Awesome Genome Analysis

A collection of papers on awesome genome analysis, e.g., architectures, systems, and algorithms.

• Architecture
• HPC System
• Algorithm
• Future System

Architecture

Genome analysis architecture at top-tier conferences (e.g., HPCA, ASPLOS, ISCA, MICRO, ISSCC, DAC).

Year	Conf.	Paper	Affiliation
2018	HPCA	Searching for Potential gRNA Off-Target Sites for CRISPR/Cas9 Using Automata Processing Across Different Platforms	UVA
2018	ASPLOS	Darwin: A Genomics Co-processor Provides up to 15000X Acceleration on Long Read Assembly	Stanford University
2018	ISCA	GenAx: A Genome Sequencing Accelerator	UofM
2019	HPCA	Darwin-WGA: A Co-processor Provides Increased Sensitivity in Whole Genome Alignments with High Speed	Stanford University
2019	HPCA	FPGA Accelerated INDEL Realignment in the Cloud	UCB
2019	MICRO	GenCache: Leveraging In-Cache Operators for Efficient Sequence Alignment	University of Utah
2019	MICRO	MEDAL: Scalable DIMM-based Near Data Processing Accelerator for DNA Seeding Algorithm	UCSB
2020	ISCA	Genesis: A Hardware Acceleration Framework for Genomic Data Analysis	SNU
2020	MICRO	SeedEx: A Genome Sequencing Accelerator for Optimal Alignments in Subminimal Space	UofM
2020	MICRO	GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis	ETHZ
2020	ISSCC	A Fully Integrated Genetic Variant Discovery SoC for Next-Generation Sequencing	NTU
2020	DAC	PIM-Assembler: A Processing-in-Memory Platform for Genome Assembly	Arizona State University
2021	HPCA	EXMA: A Genomics Accelerator for Exact-Matching	Indiana University Bloomington
2021	ISCA	Accelerated Seeding for Genome Sequence Alignment with Enumerated Radix Trees	UofM
2021	ISCA	Sieve: Scalable In-situ DRAM-based Accelerator Designs for Massively Parallel k-mer Matching	UVA
2021	MICRO	SquiggleFilter: An Accelerator for Portable Virus Detection	UofM
2022	ASPLOS	GenStore: a high-performance in-storage processing system for genome sequence analysis	ETHZ
2022	ASPLOS	ProSE: the architecture and design of a protein discovery engine	Duke
2022	ISCA	SeGraM: a universal hardware accelerator for genomic sequence-to-graph and sequence-to-sequence mapping	ETHZ
2022	ISCA	BioHD: an efficient genome sequence search platform using HyperDimensional memorization	UCI
2022	ISCA	EDAM: Edit Distance tolerant Approximate Matching content addressable memory	Technion-Israel Institute of Technology
2022	MICRO	BEACON: Scalable Near-Data-Processing Accelerators for Genome Analysis near Memory Pool with the CXL Support	UCSB
2022	MICRO	GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping	ETHZ
2023	HPCA	NvWa: Enhancing Sequence Alignment Accelerator Throughput via Hardware Scheduling	ICT, CAS
2023	ISCA	GenDP: A Framework of Dynamic Programming Acceleration for Genome Sequencing Analysis	UofM
2023	MICRO	Swordfish: A Framework for Evaluating Deep Neural Network-based Basecalling using Computation-In-Memory with Non-Ideal Memristors	ETHZ
2023	MICRO	DASH-CAM: Dynamic Approximate SearcH Content Addressable Memory for genome classification	Bar-Ilan University
2023	MICRO	CASA: An Energy-Efficient and High-Speed CAM-based SMEM Seeding Accelerator for Genome Alignment	THU
2023	MICRO	GMX: Instruction Set Extensions for Fast, Scalable, and Efficient Genome Sequence Alignment	BSC
2023	ISSCC	A Fully Integrated End-to-End Genome Analysis Accelerator for Next-Generation Sequencing	NTU
2023	DAC	Invited: Accelerating Genome Analysis via Algorithm-Architecture Co-Design	ETHZ
2023	DAC	ASMCap: An Approximate String Matching Accelerator for Genome Sequence Analysis Based on Capacitive Content Addressable Memory	THU
2023	DAC	MeG2: In-Memory Acceleration for Genome Graphs Analysis	HUST
2023	DAC	UpPipe: A Novel Pipeline Management on In-Memory Processors for RNA-seq Quantification	National Cheng Kung University
2024	HPCA	TALCO: Tiling Genome Sequence Alignment Using Convergence of Traceback Pointers	UCSD
2024	ASPLOS	Harp: Leveraging Quasi-Sequential Characteristics to Accelerate Sequence-to-Graph Mapping of Long Reads	THU
2024	ISCA	QUETZAL: Vector Acceleration Framework For Modern Genome Sequence Analysis	BSC
2024	ISCA	BLESS: Bandwidth and Locality Enhanced SMEM Seeding Acceleration for DNA Sequencing	KAIST
2024	ISCA	MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing	ETHZ

HPC System

Genome analysis systems at top-tier conferences (e.g., PPoPP, SC).

Year	Conf.	Paper	Affiliation
2018	PPoPP	High-performance genomic analysis framework with in-memory computing	ICT, CAS
2018	SC	Extreme scale de novo metagenome assembly	Intel
2018	SC	Optimizing high performance distributed memory parallel hash tables for DNA k-mer counting	Georgia Tech
2020	SC	Distributed many-to-many protein sequence alignment using sparse matrices	Lawrence Berkeley National Laboratory
2020	SC	SegAlign: a scalable GPU-based whole genome aligner	Stanford
2021	PPoPP	Asynchrony versus bulk-synchrony for a generalized N-body problem from genomics	UCB
2021	SC	Accelerating large scale de novo metagenome assembly using GPUs	Lawrence Berkeley National Laboratory
2021	SC	FastZ: accelerating gapped whole genome alignment on GPUs	Purdue University
2021	SC	High-throughput virtual screening of small molecule inhibitors for SARS-CoV-2 protein targets with deep fusion models	Lawrence Livermore National Laboratory
2022	SC	Extreme-Scale Many-Against-Many Protein Similarity Search	Lawrence Berkeley National Laboratory
2023	PPoPP	High-Performance and Scalable Agent-Based Simulation with BioDynaMo	ETHZ
2023	SC	Space Efficient Sequence Alignment for SRAM-Based Computing: X-Drop on the Graphcore IPU	Simula Research Laboratory
2024	PPoPP	AGAThA: Fast and Efficient GPU Acceleration of Guided Sequence Alignment for Long Read Mapping	Seoul National University
2024	PPoPP	FastFold: Optimizing AlphaFold Training and Inference on GPU Clusters	National University of Singapore

Algorithm

Genome analysis algorithm at top-tier journals (e.g., Bioinformatics).

Year	Journal	Paper	Affiliation
2009	Bioinformatics	Fast and accurate short read alignment with Burrows-Wheeler transform	Wellcome Trust Sanger Institute
2010	Bioinformatics	Fast and accurate long-read alignment with Burrows–Wheeler transform	Wellcome Trust Sanger Institute
2010	arXiv	Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM	Broad Institute
2022	Bioinformatics	BWA-MEME: BWA-MEM emulated with a machine learning approach	KAIST

Future System

Future genome analysis system at top-tier journals (e.g., Nature, Science).

Year	Journal	Paper	Affiliation
2021	Nature Materials	Random access DNA memory using Boolean search in an archival file storage system	MIT
2023	Nature	DNA-based programmable gate arrays for general-purpose DNA computing	SJTU
2024	Nature	Parallel molecular data storage by printing epigenetic bits on DNA	PKU

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