- Editorial from the Editor-in-Chief
- High-Performance Phylogenetic Inference
- Skip the Intersection: Quickly Counting Common Neighbors on Shared-Memory Systems
- Tailoring parallel alternating criteria search for domain specific MIPs: Application to maritime inventory routing
- A New Algorithmic Model for Graph Analysis of Streaming Data
- Accelerating GPU betweenness centrality
- Alternating criteria search: a parallel large neighborhood search algorithm for mixed integer programs
- Benchmarking for Graph Clustering and Partitioning
- Fast and Adaptive List Intersections on the GPU
- Hornet: An Efficient Data Structure for Dynamic Sparse Graphs and Matrices on GPUs
- Incrementally updating Katz centrality in dynamic graphs
- Introduction to HiCOMB 2018
- Logarithmic Radix Binning and Vectorized Triangle Counting
- Massive-scale Streaming Analytics: Models, Parallelism, & Real-world Applications
- Numerically approximating centrality for graph ranking guarantees
- Scalable Katz Ranking Computation in Large Static and Dynamic Graphs
- A Dynamic Algorithm for Updating Katz Centrality in Graphs
- A parallel local search framework for the Fixed-Charge Multicommodity Network Flow problem
- Approximating Personalized Katz Centrality in Dynamic Graphs
- Design and implementation of parallel PageRank on multicore platforms
- Designing and implementing a heuristic cross-architecture combination for graph traversal
- Editor's Note
- Editor's Note
- Exact and Parallel Triangle Counting in Dynamic Graphs
- Exemplar or Matching: Modeling DCJ Problems with Unequal Content Genome Data
- Graph Ranking Guarantees for Numerical Approximations to Katz Centrality
- Introduction to EMBRACE Workshop
- Local Community Detection in Dynamic Graphs Using Personalized Centrality
- Modeling the Power Variability of Core Speed Scaling on Homogeneous Multicore Systems
- Proceedings of the Sixteenth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2017), Orlando, FL, May 2017.
- Quickly finding a truss in a haystack
- Spectral partitioning with blends of eigenvectors
- Streaming Graph Sampling with Size Restrictions
- When Good Enough Is Better: Energy-Aware Scheduling for Multicore Servers
- A local measure of community change in dynamic graphs
- A Memory and Time Scalable Parallelization of the Reptile Error-Correction Code
- A New Parallel Method for Binary Black Hole Simulations
- Aging data in dynamic graphs: A comparative study
- cuSTINGER: Supporting dynamic graph algorithms for GPUs
- Editor's Note
- Engineering Algorithms for Computational Biology
- Evolving MPI+X Toward Exascale
- Exemplar or matching: modeling DCJ problems with unequal content genome data
- GABB 2016 Keynote
- HiCOMB Introduction and Committees
- High Performance Algorithm Engineering for Large-Scale Problems
- HPC node performance and energy modeling with the co-location of applications
- Mathematical foundations of the GraphBLAS
- New stopping criteria for spectral partitioning
- Sorting Signed Permutations by Reversal (Reversal Distance)
- Tracking local communities in streaming graphs with a dynamic algorithm
- A Dynamic Algorithm for Local Community Detection in Graphs
- A fast, energy-efficient abstraction for simultaneous breadth-first searches
- A Methodology for Co-Location Aware Application Performance Modeling in Multicore Computing
- Behavioral clusters in dynamic graphs
- Editor's Note
- Fast Execution of Simultaneous Breadth-First Searches on Sparse Graphs
- Fast Incremental Community Detection on Dynamic Graphs
- HiCOMB Introduction and Committees
- Parallel Methods for Verifying the Consistency of Weakly-Ordered Architectures
- ParLearning Keynotes
- Spectral Partitioning with Blends of Eigenvectors
- State of the Journal
- WEC: Improving Durability of SSD Cache Drives by Caching Write-Efficient Data
- A Lin-Kernighan Heuristic for the DCJ Median Problem of Genomes with Unequal Contents
- A performance evaluation of open source graph databases
- Benchmarking for Graph Clustering and Partitioning
- Designing a Heuristic Cross-Architecture Combination for Breadth-First Search
- GABB Introduction
- HiCOMB Introduction and Committees
- Introduction to Special Issue ALENEX'12
- Load balanced clustering coefficients
- Optimizing energy consumption and parallel performance for static and dynamic betweenness centrality using GPUs
- Revisiting Edge and Node Parallelism for Dynamic GPU Graph Analytics
- Scalable and High Performance Betweenness Centrality on the GPU (Best Student Paper Finalist)
- Standards for Graph Algorithm Primitives
- State of the Journal
- A Brief Study of Open Source Graph Databases
- A new parallel algorithm for connected components in dynamic graphs
- A statistical framework for streaming graph analysis
- Designing Hybrid Architectures for Massive-Scale Graph Analysis
- Detecting insider threats in a real corporate database of computer usage activity
- Energy-Efficient Scheduling for Best-Effort Interactive Services to Achieve High Response Quality
- Evaluating Multicore Processors and Accelerators for Dense Numerical Computations
- Faster Betweenness Centrality Based on Data Structure Experimentation
- Faster Clustering Coefficient Using Vertex Covers
- Graph Partitioning and Graph Clustering
- GraphCT: Multithreaded Algorithms for Massive Graph Analysis
- HiCOMB Introduction
- Investigating Graph Algorithms in the BSP Model on the Cray XMT
- Massive streaming data analytics: a graph-based approach
- Measuring the Sensitivity of Graph Metrics to Missing Data
- Multithreaded Community Monitoring for Massive Streaming Graph Data
- Parallel Community Detection for Massive Graphs
- Parallel community detection for massive graphs
- PASQUAL: Parallel Techniques for Next Generation Genome Sequence Assembly
- Standards for graph algorithm primitives
- Streaming Breakpoint Graph Analytics for Accelerating and Parallelizing the Computation of DCJ Median of Three Genomes
- Sustainable Software Development for Next-Gen Sequencing (NGS) Bioinformatics on Emerging Platforms
- A Fast Algorithm for Streaming Betweenness Centrality
- ACM journal on experimental algorithmics special issue on multicore algorithms
- Analysis of streaming social networks and graphs on multicore architectures
- Computational Challenges in Emerging Combinatorial Scientific Computing Applications
- Efficient Data Migration to Conserve Energy in Streaming Media Storage Systems
- Enhancing Cache Coherent Architectures with access patterns for embedded manycore systems
- GPU Merge Path: A GPU Merging Algorithm
- GTfold: Enabling parallel RNA secondary structure prediction on multi-core desktops
- HCW 2012 Keynote Talk: Analyzing massive data using heterogeneous computing
- HiCOMB Introduction
- Proceedings of the 14th Meeting on Algorithm Engineering & Experiments, ALENEX 2012, The Westin Miyako, Kyoto, Japan, January 16, 2012
- Scalable Multi-threaded Community Detection in Social Networks
- STINGER: High performance data structure for streaming graphs (Best Paper Award)
- Task-based parallel breadth-first search in heterogeneous environments
- Rec-DCM-Eigen: Reconstructing a Less Parsimonious but More Accurate Tree in Shorter Time
- A Waterfall Model to Achieve Energy Efficient Tasks Mapping for Large Scale GPU Clusters
- Algorithm Engineering Challenges in Multicore and Manycore Systems
- Fundamental Questions in the Analysis of Large Graphs
- GPUMemSort: A High Performance Graphic Co-processors Sorting Algorithm for Large Scale In-Memory Data
- Graph Algorithms
- Guest Editor's Introduction: Special Issue on High-Performance Computing with Accelerators
- HiCOMB Introduction
- Hybrid Programming With SIMPLE
- Large-Scale Network Analysis
- On the random access performance of Cell Broadband Engine with graph analysis application
- Parallel Community Detection for Massive Graphs
- Spanning Tree, Minimum Weight
- SWARM: A Parallel Programming Framework for Multicore Processors
- Tracking Structure of Streaming Social Networks
- Combinatorial Algorithm Design on the Cell/B.E. Processor
- Designing Fast Fourier Transform for the IBM Cell Broadband Engine
- Evaluating Cell/B.E software cache for ClustalW
- HiCOMB 2010: Message from the workshop chairs
- Large scale complex network analysis using the hybrid combination of a MapReduce cluster and a highly multithreaded system
- Massive Social Network Analysis: Mining Twitter for Social Good
- Massive streaming data analytics: A case study with clustering coefficients
- Message from general chair
- Scalable Graph Exploration on Multicore Processors
- Scientific Computing with Multi-core and Accelerators
- The Case of the Fast Financial Feed
- A faster parallel algorithm and efficient multithreaded implementations for evaluating betweenness centrality on massive datasets
- A Partition-Merge Based Cache-Conscious Parallel Sorting Algorithm for CMP with Shared Cache
- An efficient transactional memory algorithm for computing minimum spanning forest of sparse graphs
- Compact graph representations and parallel connectivity algorithms for massive dynamic network analysis
- Computing discrete transforms on the Cell Broadband Engine
- Faster FAST: multicore acceleration of streaming financial data
- Faster FAST: Multicore Acceleration of Streaming Financial Data (Best Paper Award)
- Generalizing k-Betweenness Centrality Using Short Paths and a Parallel Multithreaded Implementation
- GTfold: a scalable multicore code for RNA secondary structure prediction
- Proceedings of the Eighth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2009), Rome, Italy, May 2009.
- Simulating Individual-Based Models of Epidemics in Hierarchical Networks
- Understanding the design trade-offs among current multicore systems for numerical computations
- A graph-theoretic analysis of the human protein-interaction network using multicore parallel algorithms
- A Prediction Based CMP Cache Migration Policy
- DOSA: design optimizer for scientific applications
- Engineering Algorithms for Computational Biology
- Financial modeling on the cell broadband engine
- Guest editorial: High-performance computational biology
- High Performance Algorithm Engineering for Large-scale Problems
- High performance MPEG-2 software decoder on the cell broadband engine
- On the Design of Fast Pseudo-Random Number Generators for the Cell Broadband Engine and an Application to Risk Analysis
- Optimizing JPEG2000 Still Image Encoding on the Cell Broadband Engine
- Petascale Computing for Large-Scale Graph Problems
- Proceedings of the Seventh IEEE International Workshop on High Performance Computational Biology (HiCOMB 2008), Miami, FL, April 2008.
- SNAP, Small-world Network Analysis and Partitioning: An open-source parallel graph framework for the exploration of large-scale networks
- Sorting Signed Permutations by Reversal (Reversal Distance)
- A Graph-Theoretic Analysis of the Human Protein-Interaction Network Using Multicore Parallel Algorithms
- Advanced Shortest Paths Algorithms on a Massively-Multithreaded Architecture
- An Experimental Study of A Parallel Shortest Path Algorithm for Solving Large-Scale Graph Instances
- Approximating Betweenness Centrality
- Design of Multithreaded Algorithms for Combinatorial Problems
- DOSA: Design Optimizer for Scientific Applications
- Dynamic Load Balancing in Distributed Systems in the Presence of Delays: A Regeneration-Theory Approach
- Efficient Parallel Graph Algorithms for Shared-memory Multiprocessors
- FFTC: Fastest Fourier Transform for the IBM Cell Broadband Engine
- High performance combinatorial algorithm design on the Cell Broadband Engine processor
- High-Performance Combinatorial Techniques for Analyzing Massive Dynamic Interaction Networks
- Multithreaded Algorithms for Processing Massive Graphs
- On the Design and Analysis of Irregular Algorithms on the Cell Processor: A Case Study of List Ranking
- On the design of high-performance algorithms for aligning multiple protein sequences on mesh-based multiprocessor architectures
- Petascale Computing for Large-Scale Graph Problems
- Petascale Computing for Large-Scale Graph Problems
- Petascale Computing: Algorithms and Applications
- Proceedings of the Sixth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2007), Long Beach, CA, April 2007.
- SWARM: A Parallel Programming Framework for Multicore Processors
- Symposium Evening Tutorial: High-performance Computing Methods for Computational Genomics
- Techniques for Designing Efficient Parallel Graph Algorithms for SMPs and Multicore Processors
- Computational Grand Challenges in Assembling the Tree of Life: Problems and Solutions
- Designing irregular parallel algorithms with mutual exclusion and lock-free protocols
- Designing Multithreaded Algorithms for Breadth-First Search and st-connectivity on the Cray MTA-2
- Editorial: Special Section on High-Performance Computational Biology
- Efficient Implementation of Irregular Algorithms on Cell Multi-core Architecture. Poster Session.
- ExactMP: An Efficient Parallel Exact Solver for Phylogenetic Tree Reconstruction Using Maximum Parsimony
- Fast shared-memory algorithms for computing the minimum spanning forest of sparse graphs
- High-performance computing methods for computational genomics
- Parallel Algorithms for Evaluating Centrality Indices in Real-world Networks
- Parallel Shortest Path Algorithms for Solving Large-Scale Instances
- Performance analysis of parallel programs via message-passing graph traversal
- Proceedings of the Fifth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2006), Rhodes Island, Greece, April 2006.
- A Cache-Aware Parallel Implementation of the Push-Relabel Network Flow Algorithm and Experimental Evaluation of the Gap Relabeling Heuristic
- A fast, parallel spanning tree algorithm for symmetric multiprocessors (SMPs)
- An Empirical Analysis of Parallel Random Permutation Algorithms on SMPs
- An Experimental Study of Parallel Biconnected Components Algorithms on Symmetric Multiprocessors (SMPs)
- BioPerf: a benchmark suite to evaluate high-performance computer architecture on bioinformatics applications
- BioSPLASH: A sample workload from bioinformatics and computational biology for optimizing next-generation high-performance computer systems. Poster Session.
- Design and Implementation of the HPCS Graph Analysis Benchmark on Symmetric Multiprocessors (HiPC Most Impactful Papers Award)
- High Performance Computing - HiPC 2005, 12th International Conference, Goa, India, December 18-21, 2005, Proceedings
- High-Performance Algorithm Engineering for Large-Scale Graph Problems and Computational Biology
- High-Performance Algorithms for Phylogeny Reconstruction with Maximum Parsimony
- High-Performance Phylogeny Reconstruction Under Maximum Parsimony
- Incorporating life sciences applications in the architectural optimizations of next-generation petaflop-system
- On the Architectural Requirements for Efficient Execution of Graph Algorithms
- Parallel Algorithm Design for Branch and Bound
- Proceedings of the Fourth IEEE International Workshop on High Performance Computational Biology (HiCOMB 2005), Denver, CO, April 2005.
- Proceedings of the ISCA 17th International Conference on Parallel and Distributed Computing Systems
- A Fast, Parallel Spanning Tree Algorithm for Symmetric Multiprocessors (SMPs)
- A Framework for Measuring Supercomputer Productivity
- A Novel FDTD Application Featuring OpenMP-MPI Hybrid Parallelization
- A Parallel State Assignment Algorithm for Finite State Machines
- An improved, randomized algorithm for parallel selection with an experimental study
- Computational biology and high-performance computing
- Fast Shared-Memory Algorithms for Computing the Minimum Spanning Forest of Sparse Graphs
- High Performance Bioinformatics
- Lock-Free Parallel Algorithms: An Experimental Study
- Proceedings of the Third IEEE International Workshop on High Performance Computational Biology (HiCOMB 2004), Santa Fe, NM, April 2004.
- Special Issue: High Performance Computational Biology
- The Euler Tour Technique and Parallel Rooted Spanning Tree
- Guest Editor's Introduction: Special issue on high-performance computational biology
- Proceedings of the Second IEEE International Workshop on High Performance Computational Biology (HiCOMB 2003), Nice, France, April 2003
- Algorithm Engineering for Parallel Computation
- Broadcast on Clusters of SMPs with Optimal Concurrency
- Evaluating Arithmetic Expressions Using Tree Contraction: A Fast and Scalable Parallel Implementation for Symmetric Multiprocessors (SMPs)
- HiCOMB 2002: Workshop Introduction
- High-Performance Algorithm Engineering for Computational Phylogenetics
- A Linear-Time Algorithm for Computing Inversion Distance between Signed Permutations with an Experimental Study
- A Linear-Time Algorithm for Computing Inversion Distance Between Two Signed Permutations with an Experimental Study
- A New Implmentation and Detailed Study of Breakpoint Analysis
- Applications
- High-Performance Algorithm Engineering for Computational Phylogenetics
- Industrial applications of high-performance computing for phylogeny reconstruction
- Using PRAM Algorithms on a Uniform-Memory-Access Shared-Memory Architecture
- An Improved Randomized Selection Algorithm With an Experimental Study
- High performance computing algorithms for land cover dynamics using remote sensing data
- High-Performance Algorithms and Applications for SMP Clusters
- Kronos: A software system for the processing and retrieval of large-scale AVHRR data sets
- Tutorial A: Design and Analysis of High Performance Clusters
- A New, Architectural Paradigm for High-performance Computing
- Design and Analysis of the Alliance/University of New Mexico Roadrunner Linux SMP SuperCluster
- SIMPLE: A Methodology for Programming High Performance Algorithms on Clusters of Symmetric Multiprocessors (SMPs)
- A New Deterministic Parallel Sorting Algorithm with an Experimental Evaluation
- A Randomized Parallel Sorting Algorithm with an Experimental Study
- On the Design and Analysis of Practical Parallel Algorithms for Combinatorial Problems with Applications to Image Processing
- Parallel Algorithms for Image Enhancement and Segmentation by Region Growing with an Experimental Study
- Parallel algorithms for image enhancement and segmentation by region growing, with an experimental study
- Parallel Algorithms for Image Histogramming and Connected Components with an Experimental Study
- Parallel Algorithms for Personalized Communication and Sorting with an Experimental Study (Extended Abstract)
- Practical Parallel Algorithms for Dynamic Data Redistribution, Median Finding, and Selection
- Practical Parallel Algorithms for Personalized Communication and Integer Sorting
- Parallel Algorithms for Image Histogramming and Connected Components with an Experimental Study
- Scalable data parallel algorithms for texture synthesis using Gibbs random fields

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