Martin C. Frith

The paper introduces a simple and efficient method for detecting related genetic sequences with position-varying substitution, insertion, and deletion probabilities, and demonstrates its application to identify relics of LF-SINE in the human genome.

This study identifies ancient nuclear mitochondrial DNA segments in mammalian genomes using improved sequence comparison methods, revealing previously undetected NUMTs with origins over 100 million years ago.

This study identifies new types of ancient endogenous retroviruses in the human genome, highlighting differences among related ERVs and challenges in their annotation.

This paper introduces CFC-seq and SALA to sequence non-poly(A) RNAs, identifies 39,425 novel transcriptional units, and reveals a genomic code governing enhancer RNA fate based on promoter architecture.

This study identifies technical challenges in detecting somatic recombination of repeat elements using short and long read datasets and highlights PCR-induced artifacts.

The paper introduces a simple modification to sequence alignment that sums probabilities of alternative alignments, improving detection of distant sequence relationships.

The paper identifies 25 regulatory DNA segments conserved across bilaterian animals, including some in cnidaria, controlling developmental genes and revealing a conserved regulatory system since the Precambrian.

The paper introduces a sequence-sampling method that optimizes sensitivity for sequence comparison and improves specificity for biological DNA.

The paper identifies an immune-suppressing protein in human endogenous retroviruses, showing its presence in primates and suggesting horizontal genetic transfer.

The paper introduces software tools to analyze nanopore DNA reads for complex rearrangements, focusing on distinguishing patient-specific changes from common ones.

The paper investigates somatic recombination of Alu and L1 repeat elements in human genomes, finding tissue-specific patterns and links to neurodegenerative diseases.

The paper introduces a DNA-protein homology search method that improves detection of protein fossils, finding two previously undetected transposable element types in the human genome.

The paper identifies Paleozoic protein fossils in vertebrate genomes, revealing ancient transposable element diversity and exaptation, with implications for genome evolution and regulatory function.

The paper identifies widespread transcription initiation at microsatellites across species and develops deep learning models to predict STR-associated transcription and its impact on disease variants.

The paper identifies significant absent oligomers (nullomers) in genomes and proteomes across diverse species, suggesting negative selection and potential biological significance.

The paper uses nanopore direct RNA sequencing to analyze DUX4-induced gene expression and repetitive elements in human muscle cells, identifying new fusion transcripts and splicing events.

The paper surveys tandem repeats in 16 humans using nanopore sequencing and finds disease-associated repeats are more polymorphic in the general population.

The paper introduces a sparse-seeding method for sequence similarity search using minimally-overlapping words to improve sensitivity compared to existing methods.

This paper introduces a method to fully characterize complex germline rearrangements using long DNA reads, demonstrating its ability to reconstruct intricate chromosomal translocations.

The paper identifies a GGC repeat expansion in the NOTCH2NLC gene using long-read sequencing, linking it to neuronal intranuclear inclusion disease in both familial and sporadic cases.

This paper explains how sequence alignment scores relate to probability models, showing how scores can be converted to probabilities using a temperature parameter and how different models affect alignment reliability and significance.

The paper investigates the relationship between mRNA translation initiation rate and mitochondrial localization, finding that slow initiation correlates with mitochondrial localization.

This paper develops a method to detect tandem repeat expansions from long DNA reads, identifying pathological expansions by comparing to healthy controls.

The paper introduces a pipeline to analyze complex local DNA mutations using long-read sequencing and presents a catalog of rearrangements in a human cell line.

The paper uses nanopore sequencing to accurately sequence the D4Z4 repeat array associated with FSHD, demonstrating high accuracy and potential for molecular diagnosis.