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DNA affinity purification sequencing (DAP-seq) is a recently developed technique for transcription factor (TF) binding site discovery that produces datasets like ChIP-seq. A major advantage of the DAP-seq method is that it uses exogenously expressed TFs to directly interrogate genomic DNA, without the need for tagged transgenic lines or gene-specific antibodies while still capturing TF binding events...
Solid state fermentation processes are mediated by the collective metabolism of specialized microbial communities. Monitoring the relative abundance of dominating species is a critical task in quality control, which is traditionally done by wet lab techniques, such as quantitative PCR (qPCR). In this study, we developed a computational method to quantify microbial species in metagenomes based on their...
New tools are needed to enable rapid detection, identification, and reporting of infectious viral and microbial pathogens in a wide variety of point-of-care applications that impact human and animal health. We report the design, construction, and characterization of a platform for multiplexed analysis of disease-specific DNA sequences that utilizes a smartphone camera as the sensor in conjunction...
MapReduce has recently become very successful parallel processing technique. Latest DNA sequencing technologies are now able to generate huge DNA sequences easily and cheaper. Consequently making it a challenge for single-core processor systems to mine patterns, hence leading to unsatisfactory performance. In this paper, we explore this challenge by making use of MapReduce on Hadoop platform using...
Sequence overlap graphs, constructed based on suffix-prefix relationships between pairs of sequences, are an important data structure in computational biology. High throughput sequencers can read several million to a few billion DNA fragments in a single experiment, making the construction of overlap graphs for such datasets compute-intensive. In this paper, we present a Locality-Sensitive Hashing...
Endometriosis is a complex gynecological disorder. The diagnostic process of endometriosis involves an invasive procedure thus delaying the diagnosis for about 10 years on average. Both DNA-methylation data and RNA-seq data has the potential to uncover molecular mechanisms of diseases. The objective of this project is to identify diagnostic molecular mechanisms of endometriosis using a multi-omics...
Understanding the nature of many diseases, including cancer, requires locating somatically acquired rearrangements corresponding to large-scale chromosomal aberrations. Computational methods to detect inter-chromosomal rearrangements based on next-generation sequencing platforms face the big challenge of accurately predicting the location of sites spanned by a typically small number of reads, while...
Diseases such as enteric fever continues to be major cause of deaths globally, particularly in poor resource settings. Traditional cell viability test using bacterial culture method followed by confirmatory biochemical tests such as motility, triple sugar iron agar (TSI), citrate, urease test, agglutination tests, forms the gold standard method for diagnosis of enteric fever. However, these existing...
Protein-DNA docking is an important computational technique for generating native or near-native complex models. A docking program typically generates a number of complex conformations and predicts the docking solution based on interaction energies. However, incomplete sampling and energy function deficiencies can result in false positive protein-DNA complex models, which hampers its application in...
MicroRNA is a type of short non-coding RNAs, which post-transcriptionally regulate gene expressions. It has been well-documented that human microRNAs contribute in the disease development, such as cancers and obesity. While most microRNA functional studies heavily rely on the regulatory interactions between microRNAs and their target messenger RNAs, the accumulating evidence has shown that the altered...
DNA methylation has been identified to be widely associated to complex diseases. Among biological platforms to profile DNA methylation in human, the Illumina Infinium HumanMethylation450 BeadChip (450K) has been accepted as one of the most efficient technologies. However, challenges exist in analysis of DNA methylation data generated by this technology due to widespread biases. Here we proposed a...
DNA is considered as a good computing device because of the predictability of the double helical structure and the Watson-Crick binding thermodynamics associated with them. DNA circuits can be considered as a possible replacement of silicon transistor based circuits, in implantable medical devices, bio-nanorobots, SMART drugs etc. In this paper, we are proposing a novel five input majority logic gate...
the image is vulnerable to human attack during transmission. Image information not only involves personal privacy, but even relates to national security. Therefore, more and more countries all over the world pay more attention to picture security. Here, a single chaotic encryption method cannot meet the current demand. A new image encryption scheme is designed by combining logistic mapping, sine mapping...
Quasi-palindromes can be harmful or helpful, but most of this functionality is attributed to the formation of cruciforms. Unfortunately, the general properties a sequence must have to facilitate cruciform formation are poorly understood, as most research has focused on case studies of the unusual secondary structures of a few specific sequences. In this work, we investigate the general sequence properties...
With the advent of next-generation sequencing technologies, a considerable effort has been put into sequencing the epigenomes of different species. The efforts such as “Encode” and “Roadmap” epigenomics projects provide an opportunity to compare epigenomes across species (especially between human and mouse). This study is an effort to understand how different histone modifications vary/co-appear between...
Gastric cancer (GC) is one of the lethal cancer types as well as one of the heterogeneous cancer types. To elucidate GC molecular mechanisms, mutational co-occurrence analyses have been suggested. However, an association between mutational co-occurrences and known GC signaling contexts has yet to be identified. In this study, the known GC signaling contexts including cancer hallmarks (DNA repair,...
We study the problem of predicting human biogeographical ancestry using genomic data. While continental level ancestry is relatively simple using genomic information, distinguishing between individuals from closely associated subpopulations (e.g., from the same continent) is still a difficult challenge. In particular, we focus on the case where the analysis is constrained to using single nucleotide...
Miniature inverted-repeat transposable element (M ITE) is a type of class II non-autonomous transposable element playing a crucial role in the process of evolution in biology. Development of bioinformatics tools that are capable of effectively identifying MITEs can enable genome-wide studies of MITE patterns in eukaryotes. Here, we present a fast, accurate and memory-efficient tool, MiteFinder, for...
The rapid development of high-throughput sequencing technology provides unique opportunities for studies of transcription factor binding, while also bringing new computational challenges. Recently, a series of discriminative motif discovery (DMD) methods have been proposed and offer promising solutions for addressing these challenges. However, because of the huge computational cost, most of them have...
It is now possible to compress and decompress large-scale Next-Generation Sequencing files taking advantage of high-performance computing techniques. To this end, we have recently introduced a scalable hybrid parallel algorithm, called phyNGSC, which allows fast compression as well as decompression of big FASTQ datasets using distributed and shared memory programming models via MPI and OpenMP. In...
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