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Rye is an important European crop used for food, feed, and bioenergy. Several quality and yield-related traits are of agronomic relevance for rye breeding programs. Profound knowledge of the genetic architectu...
The transcription factor (TF) forkhead box P3 (FOXP3) is constitutively expressed at high levels in naturally occurring CD4+CD25+ regulatory T cells (nTregs). It is not only the most accepted marker for that cell...
Gene expression data are noisy due to technical and biological variability. Consequently, analysis of gene expression data is complex. Different statistical methods produce distinct sets of genes. In addition,...
The discovery of molecular pathways is a challenging problem and its solution relies on the identification of causal molecular interactions in genomics data. Causal molecular interactions can be discovered usi...
Many cancer clinical trials now specify the particular status of a genetic lesion in a patient's tumor in the inclusion or exclusion criteria for trial enrollment. To facilitate search and identification of ge...
Answering questions such as "Which genes are related to breast cancer?" usually requires retrieving relevant publications through the PubMed search engine, reading these publications, and creating gene lists. ...
Detecting the borders between coding and non-coding regions is an essential step in the genome annotation. And information entropy measures are useful for describing the signals in genome sequence. However, th...
Identifying the location of transcription factor bindings is crucial to understand transcriptional regulation. Currently, Chromatin Immunoprecipitation followed with high-throughput Sequencing (ChIP-seq) is ab...
The application of next-generation sequencing to the study of the vaginal microbiome is revealing the spectrum of microbial communities that inhabit the human vagina. High-resolution identification of bacteria...
A variety of species and experimental designs have been used to study genetic influences on alcohol dependence, ethanol response, and related traits. Integration of these heterogeneous data can be used to prod...
Since the initial annotation of microRNAs (miRNAs) in 2001, many studies have sought to identify additional miRNAs experimentally or computationally in various species. MiRNAs act with the Argonaut family of p...
Hepatocellular carcinoma (HCC) is one of the most fatal cancers in the world, and metastasis is a significant cause to the high mortality in patients with HCC. However, the molecular mechanism behind HCC metas...
MicroRNAs (miRNAs) are 19-25 nucleotides non-coding RNAs known to have important post-transcriptional regulatory functions. The computational target prediction algorithm is vital to effective experimental test...
Due to the recent rapid development in ChIP-seq technologies, which uses high-throughput next-generation DNA sequencing to identify the targets of Chromatin Immunoprecipitation, there is an increasing amount o...
Differential expression detection for RNA-seq experiments is often biased by normalization algorithms due to their sensitivity to parametric assumptions on the gene count distributions, extreme values of gene ...
RNA sequencing (RNA-seq) has become a major tool for biomedical research. A key step in analyzing RNA-seq data is to infer the origin of short reads in the source genome, and for this purpose, many read alignm...
Accurate calling of SNPs and genotypes from next-generation sequencing data is an essential prerequisite for most human genetics studies. A number of computational steps are required or recommended when transl...
DNA methylation, which mainly occurs at CpG dinucleotides, is a dynamic epigenetic regulation mechanism in most eukaryotic genomes. It is already known that methylated CpG dinucleotides can lead to a high rate...
Histone modification plays an important role in cell differentiation and tissue development. A recent study has shown that the dimethylation of lysine 4 residue on histone 3 (H3K4me2) marks the gene body area ...
Bacteria of the genus Sneathia are emerging as potential pathogens of the female reproductive tract. Species of Sneathia, which were formerly grouped with Leptotrichia, can be part of the normal microbiota of the...
High-throughput RNA interference (RNAi) screens have been used to find genes that, when silenced, result in sensitivity to certain chemotherapy drugs. Researchers therefore can further identify drug-sensitive ...
While genome-wide association studies identified some promising candidates for schizophrenia, the majority of risk genes remained unknown. We were interested in testing whether integration gene expression and ...
We present a report of the 2012 International Conference on Intelligent Biology and Medicine (ICIBM 2012) and the editorial report of the supplement to BMC Genomics that includes 22 research papers selected from ...
Genomic regions controlling abdominal fatness (AF) were studied in the Northeast Agricultural University broiler line divergently selected for AF. In this study, the chicken 60KSNP chip and extended haplotype ...
High-throughput re-sequencing is rapidly becoming the method of choice for studies of neutral and adaptive processes in natural populations across taxa. As re-sequencing the genome of large numbers of samples ...
The use of dispersants can be an effective way to deal with acute oil spills to limit environmental damage, however very little is known about whether chemically dispersed oil have the same toxic effect on mar...
State-of-the-art high-throughput sequencers, e.g., the Illumina HiSeq series, generate sequencing reads that are longer than 150 bp up to a total of 600 Gbp of data per run. The high-throughput sequencers gene...
Microarray experiments produce expression measurements in genomic scale. A way to derive functional understanding of the data is to focus on functional sets of genes, such as pathways, instead of individual ge...
The overwhelming amount of network data in functional genomics is making its visualization cluttered with jumbling nodes and edges. Such cluttered network visualization, which is known as "hair-balls", is sign...
Molecular chaperones appear to have been evolved to facilitate protein folding in the cell through entrapment of folding intermediates on the interior of a large cavity formed between GroEL and its co-chaperon...
To discover a compound inhibiting multiple proteins (i.e. polypharmacological targets) is a new paradigm for the complex diseases (e.g. cancers and diabetes). In general, the polypharmacological proteins often...
Leishmaniasis is caused by several species of leishmania protozoan and is one of the major vector-born diseases after malaria and sleeping sickness. Toxicity of available drugs and drug resistance development ...
A number of apicomplexan genomes have been sequenced successfully in recent years and this would help in understanding the biology of apicomplexan parasites. The members of the phylum Apicomplexa are important...
MicroRNAs (miRNAs) are short noncoding RNAs (approximately 22 nucleotides in length) that play important roles in breast cancer progression by downregulating gene expression. The detailed mechanisms and biolog...
Functional annotations are available only for a very small fraction of microRNAs (miRNAs) and very few miRNA target genes are experimentally validated. Therefore, functional analysis of miRNA clusters has typi...
MicroRNAs (miRNAs) have been known to play an important role in several biological processes in both animals and plants. Although several tools for miRNA and target identification are available, the number of ...
The microRNA-based gene-silencing machinery has been recognized as a promising approach to control viral replication and used for improving safety for the live attenuated virus vaccines. The effective host mic...
MicroRNAs (miRNAs) are a class of small noncoding RNAs that regulate the target gene expression at post-transcriptional level. They are widely involved in biological processes, such as embryonic development, c...
The sRNAs of bacterial pathogens are known to be involved in various cellular roles including environmental adaptation as well as regulation of virulence and pathogenicity. It is expected that sRNAs may also h...
Researches have been conducted for the identification of differentially expressed genes (DEGs) by generating and mining of cDNA expressed sequence tags (ESTs) for more than a decade. Although the availability ...
Multiple transcription factors (TFs) are involved in the generation of gene expression patterns, such as tissue-specific gene expression and pleiotropic immune responses. However, how combinations of TFs orche...
Teladorsagia circumcincta (order Strongylida) is an economically important parasitic nematode of small ruminants (including sheep and goats) in temperate climatic regions of the world. Improved insights into the ...
Recent developments in high-throughput sequencing (HTS) technologies have made it feasible to sequence the complete transcriptomes of non-model organisms or metatranscriptomes from environmental samples. The c...
Dengue is the world's most common mosquito-borne viral disease. Poor proofreading by RNA polymerase during its replication results in the accumulation of mutations in its genome. This leads to a diversity of g...
The advances and decreasing economical cost of whole genome sequencing (WGS), will soon make this technology available for routine infectious disease epidemiology. In epidemiological studies, outbreak isolates...
Mitochondrial dysfunction is associated with various aging diseases. The copy number of mtDNA in human cells may therefore be a potential biomarker for diagnostics of aging. Here we propose a new computational...
The opportunistic enterobacterium, Morganella morganii, which can cause bacteraemia, is the ninth most prevalent cause of clinical infections in patients at Changhua Christian Hospital, Taiwan. The KT strain of M...
The preferred habitat of a given bacterium can provide a hint of which types of enzymes of potential industrial interest it might produce. These might include enzymes that are stable and active at very high or...
Genome-wide association studies (GWAS) do not provide a full account of the heritability of genetic diseases since gene-gene interactions, also known as epistasis are not considered in single locus GWAS. To ad...
The theme of the 2012 International Conference on Bioinformatics (InCoB) in Bangkok, Thailand was "From Biological Data to Knowledge to Technological Breakthroughs." Besides providing a forum for life scientis...
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