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Developing whole-body tactile skins for robots remains a challenging task, as existing solutions often prioritize modular, one-size-fits-all designs, which, while versatile, fail to account for the robot's specific shape and the unique…
Reproducibility in genome-wide association studies (GWAS) is crucial for ensuring reliable genomic research outcomes. However, limited access to original genomic datasets (mainly due to privacy concerns) prevents researchers from…
Wearable Cognitive Assistance (WCA) amplifies human cognition in real time through a wearable device and low-latency wireless access to edge computing infrastructure. It is inspired by, and broadens, the metaphor of GPS navigation tools…
With the rapid advances in high-throughput sequencing technologies, the focus of survival analysis has shifted from examining clinical indicators to incorporating genomic profiles with pathological images. However, existing methods either…
The past decade has seen a rapid growth in omics technologies. Genome-wide association studies (GWAS) have uncovered susceptibility variants for a variety of complex traits. However, the functional significance of most discovered variants…
We develop a cross-platform open-source Java application (BACOM2) with graphic user interface (GUI), and users also can use a XML file to set the parameters of algorithm model, file paths and the dataset of paired samples. BACOM2 implements…
Alignment of structural RNAs is an important problem with a wide range of applications. Since function is often determined by molecular structure, RNA alignment programs should take into account both sequence and base-pairing information…
We propose a modified MSA algorithm on quantum annealers with applications in areas of bioinformatics and genetic sequencing. To understand the human genome, researchers compare extensive sets of these genetic sequences -- or their protein…
The Cancer Genome Atlas (TCGA) provides researchers with clinicopathological data and genomic characterizations of various carcinomas. These data sets include expression microarrays for genes and microRNAs -- short, non-coding strands of…
Tool planning with large language models (LLMs), referring to selecting, organizing, and preparing the tools necessary to complete a user request, bridges the gap between natural language understanding and task execution. However, current…
Summary: Coarse-grained normal mode analysis (NMA) is a fast computational technique to study the dynamics of biomolecules. Here we present the Najmanovich Research Group Toolkit for Elastic Networks (NRGTEN). NRGTEN is a Python toolkit…
Background: Coevolution within a protein family is often predicted using statistics that measure the degree of covariation between positions in the protein sequence. Mutual Information is a measure of dependence between two random variables…
BarraCUDA is a C program which uses the BWA algorithm in parallel with nVidia CUDA to align short next generation DNA sequences against a reference genome. The genetically improved (GI) code is up to three times faster on short paired end…
Most genetic algorithms (GAs) used in literature to solve control problems are time consuming and involve important storage memory requirements. In fact, the search in GAs is iteratively performed on a population of chromosomes (control…
Gene-gene interactions have long been recognized to be fundamentally important to understand genetic causes of complex disease traits. At present, identifying gene-gene interactions from genome-wide case-control studies is computationally…
GENFIT is an experiment-independent track-fitting toolkit that combines fitting algorithms, track representations, and measurement geometries into a modular framework. We report on a significantly improved version of GENFIT, based on…
Gene set analysis, a popular approach for analyzing high-throughput gene expression data, aims to identify sets of related genes that show significantly enriched or depleted expression patterns between different conditions. In the last…
Summary: Accurate phenotype prediction from genomic sequences is a highly coveted task in biological and medical research. While machine-learning holds the key to accurate prediction in a variety of fields, the complexity of biological data…
Qualitative research delves deeply into individual complex perspectives on technology and various phenomena. However, a meticulous analysis of qualitative data often requires a significant amount of time, especially during the crucial…
It is increasingly common clinically for cancer specimens to be examined using techniques that identify somatic mutations. In principle these mutational profiles can be used to diagnose the tissue of origin, a critical task for the 3-5% of…