HiCOMB 2021 Online Proceedings

Twentieth IEEE International Workshop on High Performance Computational Biology

Virtual, May 17, 2021

• Introductory Remarks
  Mehmet Koyuturk, Alba Cristina M. A. de Melo, Ananth Kalyanaraman
  
• HiCOMB Keynote: Genomic Analysis at Scale: Mapping Irregular Computations to Advanced Architectures
  Kathy Yelick, UC Berkeley   slides
  
• HiCOMB Invited talk #1: Probabilistic Models for Large-scale Human Genomic Data
  Sriram Sankararaman, UCLA   slides
  
• HiCOMB Invited talk #2: Fast Approximations of Frequent k-mers and Applications
  Fabio Vandin, U. Padoa    slides
  
• HiCOMB Invited talk #3: Designing Interventions in Networked Models of Epidemic Spread
  Anil Vullikanti, U. Virginia   slides
  
  Peer-reviewed papers:  (*all prerecorded talk videos are available on this YouTube Playlist)
  
• GYAN: Accelerating Bioinformatics tools in Galaxy with GPU-aware Computation Mapping  
  Gulsum Gudukbay, Jashwant Raj Gunasekaran, Yilin Feng, Mahmut T. Kandemir, Chita R. Das, Anton Nekrutenko, Paul Medvedev, Bjorn Gruning, Nate Caraor, Enis Afgan, Nathan Roach
  Talk video    Slides
  
• Accelerating SARS-CoV-2 Low Frequent Variant Calling on Ultra Deep Sequencing Datasets
  Bryce Kille, Yunxi Liu, Nicolae Sapoval, Michael Nute, Lawrence Rauchwerger, Nancy Amato, Todd J. Treangen
  Talk video
  
• GateKeeper-GPU: Accelerated Pre-alignment Filtering in Short Read Mapping
  Zulal Bingol, Mohammed Alser, Ozcan Ozturk, Can Alkan
  Talk video   Slides
  
• GPU Acceleration of 3D Agent-based Biological Simulations
  Ahmad Hesam, Lukas Breitwieser, Fons Rademakers, Zaid Al-Ars
  Talk video
  
• Efficient Memory Management in Likelihood-based Phylogenetic Placement
  Pierre Barbera, Alexandros Stamatakis
  Talk video
  
• Accelerating the BPMax Algorithm for RNA-RNA Interactions
  Chiranjeb Mondal, Sanjay Rajopadhye
  Talk video   Slides
  

HiCOMB 2020 Online Proceedings

Nineteenth IEEE International Workshop on High Performance Computational Biology

Virtual, May 18, 2020

• Introductory Remarks
  Ariful Azad, Alba Cristina M. A. de Melo, Ananth Kalyanaraman
• A Tropical Semiring Multiple Matrix-product Library on GPUs: A Step Towards RNA-RNA Interaction Computations  slides 
  Brandon Glidemaster, Prerna Ghalassi, Sanjay Rajopadhye
  
• Fast and High Quality Graph Alignment via Treelets slides  talk video
  Morgan Lee, George Slota
• GPU Accelerated Partial Order Multiple Sequence Alignment for Long Reads Self-correction slides
  Francesco Peverelli, Lorenzo Di Tucci, Marco Domeinico Santambrogio, Nan Ding, Steven Hofmeyr, Aydin Buluc, Leonid Oliker, Katherine Yelick
  
• Optimizing High-Performance Computing Systems for Biomedical Workloads  slides
  Patricia Kovatch, Lili Gai, Hyung Min Cho, Eugene Fluder, Dansha Jiang
• Kcollections: A Fast and Efficient Library for k-mers  slides
  M. Stanley Fujimoto, Cole Lyman, Mark Clement
  

HiCOMB 2019 Online Proceedings

Eighteenth IEEE International Workshop on High Performance Computational Biology

Rio de Janiero, Brazil, May 20, 2019

• Introductory Remarks
  Alba Cristina M. A. de Melo, Ananth Kalyanaraman, Kamesh Madduri
• HiCOMB Keynote
  Ajay Royyuru
• Accelerating Clustering using Approximate Spanning Tree and Prime Number based Filter
  Dhananjai Rao, Sutharzan Sreeskandarajan, Chun Liang
• Data Distribution for Phylogenetic Inference with Site Repeats via Judicious Hypergraph Partitioning
  Ivo Baar, Lukas Hübner, Peter Oettig, Adrian Zapletal, Sebastian Schlag, Alexandros Stamatakis, Benoit Morel
• ArrOW: Experiencing a Parallel Cloud-based De Novo Assembler Workflow
  Kary Ocaña, Thaylon Guedes, Daniel de Oliveira
• LBE: A Computational Load Balancing Algorithm for Speeding up Parallel Peptide Search in Mass-Spectrometry based Proteomics
  Muhammad Haseeb, Fatima Afzali, Fahad Saeed
• Portable GPU Framework for SNP Comparisons
  Elliott Binder, Tze Meng Low, Doru Thom Popovici
• Parallel Decompression of gzip-compressed Files and Random Access to DNA sequences
  Maël Kerbiriou, Rayan Chikhi

HiCOMB 2018 Online Proceedings

Seventeenth IEEE International Workshop on High Performance Computational Biology

Vancouver, Canada, May 21, 2018

• Introductory Remarks
  Srinivas Aluru, David Bader, Paul Medvedev
• HiCOMB Keynote 1
  James Taylor
• HICOMB Keynote 2
  Onur Mutlu
• GraphNER: Using Corpus Level Similarities and Graph Propagation for Named Entity Recognition
  Golnar Sheikhshab, Elizabeth Starks, Aly Karsan, Readman Chiu, Anoop Sarkar, Inanc Birol
• Modifying HMMER3 to Run Efficiently on the Cori Supercomputer Using OpenMP Tasking
  William Arndt
• Rerooting Trees Increases Opportunities for Concurrent Computation and Results in Markedly Improved Performance for Phylogenetic Inference
  Daniel L. Ayres, Michael P. Cummings
• Sequence Alignment Through the Looking Glass
  Raja Appuswamy, Jacques Fellay, Nimisha Chaturvedi

HiCOMB 2017 Online Proceedings

Sixteenth IEEE International Workshop on High Performance Computational Biology

Orlando, FL, May 29, 2017

• Introductory Remarks
  Alex Pothen, Ananth Grama
• HiCOMB Keynote
  Radu Marculescu
• Scalable FRaC Variants: Anomaly Detection for Precision Medicine
  Cyrus Cousins, Chirstopher M. Pietras, Donna K. Slonim
• Exploratory Modeling and Simulation of the Evolutionary Dynamics of Single-Stranded RNA Virus Populations
  Jae-Seung Yeom, Tanya Kostova-Vassilevska, Peter D. Barnes_Jr., David R. Jefferson, Tomas Oppelstrup
• Parallel NGS Assembly Using Distributed Assembly Graphs Enriched with Biological Knowledge
  Julia D. Warnke-Sommer, Hesham H. Ali
• Parallel and Memory-Efficient Preprocessing for Metagenome Assembly
  Vasudevan Rengasamy, Paul Medvedev, Kamesh Madduri
• Scalable Parallelization of a Markov Coalescent Genealogy Sampler
  Philip E. Davis, Adam M. Terwilliger, David Zeitler, Greg Wolffe
• Par-eXpress: A Tool for Analysis of Sequencing Experiments With Ambiguous Assignment of Fragments in Parallel
  Mucahid Kutlu, Gagan Agrawal, James S. Blachly

HiCOMB 2016 Online Proceedings

Fifteenth IEEE International Workshop on High Performance Computational Biology

Chicago, IL, May 23, 2016

• Introductory Remarks
  Srinivas Aluru, David A. Bader, Ananth Kalyanaraman, Jaroslaw Zola
• The Divisible Load Balance Problem with Shared Cost and Its Application to Phylogenetic Inference
  Constantin Scholl, Kassian Kobert, Tomáš Flouri, Alexandros Stamatakis
• Efficient Computation of Linkage Disequilibria as Dense Linear Algebra Operations
  Nikolaos Alachiotis, Thom Popovici, Tze Meng Low
• Improving Reaction Kernel Performance in Lattice Microbes: Particle-Wise Propensities and Run-Time Generated Code
  Michael J. Hallock, Zaida Luthey-Schulten
• SparkScore: Leveraging Apache Spark for Distributed Genomic Inference
  Amir Bahmani, Alexander B. Sibley, Mahmoud Parsian, Kouros Owzar, Frank Mueller
• A Scalable Pipeline for Transcriptome Profiling Tasks with On-Demand Computing Clouds
  Shayan Shams, Nayong Kim, Xiandong Meng, Ming Tai Ha, Shantenu Jha, Zhong Wang, Joohyun Kim
• A Memory and Time Scalable Parallelization of the Reptile Error-Correction Code
  Vipin Sachdeva, Srinivas Aluru, David A. Bader
• Real-Time Agent-Based Modeling Simulation with in-Situ Visualization of Complex Biological Systems: A Case Study on Vocal Fold Inflammation and Healing
  Nuttiiya Seekhao, Caroline Shung, Joseph JaJa, Luc Mongeau, Nicole Y. K. Li-Jessen
• A Novel Associative Memory Based Architecture for Sequence Alignment
  M. Ali Mirzaei, Francesco Crescioli, Sebastien Viret, William Tromeur, Giovanni Calderini, Giovanni Marchiori, Guillaume Baulieu, Geoffrey Galbit

HiCOMB 2015 Online Proceedings

Fourteenth IEEE International Workshop on High Performance Computational Biology

Hyderabad, India, May 25, 2015

• Introductory Remarks
  Sanguthevar Rajasekaran, Srinivas Aluru, and David A. Bader
• Keynote and Invited Talks
  Ramesh Hariharan, Ananth Kalyanaraman, Michela Taufer, Trilce Estrada, Pietro Cicotti, Pavan Balaji
• Perfect Hashing Structures for Parallel Similarity Searches
  Tuan Tu Tran, Mathieu Giraud, Jean-Stéphane Varré
• A Crossbar Interconnection Network in DNA
  Basavaraj Talawar
• Handling Heterogeneity for Efficient Implementations: A Case Study on Sequence Comparison
  Denis Trystram
• Phylogenetic Analysis Using MapReduce Programming Model
  G.M. Siddesh, K.G. Srinivasa, Ishank Mishra, Abhinav Anurag, Eklavya Uppal
• Towards Context-Aware DNA Sequence Compression for Efficient Data Exchange
  Wajeeta Lohana, Jawwad A. Shamsi, Tahir Q. Syed, Farrukh Hasan
• Generalised Implementation for Fixed-Length Approximate String Matching under Hamming Distance and Applications
  Solon Pissis, Ahmad Retha
• Fine-Grained Acceleration of HMMER 3.0 via Architecture-Aware Optimization on Massively Parallel Processors
  Hanyu Jiang, Narayan Ganesan

HiCOMB 2014 Online Proceedings

Thirteenth IEEE International Workshop on High Performance Computational Biology

Phoenix, AZ, May 19, 2014

• Introductory Remarks
  Alba Cristina Magalhaes Alves de Melo, Srinivas Aluru, and David A. Bader
• Removing Sequential Bottlenecks in Analysis of Next-Generation Sequencing Data
  Yi Wang, Gagan Agrawal, Gulcin Ozer and Kun Huang
• Parallelization of the Trinity pipeline for de novo transcriptome assembly
  Vipin Sachdeva, Chang-Sik Kim, Kirk Jordan and Martyn D Winn
• Design and Optimization of a Metagenomics Analysis Workflow for NVRAM
  Sasha Ames, Jonathan Allen, David Hysom, Scott Lloyd and Maya Gokhale
• Efficient Computation of the Phylogenetic Likelihood Function on the Intel MIC Architecture
  Alexey M Kozlov, Christian Goll and Alexandros Stamatakis
• HiPGA: A High Performance Genome Assembler for Short Read Sequence Data
  Xiaohui Duan, Kun Zhao and Weiguo Liu
• Exploring Large Scale Receptor-Ligand Pairs in Molecular Docking Workflows in HPC Clouds
  Kary Ocana, Silvia Benza, Daniel de Oliveira, Jonas Dias and Marta Mattoso
• Process Simulation of Complex Biochemical Pathways in Explicit 3D Space Enabled by Heterogeneous Computing Platform
  Jie Li, Amin Salighehdar and Narayan Ganesan
• A Comparison of a Campus Cluster and Open Science Grid Platforms for Protein-Guided Assembly using Pegasus Workflow Management System
  Natasha Pavlovikj, Kevin Begcy, Sairam Behera, Malachy Cambell, Harkamal Walia and Jitender Singh Deogun
• Constructing Similarity Graphs from Large-scale Biological Sequence Collections
  Jaroslaw Zola

HiCOMB 2013 Online Proceedings

Twelfth IEEE International Workshop on High Performance Computational Biology

Boston, MA, May 20, 2013

• Introductory Remarks
  Jaroslaw Zola, David A. Bader, and Srinivas Aluru
• Biological Sequence Comparison on Hybrid Platforms with Dynamic Workload Adjustment
  Fernando Machado Mendonca, Alba Cristina Magalhaes Alves de Melo
• Accelerating All-to-All Protein Structures Comparison with TMalign Using a NoC Many-Cores Processor Architecture
  Anuj Sharma, Antonis Papanikolaou, Elias S. Manolakos
• Secondary Structure Predictions for Long RNA Sequences Based on Inversion Excursions and MapReduce
  Daniel T. Yehdego, Boyu Zhang, Vikram K.R. Kodimala, Kyle L. Johnson, Michela Taufer, Ming-Ying Leung
• A Generic Vectorization Scheme and a GPU Kernel for the Phylogenetic Likelihood Library
  Fernando Izquierdo-Carrasco, Nikolaos Alachiotis, Simon Berger, Tomas Flouri, Solon P. Pissis, Alexandros Stamatakis
• Boosting the Performance of Bayesian Divergence Time Estimation with the Phylogenetic Likelihood Library
  Diego Darriba, Andre Aberer, Tomas Flouri, Tracy A. Heath, Fernando Izquierdo-Carrasco, Alexandros Stamatakis
• A Map-Reduce Framework for Clustering Metagenomes
  Zeehasham Rasheed, Huzefa Rangwala
• GPU-Accelerated Protein Family Identification for Metagenomics
  Changjun Wu, Ananth Kalyanaraman
• Polarization Energy on a Cluster of Multicores
  Jesmin Jahan Tithi, Rezaul A. Chowdhury
• GPU-Based Steady-State Solution of the Chemical Master Equation
  Marco Maggioni, Tanya Berger-Wolf, Jie Liang

HiCOMB 2012 Online Proceedings

Eleventh IEEE International Workshop on High Performance Computational Biology

Shanghai, China, May 21, 2012

• Introductory Remarks
  Mark J. Clement, Quinn Snell, Srinivas Aluru, and David A. Bader
• Investigating Memory Optimization of Hash-index for Next Generation Sequencing on Multi-core Architecture
  Wendi Wang, Wen Tang, Linchuan Li, Guangming Tan, Peiheng Zhang, and Ninghui Sun
• Parallel Pair-HMM SNP Detection
  Nathan L. Clement, Brent A. Shepherd, Paul Bodily, Sukhbat Tumur-Ochir, Younghoon Gim, Quinn Snell, Mark J. Clement, and W. Evan Johnson
• Evaluation of GPU-based Seed Generation for Computational Genomics Using Burrows-Wheeler Transform
  Yongchao Liu and Bertil Schmidt
• The Multi-Processor Scheduling Problem in Phylogenetics
  Jiajie Zhang and Alexandros Stamatakis
• Optimizing the Execution of Statistical Simulations for Human Evolution in Hyper-threaded Multicore Architectures
  Raquel Dias, César A.F. De Rose, Antônio Tadeu Azevedo Gomes, and Nelson J.R. Fagundes
• SlimCodeML: An Optimized Version of CodeML for the Branch-Site Model
  Hannes Schabauer, Mario Valle, Christoph Pacher, Heinz Stockinger, Alexandros Stamatakis, Marc Robinson-Rechavi, Ziheng Yang, and Nicolas Salamin
• Finding Common RNA Secondary Structures: A Case Study on the Dynamic Parallelization of a Data-driven Recurrence
  Steven T. Stewart, Eric Aubanel, and Patricia A. Evans
• The Development of Parallel Adaptive Sampling Algorithms for Analyzing Biological Networks CUDA Enabled Devices
  Kathryn Dempsey, Kanimathi Duraisamy, Sanjukta Bhowmick, and Hesham Ali
• A Speculative HMMER Search Implementation on GPU
  Xiaoqiang Li, Wenting Han, Gu Liu, Hong An, Mu Xu, Wei Zhou, and Qi Li
• Probabilistic Brain Fiber Tractography on GPUs
  Mo Xu, Xiaorui Zhang, Yu Wang, Ling Ren, Ziyu Wen, Yi Xu, Gaolang Gong, Ningyi Xu, and Huazhong Yang
• Quantitative Trait Locus Analysis Using a Partitioned Linear Model on a GPU Cluster
  Peter E. Bailey, Tapasya Patki, Gregory M. Striemer, Ali Akoglu, David K. Lowenthal, Peter Bradbury, Matt Vaughn, Liya Wang, and Stephen Goff

HiCOMB 2011 Online Proceedings

Tenth IEEE International Workshop on High Performance Computational Biology

Anchorage, AK, May 16, 2011

• Introductory Remarks
  Anantharaman Kalyanraman, Srinivas Aluru, and David A. Bader
• Parallelizing BLAST and SOM algorithms with MapReduce-MPI library
  Seung-Jin Sul, Andrey Tovchigrechko
• Improving CUDASW++, a Parallelization of Smith-Waterman for CUDA Enabled Devices
  Doug Hains, Zach Cashero, Mark Ottenberg, Wim Bohm, Sanjay Rajopadhye
• An Ultrafast Scalable Many-core Motif Discovery Algorithm for Multiple GPUs
  Yongchao Liu, Bertil Schmidt, Douglas Maskell
• Parallel Mapping Approaches for GNUMAP
  Nathan Clement, Mark J. Clement, Quinn Snell, W. Evan Johnson
• Computing the Phylogenetic Likelihood Function Out-of-Core
  Fernando Izquierdo-Carrasco, Alexandros Stamatakis
• Algorithms for a Parallel Implementation of Hidden Markov Models with a Small State Space
  Jesper Nielsen, Andreas Sand
• Efficient Nonserial Polyadic Dynamic Programming on the Cell Processor
  Li Liu, Mu Wang, Jinlei Jiang, Ruizhe Li, Guangwen Yang
• FENZI: GPU-enabled Molecular Dynamics Simulations of Large Membrane Regions based on the CHARMM force field and PME
  Narayan Ganesan, Brad Bauer, Sandeep Patel, Michela Taufer
• Divide-and-conquer approach to the parallel computation of elementary flux modes in metabolic networks
  Dimitrije Jevremovic, Daniel Boley, Carlos Sosa
• Sensitive and Specific Identification of Protein Complexes in ``Perturbed'' Protein Interaction Networks from Noisy Pull-Down Data
  William Hendrix, Tatiana Karpinets, Byung-Hoon Park, Eric Schendel, Alok Choudhary, Nagiza Samatova
• An Efficient and Scalable Implementation of SNP-pair Interaction Testing for Genetic Association Studies
  Lars Koesterke, Dan Stanzione, Matt Vaughn, Stephen Welch, Waclaw Kusnierczyk, Jinliang Wang, Cheng-Ting Yeh, Dan Nettleton, Patrick S. Schnable

HiCOMB 2010 Online Proceedings

Ninth IEEE International Workshop on High Performance Computational Biology

Atlanta, GA, April 19, 2010

• Introductory Remarks
  George Karypis, Srinivas Aluru, and David A. Bader
• GPU-Accelerated Multi-scoring Functions Protein Loop Structure Sampling
  Yaohang Li and Weihang Zhu
• Acceleration of Spiking Neural Networks in Emerging Multi-core and GPU Architectures
  Mohammad A. Bhuiyan, Vivek K. Pallipuram and Melissa C. Smith
• A Tile-based Parallel Viterbi Algorithm for Biological Sequence Alignment on GPU with CUDA
  Zhihui Du, Zhaoming Yin, and David A. Bader
• Fast Binding Site Mapping using GPU and CUDA
  Bharat Sukhwani and Martin Herbordt
• Hybrid MPI/Pthreads Parallelization of the RAxML Phylogenetics Code
  Wayne Pfeiffer and Alexandros Stamatakis
• Measuring Properties of Molecular Surfaces Using Ray Casting
  Mike Phillips, Iliyan Georgiev, Anna Dehof, Lukas Marsalek, Hans-Peter Lenhof, Andreas Hildebrandt, and Philipp Slusallek
• On the Parallelisation of MCMC-based Image Processing
  Jonathan M.R. Byrd, Stephen A. Jarvis, and Abhir H. Bhalerao
• Exploring Parallelism in Short Sequence Mapping Using Burrows-Wheeler Transform
  Doruk Bozdag, Ayat Hatem, Umit V. Catalyurek
• pFANGS: Parallel High Speed Sequence Mapping for Next Generation 454-Roche Sequencing Reads
  Sanchit Misra, Ramanathan Narayanan, Wei-keng Liao, Alok Choudhary, and Simon Lin
• Efficient and scalable parallel reconstruction of sibling relationships from genetic data in wild- populations
  Saad Sheikh, Ashfaq Khokhar, and Tanya Berger-Wolf

HiCOMB 2009 Online Proceedings

Eighth IEEE International Workshop on High Performance Computational Biology

Rome, Italy, May 25, 2009

• Introductory Remarks
  Michela Taufer, Srinivas Aluru, and David A. Bader
• De Novo Modeling of GPCR Class A Structures
  Charles L. Brooks III
• Parallel Reconstruction of Neighbor-Joining Trees for Large Multiple Sequence Alignments using CUDA
  Yongchao Liu, Bertil Schmidt, and Douglas Maskell
• Accelerating Error Correction in High-Throughput Short-Read DNA Sequencing Data with CUDA
  Haixiang Shi, Bertil Schmidt, Weiguo Liu, and Wolfgang Mueller-Wittig
• Parallel Monte Carlo Study on Caffeine-DNA Interaction in Aqueous Solution
  Michael Kalugin and Alexandr Teplukhin
• Dynamic Parallelization for RNA Structure Comparison
  Eric Aubanel, Patricia Evans, and Eric Snow
• HMMer Acceleration Using Systolic Array Based Reconfigurable Architecture
  Yanteng Sun, Peng Li, Guochang Gu, Yuan Wen, Yuan Liu, and Dong Liu
• A Resource-Efficient Computing Paradigm for Computational Protein Modeling Applications
  Yaohang Li, Dougalas Wardell, and Vincent Freeh
• Exploring FPGAs for Accelerating the Phylogenetic Likelihood Function
  Nikolaos Alachiotis, Euripides Sotiriades, Apostolos Dollas, and Alexandros Stamatakis
• Long Time-scale Simulations of in vivo Diffusion using GPU Hardware
  Elijah Roberts, John Stone, Leonardo Sepulveda, Wen-Mei Hwu, and Zaida Luthey-Schulten
• An Efficient Implementation Smith Waterman Algorithm on GPU using CUDA, for Massively Parallel Scanning of Sequence Databases
  Lukasz Ligowski and Witold Rudnicki
• A Novel Framework for Modeling Ion Channels
  May Siksik and Vikram Krishnamurthy
• High-throughput Protein Structure Determination using Grid Computing
  Jason W. Schmidberger, Blair Bethwaite, Colin Enticott, Mark A. Bate, Steve G. Androulakis, Noel Faux, Cyril F. Reboul, Jennifer M. N. Phan, James C. Whisstock, Wojtek J. Goscinski, Slavisa Garic, David Abramson, and Ashley M. Buckle
• Folding@home: Lessons From Eight Years of Volunteer Distributed Computing
  Adam L. Beberg, Guha Jayachandran, Siraj Khaliq, Vijay S. Pande

HiCOMB 2008 Online Proceedings

Seventh IEEE International Workshop on High Performance Computational Biology

Miami, FL, April 14, 2008

• Introductory Remarks
  Bertil Schmidt, Srinivas Aluru, and David A. Bader
• Ordered Index Seed Algorithm for Intensive DNA Sequence Comparison
  D. Lavenier
• Parallel, Scalable, Memory-Efficient Backtracking for Combinatorial Modeling of Large-Scale Biological Systems
  B.-H. Park, M. Schmidt, K. Thomas, T. Karpinets, N.F. Samatova
• Parallelized preprocessing algorithms for high-density oligonucleotide array data
  M. Schmidberger, U. Mansmann
• On the Effectiveness of Rebuilding RNA Secondary Structures from Sequence Chunks
  M. Taufer, T. Solorio, A. Licon, D. Mireles, M.-Y. Leung
• A Parallel Architecture for Regulatory Motif Algorithm Assessment
  D. Quest, K. Dempsey, D. Bastola, H. Ali
• Design and Development of a FPGA-based Cascade Markov Model for Recognition of Steroid Hormone Response Elements
  M. Stepanova, F. Lin, V. Lin
• Supporting High Performance Bioinformatics Flat-File Data Processing
  X. Zhang, G. Agrawal
• Sample-Align-D: A High Performance Multiple Sequence Alignment System using Phylogenetic Sampling and Domain Decomposition
  F. Saeed, A. Khokhar
• Adaptive Locality-Effective Kernel Methods for Phosphorylation Site Prediction
  P. Yoo, Y.S. Ho, B.B. Zhou, A. Zomaya
• Impacts of Multicores on Large-scale Molecular Dynamics Simulations
  S. Alam, J. Vetter, P. Agarwal, H. Ong, S. Hampton

HiCOMB 2007 Online Proceedings

Sixth IEEE International Workshop on High Performance Computational Biology

Long Beach, CA, March 26, 2007

• Introductory Remarks
  Ananth Grama, Shankar Subramaniam, Srinivas Aluru, and David A. Bader
• On the path to enable multi-scale biomolecular simulations on Petaflop supercomputer with multi-core processors
  Sadaf Alam, Pratul Agarwal
• Analysis of a Computational Biology Simulation Technique on Emerging Processing Architectures
  Jeremy Meredith, Sadaf Alam, Jeffrey S. Vetter
• A Graph-Theoretic Analysis of the Human Protein-Interaction Network Using Multicore Parallel Algorithms
  David A. Bader, Kamesh Madduri
• Biomolecular Path Sampling Enabled by Processing in Network Storage
  Paul Brenner, Justin Wozniak, Jesus Izaguirre, Aaron Striegel, Douglas Thain, Jeff Peng
• Preliminary results in accelerating profile HMM search on FPGAs
  Arpith Jacob, Joseph Lancaster, Jeremy Buhler, Roger Chamberlain
• High Performance Database Searching with HMMer on FPGAs
  Tim Oliver, Leow Yuan Yeow, Bertil Schmidt
• Exploring the viability of the Cell Broadband Engine for bioinformatics applications
  Vipin Sachdeva, Mike Kistler, Evan Speight, Tzy-Hwa Kathy Tzeng
• Data-Driven Time-Parallelization in the AFM Simulation of Proteins
  Lei Ji, Hugh Nymeyer, Ashok Srinivasan, Yanan Yu
• RNAVLab: A unified environment for computational RNA structure analysis based on grid computing technology
  Michela Taufer, Ming-Ying Leung, Kyle L. Johnson, Abel Licon
• An Automated Data Processing Pipeline for Virus Structure Determination at High Resolution
  Chen Yu, Dan C. Marinescu, John P. Morrison, Brian C. Clayton, David A. Power

HiCOMB 2006 Online Proceedings

Fifth IEEE International Workshop on High Performance Computational Biology

Rhodes Island, Greece, April 25, 2006

• Introductory Remarks
  Chau-Wen Tseng, David A. Bader, and Srinivas Aluru
• Bio-Sequence Database Scanning on a GPU
  Weiguo Liu, Bertil Schmidt, Gerrit Voss, Andre Schroder, Wolfgang Muller-wittig
• Some Initial Results on Hardware BLAST Acceleration with a Reconfigurable Architecture
  Euripides Sotiriades, Christos Kozanitis, Apostolos Dollas
• Phylospaces: Reconstructing Evolutionary Trees in Tuple Space
  Marc L. Smith, Tiffani L. Williams
• Parallel Implementation of a Quartet-Based Algorithm for Phylogenetic Analysis
  B. B. Zhou, D. Chu, M. Tarawneh, P. Wang, C. Wang, A. Y. Zomaya, R. P. Brent
• Phylogenetic Models of Rate Heterogeneity: A High Performance Computing Perspective
  Alexandros Stamatakis
• Parallel Multiple Sequence Alignment with Local Phylogeny Search by Simulated Annealing
  Jaroslaw Zola, Denis Trystram, Andrei Tchernykh, Carlos Brizuela
• MT-ClustalW: Multithreading Multiple Sequence Alignment
  Kridsadakorn Chaichoompu, Surin Kittitornkun, Sissades Tongsima
• Parallel Implementation of the Replica Exchange Molecular Dynamics Algorithm on Blue Gene/L
  M. Eleftheriou, A. Rayshubski, J. W. Pitera, B. G. Fitch, R. Zhou, R. S. Germain
• Application Re-Structuring and Data Management on a GRID Environment: a Case Study for Bioinformatics
  Giovanni Ciriello, Matteo Comin, Concettina Guerra
• A Method to Improve Structural Modeling Based on Conserved Domain Clusters
  Fa Zhang, Lin Xu, Bo Yuan
• An Experimental Study of Optimizing Bioinformatics Applications
  Guangming Tan, Lin Xu, Shengzhong Feng, Ninghui Sun

HiCOMB 2005 Online Proceedings

Fourth IEEE International Workshop on High Performance Computational Biology

Denver, CO, April 4, 2005

• Introductory Remarks
  Nancy Amato, David A. Bader, and Srinivas Aluru
• BioFilter: An architecture for parallel deployment and dynamic chaining of standalone bioinformatics tools
  Thomas Brettin and Avinash Kewalramani
• Comparison of Different Versions of Current BLAST Software on Nucleotide Sequences
  I. Elizabeth Cha and Eric Rouchka
• Statistical Methods for the Discovery of Co-operative Transcription Factors: the Co-bind code revised
  Giovanni Lavorgna, Alessandro Marongiu, Simone Melchionna, Paolo Palazzari, Vittorio Rosato, and Paolo Verrecchia
• A Case Study on Pattern-based Systems for High Performance
  Weiguo Liu and Bertil Schmidt
• High-Performance Direct Pairwise Comparison of Large Genomic Sequences
  Chris Mueller, Mehmet Dalkilic and Andrew Lumsdaine
• RC-BLAST: Towards an Open Source Hardware Implementation
  Krishna Muriki, Keith Underwood and Ron Sass
• FROST: Revisited and Distributed
  Vincent Poirriez, Antoine Marin, Rumen Andonov and Jean-Francois Gibrat
• An Efficient Program for Phylogenetic Inference Using Simulated Annealing
  Alexandros Stamatakis
• Predictor@Home: A "Protein Structure Prediction Supercomputer" Based on Public-Resource Computing
  Michela Taufer and C. An and A. Kerstens and C.L. Brooks III
• ESTmapper: Efficiently Aligning DNA Sequences to Genomes
  Xue Wu, Woei-Jyh (Adam) Lee and Chau-Wen Tseng
• Folding@Home: Advances in biophysics and biomedicine from world-wide grid computing (invited keynote)
  Vijay Pande

HiCOMB 2004 Online Proceedings

Third IEEE International Workshop on High Performance Computational Biology

Santa Fe, NM, April 26, 2004

• Introductory Remarks
  Dan C. Marinescu, David A. Bader, and Srinivas Aluru
• Three-dimensional reconstruction of viruses: challenges and strategies
  Timothy S. Baker
• Study of a Highly Accurate and Fast-Protein Ligand Docking Algorithm Based Upon Molecular Dynamics
  M. Taufer, M. Crowley, D. Price, A.A. Chien, and C. L. Brooks III
• Parallel Protein Folding with STAPL
  S. Thomas and N. Amato
• A Hypergraph Model for the Yeast Protein Complex Network
  E. Ramadan, A. Tarafdar, and A. Pothen
• Dynamic Programming for LR-PCR Segmentation of Bacterium Genomes
  R. Andonov, D. Lavenier, N. Yanev, and P. Veber
• Parallel RNA Sequence-Structure Alignment
  T. Liu and B. Schmidt
• Constrained De Novo Peptide Identification via Multiobjective Optimization
  J. M. Mallard, A. Heredia-Langner, D.J. Baxter, K. H. Jarman, and W. R. Cannon
• Identification of Mycobacteriun Species Using Curated Custom Databases
  D. Kuyper, H. Ali, A. M. Mohamed, and S. H. Hinrichs
• High Performance Computational Tools for Motif Discovery
  N. E. Baldwin, R. L. Collins, M. A. Langston, M. R. Leuze, C. T. Symons, and B. H. Voy
• High Performance Biosequence Database Scanning on Reconfigurable Platforms
  T. Oliver and B. Schmidt
• New Fast and Acurate Heuristics for Inference of Large Phylogenic Trees
  A.P. Stamatakis, T. Ludwig, and H. Meier
• Large-Scale Simulation of Eukaryotic Cell Signaling Processes
  J. H. Miller and F. Zheng
• Particle Swarm Optimization and Neural Network Application for QSAR
  Z. Wang, G. L. Durst, R.C. Eberhart, D.B. Boyd, and Z. B. Miled

HiCOMB 2003 Online Proceedings

Second IEEE International Workshop on High Performance Computational Biology

Nice, France, April 22, 2003

• Introductory Remarks
  S. Aluru and D.A. Bader
• Sequence Alignment on the Cray MTA-2
  Shahid H. Bokhari and Jon R. Sauer
• Using Hybrid Alignment for Iterative Sequence Database Searches
  Yuheng Li, Mario Lauria, and Ralf Bundschuh
• A Fast Algorithm for the Exhaustive Analysis of 12-Nucleotide-Long DNA Sequences: Applications to Human Genomics
  Vicente Arnau and Ignacio Marín
• Realtime Primer Design for DNA chips
  Harald Simmler, H. Singpiel, and R. Männer
• Accurate method for fast design of diagnostic oligonucleotide probe sets for DNA microarrays
  Andreas Krause, Markus Kräutner, and Harald Meier
• Gene Clustering using Self-Organizing Maps and Particle Swarm Optimization
  X. Xiao, E. Dow, R. Eberhart, Z. Ben Miled, and R. J. Oppelt
• Protein Structure Prediction by Applying an Evolutionary Algorithm
  Richard O. Day, Gary B. Lamont, and Ruth Pachter
• PROSIDIS: a Special Purpose Processor for PROtein SImilarity DIScovery
  A. Marongiu, P. Palazzari, and V. Rosato
• Parallelisation of IBD computation for determining genetic disease map
  Nouhad J. Rizk
• Parallel Detection of Regulatory Elements with gMP
  Bertil Schmidt, Lin Feng, Amey Laud, and Yusdi Santoso
• Solving the Protein Threading Problem in Parallel
  Nicola Yanev and Rumen Andonov
• Phylogenetic Tree Inference on PC Architectures with AxML/PAxML
  Alexandros P. Stamatakis and Thomas Ludwig

HiCOMB 2002 Online Proceedings

First IEEE International Workshop on High Performance Computational Biology

Fort Lauderdale, FL, April 15, 2002

• Introductory Remarks
  S. Aluru and D.A. Bader
• TurboBLAST: A Parallel Implementation of BLAST Based on the TurboHub Architecture for High Performance Bioinformatics
  R.D. Bjornson, A.H. Sherman, S.B. Weston, N.Willard, and J. Wing
• Improving Performance of Multiple Sequence Alignment Analysis in Multi-client Environments
  U. Catalyurek, R. Ferreira, T. Kurc, and J. Saltz
• TCS: Estimating Gene Genealogies
  M. Clement, Q. Snell, P. Walker, D. Posada, and K.A. Crandall
• Parallel Genehunter:Implementation of a linkage analysis package for distributed memory architectures
  G. Conant, A. Wagner, S. Plimpton, W. Old, and P. Fain
• Parallel EST Clustering
  A. Kalyanaraman, S. Aluru, and S. Kothari, Iowa State University
• Parallel Out-of-core Algorithm for Genome-Scale Enumeration of Metabolic Systematic Pathways
  N.F. Samatova, A. Geist, G. Ostrouchov, and A.V. Melechko
• Massively Parallel Solutions for Molecular Sequence Analysis
  B. Schmidt, H. Schröder, and M. Schimmler
• Monte Carlo Simulation of HIV-1 Evolution in Response to Selection by Antibodies
  J. Silva and A. Hughes
• Aligning Two Fragmented Sequences
  V. Veeramachaneni, P. Berman, and W. Miller
• Quasiperiodic Biosequences and Modulo Incidence Matrices
  H. Wan and E. Song