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BMC Bioinformatics

Zhongming Zhao, Yunlong Liu, Yufei Huang, Kun Huang, Jianhua Ruan
The 2015 International Conference on Intelligent Biology and Medicine (ICIBM 2015) was held on November 13-15, 2015 in Indianapolis, Indiana, USA. ICIBM 2015 included eight scientific sessions, three tutorial sessions, one poster session, and four keynote presentations that covered the frontier research in broad areas related to bioinformatics, systems biology, big data science, biomedical informatics, pharmacogenomics, and intelligent computing. Here, we present a summary of the 10 research articles that were selected from ICIBM 2015 and included in the supplement to BMC Systems Biology...
2016: BMC Systems Biology
Yongsheng Bai, Jeff Kinne, Brandon Donham, Feng Jiang, Lizhong Ding, Justin R Hassler, Randal J Kaufman
BACKGROUND: Most existing tools for detecting next-generation sequencing-based splicing events focus on generic splicing events. Consequently, special types of non-canonical splicing events of short mRNA regions (IRE1α targeted) have not yet been thoroughly addressed at a genome-wide level using bioinformatics approaches in conjunction with next-generation technologies. During endoplasmic reticulum (ER) stress, the gene encoding the RNase Ire1α is known to splice out a short 26 nt region from the mRNA of the transcription factor Xbp1 non-canonically within the cytosol...
2016: BMC Genomics
Kun Huang, Yunlong Liu, Yufei Huang, Lang Li, Lee Cooper, Jianhua Ruan, Zhongming Zhao
We summarize the 2015 International Conference on Intelligent Biology and Medicine (ICIBM 2015) and the editorial report of the supplement to BMC Genomics. The supplement includes 20 research articles selected from the manuscripts submitted to ICIBM 2015. The conference was held on November 13-15, 2015 at Indianapolis, Indiana, USA. It included eight scientific sessions, three tutorials, four keynote presentations, three highlight talks, and a poster session that covered current research in bioinformatics, systems biology, computational biology, biotechnologies, and computational medicine...
2016: BMC Genomics
Srivani L S S Nagam, Saritha Katta, Vidudala V T S Prasad
Reports on the association of TP53 polymorphisms with oral cancer are not only limited but also not specific to site and/or gender. Hence, we examined the effect of TP53 polymorphisms (EX4 215G > C, IVS3 + 40-41ins16 and IVS6 + 62G > A) on buccal mucosa cancer (BMC) and tongue cancer (TC) risk, survival of patients in relation to risk and clinical factors, gender wise [excepting for estimating hazards ratio (HR)], using Fisher's Exact Test, Kaplan-Meier analysis and Cox-proportional hazards models...
August 17, 2016: Molecular Carcinogenesis
Yang Yang, Abhishek Niroula, Bairong Shen, Mauno Vihinen
MOTIVATION: Solubility is one of the fundamental protein properties. It is of great interest because of its relevance to protein expression. Reduced solubility and protein aggregation are also associated with many diseases. RESULTS: We collected from literature the largest experimentally verified solubility affecting amino acid substitution (AAS) dataset and used it to train a predictor called PON-Sol. The predictor can distinguish both solubility decreasing and increasing variants from those not affecting solubility...
July 1, 2016: Bioinformatics
Xuan Zhu, Jian Wang, Bo Peng, Sanjay Shete
BACKGROUND: Next-generation sequencing has been used by investigators to address a diverse range of biological problems through, for example, polymorphism and mutation discovery and microRNA profiling. However, compared to conventional sequencing, the error rates for next-generation sequencing are often higher, which impacts the downstream genomic analysis. Recently, Wang et al. (BMC Bioinformatics 13:185, 2012) proposed a shadow regression approach to estimate the error rates for next-generation sequencing data based on the assumption of a linear relationship between the number of reads sequenced and the number of reads containing errors (denoted as shadows)...
2016: BMC Bioinformatics
Amrit Singh, Casey P Shannon, Young Woong Kim, Mari L DeMarco, Gail M Gauvreau, J Mark FitzGerald, Louis-Philippe Boulet, Paul M O'Byrne, Kim-Anh Le Cao, Scott J Tebbutt
RATIONALE: Individuals with allergic asthma respond differently, but reproducibly, to allergen inhalation challenge. Some individuals develop an isolated early response (early responders) (ERs), whereas others go on to develop a late response (dual responders) (DRs). It is not understood why late responses do not develop in all sensitized individuals. OBJECTIVES: The aim of this study was to identify blood biomarkers that can discriminate ERs and DRs using cellular frequencies and gene and metabolite expression from whole blood...
March 2016: Annals of the American Thoracic Society
James L McDonagh, Daniel Barker, Rosanna G Alderson
BACKGROUND: The increasing use of computers in science allows for the scientific analyses of large datasets at an increasing pace. We provided examples and interactive demonstrations at Dundee Science Centre as part of the 2015 Women in Science festival, to present aspects of computational science to the general public. We used low-cost Raspberry Pi computers to provide hands on experience in computer programming and demonstrated the application of computers to biology. Computer games were used as a means to introduce computers to younger visitors...
2016: SpringerPlus
Dirk Krüger
The editors of BMC Bioinformatics would like to thank all our reviewers who have contributed to the journal in Volume 16 (2015).
2016: BMC Bioinformatics
Kevin P Keegan, Elizabeth M Glass, Folker Meyer
Approaches in molecular biology, particularly those that deal with high-throughput sequencing of entire microbial communities (the field of metagenomics), are rapidly advancing our understanding of the composition and functional content of microbial communities involved in climate change, environmental pollution, human health, biotechnology, etc. Metagenomics provides researchers with the most complete picture of the taxonomic (i.e., what organisms are there) and functional (i.e., what are those organisms doing) composition of natively sampled microbial communities, making it possible to perform investigations that include organisms that were previously intractable to laboratory-controlled culturing; currently, these constitute the vast majority of all microbes on the planet...
2016: Methods in Molecular Biology
Perla C Reyes Fernandez, Rebecca A Replogle, Libo Wang, Min Zhang, James C Fleet
Low dietary calcium (Ca) intake during growth limits peak bone mass but physiological adaptation can prevent this adverse effect. To assess the genetic control on the physiologic response to dietary Ca restriction (RCR), we conducted a study in 51 BXD lines fed either 0.5% (basal) or 0.25% (low) Ca diets from ages 4 to 12 weeks (n = 8/line/diet). Ca absorption (CaAbs), femur bone mineral density (BMD), and bone mineral content (BMC) were examined. ANCOVA with body size as covariate was used to detect significant line and diet main effects, and line-by-diet interactions...
May 2016: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
Mihai Pop, Steven L Salzberg
Supplementary material is a ubiquitous feature of scientific articles, particularly in journals that limit the length of the articles. While the judicious use of supplementary material can improve the readability of scientific articles, its excessive use threatens the scientific review process and by extension the integrity of the scientific literature. In many cases supplementary material today is so extensive that it is reviewed superficially or not at all. Furthermore, citations buried within supplementary files rob other scientists of recognition of their contribution to the scientific record...
2015: BMC Bioinformatics
Rocio T Martinez-Nunez, Jeremy R Sanford
Gene expression profiling is widely used as a measure of the protein output of cells. However, it is becoming more evident that there are multiple layers of post-transcriptional gene regulation that greatly impact protein output (Battle et al., Science 347:664-667, 2014; Khan et al., Science 342:1100-1104, 2013; Vogel et al., Mol Syst Biol 6:400, 2010). Alternative splicing (AS) impacts the expression of protein coding genes in several ways. Firstly, AS increases exponentially the coding-capacity of genes generating multiple transcripts from the same genomic sequence...
2016: Methods in Molecular Biology
Jan Zarzycki, Onur Erbilgin, Cheryl A Kerfeld
Bacterial microcompartments (BMCs) are proteinaceous organelles encapsulating enzymes that catalyze sequential reactions of metabolic pathways. BMCs are phylogenetically widespread; however, only a few BMCs have been experimentally characterized. Among them are the carboxysomes and the propanediol- and ethanolamine-utilizing microcompartments, which play diverse metabolic and ecological roles. The substrate of a BMC is defined by its signature enzyme. In catabolic BMCs, this enzyme typically generates an aldehyde...
December 2015: Applied and Environmental Microbiology
Marília D V Braga, Jens Stoye
Rearrangements are mutations that can change the organization of a genome, but not its content. Examples are inversions of DNA segments, translocations of chromosome ends, fusions and fissions of chromosomes. All mentioned rearrangements can be represented by the generic Double Cut and Join (DCJ) operation. However, the DCJ operation also allows circular chromosomes to be created at intermediate steps, even if the compared genomes are linear. In this case it is more plausible to consider a restriction in which the reincorporation of a circular chromosome has to be done immediately after its creation...
May 2015: IEEE/ACM Transactions on Computational Biology and Bioinformatics
Catherine A Lozupone, Rob Knight
Long et al. (BMC Bioinformatics 2014, 15(1):278) describe a "discrepancy" in using UniFrac to assess statistical significance of community differences. Specifically, they find that weighted UniFrac results differ between input trees where (a) replicate sequences each have their own tip, or (b) all replicates are assigned to one tip with an associated count. We argue that these are two distinct cases that differ in the probability distribution on which the statistical test is based, because of the differences in tree topology...
2015: BMC Bioinformatics
Jianhua Ruan, Victor Jin, Yufei Huang, Hua Xu, Jeremy S Edwards, Yidong Chen, Zhongming Zhao
Here we present a summary of the 2014 International Conference on Intelligent Biology and Medicine (ICIBM 2014) and the editorial report of the supplement to BMC Genomics and BMC Systems Biology that includes 20 research articles selected from ICIBM 2014. The conference was held on December 4-6, 2014 at San Antonio, Texas, USA, and included six scientific sessions, four tutorials, four keynote presentations, nine highlight talks, and a poster session that covered cutting-edge research in bioinformatics, systems biology, and computational medicine...
2015: BMC Genomics
Irene Pala
The editors of BMC Bioinformatics would like to thank all our reviewers who have contributed their time to the journal in Volume 14 (2013).
2015: BMC Bioinformatics
Karolina Sikorska, Nahid Mostafavi Montazeri, André Uitterlinden, Fernando Rivadeneira, Paul Hc Eilers, Emmanuel Lesaffre
Analysis of genome-wide association studies with longitudinal data using standard procedures, such as linear mixed model (LMM) fitting, leads to discouragingly long computation times. There is a need to speed up the computations significantly. In our previous work (Sikorska et al: Fast linear mixed model computations for genome-wide association studies with longitudinal data. Stat Med 2012; 32.1: 165-180), we proposed the conditional two-step (CTS) approach as a fast method providing an approximation to the P-value for the longitudinal single-nucleotide polymorphism (SNP) effect...
October 2015: European Journal of Human Genetics: EJHG
Max Greenfeld, Jan-Willem van de Meent, Dmitri S Pavlichin, Hideo Mabuchi, Chris H Wiggins, Ruben L Gonzalez, Daniel Herschlag
BACKGROUND: Single-molecule techniques have emerged as incisive approaches for addressing a wide range of questions arising in contemporary biological research [Trends Biochem Sci 38:30-37, 2013; Nat Rev Genet 14:9-22, 2013; Curr Opin Struct Biol 2014, 28C:112-121; Annu Rev Biophys 43:19-39, 2014]. The analysis and interpretation of raw single-molecule data benefits greatly from the ongoing development of sophisticated statistical analysis tools that enable accurate inference at the low signal-to-noise ratios frequently associated with these measurements...
2015: BMC Bioinformatics
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