Sotabase

Career

· Assistant Professor, UC Berkeley, Department of Electrical Engineering & Computer Sciences2023–

Publications (44)

REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants.
American Journal of Human Genetics · 2016
2,227
cited
Personal transcriptome variation is poorly explained by current genomic deep learning models
bioRxiv · 2023
88
cited
Identification of Susceptibility Loci for Cutaneous Squamous Cell Carcinoma.
Journal of Investigative Dermatology · 2016
83
cited
Estimating prevalence for limb-girdle muscular dystrophy based on public sequencing databases
Genetics in Medicine · 2018
57
cited
Tissue-specific impacts of aging and genetics on gene expression patterns in humans
bioRxiv · 2021
55
cited
Cross-protein transfer learning substantially improves disease variant prediction
bioRxiv · 2023
51
cited
CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods
Genome Biology · 2022
50
cited
Two-stage Study of Familial Prostate Cancer by Whole-exome Sequencing and Custom Capture Identifies 10 Novel Genes Associated with the Risk of Prostate Cancer.
European Urology · 2020
43
cited
Cutaneous squamous cell cancer (cSCC) risk and the human leukocyte antigen (HLA) system.
Human Immunology · 2017
30
cited
FIRE: functional inference of genetic variants that regulate gene expression
Bioinform. · 2017
30
cited
Gene expression imputation identifies candidate genes and susceptibility loci associated with cutaneous squamous cell carcinoma
Nature Communications · 2018
26
cited
Critical assessment of missense variant effect predictors on disease-relevant variant data
bioRxiv · 2024
17
cited
Fine-tuning sequence-to-expression models on personal genome and transcriptome data
bioRxiv · 2024
17
cited
Genetic variants in the HLA class II region associated with risk of cutaneous squamous cell carcinoma
Cancer Immunology and Immunotherapy · 2018
13
cited
GUANinE v1.0: Benchmark Datasets for Genomic AI Sequence-to-Function Models
bioRxiv · 2023
13
cited
A Prediction Tool to Facilitate Risk-Stratified Screening for Squamous Cell Skin Cancer.
Journal of Investigative Dermatology · 2018
12
cited
Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function
Nature Genetics · 2024
11
cited
Current genomic deep learning models display decreased performance in cell type specific accessible regions
bioRxiv · 2024
9
cited
Designing Cell-Type-Specific Promoter Sequences Using Conservative Model-Based Optimization
bioRxiv · 2024
8
cited
Predicting target genes of non-coding regulatory variants with IRT
Bioinform. · 2020
7
cited
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Nilah Ioannidis | Researcher Profile | Sotabase | Sotabase