anurag Verma, Yuki Bradford, Scott Dudek, Anastasia M. Lucas, Shefali S. Verma, Sarah A. Pendergrass and Marylyn D. Ritchie

    Citation: BMC Bioinformatics 2018 19:120

    Content type: Research article

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  2. Diabetes mellitus is a common and complicated chronic lifelong disease. Hence, it is of high clinical significance to find the most relevant clinical indexes and to perform efficient computer-aided pre-diagnos...

    Authors: Peihua Chen and Chuandi Pan

    Citation: BMC Bioinformatics 2018 19:109

    Content type: Research

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  3. 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

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  4. Running multiple-chain Markov Chain Monte Carlo (MCMC) provides an efficient parallel computing method for complex Bayesian models, although the efficiency of the approach critically depends on the length of t...

    Authors: Peng Guo, Bo Zhu, Hong Niu, Zezhao Wang, Yonghu Liang, Yan Chen, Lupei Zhang, Hemin Ni, Yong Guo, El Hamidi A. Hay, Xue Gao, Huijiang Gao, Xiaolin Wu, Lingyang Xu and Junya Li

    Citation: BMC Bioinformatics 2018 19:3

    Content type: Research article

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  5. Bioinformatic tools for the enrichment of ‘omics’ datasets facilitate interpretation and understanding of data. To date few are suitable for metabolomics datasets. The main objective of this work is to give a ...

    Authors: Anna Marco-Ramell, Magali Palau-Rodriguez, Ania Alay, Sara Tulipani, Mireia Urpi-Sarda, Alex Sanchez-Pla and Cristina Andres-Lacueva

    Citation: BMC Bioinformatics 2018 19:1

    Content type: Research article

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  6. qPCR has established itself as the technique of choice for the quantification of gene expression. Procedures for conducting qPCR have received significant attention; however, more rigorous approaches to the st...

    Authors: Michael T. Ganger, Geoffrey D. Dietz and Sarah J. Ewing

    Citation: BMC Bioinformatics 2017 18:534

    Content type: Methodology Article

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  7. Autism spectrum disorders (ASD) are hereditary, heterogeneous and biologically complex neurodevelopmental disorders. Individual studies on gene expression in ASD cannot provide clear consensus conclusions. The...

    Authors: Shuyun Zhang, Libin Deng, Qiyue Jia, Shaoting Huang, Junwang Gu, Fankun Zhou, Meng Gao, Xinyi Sun, Chang Feng and Guangqin Fan

    Citation: BMC Bioinformatics 2017 18:494

    Content type: Database

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  8. The advent of array-based genome-wide DNA methylation methods has enabled quantitative measurement of single CpG methylation status at relatively low cost and sample input. Whereas the use of Infinium Human Me...

    Authors: Maria Needhamsen, Ewoud Ewing, Harald Lund, David Gomez-Cabrero, Robert Adam Harris, Lara Kular and Maja Jagodic

    Citation: BMC Bioinformatics 2017 18:486

    Content type: Methodology Article

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  9. Threshold regression models are a diverse set of non-regular regression models that all depend on change points or thresholds. They provide a simple but elegant and interpretable way to model certain kinds of ...

    Authors: Youyi Fong, Ying Huang, Peter B. Gilbert and Sallie R. Permar

    Citation: BMC Bioinformatics 2017 18:454

    Content type: Software

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  10. Recent advances in omics technology have produced a large amount of liver-related data. A comprehensive and up-to-date source of liver-related data is needed to allow biologists to access the latest data. Howe...

    Authors: Tao Chen, Mansheng Li, Qiang He, Lei Zou, Youhuan Li, Cheng Chang, Dongyan Zhao and Yunping Zhu

    Citation: BMC Bioinformatics 2017 18:452

    Content type: Database

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  11. Small insertions and deletions (indels) have a significant influence in human disease and, in terms of frequency, they are second only to single nucleotide variants as pathogenic mutations. As the majority of ...

    Authors: Michael Ferlaino, Mark F. Rogers, Hashem A. Shihab, Matthew Mort, David N. Cooper, Tom R. Gaunt and Colin Campbell

    Citation: BMC Bioinformatics 2017 18:442

    Content type: Research Article

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  12. Genome-wide microarray has enabled development of robust databases for functional genomics studies in rice. However, such databases do not directly cater to the needs of breeders. Here, we have attempted to de...

    Authors: Maninder Sandhu, V. Sureshkumar, Chandra Prakash, Rekha Dixit, Amolkumar U. Solanke, Tilak Raj Sharma, Trilochan Mohapatra and Amitha Mithra S. V.

    Citation: BMC Bioinformatics 2017 18:432

    Content type: Database

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  13. Genome-wide association studies allow us to understand the genetics of complex diseases. Human metabolism provides information about the disease-causing mechanisms, so it is usual to investigate the associatio...

    Authors: Sophie Molnos, Clemens Baumbach, Simone Wahl, Martina Müller-Nurasyid, Konstantin Strauch, Rui Wang-Sattler, Melanie Waldenberger, Thomas Meitinger, Jerzy Adamski, Gabi Kastenmüller, Karsten Suhre, Annette Peters, Harald Grallert, Fabian J. Theis and Christian Gieger

    Citation: BMC Bioinformatics 2017 18:429

    Content type: Software

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  14. The ability to efficiently search and filter datasets depends on access to high quality metadata. While most biomedical repositories require data submitters to provide a minimal set of metadata, some such as t...

    Authors: Wei Hu, Amrapali Zaveri, Honglei Qiu and Michel Dumontier

    Citation: BMC Bioinformatics 2017 18:415

    Content type: Methodology Article

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  15. Although the sequencing landscape is rapidly evolving and sequencing costs are continuously decreasing, whole genome sequencing is still too expensive for use on a routine basis. Targeted resequencing of only ...

    Authors: Steve Lefever, Filip Pattyn, Bram De Wilde, Frauke Coppieters, Sarah De Keulenaer, Jan Hellemans and Jo Vandesompele

    Citation: BMC Bioinformatics 2017 18:400

    Content type: Software

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  16. Probabilistic assessments of clinical care are essential for quality care. Yet, machine learning, which supports this care process has been limited to categorical results. To maximize its usefulness, it is imp...

    Authors: Brian Connolly, K. Bretonnel Cohen, Daniel Santel, Ulya Bayram and John Pestian

    Citation: BMC Bioinformatics 2017 18:361

    Content type: Methodology Article

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  17. Computational bioinformatics workflows are extensively used to analyse genomics data, with different approaches available to support implementation and execution of these workflows. Reproducibility is one of the ...

    Authors: Sehrish Kanwal, Farah Zaib Khan, Andrew Lonie and Richard O. Sinnott

    Citation: BMC Bioinformatics 2017 18:337

    Content type: Research Article

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  18. Systems Biology Markup Language (SBML) is the standard model representation and description language in systems biology. Enriching and analysing systems biology models by integrating the multitude of available...

    Authors: Sascha Schäuble, Anne-Kristin Stavrum, Mathias Bockwoldt, Pål Puntervoll and Ines Heiland

    Citation: BMC Bioinformatics 2017 18:314

    Content type: Software

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  19. Bioinformatics has multitudinous identities, organisational alignments and disciplinary links. This variety allows bioinformaticians and bioinformatic work to contribute to much (if not most) of life science r...

    Authors: Andrew Bartlett, Bart Penders and Jamie Lewis

    Citation: BMC Bioinformatics 2017 18:311

    Content type: Correspondence

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  20. Survival analysis is an important element of reasoning from data. Applied in a number of fields, it has become particularly useful in medicine to estimate the survival rate of patients on the basis of their co...

    Authors: Łukasz Wróbel, Adam Gudyś and Marek Sikora

    Citation: BMC Bioinformatics 2017 18:285

    Content type: Research Article

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  21. Copy number variation (CNV) is known to play an important role in the genetics of complex diseases and several methods have been proposed to detect association of CNV with phenotypes of interest. Statistical m...

    Authors: Meiling Liu, Sanghoon Moon, Longfei Wang, Sulgi Kim, Yeon-Jung Kim, Mi Yeong Hwang, Young Jin Kim, Robert C. Elston, Bong-Jo Kim and Sungho Won

    Citation: BMC Bioinformatics 2017 18:217

    Content type: Research Article

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  22. Whole blood is frequently utilized in genome-wide association studies of DNA methylation patterns in relation to environmental exposures or clinical outcomes. These associations can be confounded by cellular h...

    Authors: Akhilesh Kaushal, Hongmei Zhang, Wilfried J. J. Karmaus, Meredith Ray, Mylin A. Torres, Alicia K. Smith and Shu-Li Wang

    Citation: BMC Bioinformatics 2017 18:216

    Content type: Research article

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  23. Intrinsically unstructured or disordered proteins function via interacting with other molecules. Annotation of these binding sites is the first step for mapping functional impact of genetic variants in coding ...

    Authors: Jia-Feng Yu, Xiang-Hua Dou, Yu-Jie Sha, Chun-Ling Wang, Hong-Bo Wang, Yi-Ting Chen, Feng Zhang, Yaoqi Zhou and Ji-Hua Wang

    Citation: BMC Bioinformatics 2017 18:206

    Content type: Database

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  24. Systematic, standardized and in-depth phenotyping and data analyses of rodent behaviour empowers gene-function studies, drug testing and therapy design. However, no data repositories are currently available fo...

    Authors: Bastijn Koopmans, August B. Smit, Matthijs Verhage and Maarten Loos

    Citation: BMC Bioinformatics 2017 18:200

    Content type: Database

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  25. Population structure inference using the software STRUCTURE has become an integral part of population genetic studies covering a broad spectrum of taxa including humans. The ever-expanding size of genetic data...

    Authors: Vikram E. Chhatre and Kevin J. Emerson

    Citation: BMC Bioinformatics 2017 18:192

    Content type: Software

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  26. 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

    Content type: Methodology article

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  27. 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

    Content type: Methodology article

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  28. 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

    Content type: Software

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  29. 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

    Content type: Software

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  30. 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

    Content type: Methodology article

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  31. 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

    Content type: Software

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  32. 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

    Content type: Research Article

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

  33. 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

    Content type: Methodology article

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  34. 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

    Content type: Methodology article

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  35. 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

    Content type: Software

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  36. 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

    Content type: Research Article

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  37. 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

    Content type: Software

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