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Finding Motifs in Biological Sequences Using the Micron Automata Processor
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1007/11682462_69openalex-snapshot
RISOTTO: Fast Extraction of Motifs with Mismatches
inferredcites →https://doi.org/10.1007/978-3-540-45078-8_5openalex-snapshot
Toward Optimal Motif Enumeration
inferredcites →https://doi.org/10.1016/0022-2836(70)90150-6openalex-snapshot
A restriction enzyme from Hemophilus influenzae
inferredcites →https://doi.org/10.1016/b978-0-12-131200-8.50032-0openalex-snapshot
A Restriction Enzyme from Hemophilus influenzae II. Base Sequence of the Recognition Site
inferredcites →https://doi.org/10.1016/s0304-3975(03)00320-7openalex-snapshot
On the complexity of finding common approximate substrings
inferredcites →https://doi.org/10.1089/cmb.2005.12.1117openalex-snapshot
Exact Algorithms for Planted Motif Problems
inferredcites →https://doi.org/10.1093/bioinformatics/15.7.563openalex-snapshot
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences.
inferredcites →https://doi.org/10.1093/bioinformatics/18.suppl_1.s354openalex-snapshot
Finding composite regulatory patterns in DNA sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btg1072openalex-snapshot
Finding subtle motifs by branching from sample strings
inferredcites →https://doi.org/10.1109/iccabs.2012.6182627openalex-snapshot
PMS6: A fast algorithm for motif discovery
inferredcites →https://doi.org/10.1109/tc.2011.129openalex-snapshot
High-Performance and Compact Architecture for Regular Expression Matching on FPGA
inferredcites →https://doi.org/10.1109/tcbb.2007.70241openalex-snapshot
Fast and Practical Algorithms for Planted (l, d) Motif Search
inferredcites →https://doi.org/10.1109/tpds.2012.116openalex-snapshot
MIN-MAX: A Counter-Based Algorithm for Regular Expression Matching
inferredcites →https://doi.org/10.1109/tpds.2014.8openalex-snapshot
An Efficient and Scalable Semiconductor Architecture for Parallel Automata Processing
inferredcites →https://doi.org/10.1126/science.8211139openalex-snapshot
Detecting Subtle Sequence Signals: a Gibbs Sampling Strategy for Multiple Alignment
inferredcites →https://doi.org/10.1142/9781860947322_0026openalex-snapshot
VOTING ALGORITHMS FOR DISCOVERING LONG MOTIFS
inferredcites →https://doi.org/10.1142/9781860947322_0027openalex-snapshot
A HIGHLY SCALABLE ALGORITHM FOR THE EXTRACTION OF CIS-REGULATORY REGIONS
inferredcites →https://doi.org/10.1145/1477942.1477948openalex-snapshot
Compact architecture for high-throughput regular expression matching on FPGA
inferredcites →https://doi.org/10.1145/322326.322327openalex-snapshot
The Compilation of Regular Expressions into Integrated Circuits
inferredcites →https://doi.org/10.1145/332306.332553openalex-snapshot
Extracting structured motifs using a suffix tree—algorithms and application to promoter consensus identification
inferredcites →https://doi.org/10.1145/565196.565222openalex-snapshot
Finding motifs in the twilight zone
inferredcites →https://doi.org/10.1186/1471-2105-12-410openalex-snapshot
PMS5: an efficient exact algorithm for the (ℓ, d)-motif finding problem
inferredcites →https://doi.org/10.1186/1471-2105-15-34openalex-snapshot
Efficient sequential and parallel algorithms for planted motif search
inferredcites →https://doi.org/10.1371/journal.pone.0041425openalex-snapshot
qPMS7: A Fast Algorithm for Finding (ℓ, d)-Motifs in DNA and Protein Sequences
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/cpe.4037openalex-snapshot
Combinatorial optimization of DNA sequence analysis on heterogeneous systems
inferred← citeshttps://doi.org/10.1007/978-3-319-41321-1_11openalex-snapshot
Towards Machine Learning on the Automata Processor
inferred← citeshttps://doi.org/10.1016/j.jpdc.2018.01.010openalex-snapshot
Interval stabbing on the Automata Processor
inferred← citeshttps://doi.org/10.1016/j.nima.2016.06.119openalex-snapshot
Using the automata processor for fast pattern recognition in high energy physics experiments—A proof of concept
inferred← citeshttps://doi.org/10.1016/j.sysarc.2019.07.006openalex-snapshot
A survey on applications and architectural-optimizations of Micron’s Automata Processor
inferred← citeshttps://doi.org/10.1038/srep07813openalex-snapshot
qPMS9: An Efficient Algorithm for Quorum Planted Motif Search
inferred← citeshttps://doi.org/10.1109/acssc.2016.7869105openalex-snapshot
Feature extraction and image retrieval on an automata structure
inferred← citeshttps://doi.org/10.1109/asap.2019.000-7openalex-snapshot
An Overlay Architecture for Pattern Matching
inferred← citeshttps://doi.org/10.1109/bigdata.2015.7363776openalex-snapshot
Regular expression acceleration on the micron automata processor: Brill tagging as a case study
inferred← citeshttps://doi.org/10.1109/bigdata.2016.7840617openalex-snapshot
Entity resolution acceleration using the automata processor
inferred← citeshttps://doi.org/10.1109/bigdata.2017.8257936openalex-snapshot
Robotomata: A framework for approximate pattern matching of big data on an automata processor
inferred← citeshttps://doi.org/10.1109/globalsip.2017.8309056openalex-snapshot
Classifying images in a histopathological dataset using the cumulative distribution transform on an automata architecture
inferred← citeshttps://doi.org/10.1109/hipc.2017.00053openalex-snapshot
A Memory-Efficient GPU Method for Hamming and Levenshtein Distance Similarity
inferred← citeshttps://doi.org/10.1109/hpca.2018.00068openalex-snapshot
Searching for Potential gRNA Off-Target Sites for CRISPR/Cas9 Using Automata Processing Across Different Platforms
inferred← citeshttps://doi.org/10.1109/hpca.2018.00069openalex-snapshot
Characterizing and Mitigating Output Reporting Bottlenecks in Spatial Automata Processing Architectures
inferred← citeshttps://doi.org/10.1109/ia3.2016.008openalex-snapshot
Parallel Interval Stabbing on the Automata Processor
inferred← citeshttps://doi.org/10.1109/icosc.2015.7050812openalex-snapshot
Brill tagging on the Micron Automata Processor
inferred← citeshttps://doi.org/10.1109/icpads.2016.0139openalex-snapshot
Parallel Gene Upstream Comparison via Multi-Level Hash Tables on GPU
inferred← citeshttps://doi.org/10.1109/icpp.2016.30openalex-snapshot
Programming Techniques for the Automata Processor
inferred← citeshttps://doi.org/10.1109/iiswc.2016.7581271openalex-snapshot
ANMLzoo: a benchmark suite for exploring bottlenecks in automata processing engines and architectures
inferred← citeshttps://doi.org/10.1109/iiswc.2018.8573482openalex-snapshot
AutomataZoo: A Modern Automata Processing Benchmark Suite
inferred← citeshttps://doi.org/10.1109/ipdps.2015.101openalex-snapshot
Association Rule Mining with the Micron Automata Processor
inferred← citeshttps://doi.org/10.1109/ipdps.2016.116openalex-snapshot
Algorithmic Techniques for Solving Graph Problems on the Automata Processor
inferred← citeshttps://doi.org/10.1109/ipdps53621.2022.00053openalex-snapshot
GSpecPal: Speculation-Centric Finite State Machine Parallelization on GPUs
inferred← citeshttps://doi.org/10.1109/micro.2018.00012openalex-snapshot
CSE: Parallel Finite State Machines with Convergence Set Enumeration
inferred← citeshttps://doi.org/10.1109/micro.2018.00078openalex-snapshot
Architectural Support for Efficient Large-Scale Automata Processing
inferred← citeshttps://doi.org/10.1109/padsw.2018.8644852openalex-snapshot
A Compiler Framework for Fixed-Topology Non-Deterministic Finite Automata on SIMD Platforms
inferred← citeshttps://doi.org/10.1109/reconfig.2017.8279779openalex-snapshot
A Dynamically Reconfigurable Automata Processor Overlay
inferred← citeshttps://doi.org/10.1109/tcbb.2015.2430313openalex-snapshot
Discovering Motifs in Biological Sequences Using the Micron Automata Processor
inferred← citeshttps://doi.org/10.1109/tpds.2018.2869736openalex-snapshot
Portable Programming with RAPID
inferred← citeshttps://doi.org/10.1145/2830772.2830809openalex-snapshot
Fast support for unstructured data processing
inferred← citeshttps://doi.org/10.1145/2872362.2872393openalex-snapshot
RAPID Programming of Pattern-Recognition Processors
inferred← citeshttps://doi.org/10.1145/2903150.2903172openalex-snapshot
Sequential pattern mining with the Micron automata processor
inferred← citeshttps://doi.org/10.1145/2954679.2872393openalex-snapshot
RAPID Programming of Pattern-Recognition Processors
inferred← citeshttps://doi.org/10.1145/2954680.2872393openalex-snapshot
RAPID Programming of Pattern-Recognition Processors
inferred← citeshttps://doi.org/10.1145/2968456.2976763openalex-snapshot
An overview of micron's automata processor
inferred← citeshttps://doi.org/10.1145/2980024.2872393openalex-snapshot
RAPID Programming of Pattern-Recognition Processors
inferred← citeshttps://doi.org/10.1145/3079079.3079082openalex-snapshot
Enabling scalability-sensitive speculative parallelization for FSM computations
inferred← citeshttps://doi.org/10.1145/3079079.3079100openalex-snapshot
Demystifying automata processing
inferred← citeshttps://doi.org/10.1145/3297858.3304066openalex-snapshot
Debugging Support for Pattern-Matching Languages and Accelerators
inferred← citeshttps://doi.org/10.1145/3358200openalex-snapshot
Efficient Tracing Methodology Using Automata Processor
inferred← citeshttps://doi.org/10.1145/3373376.3378471openalex-snapshot
Why GPUs are Slow at Executing NFAs and How to Make them Faster
inferred← citeshttps://doi.org/10.1145/3373376.3378503openalex-snapshot
Accelerating Legacy String Kernels via Bounded Automata Learning
inferred← citeshttps://doi.org/10.1145/3377456openalex-snapshot
Reliability Analysis for Unreliable FSM Computations
inferred← citeshttps://doi.org/10.1145/3445814.3446705openalex-snapshot
Scalable FSM parallelization via path fusion and higher-order speculation
inferred← citeshttps://doi.org/10.1145/3466752.3480934openalex-snapshot
Sunder: Enabling Low-Overhead and Scalable Near-Data Pattern Matching Acceleration
inferred← citeshttps://doi.org/10.1145/3617232.3624848openalex-snapshot
ngAP: Non-blocking Large-scale Automata Processing on GPUs
inferred← citeshttps://doi.org/10.1145/3649329.3657378openalex-snapshot
ALVEARE: a Domain-Specific Framework for Regular Expressions
inferred← citeshttps://doi.org/10.1145/3676642.3736126openalex-snapshot
Hopps: Leveraging Sparsity to Accelerate Automata Processing
inferred← citeshttps://doi.org/10.1145/3748646openalex-snapshot
Towards Scalable and Non-blocking Automata Processing on GPUs with ngAP
inferred← citeshttps://doi.org/10.14257/ijgdc.2016.9.4.05openalex-snapshot
Automata Processor Architecture and Applications: A Survey
inferred← citeshttps://doi.org/10.1587/transinf.2017edp7051openalex-snapshot
Accelerating Weeder: A DNA Motif Search Tool Using the Micron Automata Processor and FPGA
inferred← citeshttps://doi.org/10.18130/v33970openalex-snapshot
Brill Tagging on the Micron Automata Processor
inferred← citeshttps://doi.org/10.18130/v3d50ropenalex-snapshot
Cellular Automata on the Micron Automata Processor
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IP on AP: Exploring Image Processing on the Automata Processor
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An Assessment of Algorithms for Deriving Failure Deterministic Finite Automata
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Time-division Multiplexing Automata Processor
inferred← citeshttps://doi.org/10.23919/date51398.2021.9474249openalex-snapshot
LAP: A Lightweight Automata Processor for Pattern Matching Tasks
inferred← citeshttps://doi.org/10.32469/10355/66808openalex-snapshot
Homology sequence analysis using GPU acceleration
inferred← citeshttps://doi.org/10.48550/arxiv.2007.06273openalex-snapshot
RNA-2QCFA: Evolving Two-way Quantum Finite Automata with Classical States for RNA Secondary Structures
inferred← citeshttps://doi.org/10.5555/3018843.3018846openalex-snapshot
Parallel interval stabbing on the automata processor
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