269 citations · 1.3k across the 20 of their papers we have counts for
20 papers
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…
SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping
Damla Senol Cali, Konstantinos Kanellopoulos, Joel Lindegger +15
A critical step of genome sequence analysis is the mapping of sequenced DNA fragments (i.e., reads) collected from an individual to a known linear reference genome sequence (i.e.,…
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…
Accelerating Genome Analysis: A Primer on an Ongoing Journey
Mohammed Alser, Zülal Bingöl, Damla Senol Cali +4
Genome analysis fundamentally starts with a process known as read mapping, where sequenced fragments of an organism's genome are compared against a reference genome. Read mapping i…
GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis
Damla Senol Cali, Gurpreet S. Kalsi, Zülal Bingöl +13
Genome sequence analysis has enabled significant advancements in medical and scientific areas such as personalized medicine, outbreak tracing, and the understanding of evolution. U…
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…
SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs
Mohammed Alser, Taha Shahroodi, Juan Gomez-Luna +2
Motivation: We introduce SneakySnake, a highly parallel and highly accurate pre-alignment filter that remarkably reduces the need for computationally costly sequence alignment. The…
Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm
Can Firtina, Jeremie S. Kim, Mohammed Alser +4
Long reads produced by third-generation sequencing technologies are used to construct an assembly (i.e., the subject's genome), which is further used in downstream genome analysis.…
Shouji: A Fast and Efficient Pre-Alignment Filter for Sequence Alignment
Mohammed Alser, Hasan Hassan, Akash Kumar +2
Motivation: The ability to generate massive amounts of sequencing data continues to overwhelm the processing capability of existing algorithms and compute infrastructures. In this…
Fast Characterization of Segmental Duplications in Genome Assemblies
Ibrahim Numanagić, Alim S. Gökkaya, Lillian Zhang +3
Segmental duplications (SDs), or low-copy repeats (LCR), are segments of DNA greater than 1 Kbp with high sequence identity that are copied to other regions of the genome. SDs are…
GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping Using Processing-in-Memory Technologies
Jeremie S. Kim, Damla Senol Cali, Hongyi Xin +7
Motivation: Seed location filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to id…
Nanopore Sequencing Technology and Tools for Genome Assembly: Computational Analysis of the Current State, Bottlenecks and Future Directions
Damla Senol Cali, Jeremie S. Kim, Saugata Ghose +2
Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high err…
GRIM-filter: fast seed filtering in read mapping using emerging memory technologies
Jeremie S Kim, Damla Senol, Hongyi Xin +7
Motivation: Seed filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify ge…
MAGNET: Understanding and Improving the Accuracy of Genome Pre-Alignment Filtering
Mohammed Alser, Onur Mutlu, Can Alkan
In the era of high throughput DNA sequencing (HTS) technologies, calculating the edit distance (i.e., the minimum number of substitutions, insertions, and deletions between a pair…
GateKeeper: A New Hardware Architecture for Accelerating Pre-Alignment in DNA Short Read Mapping
Mohammed Alser, Hasan Hassan, Hongyi Xin +3
Motivation: High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments -- called short reads -- that cause significant computational burde…
Coinami: A Cryptocurrency with DNA Sequence Alignment as Proof-of-work
Atalay M. Ileri, Halil I. Ozercan, Alper Gundogdu +3
Rate of growth of the amount of data generated using the high throughput sequencing (HTS) platforms now exceeds the growth stipulated by Moore's Law. The HTS data is expected to su…
Optimal Seed Solver: Optimizing Seed Selection in Read Mapping
Hongyi Xin, Richard Zhu, Sunny Nahar +5
Motivation: Optimizing seed selection is an important problem in read mapping. The number of non-overlapping seeds a mapper selects determines the sensitivity of the mapper while t…
Genome Sequencing Highlights Genes Under Selection and the Dynamic Early History of Dogs
Adam H. Freedman, Rena M. Schweizer, Ilan Gronau +27
To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we analyzed novel high-quality genome sequences of three gray wolves, one…