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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. 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

    Content type: Database

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  2. 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

    Content type: Research Article

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  3. 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

    Content type: Research article

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  4. 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

    Content type: Software

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  5. 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

    Content type: Methodology article

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  6. 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

    Content type: Software

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  7. 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

    Content type: Software

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  8. 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

    Content type: Methodology Article

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  9. 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

    Content type: Research Article

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  10. 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

    Content type: Methodology article

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  11. 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

    Content type: Software

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  12. 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

    Content type: Research article

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  13. 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

    Content type: Methodology Article

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  14. 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

    Content type: Research article

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  15. 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

    Content type: Research Article

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  16. 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

    Content type: Software

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  17. 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

    Content type: Software

    Published on:

  18. 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

    Content type: Methodology Article

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  19. 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

    Content type: Software

    Published on:

  20. 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

    Content type: Methodology article

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  21. 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

    Content type: Research Article

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  22. 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

    Content type: Research article

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  23. 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

    Content type: Database

    Published on:

  24. 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

    Content type: Methodology Article

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  25. The increase in human populations around the world has put pressure on resources, and as a consequence food security has become an important challenge for the 21st century. Wheat (Triticum aestivum) is one of the...

    Authors: Paul A. Wilkinson, Mark O. Winfield, Gary L. A. Barker, Simon Tyrrell, Xingdong Bian, Alexandra M. Allen, Amanda Burridge, Jane A. Coghill, Christy Waterfall, Mario Caccamo, Robert P. Davey and Keith J. Edwards

    Citation: BMC Bioinformatics 2016 17:256

    Content type: Database

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  26. Non-negative linear combinations of elementary flux modes (EMs) describe all feasible reaction flux distributions for a given metabolic network under the quasi steady state assumption. However, only a small su...

    Authors: Moritz von Stosch, Cristiana Rodrigues de Azevedo, Mauro Luis, Sebastiao Feyo de Azevedo and Rui Oliveira

    Citation: BMC Bioinformatics 2016 17:200

    Content type: Methodology article

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  27. G-DOC Plus is a data integration and bioinformatics platform that uses cloud computing and other advanced computational tools to handle a variety of biomedical BIG DATA including gene expression arrays, NGS and m...

    Authors: Krithika Bhuvaneshwar, Anas Belouali, Varun Singh, Robert M. Johnson, Lei Song, Adil Alaoui, Michael A. Harris, Robert Clarke, Louis M. Weiner, Yuriy Gusev and Subha Madhavan

    Citation: BMC Bioinformatics 2016 17:193

    Content type: Software

    Published on:

  28. There is growing evidence that DNA methylation alterations may contribute to carcinogenesis. Recent data also suggest that DNA methylation field defects in normal pre-neoplastic tissue represent infrequent sto...

    Authors: Andrew E. Teschendorff, Allison Jones and Martin Widschwendter

    Citation: BMC Bioinformatics 2016 17:178

    Content type: Research article

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  29. The immune system is multifaceted, structured by diverse components that interconnect using multilayered dynamic cellular processes. Genomic technologies provide a means for investigating, at the molecular lev...

    Authors: Hong Liu, Jessica Liu, Michelle Toups, Timothy Soos and Christopher Arendt

    Citation: BMC Bioinformatics 2016 17:171

    Content type: Research article

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  30. MicroRNAs (miRNAs) are about 22 nucleotides, non-coding RNAs that affect various cellular functions, and play a regulatory role in different organisms including human. Until now, more than 2500 mature miRNAs i...

    Authors: Emily Chia-Yu Su, Yu-Sing Chen, Yun-Cheng Tien, Jeff Liu, Bing-Ching Ho, Sung-Liang Yu and Sher Singh

    Citation: BMC Bioinformatics 2016 17:167

    Content type: Software

    Published on:

  31. Many popular dengue forecasting techniques have been used by several researchers to extrapolate dengue incidence rates, including the K-H model, support vector machines (SVM), and artificial neural networks (A...

    Authors: Padet Siriyasatien, Atchara Phumee, Phatsavee Ongruk, Katechan Jampachaisri and Kraisak Kesorn

    Citation: BMC Bioinformatics 2016 17:166

    Content type: Research article

    Published on:

  32. Accurate adjustment for the amplification efficiency (AE) is an important part of real-time quantitative polymerase chain reaction (qPCR) experiments. The most commonly used correction strategy is to estimate ...

    Authors: Anders E. Bilgrau, Steffen Falgreen, Anders Petersen, Malene K. Kjeldsen, Julie S. Bødker, Hans E. Johnsen, Karen Dybkær and Martin Bøgsted

    Citation: BMC Bioinformatics 2016 17:159

    Content type: Methodology Article

    Published on:

  33. Targeted next-generation sequencing is playing an increasingly important role in biological research and clinical diagnosis by allowing researchers to sequence high priority genes at much higher depths and at ...

    Authors: Likun Wang, Cong Zhang, Johnathan Watkins, Yan Jin, Michael McNutt and Yuxin Yin

    Citation: BMC Bioinformatics 2016 17:153

    Content type: Software

    Published on:

  34. In the context of a master level programming practical at the computer science department of the Karlsruhe Institute of Technology, we developed and make available an open-source code for testing all 203 possi...

    Authors: Michael Hoff, Stefan Orf, Benedikt Riehm, Diego Darriba and Alexandros Stamatakis

    Citation: BMC Bioinformatics 2016 17:143

    Content type: Research Article

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    3.242 - 2-year Impact Factor
    3.213 - 5-year Impact Factor
    1.156 - Source Normalized Impact per Paper (SNIP)
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