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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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  2. Content type: Software

    Biological interpretation of gene/protein lists resulting from -omics experiments can be a complex task. A common approach consists of reviewing Gene Ontology (GO) annotations for entries in such lists and sea...

    Authors: Mikhail Pomaznoy, Brendan Ha and Bjoern Peters

    Citation: BMC Bioinformatics 2018 19:470

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  3. 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

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  4. Content type: Research article

    Bayesian clustering algorithms, in particular those utilizing Dirichlet Processes (DP), return a sample of the posterior distribution of partitions of a set. However, in many applied cases a single clustering ...

    Authors: Thomas J. Glassen, Timo von Oertzen and Dmitry A. Konovalov

    Citation: BMC Bioinformatics 2018 19:375

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  5. Content type: Software

    With the exponential growth in available biomedical data, there is a need for data integration methods that can extract information about relationships between the data sets. However, these data sets might hav...

    Authors: Said el Bouhaddani, Hae-Won Uh, Geurt Jongbloed, Caroline Hayward, Lucija Klarić, Szymon M. Kiełbasa and Jeanine Houwing-Duistermaat

    Citation: BMC Bioinformatics 2018 19:371

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  6. Content type: Methodology article

    Data-driven methods that automatically learn relations between attributes from given data are a popular tool for building mathematical models in computational biology. Since measurements are prone to errors, a...

    Authors: Lidija Magdevska, Miha Mraz, Nikolaj Zimic and Miha Moškon

    Citation: BMC Bioinformatics 2018 19:333

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  7. Content type: Methodology article

    The inclusion of high-dimensional omics data in prediction models has become a well-studied topic in the last decades. Although most of these methods do not account for possibly different types of variables in...

    Authors: Simon Klau, Vindi Jurinovic, Roman Hornung, Tobias Herold and Anne-Laure Boulesteix

    Citation: BMC Bioinformatics 2018 19:322

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  8. Content type: Software

    Polygenic risk scores (PRS) describe the genomic contribution to complex phenotypes and consistently account for a larger proportion of variance in outcome than single nucleotide polymorphisms (SNPs) alone. Ho...

    Authors: Lawrence M. Chen, Nelson Yao, Elika Garg, Yuecai Zhu, Thao T. T. Nguyen, Irina Pokhvisneva, Shantala A. Hari Dass, Eva Unternaehrer, Hélène Gaudreau, Marie Forest, Lisa M. McEwen, Julia L. MacIsaac, Michael S. Kobor, Celia M. T. Greenwood, Patricia P. Silveira, Michael J. Meaney…

    Citation: BMC Bioinformatics 2018 19:295

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  11. Content type: Research article

    Circadian rhythms comprise oscillating molecular interactions, the disruption of the homeostasis of which would cause various disorders. To understand this phenomenon systematically, an accurate technique to i...

    Authors: Hitoshi Iuchi, Masahiro Sugimoto and Masaru Tomita

    Citation: BMC Bioinformatics 2018 19:249

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  12. Content type: Software

    GenoGAM (Genome-wide generalized additive models) is a powerful statistical modeling tool for the analysis of ChIP-Seq data with flexible factorial design experiments. However large runtime and memory requirem...

    Authors: Georg Stricker, Mathilde Galinier and Julien Gagneur

    Citation: BMC Bioinformatics 2018 19:247

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  13. Content type: Research article

    The Top Scoring Pair (TSP) classifier, based on the concept of relative ranking reversals in the expressions of pairs of genes, has been proposed as a simple, accurate, and easily interpretable decision rule f...

    Authors: Dimitri Kagaris, Alireza Khamesipour and Constantin T. Yiannoutsos

    Citation: BMC Bioinformatics 2018 19:244

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  14. Content type: Research article

    Lysine succinylation is a new kind of post-translational modification which plays a key role in protein conformation regulation and cellular function control. To understand the mechanism of succinylation profo...

    Authors: Qiao Ning, Xiaosa Zhao, Lingling Bao, Zhiqiang Ma and Xiaowei Zhao

    Citation: BMC Bioinformatics 2018 19:237

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  15. Content type: Research article

    In the rational drug design process, an ensemble of conformations obtained from a molecular dynamics simulation plays a crucial role in docking experiments. Some studies have found that Fully-Flexible Receptor...

    Authors: Renata De Paris, Christian Vahl Quevedo, Duncan D. Ruiz, Furia Gargano and Osmar Norberto de Souza

    Citation: BMC Bioinformatics 2018 19:235

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  16. 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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  20. Content type: Research article

    Thanks to a reasonable cost and simple sample preparation procedure, linear MALDI-ToF spectrometry is a growing technology for clinical microbiology. With appropriate spectrum databases, this technology can be...

    Authors: Vincent Picaud, Jean-Francois Giovannelli, Caroline Truntzer, Jean-Philippe Charrier, Audrey Giremus, Pierre Grangeat and Catherine Mercier

    Citation: BMC Bioinformatics 2018 19:123

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  21. Content type: Research article

    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

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  24. Content type: Research

    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

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  26. Content type: Research Article

    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

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  27. Content type: Research article

    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

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  28. Content type: Research article

    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

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  29. Content type: Methodology Article

    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

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  30. Content type: Database

    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

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  31. Content type: Methodology Article

    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

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  32. Content type: Software

    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

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  33. Content type: Database

    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

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  35. Content type: Research Article

    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

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  36. Content type: Database

    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

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  37. Content type: Software

    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

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  38. Content type: Methodology Article

    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

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  39. Content type: Software

    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

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  40. Content type: Methodology Article

    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

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  41. Content type: Research Article

    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

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  43. Content type: Software

    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

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  45. Content type: Correspondence

    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

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  46. Content type: Research Article

    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

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  48. Content type: Research Article

    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

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  49. Content type: Research article

    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

    Published on:

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