iDEP web application for RNA-Seq data analysis

X Ge - Rna Bioinformatics, 2021 - Springer
RNA sequencing (RNA-seq) has become a routine method for transcriptomic profiling. We
developed a user-friendly web app called iDEP (integrated differential expression and …

WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans

BL Snoek, MG Sterken, M Hartanto… - Database, 2020 - academic.oup.com
Quantitative genetics provides the tools for linking polymorphic loci to trait variation. Linkage
analysis of gene expression is an established and widely applied method, leading to the …

Construction of a high-density genetic map from RNA-Seq data for an Arabidopsis bay-0× Shahdara RIL population

EAR Serin, LB Snoek, H Nijveen, LAJ Willems… - Frontiers in …, 2017 - frontiersin.org
High-density genetic maps are essential for high resolution mapping of quantitative traits.
Here, we present a new genetic map for an Arabidopsis Bayreuth× Shahdara recombinant …

The genetics of gene expression in a Caenorhabditis elegans multiparental recombinant inbred line population

BL Snoek, MG Sterken, H Nijveen, RJM Volkers… - G3, 2021 - academic.oup.com
Studying genetic variation of gene expression provides a powerful way to unravel the
molecular components underlying complex traits. Expression quantitative trait locus (eQTL) …

Comparative analysis of transcriptomic profile, histology, and IDH mutation for classification of gliomas

PMH Tran, LKH Tran, J Nechtman, B Dos Santos… - Scientific reports, 2020 - nature.com
Gliomas are currently classified through integration of histology and mutation information,
with new developments in DNA methylation classification. However, discrepancies exist …

Right data for right patient—A precisionFDA NCI–CPTAC multi-omics mislabeling challenge

E Boja, Ž Težak, B Zhang, P Wang, E Johanson… - Nature medicine, 2018 - nature.com
To address a critical roadblock that can occur in translational and clinical research, the
National Cancer Institute and the Food and Drug Administration, in coordination with the …

Dissecting the eQTL Micro-Architecture in Caenorhabditis elegans

MG Sterken, RPJ Bevers, RJM Volkers… - Frontiers in …, 2020 - frontiersin.org
The study of expression quantitative trait loci (eQTL) using natural variation in inbred
populations has yielded detailed information about the transcriptional regulation of complex …

Multimodal learning for multi-omics: a survey

S Tabakhi, MNI Suvon, P Ahadian… - World Scientific Annual …, 2023 - World Scientific
With advanced imaging, sequencing, and profiling technologies, multiple omics data
become increasingly available and hold promises for many healthcare applications such as …

Tests of hybridisation in Tetragonula stingless bees using multiple genetic markers

JP Hereward, TJ Smith, DR Brookes, R Gloag… - BioRxiv, 2020 - biorxiv.org
Discrepancies in mitochondrial and nuclear genetic data are often interpreted as evidence
of hybridisation. We re-examined reports of hybridisation in three cryptic stingless bee …

Assessment of kinship detection using RNA-seq data

N Blay, E Casas, I Galván-Femenía… - Nucleic acids …, 2019 - academic.oup.com
Abstract Analysis of RNA sequencing (RNA-seq) data from related individuals is widely used
in clinical and molecular genetics studies. Prediction of kinship from RNA-seq data would be …