Graphics processing units in bioinformatics, computational biology and systems biology

CUDAMPF: a multi-tiered parallel framework for accelerating protein sequence search in HMMER on CUDA-enabled GPU

(2016) Hanyu Jiang et al.   BMC BIOINFORMATICS

Computational Modeling, Formal Analysis, and Tools for Systems Biology

(2016) Ezio Bartocci et al.   PLoS Computational Biology

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Accelerated application development: The ORNL Titan experience

(2015) Wayne Joubert et al.   COMPUTERS & ELECTRICAL ENGINEERING

Acceleration of discrete stochastic biochemical simulation using GPGPU

(2015) Kei Sumiyoshi et al.   Frontiers in Physiology

SYSBIONS: nested sampling for systems biology

(2014) R. Johnson et al.   BIOINFORMATICS

G-BLASTN: accelerating nucleotide alignment by graphics processors

(2014) Kaiyong Zhao et al.   BIOINFORMATICS

MEGADOCK 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers

(2014) Masahito Ohue et al.   BIOINFORMATICS

A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units

(2014) Andrea Manconi et al.   BMC BIOINFORMATICS

MaxSSmap: a GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence

(2014) Turki Turki et al.   BMC GENOMICS

Graphics processing units accelerated semiclassical initial value representation molecular dynamics

(2014) Dario Tamascelli et al.   JOURNAL OF CHEMICAL PHYSICS

A comparison between parallelization approaches in molecular dynamics simulations on GPUs

(2014) Lorenzo Rovigatti et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs

(2014) S.B. Kylasa et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Parallel implementation of 3D protein structure similarity searches using a GPU and the CUDA

(2014) Dariusz Mrozek et al.   JOURNAL OF MOLECULAR MODELING

GPU-accelerated simulations of mass-action kinetics models with cupSODA

(2014) Marco S. Nobile et al.   JOURNAL OF SUPERCOMPUTING

cuTauLeaping: A GPU-Powered Tau-Leaping Stochastic Simulator for Massive Parallel Analyses of Biological Systems

(2014) Marco S. Nobile et al.   PLoS One

Massive Exploration of Perturbed Conditions of the Blood Coagulation Cascade through GPU Parallelization

(2014) Paolo Cazzaniga et al.   Biomed Research International

SW#–GPU-enabled exact alignments on genome scale

(2013) Matija Korpar et al.   BIOINFORMATICS

CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions

(2013) Yongchao Liu et al.   BMC BIOINFORMATICS

Long Timestep Molecular Dynamics on the Graphical Processing Unit

(2013) James C. Sweet et al.   Journal of Chemical Theory and Computation

Molecular Dynamics Simulations Accelerated by GPU for Biological Macromolecules with a Non-Ewald Scheme for Electrostatic Interactions

(2013) Tadaaki Mashimo et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner

(2013) Ruibang Luo et al.   PLoS One

Fast Docking on Graphics Processing Units via Ray-Casting

(2013) Karen R. Khar et al.   PLoS One

CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows–Wheeler transform

(2012) Yongchao Liu et al.   BIOINFORMATICS

SOAP3: ultra-fast GPU-based parallel alignment tool for short reads

(2012) C.-M. Liu et al.   BIOINFORMATICS

CPU-GPU hybrid accelerating the Zuker algorithm for RNA secondary structure prediction applications

(2012) Guoqing Lei et al.   BMC GENOMICS

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations

(2012) Scott Le Grand et al.   COMPUTER PHYSICS COMMUNICATIONS

Using GPUs for the Exact Alignment of Short-Read Genetic Sequences by Means of the Burrows-Wheeler Transform

(2012) J. S. Torres et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

On the acceleration of the numerical solution of partial differential equations using radial basis functions and graphics processing units

(2012) W. Elliott Hutchcraft et al.   INTERNATIONAL JOURNAL OF NUMERICAL MODELLING-ELECTRONIC NETWORKS DEVICES AND FIELDS

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

(2012) Peter Eastman et al.   Journal of Chemical Theory and Computation

An investigation of the performance portability of OpenCL

(2012) S.J. Pennycook et al.   JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Accelerating the Gillespie τ-Leaping Method Using Graphics Processing Units

(2012) Ivan Komarov et al.   PLoS One

Accelerating the Gillespie Exact Stochastic Simulation Algorithm Using Hybrid Parallel Execution on Graphics Processing Units

(2012) Ivan Komarov et al.   PLoS One

A survey of computational molecular science using graphics processing units

(2012) M. J. Harvey et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

GPU accelerated biochemical network simulation

(2011) Yanxiang Zhou et al.   BIOINFORMATICS

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

(2011) Jochen Blom et al.   BIOINFORMATICS

Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation

(2011) Torbjørn Rognes   BMC BIOINFORMATICS

Swan: A tool for porting CUDA programs to OpenCL

(2011) M.J. Harvey et al.   COMPUTER PHYSICS COMMUNICATIONS

A GPU-Based Approach to Accelerate Computational Protein-DNA Docking

(2011) Jiadong Wu et al.   COMPUTING IN SCIENCE & ENGINEERING

Fat versus Thin Threading Approach on GPUs: Application to Stochastic Simulation of Chemical Reactions

(2011) Guido Klingbeil et al.   IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS

CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware

(2011) Weiguo Liu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Smoldyn on Graphics Processing Units: Massively Parallel Brownian Dynamics Simulations

(2011) L. Dematte   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Accelerating Molecular Docking Calculations Using Graphics Processing Units

(2011) Oliver Korb et al.   Journal of Chemical Information and Modeling

MOIL-opt: Energy-Conserving Molecular Dynamics on a GPU/CPU System

(2011) A. Peter Ruymgaart et al.   Journal of Chemical Theory and Computation

Pseudo-random number generation for Brownian Dynamics and Dissipative Particle Dynamics simulations on GPU devices

(2011) Carolyn L. Phillips et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Topical perspective on massive threading and parallelism

(2011) Robert M. Farber   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Accelerating reaction–diffusion simulations with general-purpose graphics processing units

(2010) Matthias Vigelius et al.   BIOINFORMATICS

ABC-SysBio--approximate Bayesian computation in Python with GPU support

(2010) J. Liepe et al.   BIOINFORMATICS

Ultra-fast FFT protein docking on graphics processors

(2010) David W. Ritchie et al.   BIOINFORMATICS

Fast and accurate protein substructure searching with simulated annealing and GPUs

(2010) Alex D Stivala et al.   BMC BIOINFORMATICS

Integrative multicellular biological modeling: a case study of 3D epidermal development using GPU algorithms

(2010) Scott Christley et al.   BMC Systems Biology

GPU computing for systems biology

(2010) L. Dematte et al.   BRIEFINGS IN BIOINFORMATICS

High performance cellular level agent-based simulation with FLAME for the GPU

(2010) P. Richmond et al.   BRIEFINGS IN BIOINFORMATICS

A view of cloud computing

(2010) Michael Armbrust et al.   COMMUNICATIONS OF THE ACM

OpenCL: A Parallel Programming Standard for Heterogeneous Computing Systems

(2010) John E. Stone et al.   COMPUTING IN SCIENCE & ENGINEERING

Grid Computing Workloads

(2010) Alexandru Iosup et al.   IEEE INTERNET COMPUTING

Systems Biology of Coagulation Initiation: Kinetics of Thrombin Generation in Resting and Activated Human Blood

(2010) Manash S. Chatterjee et al.   PLoS Computational Biology

Exploiting graphics processing units for computational biology and bioinformatics

(2010) Joshua L. Payne et al.   Interdisciplinary Sciences-Computational Life Sciences

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Long-timescale molecular dynamics simulations of protein structure and function

(2009) John L Klepeis et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Efficient Parallelization of the Stochastic Simulation Algorithm for Chemically Reacting Systems On the Graphics Processing Unit

(2009) Hong Li et al.   INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS

Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer

(2009) Roland Schulz et al.   Journal of Chemical Theory and Computation

Stochastic modelling for quantitative description of heterogeneous biological systems

(2009) Darren J. Wilkinson   NATURE REVIEWS GENETICS

Optimizing data intensive GPGPU computations for DNA sequence alignment

(2009) Cole Trapnell et al.   PARALLEL COMPUTING

Sending Signals Dynamically

(2009) R. G. Smock et al.   SCIENCE

CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment

(2008) Svetlin A Manavski et al.   BMC BIOINFORMATICS

Anton, a special-purpose machine for molecular dynamics simulation

(2008) David E. Shaw et al.   COMMUNICATIONS OF THE ACM

Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA

(2008) Weiguo Liu et al.   COMPUTER PHYSICS COMMUNICATIONS

Bioinformatics challenges of new sequencing technology

(2008) Mihai Pop et al.   TRENDS IN GENETICS