Variant calling and benchmarking in an era of complete human genome sequences
Genetic variant calling from DNA sequencing has enabled understanding of germline
variation in hundreds of thousands of humans. Sequencing technologies and variant-calling …
variation in hundreds of thousands of humans. Sequencing technologies and variant-calling …
Diversity and convergence of sex-determination mechanisms in teleost fish
Sexual reproduction is prevalent across diverse taxa. However, sex-determination
mechanisms are so diverse that even closely related species often differ in sex …
mechanisms are so diverse that even closely related species often differ in sex …
Telomere-to-telomere assembly of diploid chromosomes with Verkko
Abstract The Telomere-to-Telomere consortium recently assembled the first truly complete
sequence of a human genome. To resolve the most complex repeats, this project relied on …
sequence of a human genome. To resolve the most complex repeats, this project relied on …
Mouse Genome Informatics: an integrated knowledgebase system for the laboratory mouse
RM Baldarelli, CL Smith, M Ringwald, JE Richardson… - Genetics, 2024 - academic.oup.com
Abstract Mouse Genome Informatics (MGI) is a federation of expertly curated information
resources designed to support experimental and computational investigations into genetic …
resources designed to support experimental and computational investigations into genetic …
The complete sequence and comparative analysis of ape sex chromosomes
Apes possess two sex chromosomes—the male-specific Y chromosome and the X
chromosome, which is present in both males and females. The Y chromosome is crucial for …
chromosome, which is present in both males and females. The Y chromosome is crucial for …
Analysis and benchmarking of small and large genomic variants across tandem repeats
Tandem repeats (TRs) are highly polymorphic in the human genome, have thousands of
associated molecular traits and are linked to over 60 disease phenotypes. However, they …
associated molecular traits and are linked to over 60 disease phenotypes. However, they …
Robustness of cancer microbiome signals over a broad range of methodological variation
In 2020, we identified cancer-specific microbial signals in The Cancer Genome Atlas
(TCGA). Multiple peer-reviewed papers independently verified or extended our findings …
(TCGA). Multiple peer-reviewed papers independently verified or extended our findings …
Recombination between heterologous human acrocentric chromosomes
The short arms of the human acrocentric chromosomes 13, 14, 15, 21 and 22 (SAACs) share
large homologous regions, including ribosomal DNA repeats and extended segmental …
large homologous regions, including ribosomal DNA repeats and extended segmental …
Assembly of 43 human Y chromosomes reveals extensive complexity and variation
The prevalence of highly repetitive sequences within the human Y chromosome has
prevented its complete assembly to date and led to its systematic omission from genomic …
prevented its complete assembly to date and led to its systematic omission from genomic …
Genome-wide repeat landscapes in cancer and cell-free DNA
Genetic changes in repetitive sequences are a hallmark of cancer and other diseases, but
characterizing these has been challenging using standard sequencing approaches. We …
characterizing these has been challenging using standard sequencing approaches. We …