Diploid genome assemblies are now routinely available, but most read aligners were designed for haploid references, which have long been the gold standard. When reads are aligned to a diploid assembly...

The Symposium on Experimental Algorithms explores the role of experimentation and engineering techniques in the design and evaluation of algorithms and data structures.

Existing notions of pangenome coordinates rely on hard-to-compute multiple sequence alignments. On the other hand, pangenome-wide exact unique matches (multi-MUMs) can be computed efficiently, and rep...

Existing notions of pangenome coordinates rely on hard-to-compute multiple sequence alignments. On the other hand, pangenome-wide exact unique matches (multi-MUMs) can be computed efficiently, and represent conserved stretches of columns in the underlying MSA. We introduce Shredtools, which uses mul …

With improvements in sequencing and assembly have come many high-quality telomere-to-telomere assemblies and reference pangenomes. However, the long-read sequencing recipes needed for high quality ass...

Existing notions of pangenome coordinates rely on hard-to-compute multiple sequence alignments. On the other hand, pangenome-wide exact unique matches (multi-MUMs) can be computed efficiently, and rep...

Founded in 1850, The University of Utah is the flagship institution of higher learning in Utah, and offers over 100 undergraduate and more than 90 graduate degree programs to over 30,000 students. Uni...

Openings

Evolution has shaped the genetic code, with subtle pressures leading to preferences for some synonymous codons over others. Codons are translated at different speeds by the ribosome, imposing constrai...