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View article: Proteome-wide model for human disease genetics
Proteome-wide model for human disease genetics Open
Missense variants remain a challenge in genetic interpretation owing to their subtle and context-dependent effects. Although current prediction models perform well in known disease genes, their scores are not calibrated across the proteome…
View article: A Genomic Language Model for Zero-Shot Prediction of Promoter Variant Effects
A Genomic Language Model for Zero-Shot Prediction of Promoter Variant Effects Open
Disease-associated genetic variants occur extensively in noncoding regions like promoters, but current methods focus primarily on single nucleotide variants (SNVs) that typically have small regulatory effect sizes. Expanding beyond single …
View article: Deep generative modeling of the human proteome reveals over a hundred novel genes involved in rare genetic disorders
Deep generative modeling of the human proteome reveals over a hundred novel genes involved in rare genetic disorders Open
Identifying causal mutations accelerates genetic disease diagnosis, and therapeutic development. Missense variants present a bottleneck in genetic diagnoses as their effects are less straightforward than truncations or nonsense mutations. …
View article: ProteinGym: Large-Scale Benchmarks for Protein Design and Fitness Prediction
ProteinGym: Large-Scale Benchmarks for Protein Design and Fitness Prediction Open
Predicting the effects of mutations in proteins is critical to many applications, from understanding genetic disease to designing novel proteins that can address our most pressing challenges in climate, agriculture and healthcare. Despite …
View article: Proteome-wide model for human disease genetics
Proteome-wide model for human disease genetics Open
Identifying variants driving disease accelerates both genetic diagnosis and therapeutic development, but missense variants still present a bottleneck as their effects are less straightforward than truncations or nonsense mutations. While c…
View article: Pervasiveness of HLA allele-specific expression loss across tumor types
Pervasiveness of HLA allele-specific expression loss across tumor types Open
Background Efficient presentation of mutant peptide fragments by the human leukocyte antigen class I (HLA-I) genes is necessary for immune-mediated killing of cancer cells. According to recent reports, patient HLA-I genotypes can impact th…
View article: Additional file 2 of Pervasiveness of HLA allele-specific expression loss across tumor types
Additional file 2 of Pervasiveness of HLA allele-specific expression loss across tumor types Open
Additional file 2. Additional tables from the results of the association between HLA-I ASE loss and microsatellite instability, nonsense and missense mutations. Table S1. TCGA case numbers broken down by microsatellite instability and HLA-…
View article: HLA allele-specific expression loss in tumors can shorten survival and hinder immunotherapy
HLA allele-specific expression loss in tumors can shorten survival and hinder immunotherapy Open
Efficient presentation of aberrant peptide fragments by the human leukocyte antigen class I (HLA-I) genes is necessary for immune detection and killing of cancer cells. Patient HLA-I genotypes are known to impact the efficacy of cancer imm…
View article: arcasHLA: high-resolution HLA typing from RNAseq
arcasHLA: high-resolution HLA typing from RNAseq Open
Motivation The human leukocyte antigen (HLA) locus plays a critical role in tissue compatibility and regulates the host response to many diseases, including cancers and autoimmune di3orders. Recent improvements in the quality and accessibi…
View article: arcasHLA: high resolution HLA typing from RNA seq
arcasHLA: high resolution HLA typing from RNA seq Open
Human leukocyte antigen (HLA) locus makes up the major compatibility complex (MHC) and plays a critical role in host response to disease, including cancers and autoimmune disorders. In the clinical setting, HLA typing is necessary for dete…