Related papers: SeqManager: A Web-Based Tool for Efficient Sequenc…
The wide array of currently available genomes display a wonderful diversity in size, composition and structure with many more to come thanks to several global biodiversity genomics initiatives starting in recent years. However, sequencing…
Segmental duplications (SDs), or low-copy repeats (LCR), are segments of DNA greater than 1 Kbp with high sequence identity that are copied to other regions of the genome. SDs are among the most important sources of evolution, a common…
We here present SIMLR (Single-cell Interpretation via Multi-kernel LeaRning), an open-source tool that implements a novel framework to learn a sample-to-sample similarity measure from expression data observed for heterogenous samples. SIMLR…
Novel technologies in genomics allow creating data in exascale dimension with relatively minor effort of human and laboratory and thus monetary resources compared to capabilities only a decade ago. While the availability of this data…
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer…
Generative AI and large language models (LLMs) have shown strong capabilities in code understanding, but their use in cybersecurity, particularly for malware detection and analysis, remains limited. Existing detection systems often fail to…
GenoML is a Python package automating machine learning workflows for genomics (genetics and multi-omics) with an open science philosophy. Genomics data require significant domain expertise to clean, pre-process, harmonize and perform…
Deep learning, a rebranding of deep neural network research works, has achieved a remarkable success in recent years. With multiple hidden layers, deep learning models aim at computing the hierarchical feature representations of the…
Learning representations of user behavior sequences is crucial for various online services, such as online fraudulent transaction detection mechanisms. Graph Neural Networks (GNNs) have been extensively applied to model sequence…
Motivation: High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments -- called short reads -- that cause significant computational burden. To analyze the entire genome, each of the billions of…
Next Generation Sequencing (NGS), a recently evolved technology, have served a lot in the research and development sector of our society. This novel approach is a newbie and has critical advantages over the traditional Capillary…
Merging datafiles containing information on overlapping sets of entities is a challenging task in the absence of unique identifiers, and is further complicated when some entities are duplicated in the datafiles. Most approaches to this…
Large language model (LLM) inference often suffers from high latency, particularly in resource-constrained environments such as on-device or edge deployments. To address this challenge, we present StorInfer, a novel storage-assisted LLM…
In data warehouse and data mart systems, queries often take a long time to execute due to their complex nature. Query response times can be greatly improved by caching final/intermediate results of previous queries, and using them to answer…
The integration of knowledge graphs and graph machine learning (GML) in genomic data analysis offers several opportunities for understanding complex genetic relationships, especially at the RNA level. We present a comprehensive approach for…
Semantic web is a web of future. The Resource Description Framework (RDF) is a language to represent resources in the World Wide Web. When these resources are queried the problem of duplicate query results occurs. The present techniques…
Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating…
Isochores are long genome segments relatively homogeneous in G+C. A heuristic algorithm based on entropic segmentation has been developed by our group, and a web server implementing all the required components is available. However, a…
DNA is emerging as an increasingly attractive medium for data storage due to a number of important and unique advantages it offers, most notably the unprecedented durability and density. While the technology is evolving rapidly, the…
Background: Since the invention of next-generation RNA sequencing (RNA-seq) technologies, they have become a powerful tool to study the presence and quantity of RNA molecules in biological samples and have revolutionized transcriptomic…