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Bioinformatics

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  1. Content type: Research article

    The determination of specific kinase substrates in vivo is challenging due to the large number of protein kinases in cells, their substrate specificity overlap, and the lack of highly specific inhibitors. In t...

    Authors: Valentina Romano, Tjaart A. P. de Beer and Torsten Schwede

    Citation: BMC Research Notes 2017 10:104

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  2. Content type: Technical Note

    Several methods have been developed to identify differential correlation (DC) between pairs of molecular features from –omics studies. Most DC methods have only been tested with microarrays and other platforms...

    Authors: Charlotte Siska and Katerina Kechris

    Citation: BMC Research Notes 2017 10:54

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  3. Content type: Research article

    The taxonomic and phylogenetic classification based on sequence analysis of the ITS1 genomic region has become a crucial component of fungal ecology and diversity studies. Nowadays, there is no accurate alignm...

    Authors: Luisa Delgado-Serrano, Silvia Restrepo, Jose Ricardo Bustos, Maria Mercedes Zambrano and Juan Manuel Anzola

    Citation: BMC Research Notes 2016 9:402

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  4. Content type: Technical Note

    DNA metabarcoding is an approach for identifying multiple taxa in an environmental sample using specific genetic loci and taxa-specific primers. When combined with high-throughput sequencing it enables the tax...

    Authors: Marie Lisandra Zepeda-Mendoza, Kristine Bohmann, Aldo Carmona Baez and M. Thomas P. Gilbert

    Citation: BMC Research Notes 2016 9:255

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  5. Content type: Technical Note

    Basic local alignment search tool (BLAST) searches are frequently used to look for homologous sequences and to annotate a query protein, but the increasing size of protein databases makes it difficult to revie...

    Authors: Pablo Mier and Miguel A. Andrade-Navarro

    Citation: BMC Research Notes 2016 9:253

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  6. Content type: Research Article

    The influenza genome is highly variable due primarily to two mechanisms: antigenic drift and antigenic shift. A third mechanism for genetic change, known as copy choice or template switching, can arise during ...

    Authors: Antara De, Tapati Sarkar and Ashesh Nandy

    Citation: BMC Research Notes 2016 9:222

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  7. Content type: Short Report

    An absent word with respect to a sequence is a word that does not occur in the sequence as a factor; an absent word is minimal if all its factors on the other hand occur in that sequence. In this paper we expl...

    Authors: Mohammad Saifur Rahman, Ali Alatabbi, Tanver Athar, Maxime Crochemore and M. Sohel Rahman

    Citation: BMC Research Notes 2016 9:186

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  8. Content type: Technical Note

    Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with complex traits and diseases. However, most of them are located in the non-protein coding regions, and theref...

    Authors: Zheng Xu, Guosheng Zhang, Qing Duan, Shengjie Chai, Baqun Zhang, Cong Wu, Fulai Jin, Feng Yue, Yun Li and Ming Hu

    Citation: BMC Research Notes 2016 9:159

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  9. Content type: Research article

    Genetic comparisons of clinical and environmental Legionella strains form an essential part of outbreak investigations. DNA microarrays often comprise many DNA markers (features). Feature selection and the dev...

    Authors: Tjeerd van der Ploeg and Ewout W. Steyerberg

    Citation: BMC Research Notes 2016 9:147

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  10. Content type: Technical Note

    To cope with the ever-increasing amount of sequence data generated in the field of genomics, the demand for efficient and fast database searches that drive functional and structural annotation in both large- a...

    Authors: Martin Page, Dan MacLean and Christian Schudoma

    Citation: BMC Research Notes 2016 9:130

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  11. Content type: Technical Note

    Keeping up with journal articles on a daily basis is an important activity of scientists engaged in biomedical research. Usually, journal articles and papers in the field of biomedicine are accessed through th...

    Authors: Pavel Evdokimov, Alexey Kudryavtsev, Ekaterina Ilgisonis, Elena Ponomarenko and Andrey Lisitsa

    Citation: BMC Research Notes 2016 9:113

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  12. Content type: Research article

    The cost per patient of next generation sequencing for detection of rare mutations may be significantly reduced using pooled experiments. Recently, some techniques have been proposed for the planning of pooled...

    Authors: Daniela Evangelista, Antonio Zuccaro, Algirdas Lančinskas, Julius Žilinskas and Mario R. Guarracino

    Citation: BMC Research Notes 2016 9:111

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  13. Content type: Research article

    Accurate detection of somatic single nucleotide variants and small insertions and deletions from DNA sequencing experiments of tumour-normal pairs is a challenging task. Tumour samples are often contaminated w...

    Authors: Robert E. Denroche, Laura Mullen, Lee Timms, Timothy Beck, Christina K. Yung, Lincoln Stein, John D. McPherson and Andrew M. K. Brown

    Citation: BMC Research Notes 2015 8:823

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  14. Content type: Technical Note

    Organisms are subject to various stress conditions, which affect both the organism’s gene expression and phenotype. It is critical to understand microbial responses to stress conditions and uncover the underly...

    Authors: Niveda Sundararaman, Christine Ash, Weihua Guo, Rebecca Button, Jugroop Singh and Xueyang Feng

    Citation: BMC Research Notes 2015 8:771

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  15. Content type: Technical Note

    Genome assembly is a fundamental problem with multiple applications. Current technological limitations do not allow assembling of entire genomes and many programs have been designed to produce longer and more ...

    Authors: Nilesh Khiste and Lucian Ilie

    Citation: BMC Research Notes 2015 8:709

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  16. Content type: Research article

    Under postharvest physiological deterioration cassava root tubers alter the expression of biosynthetic pathways of certain primary and secondary metabolites, as well as the activity of some scavenging enzymes....

    Authors: Virgílio Gavicho Uarrota and Marcelo Maraschin

    Citation: BMC Research Notes 2015 8:648

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  17. Content type: Technical Note

    One of the requirements for a successful scientific tool is its availability. Developing a functional web service, however, is usually considered a mundane and ungratifying task, and quite often neglected. Whe...

    Authors: Paweł Daniluk, Bartek Wilczyński and Bogdan Lesyng

    Citation: BMC Research Notes 2015 8:628

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  18. Content type: Short Report

    To demonstrate the bioinformatics capabilities of a low-cost computer, the Raspberry Pi, we present a comparison of the protein-coding gene content of two species in phylum Chlamydiae: Chlamydia trachomatis, a co...

    Authors: James F. Robson and Daniel Barker

    Citation: BMC Research Notes 2015 8:561

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  19. Content type: Technical Note

    With the advent of high-throughput sequencing technologies large-scale identification of microsatellites became affordable and was especially directed to non-model species. By contrast, few efforts have been p...

    Authors: Concita Cantarella and Nunzio D’Agostino

    Citation: BMC Research Notes 2015 8:525

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  20. Content type: Research article

    Inflammatory disease processes involve complex and interrelated systems of mediators. Determining the causal relationships among these mediators becomes more complicated when two, concurrent inflammatory condi...

    Authors: Jean A. Nemzek, Andrew P. Hodges and Yongqun He

    Citation: BMC Research Notes 2015 8:516

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  21. Content type: Technical Note

    For decades there has been increasing interest in understanding the relationships between microbial communities and ecosystem functions. Current DNA sequencing technologies allows for the exploration of microb...

    Authors: Se-Ran Jun, Michael S. Robeson, Loren J. Hauser, Christopher W. Schadt and Andrey A. Gorin

    Citation: BMC Research Notes 2015 8:479

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  22. Content type: Research article

    Every next generation sequencing (NGS) platform relies on proprietary and open source computational tools to analyze sequencing data. NGS tools for Illumina platforms are well documented which is not the case ...

    Authors: Erinija Pranckevičiene, Tautvydas Rančelis, Aidas Pranculis and Vaidutis Kučinskas

    Citation: BMC Research Notes 2015 8:421

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  23. Content type: Technical Note

    Next-generation sequencing allows for determining the genetic composition of a mixed sample. For instance, when performing resistance testing for BCR-ABL1 it is necessary to identify clones and define compound mu...

    Authors: Norbert Niklas, Julia Hafenscher, Agnes Barna, Karin Wiesinger, Johannes Pröll, Stephan Dreiseitl, Sandra Preuner-Stix, Peter Valent, Thomas Lion and Christian Gabriel

    Citation: BMC Research Notes 2015 8:422

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  24. Content type: Technical Note

    Next generation sequencing (NGS) data treatment often requires mapping sequenced reads onto a reference genome for further analysis. Mapped data are commonly visualized using genome browsers. However, such sof...

    Authors: Marc Descrimes, Yousra Ben Zouari, Maxime Wery, Rachel Legendre, Daniel Gautheret and Antonin Morillon

    Citation: BMC Research Notes 2015 8:419

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  25. Content type: Research article

    Genotype imputation is an important procedure in current genomic analysis such as genome-wide association studies, meta-analyses and fine mapping. Although high quality tools are available that perform the ste...

    Authors: Alexandros Kanterakis, Patrick Deelen, Freerk van Dijk, Heorhiy Byelas, Martijn Dijkstra and Morris A Swertz

    Citation: BMC Research Notes 2015 8:359

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  26. Content type: Research article

    In recent years the emergence of multidrug resistant Klebsiella pneumoniae strains has been an increasingly common event. This opportunistic species is one of the five main bacterial pathogens that cause hospital...

    Authors: Martha Lorena Ostria-Hernández, Carlos Javier Sánchez-Vallejo, J Antonio Ibarra and Graciela Castro-Escarpulli

    Citation: BMC Research Notes 2015 8:332

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  27. Content type: Technical Note

    Functional metagenomic selections represent a powerful technique that is widely applied for identification of novel genes from complex metagenomic sources. However, whereas hundreds to thousands of clones can ...

    Authors: Eric van der Helm, Henrik Marcus Geertz-Hansen, Hans Jasper Genee, Sailesh Malla and Morten Otto Alexander Sommer

    Citation: BMC Research Notes 2015 8:328

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  28. Content type: Technical Note

    When modeling single-molecule fluorescence lifetime experimental data, the analysis often involves fitting a biexponential distribution to binned data. When dealing with small sample sizes, there is the potent...

    Authors: Daniel Sewell, Hajin Kim, Taekjip Ha and Ping Ma

    Citation: BMC Research Notes 2015 8:230

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  29. Content type: Research article

    Proteolytic enzymes are ubiquitous and active in a myriad of biochemical pathways. One type, the rhomboids are intramembrane serine proteases that release their products extracellularly. These proteases are pr...

    Authors: Peter A Novick, Naydu M Carmona and Monica Trujillo

    Citation: BMC Research Notes 2015 8:234

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  30. Content type: Research article

    Tests for the evolutionary conservation of associations between genes coding for transcription factors (TFs) and other genes have been limited to a few model organisms due to the lack of experimental informati...

    Authors: Marc del Grande and Gabriel Moreno-Hagelsieb

    Citation: BMC Research Notes 2014 7:928

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  31. Content type: Short Report

    Computational methods have been widely used for the prediction of protein subcellular localization. However, these predictions are rarely validated experimentally and as a result remain questionable. Therefore...

    Authors: Nagendra K Chaturvedi, Riyaz A Mir, Vimla Band, Shantaram S Joshi and Chittibabu Guda

    Citation: BMC Research Notes 2014 7:912

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  32. Content type: Technical Note

    To gain statistical power or to allow fine mapping, researchers typically want to pool data before meta-analyses or genotype imputation. However, the necessary harmonization of genetic datasets is currently er...

    Authors: Patrick Deelen, Marc Jan Bonder, K Joeri van der Velde, Harm-Jan Westra, Erwin Winder, Dennis Hendriksen, Lude Franke and Morris A Swertz

    Citation: BMC Research Notes 2014 7:901

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  33. Content type: Technical Note

    Analyzing the microarray data of different conditions, one can identify the conserved and condition-specific genes and gene modules, and thus can infer the underlying cellular activities. All the available too...

    Authors: Chittabrata Mal, Md Aftabuddin and Sudip Kundu

    Citation: BMC Research Notes 2014 7:886

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  34. Content type: Research article

    Next Generation Sequencing (NGS) machines extract from a biological sample a large number of short DNA fragments (reads). These reads are then used for several applications, e.g., sequence reconstruction, DNA ass...

    Authors: Emanuel Weitschek, Daniele Santoni, Giulia Fiscon, Maria Cristina De Cola, Paola Bertolazzi and Giovanni Felici

    Citation: BMC Research Notes 2014 7:869

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  35. Content type: Data Note

    The angel’s wing oyster mushroom (Pleurocybella porrigens, Sugihiratake) is a well-known delicacy. However, its potential risk in acute encephalopathy was recently revealed by a food poisoning incident. To disclo...

    Authors: Naoki Yamamoto, Tomohiro Suzuki, Masaaki Kobayashi, Hideo Dohra, Yohei Sasaki, Hirofumi Hirai, Koji Yokoyama, Hirokazu Kawagishi and Kentaro Yano

    Citation: BMC Research Notes 2014 7:866

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  36. Content type: Short Report

    Over the past ten years, there has been an explosion of microbiome research. Many software packages for analyzing microbial sequences such as the 16S gene from 454 sequencers and Illumina platforms are availab...

    Authors: Haema Nilakanta, Kimberly L Drews, Suzanne Firrell, Mary A Foulkes and Kathleen A Jablonski

    Citation: BMC Research Notes 2014 7:830

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