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PSAP-Genomic-Regions: A Method Leveraging Population Data to Prioritize Coding and Non-Coding Variants in Whole Genome Sequencing for Rare Disease Diagnosis

Marie-Sophie, who was a visiting scholar in the Conrad lab last summer, just had had paper published on extending PSAP to the non-coding genomes in Genetic Epidemiology. Congratulations! Abstract The introduction of Next-Generation Sequencing technologies in the clinics has improved rare disease diagnosis. Nonetheless, for very heterogeneous or very rare diseases, more than half of […]

The human infertility single-cell testis atlas (HISTA): an interactive molecular scRNA-Seq reference of the human testis

Eisa’s new paper is now available online in Andrology. Congratulations! Abstract Background: Single-cell RNA-seq (scRNA-Seq) has been widely adopted to study gene expression of the human testis. Several datasets of scRNA-Seq from human testis have been generated from different groups processed with different informatics pipelines. An integrated atlas of scRNA-Seq expression constructed from multiple donors, developmental […]

A naturally occurring variant of MBD4 causes maternal germline hypermutation in primates

Alex’s paper is now available online in Genome Research. Congratulations! Abstract As part of an ongoing genome sequencing project at the Oregon National Primate Research Center, we identified a rhesus macaque with a rare homozygous frameshift mutation in the gene methyl-CpG binding domain 4, DNA glycosylase (MBD4). MBD4 is responsible for the repair of C […]

Consensus label propagation with graph convolutional networks for single-cell RNA sequencing cell type annotation

Daniel’s paper is now available online in Bioinformatics. Congratulations! Abstract Motivation: Single-cell RNA sequencing (scRNA-seq) data, annotated by cell type, is useful in a variety of downstream biological applications, such as profiling gene expression at the single-cell level. However, manually assigning these annotations with known marker genes is both time-consuming and subjective. Results: We present a Graph […]

The origins and functional effects of postzygotic mutations throughout the human life span

Former grad student Nicole’s paper on detecting and analyzing PZMs in GTEx data is now available online in Science. Congratulations! Abstract Postzygotic mutations (PZMs) begin to accrue in the human genome immediately after fertilization, but how and when PZMs affect development and lifetime health remain unclear. To study the origins and functional consequences of PZMs, […]

Diverse monogenic subforms of human spermatogenic failure

Our main GEMINI paper is now available online in Nature Communications. Congratulations to all! Abstract Non-obstructive azoospermia (NOA) is the most severe form of male infertility and typically incurable. Defining the genetic basis of NOA has proven challenging, and the most advanced classification of NOA subforms is not based on genetics, but simple description of […]

SATINN: An automated neural network-based classification of testicular sections allows for high-throughput histopathology of mouse mutants

Ran and Ana’s paper is now available online in Bioinformatics. Congratulations! Abstract Motivation: The mammalian testis is a complex organ with a cellular composition that changes smoothly and cyclically in normal adults. While testis histology is already an invaluable tool for identifying and describing developmental differences in evolution and disease, methods for standardized, digital image analysis […]