269 citations · 752 across the 16 of their papers we have counts for
17 papers
GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping
Haiyu Mao, Mohammed Alser, Mohammad Sadrosadati +6
Nanopore sequencing is a widely-used high-throughput genome sequencing technology that can sequence long fragments of a genome into raw electrical signals at low cost. Nanopore seq…
Scrooge: A Fast and Memory-Frugal Genomic Sequence Aligner for CPUs, GPUs, and ASICs
Joël Lindegger, Damla Senol Cali, Mohammed Alser +3
Pairwise sequence alignment is a very time-consuming step in common bioinformatics pipelines. Speeding up this step requires heuristics, efficient implementations, and/or hardware…
ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-Efficient Genome Analysis
Can Firtina, Kamlesh Pillai, Gurpreet S. Kalsi +10
Profile hidden Markov models (pHMMs) are widely employed in various bioinformatics applications to identify similarities between biological sequences, such as DNA or protein sequen…
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.,…
Algorithmic Improvement and GPU Acceleration of the GenASM Algorithm
Joël Lindegger, Damla Senol Cali, Mohammed Alser +2
We improve on GenASM, a recent algorithm for genomic sequence alignment, by significantly reducing its memory footprint and bandwidth requirement. Our algorithmic improvements redu…
GenStore: A High-Performance and Energy-Efficient In-Storage Computing System for Genome Sequence Analysis
Nika Mansouri Ghiasi, Jisung Park, Harun Mustafa +11
Read mapping is a fundamental, yet computationally-expensive step in many genomics applications. It is used to identify potential matches and differences between fragments (called…
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 Sequence Analysis via Efficient Hardware/Algorithm Co-Design
Damla Senol Cali
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis…
FPGA-Based Near-Memory Acceleration of Modern Data-Intensive Applications
Gagandeep Singh, Mohammed Alser, Damla Senol Cali +4
Modern data-intensive applications demand high computation capabilities with strict power constraints. Unfortunately, such applications suffer from a significant waste of both exec…
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…
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…
Understanding the Interactions of Workloads and DRAM Types: A Comprehensive Experimental Study
Saugata Ghose, Tianshi Li, Nastaran Hajinazar +2
It has become increasingly difficult to understand the complex interaction between modern applications and main memory, composed of DRAM chips. Manufacturers are now selling and pr…
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.…
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…