Publications in collaboration with researchers from Johannes Gutenberg University of Mainz (18)

2018

  1. parSRA: A framework for the parallel execution of short read aligners on compute clusters

    Journal of Computational Science, Vol. 25, pp. 134-139

2017

  1. Parallel programming: Concepts and practice

    Elsevier Inc., pp. 1-403

  2. Speed and accuracy improvement of higher-order epistasis detection on CUDA-enabled GPUs

    Cluster Computing, Vol. 20, Núm. 3, pp. 1899-1908

  3. Ultra-fast detection of higher-order epistatic interactions on GPUs

    Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

2016

  1. Combining GPU and FPGA Technology for Efficient Exhaustive Interaction Analysis in GWAS

    2016 IEEE 27TH INTERNATIONAL CONFERENCE ON APPLICATION-SPECIFIC SYSTEMS, ARCHITECTURES AND PROCESSORS (ASAP)

  2. Combining GPU and FPGA technology for efficient exhaustive interaction analysis in GWAS

    Proceedings of the International Conference on Application-Specific Systems, Architectures and Processors

  3. MSAProbs-MPI: Parallel multiple sequence aligner for distributed-memory systems

    Bioinformatics, Vol. 32, Núm. 24, pp. 3826-3828

  4. ParDRe: Faster parallel duplicated reads removal tool for sequencing studies

    Bioinformatics, Vol. 32, Núm. 10, pp. 1562-1564

  5. Parallel and scalable short-read alignment on multi-core clusters using UPC++

    PLoS ONE, Vol. 11, Núm. 1

  6. Parallel pairwise epistasis detection on heterogeneous computing architectures

    IEEE Transactions on Parallel and Distributed Systems, Vol. 27, Núm. 8, pp. 2329-2340

2015

  1. GPU-accelerated exhaustive search for third-order epistatic interactions in case-control studies

    Journal of Computational Science, Vol. 8, pp. 93-100

  2. High-speed exhaustive 3-locus interaction epistasis analysis on FPGAs

    Journal of Computational Science, Vol. 9, pp. 131-136

  3. Large-scale genome-wide association studies on a GPU cluster using a CUDA-accelerated PGAS programming model

    International Journal of High Performance Computing Applications, Vol. 29, Núm. 4, pp. 506-510

  4. Parallelizing epistasis detection in GWAS on FPGA and GPU-accelerated computing systems

    IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 12, Núm. 5, pp. 982-994

2014

  1. A 2D algorithm with asymmetric workload for the UPC conjugate gradient method

    Journal of Supercomputing, Vol. 70, Núm. 2, pp. 816-829

  2. FPGA-based acceleration of detecting statistical epistasis in GWAS

    Procedia Computer Science

  3. Hybrid CPU/GPU acceleration of detection of 2-SNP epistatic interactions in GWAS

    Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

  4. UPC++ for bioinformatics: A case study using genome-wide association studies

    2014 IEEE International Conference on Cluster Computing, CLUSTER 2014