Cover Image

Benchmarking end-to-end genotype-to-phenotype prediction workflows across 80 openSNP phenotypes

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Muneeb, Muhammad, Ascher, David B., Myung, YooChan, Feng, Samuel F., Henschel, Andreas
Format:	Preprint
Published:	2026
Subjects:	Genomics
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

Identifying genes associated with phenotypes using machine and deep learning
by: Muneeb, Muhammad, et al.
Published: (2026)

EFGPP: Exploratory framework for genotype-phenotype prediction
by: Muneeb, Muhammad, et al.
Published: (2026)

A harmonized benchmarking framework for implementation-aware evaluation of 46 polygenic risk score tools across binary and continuous phenotypes
by: Muneeb, Muhammad, et al.
Published: (2026)

PhenotypeToGeneDownloaderR: automated multi-source retrieval and validation of phenotype-associated genes
by: Muneeb, Muhammad, et al.
Published: (2026)

Benchmarking Heritability Estimation Strategies Across 86 Configurations and Their Downstream Effect on Polygenic Risk Score Performance
by: Muneeb, Muhammad, et al.
Published: (2026)

AnnotateMissense: a genome-wide annotation and benchmarking framework for missense pathogenicity prediction
by: Muneeb, Muhammad, et al.
Published: (2026)

G2DR: A Genotype-First Framework for Genetics-Informed Target Prioritization and Drug Repurposing
by: Muneeb, Muhammad, et al.
Published: (2026)

Further delineation of phenotype and genotype of Kenny–Caffey syndrome type 2 (phenotype and genotype of KCS type 2)
by: Xuefei Chen, et al.
Published: (2024)

Inferring genotype-phenotype maps using attention models
by: Rijal, Krishna, et al.
Published: (2025)

inMOTIFin: a lightweight end-to-end simulation software for regulatory sequences
by: Ferenc, Katalin, et al.
Published: (2025)

Leveraging genomics and temporal high‐throughput phenotyping to enhance association mapping and yield prediction in sesame
by: Idan Sabag, et al.
Published: (2024)

Genetic analysis of predicted vegetative biomass and biomass‐related traits from digital phenotyping of strawberry
by: Cheryl Dalid, et al.
Published: (2025)

The PERPETUAL FLOWERING locus: Necessary but insufficient for genomic prediction of runnerless and other asexual reproduction phenotypes in strawberry
by: Hillel Brukental, et al.
Published: (2025)

Correction to “In silico validation revealed the role of SCN5A mutations and their genotype–phenotype correlations in Brugada syndrome”
Published: (2024)

Genome‐wide SNP discovery and genotyping delineates potential QTLs underlying major yield‐attributing traits in buckwheat
by: Samiullah Naik, et al.
Published: (2024)

Association mapping and genomic prediction for processing and end‐use quality traits in wheat ( Triticum aestivum L.)
by: Harsimardeep S. Gill, et al.
Published: (2024)

Genomic prediction of stalk lodging resistance and the associated intermediate phenotypes in maize using whole‐genome resequence and multi‐environmental data
by: Caique Machado e Silva, et al.
Published: (2025)

Effects of SNP marker density and training population size on prediction accuracy in alfalfa ( Medicago sativa L.) genomic selection
by: Hu Wang, et al.
Published: (2024)

TorchGWAS : GPU-accelerated GWAS for thousands of quantitative phenotypes
by: Zhao, Xingzhong, et al.
Published: (2026)

Genetic control of wheat flour end‐use quality and rheology by genome‐wide association studies
by: Juan Menor de Gaspar, et al.
Published: (2026)

Mutation profiling in South African patients with Cornelia de Lange syndrome phenotype
by: Heather Seymour, et al.
Published: (2024)

MicroTrace: A Lightweight R Tool for SNP-Based Pathogen Clustering in Outbreak Detection
by: Lai, Kaitao
Published: (2025)

A new phenotype of EVEN‐PLUS syndrome in a Chinese family and literature review
by: Ming Liu, et al.
Published: (2024)

Genotype–phenotype correlations in carriers of the PMS2 founder variant c.1831dup
by: Melanie Gass, et al.
Published: (2024)

Pitfalls of multi‐species SNP arrays introducing new forms of ascertainment bias
by: Abdulqader Jighly
Published: (2024)

How Effectively Can Large Language Models Connect SNP Variants and ECG Phenotypes for Cardiovascular Risk Prediction?
by: Menon, Niranjana Arun, et al.
Published: (2025)

ImmunoNX: a robust bioinformatics workflow to support personalized neoantigen vaccine trials
by: Singhal, Kartik, et al.
Published: (2025)

Exploring chromosomal variations in garden roses: Insights from high‐density SNP array data and a new tool, Qploidy
by: Cristiane H. Taniguti, et al.
Published: (2025)

Low density marker‐based effectiveness and efficiency of early‐generation genomic selection relative to phenotype‐based selection in dolichos bean ( Lablab purpureus L. Sweet)
by: Mugali Pundalik Kalpana, et al.
Published: (2025)

Mexican patient with Ellis‐van Creveld syndrome and cleft palate: Importance of functional hemizygosity and phenotype expansion
by: Luis Felipe León‐Madero, et al.
Published: (2024)

Development and implementation of nested single‐nucleotide polymorphism (SNP) assays for breeding and genetic research applications
by: Qijian Song, et al.
Published: (2024)

Effects of genotype × environment interactions on the morphological and genetic aspects of the seed characteristics of faba beans
by: Ahmed Sallam, et al.
Published: (2025)

Shotgun DNA sequencing for human identification: Dynamic SNP selection and likelihood ratio calculations accounting for errors
by: Andersen, Mikkel Meyer, et al.
Published: (2024)

A Linear-Transformer Hybrid for SNP-Based Genotype-to-Phenotype Prediction in Grapevine
by: Wang, Yibin, et al.
Published: (2026)

DuAL-Net: A Hybrid Framework for Alzheimer's Disease Prediction from Whole-Genome Sequencing via Local SNP Windows and Global Annotations
by: Lee, Eun Hye, et al.
Published: (2025)

BMFM-DNA: A SNP-aware DNA foundation model to capture variant effects
by: Li, Hongyang, et al.
Published: (2025)

Near‐infrared reflectance spectroscopy phenomic prediction can perform similarly to genomic prediction of maize agronomic traits across environments
by: Aaron J. DeSalvio, et al.
Published: (2024)

Genome‐wide association mapping for field spot blotch resistance in South Asian spring wheat genotypes
by: Umesh Kamble, et al.
Published: (2024)

Studies of genetic diversity and genome‐wide association for vitamin C content in lettuce ( Lactuca sativa L.) using high‐throughput SNP arrays
by: Inés Medina‐Lozano, et al.
Published: (2024)

Traversing the effects of ploidy changes in different Eragrostis curvula genotypes through high‐throughput RNA sequencing
by: D. F. Santoro, et al.
Published: (2026)