17 citations · 32 across the 3 of their papers we have counts for
8 papers
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…
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 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…