Heidi J. Sofia
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View article: FAVOR: functional annotation of variants online resource and annotator for variation across the human genome
FAVOR: functional annotation of variants online resource and annotator for variation across the human genome Open
Large biobank-scale whole genome sequencing (WGS) studies are rapidly identifying a multitude of coding and non-coding variants. They provide an unprecedented resource for illuminating the genetic basis of human diseases. Variant functiona…
View article: FAVOR: Functional Annotation of Variants Online Resource and Annotator for Variation across the Human Genome
FAVOR: Functional Annotation of Variants Online Resource and Annotator for Variation across the Human Genome Open
Large-scale whole genome sequencing (WGS) studies and biobanks are rapidly generating a multitude of coding and non-coding variants. They provide an unprecedented resource for illuminating the genetic basis of human diseases. Variant funct…
View article: SCOR: A secure international informatics infrastructure to investigate COVID-19
SCOR: A secure international informatics infrastructure to investigate COVID-19 Open
Global pandemics call for large and diverse healthcare data to study various risk factors, treatment options, and disease progression patterns. Despite the enormous efforts of many large data consortium initiatives, scientific community st…
View article: Ultra-Fast Homomorphic Encryption Models enable Secure Outsourcing of Genotype Imputation
Ultra-Fast Homomorphic Encryption Models enable Secure Outsourcing of Genotype Imputation Open
Genotype imputation is a fundamental step in genomic data analysis such as GWAS, where missing variant genotypes are predicted using the existing genotypes of nearby ‘tag’ variants. Imputation greatly decreases the genotyping cost and prov…
View article: Publisher Correction: Butler enables rapid cloud-based analysis of thousands of human genomes
Publisher Correction: Butler enables rapid cloud-based analysis of thousands of human genomes Open
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
View article: Comprehensive Molecular Characterization of the Hippo Signaling Pathway in Cancer
Comprehensive Molecular Characterization of the Hippo Signaling Pathway in Cancer Open
Hippo signaling has been recognized as a key tumor suppressor pathway. Here, we perform a comprehensive molecular characterization of 19 Hippo core genes in 9,125 tumor samples across 33 cancer types using multidimensional "omic" data from…
View article: A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily
A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily Open
We present an integromic analysis of gene alterations that modulate transforming growth factor β (TGF-β)-Smad-mediated signaling in 9,125 tumor samples across 33 cancer types in The Cancer Genome Atlas (TCGA). Focusing on genes that encode…
View article: Visualization and Integrated Data Mining of Disparate Information
Visualization and Integrated Data Mining of Disparate Information Open
The volumes and diversity of information in the discovery, development, and business processes within the chemical and life sciences industries require new approaches for analysis. Traditional list- or spreadsheet-based methods are easily …
View article: The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma
The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma Open
Renal cell carcinoma (RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic…