Genetics

Developmental validation of PACE™: Automated artifact identification and contributor estimation for use with GlobalFiler™ and PowerPlex® fusion 6c generated data.

DNA mixture interpretation remains one of the major challenges in forensic DNA analysis. DNA mixture samples are inherently complex due to several factors including the variations in the quantity of DNA, the presence of non-allelic artifactual peaks and the presence of multiple contributors with variable levels of allele sharing. The Probabilistic Assessment for Contributor Estimation (PACE) is a ...

Cross-registry neural domain adaptation to extract mutational test results from pathology reports.

OBJECTIVE: We study the performance of machine learning (ML) methods, including neural networks (NNs), to extract mutational test results from pathology reports collected by cancer registries. Given the lack of hand-labeled datasets for mutational test result extraction, we focus on the particular use-case of extracting Epidermal Growth Factor Receptor mutation results in non-small cell lung cance...

Hierarchical Hidden Markov models enable accurate and diverse detection of antimicrobial resistance sequences.

The characterization of antimicrobial resistance genes from high-throughput sequencing data has become foundational in public health research and regu...

Gene Ontology and Expression Studies of Strigolactone Analogues on a Hepatocellular Carcinoma Cell Line.

Human hepatocellular carcinoma (HCC) is the most common and recurrent type of primary adult liver cancer without any effective therapy. Plant-derived ...

Low-rank analysis-synthesis dictionary learning with adaptively ordinal locality.

Analysis dictionary learning (ADL) has been successfully applied to a variety of learning systems. However, the ordinal locality of analysis dictionar...

Characterizing Alzheimer's Disease With Image and Genetic Biomarkers Using Supervised Topic Models.

Neuroimaging and genetic biomarkers have been widely studied from discriminative perspectives towards Alzheimer's disease (AD) classification, since n...

Automated lesion segmentation with BIANCA: Impact of population-level features, classification algorithm and locally adaptive thresholding.

White matter hyperintensities (WMH) or white matter lesions exhibit high variability in their characteristics both at population- and subject-level, m...

Single T Cell Sequencing Demonstrates the Functional Role of TCR Pairing in Cell Lineage and Antigen Specificity.

Although structural studies of individual T cell receptors (TCRs) have revealed important roles for both the α and β chain in directing MHC and antige...

Inferring Gene Regulatory Networks of Metabolic Enzymes Using Gradient Boosted Trees.

Metabolic reprogramming is a hallmark of cancer. In cancer cells, transcription factors (TFs) govern metabolic reprogramming through abnormally increa...

Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne).

Perennial ryegrass (Lolium perenne) is a forage and amenity grass species widely cultivated in temperate regions worldwide. As such, perennial ryegras...

A novel bio-heuristic computing algorithm to solve the capacitated vehicle routing problem based on Adleman-Lipton model.

DNA computing, as one of potential means to solve complicated computational problems, is a new field of interdisciplinary research, including computat...

Identification of city specific important bacterial signature for the MetaSUB CAMDA challenge microbiome data.

BACKGROUND: Metagenomic data of whole genome sequences (WGS) from samples across several cities around the globe may unravel city specific signatures ...

A New Nonlinear Sparse Component Analysis for a Biologically Plausible Model of Neurons.

It is known that brain can create a sparse representation of the environment in both sensory and mnemonic forms (Olshausen & Field, 2004). Such sparse...

A Guide for Using Deep Learning for Complex Trait Genomic Prediction.

Deep learning (DL) has emerged as a powerful tool to make accurate predictions from complex data such as image, text, or video. However, its ability t...

Wx: a neural network-based feature selection algorithm for transcriptomic data.

Next-generation sequencing (NGS), which allows the simultaneous sequencing of billions of DNA fragments simultaneously, has revolutionized how we stud...

Opportunities and Challenges in Phenotypic Screening for Neurodegenerative Disease Research.

Toxic misfolded proteins potentially underly many neurodegenerative diseases, but individual targets which regulate these proteins and their downstrea...

Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data.

Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). Howe...

PolyCRACKER, a robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution.

BACKGROUND: Our understanding of polyploid genomes is limited by our inability to definitively assign sequences to a specific subgenome without extens...

Multivariate Cluster-Based Multifactor Dimensionality Reduction to Identify Genetic Interactions for Multiple Quantitative Phenotypes.

To understand the pathophysiology of complex diseases, including hypertension, diabetes, and autism, deleterious phenotypes are unlikely due to the ef...

Future of Radiotherapy in Nasopharyngeal Carcinoma.

Nasopharyngeal carcinoma (NPC) is a malignancy with unique clinical biological profiles such as associated Epstein-Barr virus infection and high radio...