269 citations · 3.4k across the 186 of their papers we have counts for
12 papers · 1 filter
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering
Meryem Banu Cavlak, Gagandeep Singh, Mohammed Alser +6
Basecalling is an essential step in nanopore sequencing analysis where the raw signals of nanopore sequencers are converted into nucleotide sequences, i.e., reads. State-of-the-art…
Going From Molecules to Genomic Variations to Scientific Discovery: Intelligent Algorithms and Architectures for Intelligent Genome Analysis
Mohammed Alser, Joel Lindegger, Can Firtina +5
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enoug…
FastRemap: A Tool for Quickly Remapping Reads between Genome Assemblies
Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak +3
A genome read data set can be quickly and efficiently remapped from one reference to another similar reference (e.g., between two reference versions or two similar species) using a…
BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches in Genome Analysis
Can Firtina, Jisung Park, Mohammed Alser +8
Generating the hash values of short subsequences, called seeds, enables quickly identifying similarities between genomic sequences by matching seeds with a single lookup of their h…
Technology dictates algorithms: Recent developments in read alignment
Mohammed Alser, Jeremy Rotman, Kodi Taraszka +13
Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. M…
AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes
Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak +5
AirLift is the first read remapping tool that enables users to quickly and comprehensively map a read set, that had been previously mapped to one reference genome, to another simil…