Genome Rearrangement Algorithms

Maximum Parsimony Reconciliation in the DTLOR Model

The paper extends the DTL model to account for gene family entry outside the species tree and genomic rearrangements, introducing an efficient algorithm for maximum parsimony reconciliation and preliminary integration into a tool for reconstructing genomic island histories.

Short-range template switching in great ape genomes explored using a pair hidden Markov model

The paper introduces a pair hidden Markov model to detect short-range template switch mutations in great ape genomes and shows their prevalence in evolutionary history.

State-of-the-art structural variant calling: What went conceptually wrong and how to fix it?

This paper identifies conceptual issues in structural variant calling and proposes a graph-based approach to resolve them, demonstrating accuracy on yeast genomes.

Longest Order Conserved Exemplar Subsequences

The paper introduces an algorithm to find longest common exemplar subsequences between genomes, validated on human and gorilla chromosomes, identifying conserved pseudo genes.

rearrvisr: an R package to detect, classify, and visualize genome rearrangements

rearrvisr detects, classifies, and visualizes genome rearrangements by projecting them onto a reference genome, achieving high precision and recall on simulated data.

Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements

Smash++ identifies genomic rearrangements without sequence alignment, using data compression, and validates results against existing methods and FISH analysis.

Phylogenetic reconstruction based on synteny block and gene adjacencies

PhyChro reconstructs phylogenetic trees using synteny breakpoints and gene adjacencies, achieving high accuracy and speed on vertebrate and yeast genomes.

Short-range, orientation-reversing template-switching events occur at a high frequency in the human and yeast genomes

The paper develops SCARR to identify DNA rearrangements and finds high-frequency short-range orientation-reversing events in human and yeast genomes, likely via template-switching during replication.

SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies

SyRI identifies genomic rearrangements and local variations from whole-genome assemblies by analyzing co-linear regions and classifying structural differences.

Recovering rearranged cancer chromosomes from karyotype graphs

This paper introduces a method to recover rearranged cancer chromosomes from karyotype graphs, demonstrating its effectiveness on a prostate cancer dataset.

Revisiting the landscape of evolutionary breakpoints across human genome using multi-way comparison

The paper identifies human lineage-specific evolutionary breakpoints and refractory regions using multi-way conservation alignments, revealing associations with biological processes and developmental genes.

Prefix Block-Interchanges on Binary and Ternary Strings

The paper presents upper bounds and algorithms for sorting binary and ternary strings using prefix block-interchange operations and provides a classification for ternary strings based on required operations.

Estimation of Rearrangement Break Rates Across the Genome

The paper estimates double-strand break rates across the genome in Neurospora crassa and finds higher rates in subtelomeric regions associated with novel gene evolution.

deStruct: Accurate Rearrangement Detection using Breakpoint Specific Realignment

deStruct improves breakpoint prediction by using specific realignment and clustering, achieving higher sensitivity and specificity than existing tools on simulated data.

Rearrangement Scenarios Guided By Chromatin Structure

The paper evaluates a model for inferring ancestral rearrangement scenarios by correlating Hi-C data clustering quality with rearrangement scenario accuracy between Drosophila species.

SplitThreader: Exploration and analysis of rearrangements in cancer genomes

SplitThreader analyzes genomic rearrangements and copy number changes in cancer genomes to identify gene fusions and variant categories.