Related papers: Automated family-based naming of small RNAs for ne…
Sequencing by Emergence (SEQE) is a new single-molecule nucleic acid (DNA/RNA) sequencing technology that estimates sequence as an emergent property of the binding and localization of a repertoire of short oligonucleotide probes. SEQE…
DNA microarrays are a relatively new technology that can simultaneously measure the expression level of thousands of genes. They have become an important tool for a wide variety of biological experiments. One of the most common goals of DNA…
Next-generation sequencing (NGS) technologies have enabled affordable sequencing of billions of short DNA fragments at high throughput, paving the way for population-scale genomics. Genomics data analytics at this scale requires overcoming…
We present GobyWeb, a web-based system to facilitate the management and analysis of high-throughput sequencing (HTS) projects. The software provides integrated support for a broad set of HTS analyses and offers a simple plugin extension…
Motivation: Protein-to-genome alignment is critical to annotating genes in non-model organisms. While there are a few tools for this purpose, all of them were developed over ten years ago and did not incorporate the latest advances in…
Rapidly growing public gene expression databases contain a wealth of data for building an unprecedentedly detailed picture of human biology and disease. This data comes from many diverse measurement platforms that make integrating it all…
RNA secondary structure prediction and classification are two important problems in the field of RNA biology. Here, we propose a new permutation based approach to create logical non-disjoint clusters of different secondary structures of a…
For most diseases, building large databases of labeled genetic data is an expensive and time-demanding task. To address this, we introduce genetic Generative Adversarial Networks (gGAN), a semi-supervised approach based on an innovative GAN…
Motivation: Microarray data has been recently been shown to be efficacious in distinguishing closely related cell types that often appear in the diagnosis of cancer. It is useful to determine the minimum number of genes needed to do such a…
Next-generation sequencing technologies provide a revolutionary tool for generating gene expression data. Starting with a fixed RNA sample, they construct a library of millions of differentially abundant short sequence tags or "reads",…
With recent high-throughput technology we can synthesize large heterogeneous collections of DNA structures, and also read them all out precisely in a single procedure. Can we use these tools, not only to do things faster, but also to devise…
An important aspect of many botnets is their capability to generate pseudorandom domain names using Domain Generation Algorithms (DGAs). A cyber criminal can register such domains to establish periodically changing rendezvous points with…
In real-world, our DNA is unique but many people share names. This phenomenon often causes erroneous aggregation of documents of multiple persons who are namesake of one another. Such mistakes deteriorate the performance of document…
Portable genome sequencing technology is revolutionizing genomic research by providing a faster, more flexible method of sequencing DNA and RNA [1, 2]. The unprecedented shift from bulky stand-alone benchtop equipment confined in a…
Whole and targeted sequencing of human genomes is a promising, increasingly feasible tool for discovering genetic contributions to risk of complex diseases. A key step is calling an individual's genotype from the multiple aligned short read…
The identification of disease-gene associations is instrumental in understanding the mechanisms of diseases and developing novel treatments. Besides identifying genes from RNA-Seq datasets, it is often necessary to identify gene clusters…
Printing custom DNA sequences is essential to scientific and biomedical research, but the technology can be used to manufacture plagues as well as cures. Just as ink printers recognize and reject attempts to counterfeit money, DNA…
A critical step of genome sequence analysis is the mapping of sequenced DNA fragments (i.e., reads) collected from an individual to a known linear reference genome sequence (i.e., sequence-to-sequence mapping). Recent works replace the…
RNA sequencing (RNA-seq) has been rapidly adopted for the profiling of transcriptomes in many areas of biology, including studies into gene regulation, development and disease. Of particular interest is the discovery of differentially…
Computational complexity is a key limitation of genomic analyses. Thus, over the last 30 years, researchers have proposed numerous fast heuristic methods that provide computational relief. Comparing genomic sequences is one of the most…