Publications

[2019] - [2018] - [2017] - [2016] - [2015] - [2014] - [2013] - [2012] - [2011] - [2010] - [2009] - [2008] - [2007] - [2006]

2019

H. Lan, J. Meng, C. Hundt, B. Schmidt, M. Deng, X. Wang, W. Liu, Y. Qiao, S. Feng:
FeatherCNN: Fast Inference Computation with TensorGEMM on ARM Architectures,
IEEE Transactions on Parallel and Distributed Systems (TPDS), in press, 2019 (IF: 3.402)

H. Winther, M. Gutberlet, C. Hundt, T. Kaireit, T. Alsady, B. Schmidt, F. Wacker, Y. Sun, S. Dettmer, S.. Maschke, J. Hinrichs, S. Jambawalikar, M.R. Prince, G. Barr, J. Vogel‐Claussen:
Deep semantic lung segmentation for tracking potential pulmonary perfusion biomarkers in chronic obstructive pulmonary disease (COPD): The multi‐ethnic study of atherosclerosis COPD study,
Journal of Magnetic Resonance Imaging (JMRI), in press, 2019 (IF: 3.732)

L. Schmidt, S. Werner, T. Kemmer, S. Niebler, L. Ayadi, P. Johe, V. Marchand, T. Schirmeister, Y. Motorin, A. Hildebrandt, B. Schmidt, M. Helm:
Graphical workflow system for modification calling by machine learning of reverse transcription signatures Frontiers in Genetics,
in press, 2019 (IF: 3.517)

P. Jiang, J. Luo, Y. Wang, P. Deng, B. Schmidt, X. Tang, N. Chen, Limsoon Wong, L. Zhao:
kmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers,
Bioinformatics, in press, 2019 (IF: 5.481)

J. Zhang, H. Lan, Y. Chan, Y. Shang, B. Schmidt, W. Liu:
BGSA: a bit-parallel global sequence alignment toolkit for multi-core and many-core architectures,
Bioinformatics, in press, 2019 (IF: 5.481)

F. Kallenborn, C. Hundt, S. Böser, B. Schmidt:
Massively Parallel Computation of Atmospheric Neutrino Oscillation on CUDA-enabled Accelerators,
Computer Physics Communications, in press, 2018, doi:10.1016/j.cpc.2018.07.022 (IF: 3.74)

F. Büren, D. Jünger, R. Kobus, C. Hundt, B. Schmidt:
Suffix Array Construction on multi-GPU Systems,
ACM HPDC 2019 (acceptance rate: 20.5%)

R. Kobus, D. Jünger, C. Hundt, B. Schmidt:
Gossip: Efficient Communication Primitives for Multi-GPU Systems,
ACM ICPP 2019, (acceptance rate: 26%)

A. Weißenberger, B. Schmidt:
Massively Parallel ANS Decoding on GPUs,
ACM ICPP 2019, (acceptance rate: 26%)

Z. Yin, T. Zhang, A. Müller, H. Liu, Y. Wei, B. Schmidt, W. Liu:
Efficient Sort on AVX-512-based Multi-core and Many-Core Architectures,
IEEE HPCC 2019, accepted

Z. Yin, H. Zhang, K. Xu, Y. Chan, S. Peng, X. Wang, B. Schmidt, W. Liu:
XLCS: A New Bit-Parallel Longest Common Subsequence Algorithm on Xeon Phi Clusters,
IEEE HPCC 2019, accepted

2018

R. Leißa, K. Boesche, S. Hack, A. Pérard-Gayot, R. Membarth, P. Slusallek, A. Müller, B. Schmidt:
AnyDSL: A Partial Evaluation Framework for Programming High-Performance Libraries.
OOPSLA 2018

A. Weißenberger, B. Schmidt:
Massively Parallel Huffman Decoding on GPUs.
ICPP 2018, 27:1-27:10

K. Xu, R. Kobus, Y. Chan, P. Gao, X. Meng, Y. Wei, B. Schmidt, W. Liu:
SPECTR: Scalable Parallel Short Read Error Correction on Multi-core and Many-core Architectures.
ICPP 2018, 39:1-39:10

Jünger D, Hundt C, and Schmidt B (2018).
WarpDrive: Massively Parallel Hashing on Multi-GPU Nodes.
IPDPS 2018.

Winther H, Hundt C, Schmidt B, Czerner C, Bauersachs J, Wacker F, Vogel-Claussen J (2018).
ν-net: Deep Learning for Generalized Biventricular Cardiac Mass and Function Parameters,
JACC: Cardiovascular Imaging, in press, 2018 (IF: 10.19)

H. Zhang, Y. Chan, K. Fan, B. Schmidt, W. Liu:
Fast and Efficient Short Read Mapping based on a Succinct Hash Index,
BMC Bioinformatics, in press, 2018 (IF: 2.45)

Y. Liu, B. Schmidt:
LightSpMV: faster CUDA-compatible sparse matrix-vector multiplication using compressed sparse rows
Journal of Signal Processing Systems, 90(1):69-86, 2018 (IF:0.89)

J. Gonzalez-Dominguez, C. Hundt, B. Schmidt:
parSRA: A Portable Framework for the Parallel Execution of Short Read Aligners on Compute Clusters
Journal of Computational Science, in press, 2018 (IF: 1.75)

B. Schmidt, A. Hildebrandt:
Dedicated Bioinformatics Analysis Hardware,
in: Encyclopedia of Bioinformatics and Computational Biology (Elsevier), to appear

2017

Müller A, Hundt C, Hildebrandt A, Hankeln T, Schmidt B (2017).
MetaCache: Context-aware classification of metagenomic reads using minhashing,
Bioinformatics, btx520, https://doi.org/10.1093/bioinformatics/btx520

Kobus R, Hundt C, Müller A, and Schmidt, B (2017)
Accelerating metagenomic read classification on CUDA-enabled GPUs
BMC Bioinformatics, DOI 10.1186/s12859-016-1434-6

Duan X, Xu K, Chan Y, Hundt C, Schmidt B, Balaji P, Liu W (2017).
S-Aligner: Ultrascalable Read Mapping on Sunway Taihu Light.
2017 IEEE International Conference on Cluster Computing (CLUSTER), Honolulu, HI, 2017, pp. 36-46.

Schlarb M, Hundt C, and Schmidt B (2017).
SAUCE: A Web-Based Automated Assessment Tool for Teaching Parallel Programming.
Euro-Par 2015 International Workshops, Vienna, Austria, August 24-25, Revised Selected Papers, 2015, pp. 54–65.

Hundt C, Schlarb M, and Schmidt B.
SAUCE: A Web Application for Interactive Teaching and Learning of Parallel Programming.
Journal of Parallel and Distributed Computing, Volume 105, 2017, pp. 163–173, ISSN 0743-7315. (invited paper)

J. Schröder, A. Wirawan, B. Schmidt, A. Papenfuss:
CLOVE: classification of genomic fusions into structural variation events
BMC Bioinformatics 18(1): 346, 2017 (IF: 2.45)

B. Schmidt, A. Hildebrandt:
Next-Generation Sequencing: Big Data meets High Performance Computing
Drug Discovery Today, 22(4), pp. 712-717. 2017 (IF: 5.63),

Y. Liu, F. Ripp, R. Koeppel, H. Schmidt, S. Hellmann, M. Weber, C. Krombholz, B. Schmidt, T. Hankeln:
AFS: identification and quantification of species composition by metagenomic sequencing
Bioinformatics, 33(9): 1396-1398, 2017 (IF: 7.31)

S. Zhang, Z. Wang, Y. Peng, B. Schmidt, W. Liu:
Mapping of Option Pricing Algorithms onto Heterogeneous Many-Core Architectures,
The Journal of Supercomputing, 73(9): 3715-3737, 2017 (IF: 1.33)

D. Jünger, C.Hundt, J. González-Domínguez, B. Schmidt:
Speed and Accuracy Improvement of Higher-Order Epistasis Detection on CUDA-Enabled GPUs
Cluster Computing, 20(3): 1899-1908, 2017 (IF: 2.04)

H. Lan, W. Liu, Y. Liu, B. Schmidt:
SWhybrid: A Hybrid Parallel Framework for Large-Scale Protein Sequence Database Search,
IEEE IPDPS 2017, pp. 42-51, 2017 (acceptance rate: 22.8%)

Y. Chan, K. Xu, H. Lan, W. Liu, Y. Liu, B. Schmidt:
PUNAS: A Parallel Ungapped-Alignment-Featured Seed Verification Algorithm for Next-Generation Sequencing Read Alignment,
IEEE IPDPS 2017, pp. 52-61, 2017 (acceptance rate: 22.8%)

S. Peng, X: Zhang, S. Yang, W. Su, Z. Zhang, D. Dong, K. Lu, Y. Lu, X. Liao, B. Schmidt, W. Zhu, K.C. Li :
mD3DOCKxb: An Ultra-Scalable CPU-MIC Coordinated Virtual Screening Framework,
IEEE/ACM CCGRID 2017, pp. 671-676, 2017

2016

Hundt C, Hildebrandt A, and Schmidt B (2016).
rapidGSEA: Speeding Up Gene Set Enrichment Analysis on Multi-core CPUs and CUDA-Enabled GPUs.
BMC Bioinformatics 17 (2016): 394.

Jünger D, Hundt C, González-Domínguez J, and Schmidt B (2016).
Ultra-Fast Detection of Higher-Order Epistatic Interactions on GPUs.
4th International Workshop on Parallelism in Bioinformatics (PBio 2016), Grenoble, France, August 2016.

J. Gonzalez-Dominguez, Y. Liu, J. Tourino, B. Schmidt:
MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems, Bioinformatics,
32(24):3826-3828 (IF: 5.76)

J. Shao, Q. Yang, H.V. Dang, B. Schmidt, S. Kramer:
Scalable Clustering by Iterative Partitioning and Point Attractor Representations,
ACM Transactions on Knowledge Discovery from Data (TKDD), 11(1):5, 2016 (IF: 1.147)

J. González-Domínguez, B. Schmidt:
ParDRe: Faster Parallel Duplicated Reads Removal Tool for Sequencing Studies,
Bioinformatics, 32(10):1562-4, 2016 (IF: 4.98)

Z. Zheng, X. Wei, A. Hildebrandt, B. Schmidt:
A computational method for studying the relation between alternative splicing and DNA methylation,
Nucleic Acids Research, 44 (2): e19, 2016 (IF: 9.11)

J. González-Domínguez, Y. Liu, B. Schmidt:
Parallel and scalable short-read alignment on multi-core clusters using UPC++,
PLOS One, 11(1), 2016 (IF: 3.23)

J. González-Domínguez, J, S. Ramos, J. Touriño, B. Schmidt:
Parallel Pairwise Epistasis Detection on Heterogeneous Computing Architectures,
IEEE Transactions on Parallel and Distributed Systems, 27(8):2329-2340, 2016 (IF: 2.17)

T.T. Tran, Y. Liu, B. Schmidt:
Bit-parallel approximate pattern matching: Kepler GPU versus Xeon Phi,
Parallel Computing, 54:128-138, 2016 (IF: 1.51)

H.V. Dang, B. Schmidt, A. Hildebrandt, T.T Tran, A.K. Hildebrandt:
CUDA-enabled Hierarchical Ward Clustering of Protein Structures based on the Nearest Neighbour Chain Algorithm,
International Journal of High Performance Computing Applications, 30(2): 200-211, 2016 (IF: 1.63)

Y. Liu, T. Hankeln, B. Schmidt:
Parallel and space-efficient construction of Burrows-Wheeler transform and suffix array for big genome data,
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 13(3):592-598, 2016 (IF: 1.536)

Y. Liu, M. Loewer, S. Aluru, B. Schmidt:
SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations,
BMC Systems Biology 10(S2): 47, 2016 (IF: 2.43)

H. Lan, Y. Chan, K. Xu, B. Schmidt, S. Peng, W. Liu:
Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters,
BMC Bioinformatics 17(S-9): 267, 2016 (IF: 2.58)

J.C. Kaessens, L. Wienbrandt, J. González-Domínguez, B. Schmidt, M. Schimmler,
Combining GPU and FPGA Technology for Efficient Exhaustive Interaction Analysis in GWAS,
27th IEEE International Conference on Application-specific Systems, Architectures and Processors (IEEE ASAP 2016), 2016

2015

Liu, Y and Schmidt, B (2015).
LightSpMV: faster CSR-based sparse matrix-vector multiplication on CUDA-enabled GPUs
26th IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP 2015), 2015, in press. (Best Paper Award)

Dang, H, Schmidt, B, Hildebrandt, A, Tran, T.T and Hildebrandt, A.K (2015).
CUDA-enabled Hierarchical Ward Clustering of Protein Structures based on the Nearest Neighbour Chain Algorithm
International Journal of High Performance Computing Applications, 2015.

González-Domínguez, J and Schmidt, B (2015).
GPU-Accelerated Exhaustive Search for Third-Order Epistatic Interactions in Case-Control Studies
The Journal of Computational Science, 8:93-100.

González-Domínguez, J and Schmidt, B (2015).
Using a CUDA-Accelerated PGAS Model on a GPU Cluster for Bioinformatics
In: GPU Technology Conference (GTC 2015).

González-Domínguez, J, Kässens, JC, Wienbrandt, L, and Schmidt, B (2015).
Large-Scale Genome-Wide Association Studies on a GPU Cluster Using a CUDA-Accelerated PGAS Programming Model
International journal of High Performance Computing Applications, Accepted.

González-Domínguez, J, Ramos, S, Touriño, J, and Schmidt, B (2015).
Parallel Pairwise Epistasis Detection on Heterogeneous Computing Architectures
IEEE Transactions on Parallel and Distributed Systems, Accepted.

González-Domínguez, J, Wienbrandt, L, Kässens, JC, Ellinghaus, D, Schimmler, M, and Schmidt, B (2015).
Parallelizing Epistasis Detection in GWAS on FPGA and GPU-accelerated Computing Systems
IEEE/ACM Transactions on Computational Biology and Bioinformatics, Accepted.

Kässens, JC, Wienbrandt, L, González-Domínguez, J, Schmidt, B, and Schimmler, M (2015).
High-Speed Exhaustive 3-locus Interaction Epistasis Analysis on FPGAs
The Journal of Computational Science, 9:131-136.

Liu, Y, González-Domínguez, J, and Schmidt, B (2015).
Faster Compressed Sparse Row (CSR)-based Sparse Matrix-Vector Multiplication using CUDA
In: GPU Technology Conference (GTC 2015).

Tran, T.T, Giraud, M, and Varré, J (2015)
Perfect hashing structures for parallel similarity searches
In: Proceedings of the 14th IEEE International Workshop on High Performance Computational Biology (HICOMB), Hyderabad, India, pp. 332-341.

2014

Catalán, S, González-Domínguez, J, Mayo, R, and Quintana-Ortí, ES (2014).
Analyzing the Energy Efficiency of the Memory Subsystem in Multicore Processors
In: 12th IEEE International Symposium on Parallel and Distributed Processing with Applications (ISPA 2012), pp. 10-17.

González-Domínguez, J, Marques, OA, Martín, MJ, and Touriño, J (2014).
A 2D Algorithm with Asymmetric Workload for the UPC Conjugate Gradient Method
Journal of Supercomputing, 70(2):816-829.

González-Domínguez, J, Schmidt, B, Kässens, JC, and Wienbrandt, L (2014).
Hybrid CPU/GPU Acceleration of Detection of 2-SNP Epistatic Interactions in GWAS
In: 20th International European Conference on Parallel and Distributed Computing (Euro-Par 2014), ed. by Lecture Notes on Computer Science, vol. 8632, pp. 680-691.

Kässens, JC, González-Domínguez, J, Wienbrandt, L, and Schmidt, B (2014).
UPC++ for Bioinformatics: A Case Study Using Genome-Wide Association Studies
In: 15th IEEE International Conference on Cluster Computing, pp. 248-256.

Liu, Y and Schmidt, B (2014).
CUSHAW2-GPU: empowering faster gapped short-read alignment using GPU computing
IEEE Design & Test of Computers, 31(1):31 - 39.

Liu, Y and Schmidt, B (2014).
Multiple Protein Sequence Alignment with MSAProbs
In: Multiple Sequence Alignment Methods, ed. by Russell, David J. Springer, vol. 1079, chap. 14, pp. 211-218. Methods in Molecular Biology.

Liu, Y and Schmidt, B (2014).
SWAPHI: Smith-Waterman protein database search on Xeon Phi coprocessors
In: 25th IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP 2014), pp. 184-185.

Liu, Y and Schmidt, B (2014).
GSWABE: faster GPU-accelerated sequence alignment with optimal alignment retrieval for short DNA sequences
Concurrency and Computation: Practice and Experience, accepted.

Liu, Y and Schmidt, B (2014).
CUSHAW Software Package: Harnessing CUDA-enabled GPUs for Next Generation Sequencing Read Alignment
In: GPU Technology Conference 2014.

Liu, Y and Schmidt, B (2014).
Faster GPU-accelerated Smith-Waterman algorithm with alignment backtracking for short DNA sequences
In: Lecture Notes in Computer Science, vol. 8385, Springer.

Liu, Y, Popp, B, and Schmidt, B (2014).
CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding
PLOS ONE, 9(1): e86869.

Liu, Y, Tran, T.T, Lauenroth F, and Schmidt, B (2014).
SWAPHI-LS: Smith-Waterman Algorithm on Xeon Phi Coprocessors for Long DNA Sequences
In: IEEE Cluster 2014, pp. 257-265.

Mallón, DA, Taboada, GL, Teijeiro, C, González-Domínguez, J, Gómez, A, and Wibecan, B (2014).
Scalable PGAS Collective Operations in NUMA Clusters
Cluster Computing, 17(4):1473-1495.

Ripp, F, Krombholz, CF, Liu, Y, Weber, M, Schäfer, A, Schmidt, B, Köppel, R, and Hankeln, T (2014).
All-Food-Seq (AFS): a quantifiable screen for species in biological samples by deep DNA sequencing
BMC Genomics, 15(639).

Tran, T.T, Schindel, S, Liu, Y, and Schmidt, B (2014).
Bit-Parallel approximate pattern matching on the Xeon Phi coprocessor
In: 26th International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD 2014), pp. 81-88.

Wienbrandt, L, Kässens, JC, González-Domínguez, J, Schmidt, B, Ellinghaus, D, and Schimmler, M (2014).
FPGA-Based Acceleration of Detecting Statistical Epistasis in GWAS
In: 14th International Conference on Computational Science (ICCS 2014).

Wirawan, A, Harris, RS, Liu, Y, Schmidt, B, and Schröder, J (2014).
HECTOR: A parallel multistage homopolymer spectrum based error corrector for 454 sequencing data
BMC Bioinformatics, 15(131).

2013

Dang, H and Schmidt, B (2013).
CUDA-enabled Sparse Matrix–Vector Multiplication on GPUs using atomic operations
Parallel Computing, Volume 39, Issue 11, November 2013, Pages 737-750, ISSN 0167-8191.

Expósito, RR, Taboada, GL, Ramos, S, González-Domínguez, J, Touriño, J, and Doallo, R (2013).
Analysis of I/O Performance on an Amazon EC2 Cluster Compute and High I/O Platform
The Journal of Grid Computing, 11(4):613-631.

González-Domínguez, J (2013).
UPCBLAS: A Numerical Library for Unified Parallel C with Architecture-Aware Optimizations
PhD Thesis, University of A Coruña.

González-Domínguez, J, García-López, O, Taboada, GL, Martín, MJ, and Touriño, J (2013).
Performance Evaluation of Sparse Matrix Products in UPC
The Journal of Supercomputing, 64(1):100–109.

González-Domínguez, J, Martín, MJ, Taboada, GL, Expósito, RR, and Touriño, J (2013).
The Servet 3.0 Benchmark Suite: Characterization of Network Performance Degradation
Computers and Electrical Engineering, 39(8):2483-2493.

Liu, Y, Schroeder, J, and Schmidt, B (2013).
Musket: a multistage k-mer spectrum based error corrector for Illumina sequence data
Bioinformatics, 29(3):308-315.

Liu, Y, Wirawan, A, and Schmidt, B (2013).
CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions
BMC Bioinformatics, 14(117).

2012

Dang, H and Schmidt, B (2012).
The Sliced COO format for Sparse Matrix-Vector Multiplication on CUDA-enabled GPUs
In: International Conference on Computational Science.

Georganas, E, González-Domínguez, J, Solomonik, E, Zheng, Y, Touriño, J, and Yelick, K (2012).
Communication Avoiding and Overlapping for Numerical Linear Algebra
In: 24th ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis (SC'12).

González-Domínguez, J, Marques, OA, Martín, MJ, Taboada, GL, and Touriño, J (2012).
Design and Performance Issues of Cholesky and LU Solvers using UPCBLAS
In: 10th IEEE International Symposium on Parallel and Distributed Processing with Applications (ISPA 2012), pp. 40–47.

González-Domínguez, J, Martín, MJ, Taboada, GL, Touriño, J, Doallo, R, Mallón, DA, and Wibecan, B (2012).
UPCBLAS: A Library for Parallel Matrix Computations in Unified Parallel C
Concurrency and Computation: Practice and Experience, 24(14):1645–1667.

González-Domínguez, J, Taboada, GL, Fraguela, BB, Martín, MJ, and Touriño, J (2012).
Automatic Mapping of Parallel Applications on Multicore Architectures using the Servet Benchmark Suite
Computers and Electrical Engineering, 32(2):258–269.

Lim, KG, Kwoh, CK, Hsu, LY, and Wirawan, A (2012).
Review of tandem repeat search tools: a systematic approach to evaluating algorithmic performance
Briefings in Bioinformatics.

Liu, Y (2012).
Design and implementation of parallel bioinformatics algorithms on heterogeneous computing architectures
PhD thesis, Nanyang Technological University (Singapore).

Liu, Y and Schmidt, B (2012).
Long read alignment based on maximal exact match seeds
Bioinformatics, 28(18):i318-i324.

Liu, Y and Schmidt, B (2012).
Evaluation of GPU-based seed generation for computational genomics using Burrows-Wheeler transform
In: 11th IEEE International Workshop on High Performance Computational Biology (HiCOMB 2012), pp. 684-690, IEEE.

Liu, Y, Schmidt, B, and Maskell, DL (2012).
A fast CUDA compatible short read aligner to large genomes
In: GPU Technology Conference 2012 (GTC 2012).

Liu, Y, Schmidt, B, and Maskell, DL (2012).
CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform
Bioinformatics, 28(14):1830-1837.

Nguyen, TD, Schmidt, B, Zheng, Z, and Kwoh, CK (2012).
Large-Scale Clustering of Short Reads for Metagenomics on GPUs
In: Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data, ed. by Mourad Elloumi and Albert Y. Zomaya. Wiley-Blackwell, chap. 44, pp. 1003-1022.

Schmidt, B, Aribowo, H, and Dang, H (2012).
Iterative Sparse Matrix-Vector Multiplication for Accelerating the Block Wiedemann Algorithm over GF(2) on Multi-GPU Systems
Concurrency and Computation: Practice and Experience.

Wirawan, A, Kwoh, CK, Chew, PTK, Aquino, MCD, Loon, SC, See, J, Zheng, C, and Lin, W (2012).
Feature Selection for Computer-Aided Angle Closure Glaucoma Mechanism Detection
Journal of Medical Imaging and Health Informatics , 2(4):438-444.

2011

Giraud, M, Schmidt, B, Janot, S, and Varre, JS (2011).
Many-core high-performance computing in Bioinformatics
In: Advances in Genomic Sequence Analysis and Pattern Discovery, ed. by Laura Elnitski, Helen Piontkivska, Lonnie R Welch. World Scientific, chap. 8, pp. 179-208.

González-Domínguez, J, García-López, O, Taboada, GL, Martín, MJ, and Touriño, J (2011).
SparseBLAS Products in UPC: An Evaluation of Storage Formats
In: 11th International Conference on Computational and Mathematical Methods in Science and Engineering (CMMSE 2011), pp. 605–617.

González-Domínguez, J, Martín, MJ, Taboada, GL, and Touriño, J (2011).
Dense Triangular Solvers on Multicore Clusters using UPC
In: 11th International Conference on Computational Science (ICCS 2011).

Kuttippurathu, L, Hsing, M, Liu, Y, Schmidt, B, Maskell, DL, Lee, K, He, A, Pu, WT, and Kong, SW (2011).
CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments.
Bioinformatics, 27(5):715-7.

Ligowski, L, Rudnicki, W, Liu, Y, and Schmidt, B (2011).
Accurate scanning of sequence databases with the Smith-Waterman algorithm
GPU Computing Gems:155-172.

Liu, W, Schmidt, B, Liu, Y, and Müller-Wittig, W (2011).
Mapping of the BLASTP algorithm onto GPU clusters
17th IEEE International Conference on Parallel and Distributed Systems (ICPADS 2011):236-243.

Liu, Y, Schmidt, B, and Maskell, DL (2011).
Parallelized short read assembly of large genomes using de Bruijn graphs.
BMC Bioinformatics, 12:354.

Liu, Y, Schmidt, B, and Maskell, DL (2011).
DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI.
BMC Bioinformatics, 12:85.

Liu, Y, Schmidt, B, and Maskell, DL (2011).
An ultrafast scalable many-core motif discovery algorithm for multiple GPUs
10th IEEE International Workshop on High Performance Computational Biology (HiCOMB 2011):428-434.

Schmidt, B, Aribowo, H, and Dang, H (2011).
Iterative Sparse Matrix-Vector Multiplication for Integer Factorization on GPUs
In: Euro-Par 2011 Parallel Processing - 17th International Conference, Euro-Par 2011, Bordeaux, France, August 29 - September 2, 2011, vol. 6853, pp. 413-424, Springer. Lecture Notes in Computer Science.

Tran, TT, Giraud, M, and Varré, J (2011).
Bit-Parallel Multiple Pattern Matching
In: 9th Parallel Processing and Applied Mathematics, vol. 2, pp. 292 - 301, Springer. Lecture Notes in Computer Science.

Zhang, Z, Kwoh, CK, Liu, J, Yin, F, Wirawan, A, Cheung, C, Baskarang, M, Aung, T, and Wong, TY (2011).
MRMR Optimized Classification for Automatic Glaucoma Diagnosis
In: IEEE Engineering in Medicine and Biology Society, pp. 6228 - 6231 .

2010

González-Domínguez, J, Taboada, GL, Fraguela, BB, Martín, MJ, and Touriño, J (2010).
Servet: A Benchmark Suite for Autotuning on Multicore Clusters
In: 24th IEEE International Parallel and Distributed Processing Symposium (IPDPS 2010).

Liu, Y, Schmidt, B, and Maskell, DL (2010).
MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities.
Bioinformatics, 26(16):1958-64.

Liu, Y, Schmidt, B, and Maskell, DL (2010).
CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions.
BMC Res Notes, 3:93.

Liu, Y, Schmidt, B, and Maskell, DL (2010).
Parallel bioinformatics algorithms for CUDA-enabled GPUs
Bioinformatics: High Performance Parallel Computer Architectures:117–137.

Liu, Y, Schmidt, B, Liu, W, and Maskell, DL (2010).
CUDA-MEME: accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units
Pattern Recognition Letters, 31(14):2170 - 2177.

Schmidt, B (2010).
Bioinformatics: High Performance Parallel Computer Architectures
Taylor & Francis/CRC Press.

Wirawan, A, Kwoh, CK, and Schmidt, B (2010).
Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures
BIOINFORMATICS, 26(10):1368-1369.

Wirawan, A, Kwoh, CK, Hsu, LY, and Koh, TH (2010).
INVERTER: INtegrated Variable numbER Tandem rEpeat findeR
In: Computational Systems-Biology and Bioinformatics, ed. by Chan, J. H. Ong Y. S. Cho S. B.. Springer, vol. 115, chap. 4, pp. 151-164. Communications in Computer and Information Science.

2009

González-Domínguez, J, Martín, MJ, Taboada, GL, Touriño, J, Doallo, R, and Gómez, A (2009).
A Parallel Numerical Library for UPC
In: 15th International European Conference on Parallel and Distributed Computing (Euro-Par 2009), vol. 5704, pp. 630-641. Lecture Notes on Computer Science.

Liu, Y, Maskell, DL, and Schmidt, B (2009).
CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units.
BMC Res Notes, 2:73.

Liu, Y, Schmidt, B, and Maskell, DL (2009).
MSA-CUDA: multiple sequence alignment on graphics processing units with CUDA
20th IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP 2009):121-128. (Best Paper Award)

Liu, Y, Schmidt, B, and Maskell, DL (2009).
Parallel reconstruction of neighbor-Joining trees for large multiple sequence alignments using CUDA
8th IEEE International Workshop on High Performance Computational Biology (HiCOMB 2009):1-8.

Schmidt, B, Chen, C, Liu, W, and Mitchell, W (2009).
PheGee@Home: A Grid-based Tool for Comparative Genomics
In: Handbook of Research on Compuational Grid Technologies for Life Science, Biomedicine and Healthcare, ed. by Mario Cannataro. IGI Global, chap. 808, pp. 1885-1903.

Wirawan, A, Schmidt, B, and Kwoh, CK (2009).
Pairwise Distance Matrix Computation for Multiple Sequence Alignment on the Cell Broadband Engine
In: Computational Science - Iccs 2009, Part I, ed. by Allen, G. Nabrzyski J. Seidel E. Dongarra J. VanAlbada G. D. Sloot and Pma. Springer, vol. 5544, chap. 1, pp. 954-963. Lecture Notes in Computer Science.

Wirawan, A, Schmidt, B, Zhang, H, and Kwoh, CK (2009).
High performance protein sequence database scanning on the Cell Broadband Engine
Scientific Computing, 17(1-2):97-111.

2008

Hieu, NT, Kwoh, CK, Wirawan, A, and Schmidt, B (2008).
Applications of Heterogeneous Structure of Cell Broadband Engine Architecture for Biological Database Similarity Search
In: The 2nd International Conference onBioinformatics and Biomedical Engineering, pp. 5-8.

Le, M, Dang, H, Lim, E, and Datta, A (2008).
WikiNetViz: Visualizing friends and adversaries in implicit social networks
In: IEEE International Conference on Intelligence and Security Informatics, ISI 2008, Taipei, Taiwan, June 17-20, 2008, Proceedings, pp. 52-57, IEEE.

Wirawan, A, Kwoh, CK, Hieu, NT, and Schmidt, B (2008).
CBESW: Sequence Alignment on the Playstation 3
BMC Bioinformatics, 9:377.

Wirawan, A, Schmidt, B, and Kwoh, CK (2008).
Parallel DNA sequence alignment on the Cell Broadband Engine
In: Parallel Processing and Applied Mathematics, ed. by Wyrzykowski, R. Dongarra J. Karczewski K. Wasniewski J.. Springer, vol. 4967, chap. 1, pp. 1249-1256. Lecture Notes in Computer Science.

2007

Schmidt, B, Liu, W, and Chen, C (2007).
Hierarchical Grid Computing for High Performance Bioinformatics
In: Grids for Bioinformatics and Computational Biology, ed. by El-Ghazali Talbi, Albert Y. Zomaya. Wiley & Sons, chap. 5, pp. 87-121.

2006

Wirawan, A and Schmidt, B (2006).
Parallel discovery of transcription factor binding sites
In: IEEE Asia Pacific Conference on Circuits and Systems, pp. 700-703, IEEE.