Our group focuses on the design, implementation and evaluation of scalable tools for genomic sequence analysis (Bioinformatics) and computational science applications. Our approach is based on using modern high performance computing (HPC) technologies, such as
Using these platforms, we design efficient parallel algorithms that can serve as a foundation for a wide variety of tools.
2018
Parallel Programming. (2018). Elsevier. DOI
2017
Schmidt, B., Gonzalez-Dominguez, J., Hundt, C., and Schlarb, M. (2017). Parallel Programming Concepts and Practice. Morgan Kaufmann.
2011
Schmidt, B. (2011). Bioinformatics High Performance Parallel Computer Architectures. CRC Press.
2025
Beyer, A., Henkys, V., Kobus, R., et al. (2025). cuTeBool: Fast and Scalable Boolean Matrix Factorization on GPUs Using Tensor Cores. In Lecture Notes in Computer Science (pp. 249-264). Springer Nature Switzerland. DOI
2024
Heilmann, X., Henkys, V., Apeldoorn, D., et al. (2024). Studying Privacy Aspects of Learned Knowledge Bases in the Context of Synthetic and Medical Data. In Studies in Health Technology and Informatics. IOS Press. DOI
2023
Kobus, R., Nelgen, J., Henkys, V., and Schmidt, B. (2023). Faster Segmented Sort on GPUs (Vols. 14100, pp. 664-678). DOI Author/Publisher URL
Niebler, S., Schmidt, B., Tost, H., and Spichtinger, P. (2023). Automated Identification and Location of Three Dimensional Atmospheric Frontal Systems. In Lecture Notes in Computer Science (pp. 3-17). Springer Nature Switzerland. DOI
2019
Schmidt, B., and Hildebrandt, A. (2019). Dedicated Bioinformatics Analysis Hardware. In Encyclopedia of Bioinformatics and Computational Biology (pp. 1142-1150). Academic Press.
2017
Liu, Y., and Schmidt, B. (2017). CUSHAW Suite: Parallel and Efficient Algorithms for NGS Read Alignment. In Algorithms for Next-Generation Sequencing Data (pp. 203-233). Springer International Publishing. DOI
2014
Liu, Y., and Schmidt, B. (2014). Multiple Protein Sequence Alignment with MSAProbs. In MULTIPLE SEQUENCE ALIGNMENT METHODS (Vols. 1079, pp. 211-218). DOI Author/Publisher URL
2011
Varré, J.-S., Schmidt, B., Janot, S., and Giraud, M. (2011). Manycore High-Performance Computing in Bioinformatics. In Science, Engineering, and Biology Informatics (pp. 179-207). WORLD SCIENTIFIC. DOI
Ligowski, Łukasz, Rudnicki, W. R., Liu, Y., and Schmidt, B. (2011). Accurate Scanning of Sequence Databases with the Smith-Waterman Algorithm. In GPU Computing Gems Emerald Edition (pp. 155-171). Elsevier. DOI
2007
Schmidt, B., Chen, C., and Liu, W. (2007). Hierarchical Grid Computing for High‐Performance Bioinformatics (pp. 87-121). Wiley. DOI
2026
Yan, L., Yin, Z., Chang, Q., et al. (2026). SWBWA: A Highly Efficient NGS Aligner on the New Sunway Architecture. EURO-PAR 2025: PARALLEL PROCESSING, PT III, 15902, 183-196. DOI Author/Publisher URL
2025
Zhang, T., Xu, X., Yin, Z., et al. (2025). RabbitTClust2: Fast, Scalable, and Versatile Clustering for Massive Genomic Datasets. 2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 1495-1502. DOI
2024
Niebler, S., Schmidt, B., Spichtinger, P., Tost, H. (2024). Scalable GPU-Enabled Creation of Three DimensionalWeather Fronts. PASC 2024: PROCEEDINGS OF THE PLATFORM FOR ADVANCED SCIENTIFIC COMPUTING CONFERENCE. Published. DOI Author/Publisher URL
Wang, M., Yin, Z., Yan, L., et al. (2024). RabbitTrim: Highly Optimized Trimming of Illumina Sequencing Data on Multi-core Platforms. BIOINFORMATICS RESEARCH AND APPLICATIONS, PT II, ISBRA 2024, 14955, 26-37. DOI Author/Publisher URL
Weissenberger, A., Schmidt, B. (2024). Massively Parallel Inverse Block-sorting Transforms for bzip2 Decompression on GPUs. 53RD INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING, ICPP 2024, 856-865. DOI Author/Publisher URL
Yan, L., Yin, Z., Li, J., et al. (2024). RabbitSAlign: Accelerating Short-Read Alignment for CPU-GPU Heterogeneous Platforms. BIOINFORMATICS RESEARCH AND APPLICATIONS, PT II, ISBRA 2024, 14955, 83-94. DOI Author/Publisher URL
2022
Müller, A., Schmidt, B., Membarth, R., et al. (2022). AnySeq/GPU. Proceedings of the 36th ACM International Conference on Supercomputing, 1-11. DOI
Henkys, V., Schmidt, B., Berger, N. (2022). Online Event Selection for Mu3e using GPUs. 2022 21ST INTERNATIONAL SYMPOSIUM ON PARALLEL AND DISTRIBUTED COMPUTING (ISPDC 2022), 17-24. DOI Author/Publisher URL
Henkys, V., Schmidt, B., Berger, N. (2022). Online Event Selection for Mu3e using GPUs. ISPDC, 17-24. Author/Publisher URL
Müller, A., Schmidt, B., Membarth, R., et al. (2022). AnySeq/GPU: a novel approach for faster sequence alignment on GPUs. In L. Rauchwerger, K. W. Cameron, D. S. Nikolopoulos, and D. N. Pnevmatikatos (eds.), ICS (pp. 20:1-20:1). ACM. Author/Publisher URL
Yan, L., Yin, Z., Zhang, H., et al. (2022). RabbitQCPlus: More Efficient Quality Control for Sequencing Data. 2022 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE, BIBM, 619-626. DOI Author/Publisher URL
2021
Cascitti, J., Niebler, S., Müller, A., Schmidt, B. (2021). RNACache: Fast Mapping of RNA-Seq Reads to Transcriptomes Using MinHashing. 367-381. DOI
Kobus, R., Mueller, A., Juenger, D., et al. (2021). MetaCache-GPU: Ultra-Fast Metagenomic Classification. 50TH INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING. Published. DOI Author/Publisher URL
Weissenberger, A., Schmidt, B. (2021). Accelerating JPEG Decompression on GPUs. 2021 IEEE 28TH INTERNATIONAL CONFERENCE ON HIGH PERFORMANCE COMPUTING, DATA, AND ANALYTICS (HIPC 2021), 121-130. DOI Author/Publisher URL
2020
Duan, X., Gao, P., Zhang, M., et al. (2020). Cell-List based Molecular Dynamics on Many-Core Processors: A Case Study on Sunway TaihuLight Supercomputer. PROCEEDINGS OF SC20: THE INTERNATIONAL CONFERENCE FOR HIGH PERFORMANCE COMPUTING, NETWORKING, STORAGE AND ANALYSIS (SC20). Published. DOI Author/Publisher URL
Duan, X., Gao, P., Zhang, M., et al. (2020). Neighbor-list-free Molecular Dynamics on Sunway TaihuLight Supercomputer. PROCEEDINGS OF THE 25TH ACM SIGPLAN SYMPOSIUM ON PRINCIPLES AND PRACTICE OF PARALLEL PROGRAMMING (PPOPP ’20), 413-414. DOI Author/Publisher URL
Juenger, D., Kobus, R., Mueller, A., et al. (2020). WarpCore: A Library for fast Hash Tables on GPUs. 2020 IEEE 27TH INTERNATIONAL CONFERENCE ON HIGH PERFORMANCE COMPUTING, DATA, AND ANALYTICS (HIPC 2020), 11-20. DOI Author/Publisher URL
Müller, A., Schmidt, B., Hildebrandt, A., et al. (2020). AnySeq: A High Performance Sequence Alignment Library based on Partial Evaluation. IPDPS, 1030-1040. Author/Publisher URL
Schmidt, B., Hundt, C. (2020). cuDTW plus plus : Ultra-Fast Dynamic Time Warping on CUDA-Enabled GPUs. EURO-PAR 2020: PARALLEL PROCESSING, 12247, 597-612. DOI Author/Publisher URL
Xu, K., Duan, X., Meng, X., et al. (2020). SWMapper: Scalable Read Mapper on SunWay TaihuLight. PROCEEDINGS OF THE 49TH INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING, ICPP 2020. Published. DOI Author/Publisher URL
2019
Kobus, R., Jünger, D., Hundt, C., Schmidt, B. (2019). Gossip. Proceedings of the 48th International Conference on Parallel Processing, 1-10. DOI
Yin, Z., Zhang, T., Muller, A., et al. (2019). Efficient Parallel Sort on AVX-512-Based Multi-Core and Many-Core Architectures. 2019 IEEE 21st International Conference on High Performance Computing and Communications; IEEE 17th International Conference on Smart City; IEEE 5th International Conference on Data Science and Systems (HPCC/SmartCity/DSS), 168-176. DOI
Büren, F., Jünger, D., Kobus, R., et al. (2019). Suffix Array Construction on Multi-GPU Systems. Proceedings of the 28th International Symposium on High-Performance Parallel and Distributed Computing, 183-194. DOI
Weissenberger, A., Schmidt, B. (2019). Massively Parallel ANS Decoding on GPUs. PROCEEDINGS OF THE 48TH INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING (ICPP 2019). Published. DOI Author/Publisher URL
Yin, Z., Zhang, H., Xu, K., et al. (2019). XLCS: A New Bit-Parallel Longest Common Subsequence Algorithm on Xeon Phi Clusters. In Z. Xiao, L. T. Yang, P. Balaji, et al. (eds.), HPCC/SmartCity/DSS (pp. 1477-1483). IEEE. Author/Publisher URL
2018
Xu, K., Kobus, R., Chan, Y., et al. (2018). SPECTR. Proceedings of the 47th International Conference on Parallel Processing, 1-10. DOI
Juenger, D., Hundt, C., Schmidt, B. (2018). WarpDrive: Massively Parallel Hashing on Multi-GPU Nodes. 2018 32ND IEEE INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM (IPDPS), 441-450. DOI Author/Publisher URL
Kobus, R., Lamoth, A., Mueller, A., et al. (2018). cuBool: Bit-Parallel Boolean Matrix Factorization on CUDA-enabled Accelerators. 2018 IEEE 24TH INTERNATIONAL CONFERENCE ON PARALLEL AND DISTRIBUTED SYSTEMS (ICPADS 2018), 465-472. DOI Author/Publisher URL
Kobus, R., Lamoth, A., Müller, A., et al. (2018). cuBool: bit-parallel Boolean Matrix Factorization on CUDA-enabled accelerators. Seiten: 465-472. Author/Publisher URL
Weissenberger, A., Schmidt, B. (2018). Massively Parallel Huffman Decoding on GPUs. PROCEEDINGS OF THE 47TH INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING. Published. DOI Author/Publisher URL
Xu, K., Kobus, R., Chan, Y., et al. (2018). SPECTR: Scalable Parallel Short Read Error Correction on Multi-core and Many-core Architectures. PROCEEDINGS OF THE 47TH INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING. Published. DOI Author/Publisher URL
2017
Chan, Y., Xu, K., Lan, H., et al. (2017). PUNAS: A Parallel Ungapped-Alignment-Featured Seed Verification Algorithm for Next-Generation Sequencing Read Alignment. 2017 31ST IEEE INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM (IPDPS), 52-61. DOI Author/Publisher URL
Duan, X., Xu, K., Chan, Y., et al. (2017). S-Aligner: Ultrascalable read mapping on Sunway Taihu Light. 2017 IEEE INTERNATIONAL CONFERENCE ON CLUSTER COMPUTING (CLUSTER), 36-46. DOI Author/Publisher URL
Junger, D., Hundt, C., Gonzalez-Dominguez, J., Schmidt, B. (2017). Ultra-Fast Detection of Higher-Order Epistatic Interactions on GPUs. EURO-PAR 2016: PARALLEL PROCESSING WORKSHOPS, 10104, 421-432. DOI Author/Publisher URL
Lan, H., Liu, W., Liu, Y., Schmidt, B. (2017). SWhybrid: A Hybrid-Parallel Framework for Large-Scale Protein Sequence Database Search. 2017 31ST IEEE INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM (IPDPS), 42-51. DOI Author/Publisher URL
Peng, S., Zhang, X., Yang, S., et al. (2017). mD3DOCKxb: An Ultra-Scalable CPU-MIC Coordinated Virtual Screening Framework. 2017 17TH IEEE/ACM INTERNATIONAL SYMPOSIUM ON CLUSTER, CLOUD AND GRID COMPUTING (CCGRID), 671-676. DOI Author/Publisher URL
2016
Kaessens, J. C., Wienbrandt, L., Schimmler, M., et al. (2016). 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), 170-175. Author/Publisher URL
2015
Liu, Y., Loewer, M., Aluru, S., and Schmidt, B. (2015). SNVSniffer: An integrated caller for germline and somatic SNVs based on Bayesian models. 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 83-90. DOI
Lan, H., Liu, W., Schmidt, B., and Wang, B. (2015). Accelerating Large-Scale Biological Database Search on Xeon Phi-based Neo-Heterogeneous Architectures. PROCEEDINGS 2015 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE, 503-510. Author/Publisher URL
Liu, Y., and Schmidt, B. (2015). LightSpMV: Faster CSR-based Sparse Matrix-Vector Multiplication on CUDA-enabled GPUs. PROCEEDINGS OF THE ASAP2015 2015 IEEE 26TH INTERNATIONAL CONFERENCE ON APPLICATION-SPECIFIC SYSTEMS, ARCHITECTURES AND PROCESSORS, 82-89. Author/Publisher URL
Schlarb, M., Hundt, C., and Schmidt, B. (2015). SAUCE: A Web-Based Automated Assessment Tool for Teaching Parallel Programming. EURO-PAR 2015: PARALLEL PROCESSING WORKSHOPS, 9523, 54-65. DOI Author/Publisher URL
2014
Tran, T. T., Schindel, S., Liu, Y., Schmidt, B. (2014). Bit-Parallel Approximate Pattern Matching on the Xeon Phi Coprocessor. 2014 IEEE 26th International Symposium on Computer Architecture and High Performance Computing, 81-88. DOI
Nguyen, T.-D., Schmidt, B., Kwoh, C.-K. (2014). Fast dendrogram-based OTU clustering using sequence embedding. Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, 63-72. DOI
Kassens, J. C., Gonzalez-Dominguez, J., Wienbrandt, L., Schmidt, B. (2014). UPC++ for bioinformatics: A case study using genome-wide association studies. 2014 IEEE International Conference on Cluster Computing (CLUSTER), 248-256. DOI
Liu, Y., Schmidt, B. (2014). SWAPHI: Smith-waterman protein database search on Xeon Phi coprocessors. 2014 IEEE 25th International Conference on Application-Specific Systems, Architectures and Processors, 184-185. DOI
Dang, H.-V., Schmidt, B., Hildebrandt, A., Hildebrandt, A. K. (2014). Parallelized clustering of protein structures on cuda-enabled gpus. 2014 22nd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing, 1-8.
Gonzalez-Dominguez, J., Schmidt, B., Kaessens, J. C., Wienbrandt, L. (2014). Hybrid CPU/GPU Acceleration of Detection of 2-SNP Epistatic Interactions in GWAS. EURO-PAR 2014 PARALLEL PROCESSING, 8632, 680-691. Author/Publisher URL
Hundt, C., Schmidt, B., Schoemer, E. (2014). CUDA-Accelerated Alignment of Subsequences in Streamed Time Series Data. 2014 43RD INTERNATIONAL CONFERENCE ON PARALLEL PROCESSING (ICPP), 10-19. DOI Author/Publisher URL
Hundt, C., Schmidt, B., Schömer, E., et al. (2014). GEM: an elastic and translation-invariant similarity measure with automatic trend adjustment. In Y. Cho, S. Y. Shin, S.-W. Kim, et al. (eds.), SAC (pp. 105-112). ACM. Author/Publisher URL
Kaessens, J. C., Gonzalez-Dominguez, J., Wienbrandt, L., Schmidt, B. (2014). UPC plus plus for Bioinformatics: A Case Study Using Genome-Wide Association Studies. 2014 IEEE INTERNATIONAL CONFERENCE ON CLUSTER COMPUTING (CLUSTER), 248-256. Author/Publisher URL
Liu, Y., Schmidt, B. (2014). Faster GPU-Accelerated Smith-Waterman Algorithm with Alignment Backtracking for Short DNA Sequences. PARALLEL PROCESSING AND APPLIED MATHEMATICS (PPAM 2013), PT II, 8385, 247-257. DOI Author/Publisher URL
Liu, Y., Tran, T.-T., Lauenroth, F., Schmidt, B. (2014). SWAPHI-LS: Smith-Waterman Algorithm on Xeon Phi Coprocessors for Long DNA Sequences. 2014 IEEE INTERNATIONAL CONFERENCE ON CLUSTER COMPUTING (CLUSTER), 257-265. Author/Publisher URL
Thuy-Diem, N., Schmidt, B., Kwoh, C.-K. (2014). SparseHC: a memory-efficient online hierarchical clustering algorithm. 2014 INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE, 29, 8-19. DOI Author/Publisher URL
Wienbrandt, L., Kaessens, J. C., Gonzalez-Dominguez, J., et al. (2014). FPGA-based acceleration of detecting statistical epistasis in GWAS. 2014 INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE, 29, 220-230. DOI Author/Publisher URL
2012
Chen, Y., Schmidt, B., and Maksell, D. L. (2012). An FPGA aligner for short read mapping. 22nd International Conference on Field Programmable Logic and Applications (FPL), 511-514. DOI
Liu, Y., and Schmidt, B. (2012). Evaluation of GPU-based Seed Generation for Computational Genomics Using Burrows-Wheeler Transform. 2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops & PhD Forum, 684-690. DOI
Chen, Y., Schmidt, B., and Maskell, D. L. (2012). Accelerating short read mapping on an FPGA (abstract only). Proceedings of the ACM/SIGDA international symposium on Field Programmable Gate Arrays, 265-265. DOI
Dang, H.-V., and Schmidt, B. (2012). The Sliced COO Format for Sparse Matrix-Vector Multiplication on CUDA-enabled GPUs. Procedia Computer Science, 9, 57-66. DOI
Schmidt, B., and Maskell, D. (2012). Fourth Workshop on using Emerging Parallel Architectures. Procedia Computer Science, 9, 1867-1869. DOI
2011
Liu, W., Schmidt, B., Liu, Y., et al. (2011). Mapping of BLASTP Algorithm onto GPU Clusters. 2011 IEEE 17th International Conference on Parallel and Distributed Systems, 236-243. DOI
Liu, Y., Schmidt, B., Maskell, D. L. (2011). An Ultrafast Scalable Many-Core Motif Discovery Algorithm for Multiple GPUs. 2011 IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum, 428-434. DOI
Aluru, S., Bandyopadhyay, S., Çatalyürek, Ümit V., … Schmidt, B. (eds.). (2011). Contemporary Computing – 4th International Conference, IC3 2011, Noida, India, August 8-10, 2011. Proceedings. IC3, 168.
Schmidt, B., Maskell, D. (2011). Third Workshop on using Emerging Parallel Architectures. Procedia Computer Science, 4, 1964-1966. DOI
Schmidt, B., Aribowo, H., Dang, H.-V. (2011). Iterative Sparse Matrix-Vector Multiplication for Integer Factorization on GPUs. 413-424. DOI
Zheng, Z., Nguyen, T.-D., Schmidt, B. (2011). CRiSPy-CUDA: Computing Species Richness in 16S rRNA Pyrosequencing Datasets with CUDA. 37-49. DOI
2010
Zheng, Z., Schmidt, B., and Bourque, G. (2010). Prediction of low coverage prone regions for Illumina sequencing projects using a support vector machine. 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 13-16. DOI
Schmidt, B., and Maskell, D. (2010). Second Workshop on using Emerging Parallel Architectures. Procedia Computer Science, 1(1), 1015-1017. DOI
Shi, H., Schmidt, B., Liu, W., and Müller-Wittig, W. (2010). Quality-score guided error correction for short-read sequencing data using CUDA. Procedia Computer Science, 1(1), 1129-1138. DOI
2009
Yongchao Liu, Schmidt, B., and Maskell, D. L. (2009). MSA-CUDA: Multiple Sequence Alignment on Graphics Processing Units with CUDA. 2009 20th IEEE International Conference on Application-specific Systems, Architectures and Processors, 121-128. DOI
Haixiang Shi, Schmidt, B., Weiguo Liu, and Muller-Wittig, W. (2009). Accelerating error correction in high-throughput short-read DNA sequencing data with CUDA. 2009 IEEE International Symposium on Parallel & Distributed Processing, 1-8. DOI
Yongchao Liu, Schmidt, B., and Maskell, D. L. (2009). Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA. 2009 IEEE International Symposium on Parallel & Distributed Processing, 1-8. DOI
Chen, Y., Schmidt, B., and Maskell, D. L. (2009). A Reconfigurable Bloom Filter Architecture for BLASTN. 40-49. DOI
Schmidt, B., and Maskell, D. L. (2009). Workshop on Using Emerging Parallel Architectures for Computational Science. In G. Allen, J. Nabrzyski, E. Seidel, et al. (eds.), ICCS (1) (Vols. 5544, pp. 861-863). Springer. Author/Publisher URL
Wirawan, A., Schmidt, B., and Kwoh, C. K. (2009). Pairwise Distance Matrix Computation for Multiple Sequence Alignment on the Cell Broadband Engine. 954-963. DOI
2008
2007
Liu, W., Muller-Wittig, W., Schmidt, B. (2007). Performance Predictions for General-Purpose Computation on GPUs. 2007 International Conference on Parallel Processing (ICPP 2007), 50-50. DOI
Feng, J., Chakraborty, S., Schmidt, B., et al. (2007). Fast Schedulability Analysis Using Commodity Graphics Hardware. 13th IEEE International Conference on Embedded and Real-Time Computing Systems and Applications (RTCSA 2007), 400-408. DOI
Aung, Y. L., Maskell, D. L., Oliver, T. F., et al. (2007). C-Based Design Methodology for FPGA Implementation of ClustalW MSA. 11-18. DOI
Oliver, T., Yeow, L. Y., Schmidt, B. (2007). High Performance Database Searching with HMMer on FPGAs. 2007 IEEE International Parallel and Distributed Processing Symposium, 1-7. DOI
Rajapakse, J. C., Schmidt, B., … Volkert, L. G. (eds.). (2007). Pattern Recognition in Bioinformatics, Second IAPR International Workshop, PRIB 2007, Singapore, October 1-2, 2007, Proceedings. PRIB, 4774.
Rajapakse, M., Lin, F. (2007). Predicting Binding Peptides with Simultaneous Optimization of Entropy and Evolutionary Distance. In J. C. Rajapakse, B. Schmidt, and L. G. Volkert (eds.), PRIB (Vols. 4774, pp. 349-355). Springer. Author/Publisher URL
2006
Liu, W., Schmidt, B., Voss, G., Müller-Wittig, W. (2006). GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment. 363-374. DOI
Oliver, T. F., Schmidt, B., Jakop, Y., Maskell, D. L. (2006). Accelerating the Viterbi algorithm for Profile Hidden Markov Models using reconfigurable hardware. COMPUTATIONAL SCIENCE – ICCS 2006, PT 1, PROCEEDINGS, 3991, 522-529. Author/Publisher URL
Rajapakse, M., Schmidt, B., Brusic, V. (2006). Multi-objective evolutionary algorithm for discovering peptide binding motifs. APPLICATIONS OF EVOLUTIONARY COMPUTING, PROCEEDINGS, 3907, 149-158. Author/Publisher URL
Weiguo Liu, Schmidt, B., Voss, G., et al. (2006). Bio-sequence database scanning on a GPU. Proceedings 20th IEEE International Parallel & Distributed Processing Symposium, 8 pp.-8 pp. DOI
Wirawan, A., Schmidt, B. (2006). Parallel Discovery of Transcription Factor Binding Sites. APCCAS, 700-703. Author/Publisher URL
2005
Oliver, T., Schmidt, B., and Maskell, D. (2005). Hyper customized processors for bio-sequence database scanning on FPGAs. Proceedings of the 2005 ACM/SIGDA 13th international symposium on Field-programmable gate arrays, 229-237. DOI
Chen, C., and Schmidt, B. (2005). Parallel Construction of Large Suffix Trees on a PC Cluster. In J. C. Cunha and P. D. Medeiros (eds.), Euro-Par (Vols. 3648, pp. 1227-1236). Springer. Author/Publisher URL
Oliver, T. F., Schmidt, B., Maskell, D. L., and Vinod, A. P. (2005). A reconfigurable architecture for scanning biosequence databases. ISCAS (5), 4799-4802. Author/Publisher URL
Rajapakse, M., Wyse, L., Schmidt, B., and Brusic, V. (2005). Deriving matrix of peptide-MHC interactions in diabetic mouse by genetic algorithm. INTELLIGENT DATA ENGINEERING AND AUTOMATED LEARNING IDEAL 2005, PROCEEDINGS, 3578, 440-447. Author/Publisher URL
Yanto, J., Oliver, T. F., Schmidt, B., and Maskell, D. L. (2005). Biological Sequence Analysis with Hidden Markov Models on an FPGA. In T. Srikanthan, J. Xue, and C.-H. Chang (eds.), Asia-Pacific Computer Systems Architecture Conference (Vols. 3740, pp. 429-439). Springer. Author/Publisher URL
2004
Chen, C., and Schmidt, B. (2004). Load Balancing for Hierarchical Grid Computing: A Case Study. In L. Bougé and V. K. Prasanna (eds.), HiPC (Vols. 3296, pp. 353-362). Springer. Author/Publisher URL
Liu, W. G., and Schmidt, B. (2004). A generic parallel pattern-based system for bioinformatics. EURO-PAR 2004 PARALLEL PROCESSING, PROCEEDINGS, 3149, 989-996. Author/Publisher URL
Liu, W., and Schmidt, B. (2004). A Tunable Coarse-Grained Parallel Algorithm for Irregular Dynamic Programming Applications. In L. Bougé and V. K. Prasanna (eds.), HiPC (Vols. 3296, pp. 91-100). Springer. Author/Publisher URL
2003
Ahmad, I., Jonker, P., Schmidt, B., and Uhl, A. (2003). Topic Introduction. In H. Kosch, L. Böszörményi, and H. Hellwagner (eds.), Euro-Par (Vols. 2790, pp. 850-850). Springer. Author/Publisher URL
Cehn, and Schmidt. (2003). Computing large-scale alignments on a multi-cluster. Proceedings IEEE International Conference on Cluster Computing CLUSTR-03, 38-45. DOI
Schimmler, M., Schmidt, B., and Lang, H.-W. (2003). Design of a Bit-Serial Floating Point Unit for a Fine Grained Parallel Processor Array. In H. R. Arabnia and Y. Mun (eds.), PDPTA (pp. 255-261). CSREA Press. Author/Publisher URL
Schimmler, M., Schmidt, B., Lang, H.-W., and Heithecker, S. (2003). An Area-Efficient Bit-Serial Integer Multiplier. In H. R. Arabnia and L. T. Yang (eds.), VLSI (pp. 131-137). CSREA Press. Author/Publisher URL
Weiguo Liu, and Schmidt. (2003). Parallel design pattern for computational biology and scientific computing applications. Proceedings IEEE International Conference on Cluster Computing CLUSTR-03, 456-459. DOI
2002
Schmidt, B., Schroder, H., and Schimmler, M. (2002). Massively parallel solutions for molecular sequence analysis. Proceedings 16th International Parallel and Distributed Processing Symposium, 8 pp-8 pp. DOI
2001
Schmidt, B., Schröder, H., and Schimmler, M. (2001). Protein Sequence Comparison on the Instruction Systolic Array. In V. E. Malyshkin (ed.), PaCT (Vols. 2127, pp. 498-509). Springer. Author/Publisher URL
Schmidt, B., Schröder, H., and Schimmler, M. (2001). Scanning Biosequence Databases on a Hybrid Parallel Architecture. In R. Sakellariou, J. A. Keane, J. R. Gurd, and L. Freeman (eds.), Euro-Par (Vols. 2150, pp. 360-370). Springer. Author/Publisher URL
2000
Schmidt, B. (2000). Design of a parallel accelerator for volume rendering. EURO-PAR 2000 PARALLEL PROCESSING, PROCEEDINGS, 1900, 1095-1104. Author/Publisher URL
1999
Schmidt, B., and Schimmler, M. (1999). A parallel accelerator architecture for multimedia video compression. EURO-PAR’99: PARALLEL PROCESSING, 1685, 950-960. Author/Publisher URL
1998
Schmidt, B., Schimmler, M., and Schröder, H. (1998). Long operand arithmetic on instruction systolic computer architectures and its application in RSA cryptography. EURO-PAR ’98 PARALLEL PROCESSING, 1470, 916-922. Author/Publisher URL
1997
Schmidt, B., Schimmler, M., and Schröder, H. (1997). Morphological Hough Transform on the Instruction Systolic Array. In C. Lengauer, M. Griebl, and S. Gorlatch (eds.), Euro-Par (Vols. 1300, pp. 798-806). Springer. Author/Publisher URL
1995
Mahlmeister, U., Schmidt, B., and Sommer, G. (1995). Preattentive Colour Features by Steerable Filters. In G. Sagerer, S. Posch, and F. Kummert (eds.), DAGM-Symposium (pp. 464-472). Springer. Author/Publisher URL
Not dated
Chunxi Chen, Schmidt, B. Performance analysis of computational biology applications on hierarchical grid systems. IEEE International Symposium on Cluster Computing and the Grid, 2004. CCGrid 2004., 426-433. DOI
Liu, W., Schmidt, B., Voss, G., Müller-Wittig, W. Molecular Dynamics Simulations on Commodity GPUs with CUDA. 185-196. DOI
Low, M. Y. H., Liu, W., Schmidt, B. A Parallel BSP Algorithm for Irregular Dynamic Programming. 151-160. DOI
Oliver, T., Schmidt, B. High performance biosequence database scanning on reconfigurable platforms. 18th International Parallel and Distributed Processing Symposium, 2004. Proceedings., 192-199. DOI
Oliver, T., Schmidt, B., Maskell, D., et al. Multiple Sequence Alignment on an FPGA. 11th International Conference on Parallel and Distributed Systems (ICPADS’05), 2, 326-330. DOI
Schmidt, B., Lin Feng, Laud, A., Santoso, Y. Parallel detection of regulatory elements with gMP. Proceedings International Parallel and Distributed Processing Symposium, 8-8. DOI
Tong Liu, Schmidt, B. Parallel RNA sequence-structure alignment. 18th International Parallel and Distributed Processing Symposium, 2004. Proceedings., 190-197. DOI
Weiguo Liu, Schmidt, B. A Case Study on Pattern-Based Systems for High Performance Computational Biology. 19th IEEE International Parallel and Distributed Processing Symposium, 197b-197b. DOI
Wirawan, A., Keong, K. C., Schmidt, B. Parallel DNA Sequence Alignment on the Cell Broadband Engine. 1249-1256. DOI
2026
Zhang, H., Gan, L., Yin, Z., et al. (2026). RabbitVar: Ultra-fast and accurate somatic small-variant calling on multi-core architectures. FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE, 182. DOI Author/Publisher URL
Chen, R., An, H., Sa, Z., et al. (2026). Accelerating Molecular Dynamics Simulations on ARM Multi-Core Processors. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 37(4), 805-821. DOI Author/Publisher URL
Wei, Y., Liu, W., Schmidt, B., et al. (2026). HPC and AI in bioinformatics. FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE, 174. DOI Author/Publisher URL
Schmidt, B., Kallenborn, F., Wichmann, A., et al. (2026). gpuPairHMM: High-Speed Pair-HMM Forward Algorithm for DNA Variant Calling on GPUs. IEEE Transactions on Computational Biology and Bioinformatics, 1-8. DOI
2025
Jünger, D., Kristensen, K., Wang, Y., et al. (2025). Optimizing Bloom Filters for Modern GPU Architectures. CoRR, abs/2512.15595.
Wang, M., Yang, Y., Yin, Z., et al. (2025). RabbitTrim: An Efficient and Versatile Trimmer on Multi-Core Platforms. IEEE TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 22(6), 2442-2452. DOI Author/Publisher URL
Kruger, M., Galeazzo, T., Eremets, I., et al. (2025). Improved vapor pressure predictions using group contribution-assisted graph convolutional neural networks (GC<SUP>2</SUP>NN). GEOSCIENTIFIC MODEL DEVELOPMENT, 18(20), 7357-7371. DOI Author/Publisher URL
Kallenborn, F., Chacon, A., Hundt, C., et al. (2025). GPU-accelerated homology search with MMseqs2. NATURE METHODS, 22(10), 2024-2027. DOI Author/Publisher URL
Yan, L., Zhao, Z., Yin, Z., et al. (2025). RabbitBAM: Accelerating BAM File Manipulation on Multi-Core Platforms. IEEE TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 22(5), 2320-2326. DOI Author/Publisher URL
Zhang, T., Yin, Z., Xu, X., et al. (2025). RabbitSketch: a high-performance sketching library for genome analysis. BIOINFORMATICS, 41(5). DOI Author/Publisher URL
Yan, L., Yin, Z., Zhang, T., et al. (2025). SWQC: Efficient sequencing data quality control on the next-generation sunway platform. FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE, 164. DOI Author/Publisher URL
Mueller, A., Wichmann, A., Kallenborn, F., et al. (2025). RMapAlign3N: fast mapping of 3N-Reads. BIOINFORMATICS ADVANCES, 5(1). DOI Author/Publisher URL
2024
Schmidt, B., Kallenborn, F., Chacon, A., and Hundt, C. (2024). CUDASW++4.0: ultra-fast GPU-based Smith-Waterman protein sequence database search. BMC BIOINFORMATICS, 25(1). DOI Author/Publisher URL
Schmidt, B., and Hildebrandt, A. (2024). From GPUs to AI and quantum: three waves of acceleration in bioinformatics. DRUG DISCOVERY TODAY, 29(6). DOI Author/Publisher URL
Kallenborn, F., and Schmidt, B. (2024). CAREx: context-aware read extension of paired-end sequencing data. BMC BIOINFORMATICS, 25(1). DOI Author/Publisher URL
2023
Gao, P., Duan, X., Schmidt, B., et al. (2023). Redesign and Accelerate the AIREBO Bond-Order Potential on the New Sunway Supercomputer. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 34(12), 3117-3132. DOI Author/Publisher URL
Xu, X., Yin, Z., Yan, L., et al. (2023). RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures. BIOINFORMATICS, 39(11). DOI Author/Publisher URL
Yan, L., Yin, Z., Zhang, H., et al. (2023). RabbitQCPlus 2.0: More efficient and versatile quality control for sequencing data. METHODS, 216, 39-50. DOI Author/Publisher URL
Zhang, H., Yin, Z., Wei, Y., et al. (2023). DeepFilter: A Deep Learning Based Variant Filter for VarDict. TSINGHUA SCIENCE AND TECHNOLOGY, 28(4), 665-672. DOI Author/Publisher URL
Wichmann, A., Buschong, E., Mueller, A., et al. (2023). MetaTransformer: deep metagenomic sequencing read classification using self-attention models. NAR GENOMICS AND BIOINFORMATICS, 5(3). DOI Author/Publisher URL
Kemmer, T., Hack, S., Schmidt, B., Hildebrandt, A. (2023). CUDA-accelerated protein electrostatics in linear space. JOURNAL OF COMPUTATIONAL SCIENCE, 70. DOI Author/Publisher URL
Duan, X., Shao, Q., Weng, J., et al. (2023). Bio-ESMD: A Data Centric Implementation for Large-Scale Biological System Simulation on Sunway TaihuLight Supercomputer. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 34(3), 881-893. DOI Author/Publisher URL
Zhang, H., Song, H., Xu, X., et al. (2023). RabbitFX: Efficient Framework for FASTA/Q File Parsing on Modern Multi-Core Platforms. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 20(3), 2341-2348. DOI Author/Publisher URL
2022
Xu, K., Zhang, J., Duan, X., et al. (2022). Redesigning and Optimizing UCSF DOCK3.7 on Sunway TaihuLight. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 33(12), 4458-4471. DOI Author/Publisher URL
Meng, J., Zhuang, C., Chen, P., et al. (2022). Automatic Generation of High-Performance Convolution Kernels on ARM CPUs for Deep Learning. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 33(11), 2885-2899. DOI Author/Publisher URL
Krueger, M., Wilson, J., Wietzoreck, M., et al. (2022). Convolutional neural network prediction of molecular properties for aerosol chemistry and health effects. NATURAL SCIENCES, 2(4). DOI Author/Publisher URL
Bob, K., Teschner, D., Kemmer, T., et al. (2022). Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data. BMC BIOINFORMATICS, 23(1). DOI Author/Publisher URL
Kallenborn, F., Cascitti, J., Schmidt, B. (2022). CARE 2.0: reducing false-positive sequencing error corrections using machine learning. BMC BIOINFORMATICS, 23(1). DOI Author/Publisher URL
Juenger, D., Kobus, R., Mueller, A., et al. (2022). General-purpose GPU hashing data structures and their application in accelerated genomics. JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING, 163, 256-268. DOI Author/Publisher URL
Cascitti, J., Niebler, S., Mueller, A., Schmidt, B. (2022). RNACache: A scalable approach to rapid transcriptomic read mapping using locality sensitive hashing. JOURNAL OF COMPUTATIONAL SCIENCE, 60. DOI Author/Publisher URL
Xu, K., Duan, X., Muller, A., et al. (2022). FMapper: Scalable read mapper based on succinct hash index on SunWay TaihuLight. JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING, 161, 72-82. DOI Author/Publisher URL
Gao, P., Duan, X., Schmidt, B., et al. (2022). Optimization of Reactive Force Field Simulation: Refactor, Parallelization, and Vectorization for Interactions. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 33(2), 359-373. DOI Author/Publisher URL
Niebler, S., Miltenberger, A., Schmidt, B., Spichtinger, P. (2022). Automated detection and classification of synoptic-scale fronts from atmospheric data grids. WEATHER AND CLIMATE DYNAMICS, 3(1), 113-137. DOI Author/Publisher URL
Mueller, A., Schmidt, B., Membarth, R., et al. (2022). AnySeq/GPU: A Novel Approach for Faster Sequence Alignment on GPUs. PROCEEDINGS OF THE 36TH ACM INTERNATIONAL CONFERENCE ON SUPERCOMPUTING, ICS 2022. Published. DOI Author/Publisher URL
Zhang, H., Chang, Q., Yin, Z., et al. (2022). RabbitV: fast detection of viruses and microorganisms in sequencing data on multi-core architectures. Bioinform., 38, 2932-2933.
2021
Kallenborn, F., Hildebrandt, A., and Schmidt, B. (2021). CARE: context-aware sequencing read error correction. Bioinformatics, 37(7), 889-895. DOI Author/Publisher URL
Yin, Z., Xu, X., Zhang, J., et al. (2021). RabbitMash: accelerating hash-based genome analysis on modern multi-core architectures. Bioinformatics, 37(6), 873-875. DOI
Ringe, K. I., Vo Chieu, V. D., Wacker, F., et al. (2021). Fully automated detection of primary sclerosing cholangitis (PSC)-compatible bile duct changes based on 3D magnetic resonance cholangiopancreatography using machine learning. EUROPEAN RADIOLOGY, 31(4), 2482-2489. DOI Author/Publisher URL
Winther, H., Hundt, C., Ringe, K. I., et al. (2021). A 3D Deep Neural Network for Liver Volumetry in 3T Contrast-Enhanced MRI. ROFO-FORTSCHRITTE AUF DEM GEBIET DER RONTGENSTRAHLEN UND DER BILDGEBENDEN VERFAHREN, 193(03), 305-314. DOI Author/Publisher URL
Yin, Z., Zhang, H., Liu, M., et al. (2021). RabbitQC: high-speed scalable quality control for sequencing data. BIOINFORMATICS, 37(4), 573-574. DOI Author/Publisher URL
Weißenberger, A., Schmidt, B. (2021). Accelerating JPEG Decompression on GPUs. CoRR, abs/2111.09219.
2020
Gao, P., Duan, X., Zhang, T., et al. (2020). Millimeter-Scale and Billion-Atom Reactive Force Field Simulation on Sunway Taihulight. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 31(12), 2954-2967. DOI Author/Publisher URL
Abuin, J. M., Lopes, N., Ferreira, L., et al. (2020). Big Data in metagenomics: Apache Spark vs MPI. PLOS ONE, 15(10). DOI Author/Publisher URL
Niebler, S., Mueller, A., Hankeln, T., Schmidt, B. (2020). RainDrop: Rapid activation matrix computation for droplet-based single-cell RNA-seq reads. BMC BIOINFORMATICS, 21(1). DOI Author/Publisher URL
Kobus, R., Abuin, J. M., Mueller, A., et al. (2020). A big data approach to metagenomics for all-food-sequencing. BMC BIOINFORMATICS, 21(1). DOI Author/Publisher URL
Lan, H., Meng, J., Hundt, C., et al. (2020). FeatherCNN: Fast Inference Computation with TensorGEMM on ARM Architectures. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 31(3), 580-594. DOI Author/Publisher URL
Winther, H. B., Gutberlet, M., Hundt, C., et al. (2020). 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, 51(2), 571-579. DOI Author/Publisher URL
Hellmann, S. L., Ripp, F., Bikar, S.-E., et al. (2020). Identification and quantification of meat product ingredients by whole-genome metagenomics (All-Food-Seq). EUROPEAN FOOD RESEARCH AND TECHNOLOGY, 246(1), 193-200. DOI Author/Publisher URL
Hieronymus, M., Schmidt, B., Böser, S. (2020). Reconstruction of Low Energy Neutrino Events with GPUs at IceCube. ICCS (1), 12137, 118-131. Author/Publisher URL
Jünger, D., Kobus, R., Müller, A., et al. (2020). WarpCore: A Library for fast Hash Tables on GPUs. CoRR, abs/2009.07914.
Mueller, A., Schmidt, B., Hildebrandt, A., et al. (2020). AnySeq: A High Performance Sequence Alignment Library based on Partial Evaluation. 2020 IEEE 34TH INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM IPDPS 2020, 1030-1040. DOI Author/Publisher URL
Schmidt, B., Hildebrandt, A. (2020). Deep learning in next-generation sequencing. Drug Discovery Today.
2019
Jiang, P., Luo, J., Wang, Y., et al. (2019). kmcEx: memory-frugal and retrieval-efficient encoding of counted <i>k</i>-mers. BIOINFORMATICS, 35(23), 4871-4878. DOI Author/Publisher URL
Zhang, J., Lan, H., Chan, Y., et al. (2019). BGSA: a bit-parallel global sequence alignment toolkit for multi-core and many-core architectures. BIOINFORMATICS, 35(13), 2306-2308. DOI Author/Publisher URL
Kallenborn, F., Hundt, C., Boeser, S., Schmidt, B. (2019). Massively parallel computation of atmospheric neutrino oscillations on CUDA-enabled accelerators. COMPUTER PHYSICS COMMUNICATIONS, 234, 235-244. DOI Author/Publisher URL
Schmidt, L., Werner, S., Kemmer, T., et al. (2019). Graphical workflow system for modification calling by machine learning of reverse transcription signatures. Frontiers in genetics, 10, 876-876.
2018
Leißa, R., Boesche, K., Hack, S., et al. (2018). AnyDSL: a partial evaluation framework for programming high-performance libraries. Proceedings of the ACM on Programming Languages, 2(OOPSLA), 1-30. DOI
Winther, H. B., Hundt, C., Schmidt, B., et al. (2018). Poor Correlation, Reproducibility, and Agreement Between Volumetric Versus Linear Epicardial Adipose Tissue Measurement. JACC-CARDIOVASCULAR IMAGING, 11(7), 1036-1038. DOI Author/Publisher URL
Zhang, H., Chan, Y., Fan, K., et al. (2018). Fast and efficient short read mapping based on a succinct hash index. BMC BIOINFORMATICS, 19. DOI Author/Publisher URL
Gonzalez-Dominguez, J., Hundt, C., Schmidt, B. (2018). parSRA: A framework for the parallel execution of short read aligners on compute clusters. JOURNAL OF COMPUTATIONAL SCIENCE, 25, 134-139. DOI Author/Publisher URL
Liu, Y., Schmidt, B. (2018). LightSpMV: Faster CUDA-Compatible Sparse Matrix-Vector Multiplication Using Compressed Sparse Rows. JOURNAL OF SIGNAL PROCESSING SYSTEMS FOR SIGNAL IMAGE AND VIDEO TECHNOLOGY, 90(1), 69-86. DOI Author/Publisher URL
Chan, Y., Xu, K., Lan, H., et al. (2018). MyPhi: Efficient Levenshtein Distance Computation on Xeon Phi Based Architectures. CURRENT BIOINFORMATICS, 13(5), 479-486. DOI Author/Publisher URL
Leissa, R., Boesche, K., Hack, S., et al. (2018). AnyDSL: A Partial Evaluation Framework for Programming High-Performance Libraries. PROCEEDINGS OF THE ACM ON PROGRAMMING LANGUAGES-PACMPL, 2. DOI Author/Publisher URL
2017
Juenger, D., Hundt, C., Gonzalez Dominguez, J., Schmidt, B. (2017). Speed and accuracy improvement of higher-order epistasis detection on CUDA-enabled GPUs. CLUSTER COMPUTING-THE JOURNAL OF NETWORKS SOFTWARE TOOLS AND APPLICATIONS, 20(3), 1899-1908. DOI Author/Publisher URL
Zhang, S., Wang, Z., Peng, Y., et al. (2017). Mapping of option pricing algorithms onto heterogeneous many-core architectures. JOURNAL OF SUPERCOMPUTING, 73(9), 3715-3737. DOI Author/Publisher URL
Schroder, J., Wirawan, A., Schmidt, B., Papenfuss, A. T. (2017). CLOVE: classification of genomic fusions into structural variation events. BMC BIOINFORMATICS, 18. DOI Author/Publisher URL
Hundt, C., Schlarb, M., Schmidt, B. (2017). SAUCE: A web application for interactive teaching and learning of parallel programming. JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING, 105, 163-173. DOI Author/Publisher URL
Liu, Y., Ripp, F., Koeppel, R., et al. (2017). AFS: identification and quantification of species composition by metagenomic sequencing. BIOINFORMATICS, 33(9), 1396-1398. DOI Author/Publisher URL
Dang, H.-V., Schmidt, B., Hildebrandt, A., et al. (2017). CUDA-enabled hierarchical ward clustering of protein structures based on the nearest neighbour chain algorithm (Reprinted from vol 30, pg 200-211, 2016). INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS, 31, 181-+.
Kobus, R., Hundt, C., Müller, A., Schmidt, B. (2017). Accelerating metagenomic read classification on CUDA-enabled GPUs. BMC Bioinformatics, 18(11), 10 S. Author/Publisher URL
Müller, A., Hundt, C., Hildebrandt, A., et al. (2017). MetaCache: context-aware classification of metagenomic reads using minhashing. Bioinformatics, 33, 3740-3748.
Schmidt, B., Hildebrandt, A. (2017). Next-generation sequencing: big data meets high performance computing. Drug discovery today, 22, 712-717.
Winther, H. B., Hundt, C., Schmidt, B., et al. (2017). $ν$-net: Deep Learning for Generalized Biventricular Cardiac Mass and Function Parameters. CoRR, abs/1706.04397.
2016
Gonzalez-Dominguez, J., Liu, Y., Tourino, J., Schmidt, B. (2016). MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems. BIOINFORMATICS, 32(24), 3826-3828. DOI Author/Publisher URL
Liu, Y., Loewer, M., Aluru, S., Schmidt, B. (2016). SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations. BMC SYSTEMS BIOLOGY, 10. DOI Author/Publisher URL
Gonzalez-Dominguez, J., Ramos, S., Tourino, J., Schmidt, B. (2016). Parallel Pairwise Epistasis Detection on Heterogeneous Computing Architectures. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 27(8), 2329-2340. DOI Author/Publisher URL
Lan, H., Chan, Y., Xu, K., et al. (2016). Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters. BMC BIOINFORMATICS, 17. DOI Author/Publisher URL
Gonzalez-Dominguez, J., Schmidt, B. (2016). ParDRe: faster parallel duplicated reads removal tool for sequencing studies. BIOINFORMATICS, 32(10), 1562-1564. DOI Author/Publisher URL
Tuan, T. T., Liu, Y., Schmidt, B. (2016). Bit-parallel approximate pattern matching: Kepler GPU versus Xeon Phi. PARALLEL COMPUTING, 54, 128-138. DOI Author/Publisher URL
Dang, H.-V., Schmidt, B., Hildebrandt, A., et al. (2016). CUDA-enabled hierarchical ward clustering of protein structures based on the nearest neighbour chain algorithm. The International Journal of High Performance Computing Applications, 30, 200-211.
González-Domínguez, J., Liu, Y., Schmidt, B. (2016). Parallel and scalable short-read alignment on multi-core clusters using UPC++. PLoS one, 11(1), e0145490. Author/Publisher URL
Hundt, C., Hildebrandt, A., Schmidt, B. (2016). rapidGSEA: Speeding up gene set enrichment analysis on multi-core CPUs and CUDA-enabled GPUs. BMC bioinformatics, 17, 394-394.
Liu, Y., Hankeln, T., Schmidt, B. (2016). 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. DOI Author/Publisher URL
Shao, J., Yang, Q., Dang, H.-V., et al. (2016). Scalable clustering by iterative partitioning and point attractor representation. ACM transactions on knowledge discovery from data, 11(1), Art. 5. Author/Publisher URL
Zheng, Z., Wei, X., Hildebrandt, A., Schmidt, B. (2016). A computational method for studying the relation between alternative splicing and DNA methylation. Nucleic acids research, 44, e19-e19.
2015
Gonzalez-Dominguez, J., Kaessens, J. C., Wienbrandt, L., 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, 29(4), 506-510. DOI Author/Publisher URL
Gomez-Pulido, J. A., Schmidt, B., Feng, W.- chun. (2015). Accelerating bioinformatics applications via emerging parallel computing systems [Guest editorial]. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 12(5), 971-972. DOI
Kaessens, J. C., Wienbrandt, L., Gonzalez-Dominguez, J., et al. (2015). High-speed exhaustive 3-locus interaction epistasis analysis on FPGAs. JOURNAL OF COMPUTATIONAL SCIENCE, 9, 131-136. DOI Author/Publisher URL
Gonzalez-Dominguez, J., Schmidt, B. (2015). GPU-accelerated exhaustive search for third-order epistatic interactions in case-control studies. JOURNAL OF COMPUTATIONAL SCIENCE, 8, 93-100. DOI Author/Publisher URL
Liu, Y., Schmidt, B. (2015). GSWABE: faster GPU-accelerated sequence alignment with optimal alignment retrieval for short DNA sequences. CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, 27(4), 958-972. DOI Author/Publisher URL
Gonzalez-Dominguez, J., Wienbrandt, L., Kaessens, J. C., et al. (2015). Parallelizing Epistasis Detection in GWAS on FPGA and GPU-Accelerated Computing Systems. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 12(5), 982-994. DOI Author/Publisher URL
Thuy-Diem, N., Schmidt, B., Zheng, Z., Kwoh, C.-K. (2015). Efficient and Accurate OTU Clustering with GPU-Based Sequence Alignment and Dynamic Dendrogram Cutting. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 12(5), 1060-1073. DOI Author/Publisher URL
2014
Staib, F., Krupp, M., Maass, T., et al. (2014). CellMinerHCC: a microarray-based expression database for hepatocellular carcinoma cell lines. LIVER INTERNATIONAL, 34(4), 621-631. DOI Author/Publisher URL
Liu, Y., Popp, B., Schmidt, B. (2014). CUSHAW3 : sensitive and accurate base-space and color-space short-read alignment with hybrid seeding. PLoS one, 9(1), e86869. Author/Publisher URL
Liu, Y., Schmidt, B. (2014). CUSHAW2-GPU: Empowering Faster Gapped Short-Read Alignment Using GPU Computing. IEEE DESIGN & TEST, 31(1), 31-39. DOI Author/Publisher URL
Liu, Y., Schmidt, B. (2014). SWAPHI: Smith-Waterman Protein Database Search on Xeon Phi Coprocessors. PROCEEDINGS OF THE 2014 IEEE 25TH INTERNATIONAL CONFERENCE ON APPLICATION-SPECIFIC SYSTEMS, ARCHITECTURES AND PROCESSORS (ASAP 2014), 184-185. Author/Publisher URL
Ripp, F., Krombholz, C. F., Liu, Y., et al. (2014). All-Food-Seq (AFS) : a quantifiable screen for species in biological samples by deep DNA sequencing. BMC genomics, 15, Art. 639. Author/Publisher URL
Wirawan, A., Harris, R. S., Liu, Y., et al. (2014). HECTOR : a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data. BMC bioinformatics, 15, Art. 131. Author/Publisher URL
2013
Dang, H.-V., and Schmidt, B. (2013). CUDA-enabled Sparse Matrix-Vector Multiplication on GPUs using atomic operations. PARALLEL COMPUTING, 39(11), 737-750. DOI Author/Publisher URL
Chen, Y., Schmidt, B., and Maskell, D. L. (2013). Reconfigurable Accelerator for the Word-Matching Stage of BLASTN. IEEE TRANSACTIONS ON VERY LARGE SCALE INTEGRATION (VLSI) SYSTEMS, 21(4), 659-669. DOI Author/Publisher URL
Chen, Y., Schmidt, B., and Maskell, D. L. (2013). A hybrid short read mapping accelerator. BMC BIOINFORMATICS, 14. DOI Author/Publisher URL
Liu, Y., Schroeder, J., and Schmidt, B. (2013). Musket: a multistage <i>k-</i>mer spectrum-based error corrector for Illumina sequence data. BIOINFORMATICS, 29(3), 308-315. DOI Author/Publisher URL
Liu, Y., Schröder, J., and Schmidt, B. (2013). Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data. [Print-Electronic]. Bioinformatics (Oxford, England), 29(3), 308-315. DOI
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, Art. 117. Author/Publisher URL
Schmidt, B., Aribowo, H., and Hoang-Vu, D. (2013). Iterative sparse matrix-vector multiplication for accelerating the block Wiedemann algorithm over GF(2) on multi-graphics processing unit systems. CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, 25(4), 586-603. DOI Author/Publisher URL
2012
Liu, Y., and Schmidt, B. (2012). Long read alignment based on maximal exact match seeds. BIOINFORMATICS, 28(18), I318-I324. DOI Author/Publisher URL
Liu, Y., Schmidt, B., and Maskell, D. L. (2012). CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform. BIOINFORMATICS, 28(14), 1830-1837. DOI Author/Publisher URL
Zheng, Z., Kramer, S., and Schmidt, B. (2012). DySC : software for greedy clustering of 16S rRNA reads. Bioinformatics, 28(16), Seiten: 2182-2183. Author/Publisher URL
2011
Shi, H., Schmidt, B., Liu, W., and Müller-Wittig, W. (2011). Parallel mutual information estimation for inferring gene regulatory networks on GPUs. BMC Research Notes, 4(1). DOI
Liu, Y., Schmidt, B., and Maskell, D. L. (2011). DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI. BMC BIOINFORMATICS, 12. DOI Author/Publisher URL
Kuttippurathu, L., Hsing, M., Liu, Y., et al. (2011). CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments. BIOINFORMATICS, 27(5), 715-717. DOI Author/Publisher URL
Liu, W., Schmidt, B., Mueller-Wittig, W. (2011). CUDA-BLASTP: Accelerating BLASTP on CUDA-Enabled Graphics Hardware. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 8(6), 1678-1684. DOI Author/Publisher URL
Liu, Y., Schmidt, B., Maskell, D. L. (2011). Parallelized short read assembly of large genomes using de Bruijn graphs. BMC bioinformatics, 12, Art. 354. Author/Publisher URL
2010
Liu, Y., Schmidt, B., and Maskell, D. L. (2010). CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions. BMC Research Notes, 3(1). DOI
Liu, Y., Schmidt, B., Liu, W., and Maskell, D. L. (2010). CUDA-MEME: Accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units. PATTERN RECOGNITION LETTERS, 31(14), 2170-2177. DOI Author/Publisher URL
Ahmad, S., Chetty, M., and Schmidt, B. (2010). Pattern Recognition in Bioinformatics. Pattern Recognition Letters, 31(14), 2071-2072. DOI
Liu, Y., Schmidt, B., and Maskell, D. L. (2010). MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities. BIOINFORMATICS, 26(16), 1958-1964. DOI Author/Publisher URL
Schmidt, B. (ed.). (2010). Bioinformatics. Published online. DOI
Wirawan, A., Kwoh, C. K., and Schmidt, B. (2010). Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures. BIOINFORMATICS, 26(10), 1368-1369. DOI Author/Publisher URL
Shi, H., Schmidt, B., Liu, W., and Mueller-Wittig, W. (2010). A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-Enabled Graphics Hardware. JOURNAL OF COMPUTATIONAL BIOLOGY, 17(4), 603-615. DOI Author/Publisher URL
2009
Schmidt, B., Sinha, R., Beresford-Smith, B., Puglisi, S. J. (2009). A fast hybrid short read fragment assembly algorithm. BIOINFORMATICS, 25(17), 2279-2280. DOI Author/Publisher URL
Schroeder, J., Schroeder, H., Puglisi, S. J., et al. (2009). SHREC: a short-read error correction method. BIOINFORMATICS, 25(17), 2157-2163. DOI Author/Publisher URL
Oliver, T. F., Schmidt, B., Jakop, Y., Maskell, D. L. (2009). High Speed Biological Sequence Analysis With Hidden Markov Models on Reconfigurable Platforms. IEEE TRANSACTIONS ON INFORMATION TECHNOLOGY IN BIOMEDICINE, 13(5), 740-746. DOI Author/Publisher URL
Liu, Y., Maskell, D. L., Schmidt, B. (2009). CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units. BMC Research Notes, 2(1), 73-73. DOI
Wirawan, A., Schmidt, B., Zhang, H., Kwoh, C. K. (2009). High performance protein sequence database scanning on the Cell Broadband Engine. Sci. Program., 17, 97-111.
2008
Liu, W., Schmidt, B., Voss, G., and Mueller-Wittig, W. (2008). Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA. COMPUTER PHYSICS COMMUNICATIONS, 179(9), 634-641. DOI Author/Publisher URL
Oliver, T., Yeow, L. Y., and Schmidt, B. (2008). Integrating FPGA acceleration into HMMer. PARALLEL COMPUTING, 34(11), 681-691. DOI Author/Publisher URL
Wirawan, A., Kwoh, C. K., Hieu, N. T., and Schmidt, B. (2008). CBESW: Sequence Alignment on the Playstation 3. BMC BIOINFORMATICS, 9. DOI Author/Publisher URL
Singh, A., Chen, C., Liu, W., et al. (2008). A hybrid computational grid architecture for comparative genomics. IEEE TRANSACTIONS ON INFORMATION TECHNOLOGY IN BIOMEDICINE, 12(2), 218-225. DOI Author/Publisher URL
Singh, D. T., Trehan, R., Schmidt, B., Bretschneider, T. (2008). Comparative phyloinformatics of virus genes at micro and macro levels in a distributed computing environment. BMC Bioinformatics, 9(S1). DOI
2007
Rajapakse, M., Schmidt, B., Feng, L., Brusic, V. (2007). Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms. BMC BIOINFORMATICS, 8. DOI Author/Publisher URL
Liu, W., Mueller-Wittig, W., Schmidt, B. (2007). Performance analysis of general-purpose computation on commodity graphics hardware:: A case study using bioinformatics. JOURNAL OF VLSI SIGNAL PROCESSING SYSTEMS FOR SIGNAL IMAGE AND VIDEO TECHNOLOGY, 48(3), 209-221. DOI Author/Publisher URL
Liu, W., Schmidt, B., Voss, G., Mueller-Wittig, W. (2007). Streaming algorithms for biological sequence alignment on GPUs. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 18(9), 1270-1281. DOI Author/Publisher URL
Walters, J. P., Meng, X., Chaudhary, V., et al. (2007). MPI-HMMER-Boost: Distributed FPGA acceleration. JOURNAL OF VLSI SIGNAL PROCESSING SYSTEMS FOR SIGNAL IMAGE AND VIDEO TECHNOLOGY, 48(3), 223-238. DOI Author/Publisher URL
Lin, F., Schröder, H., Schmidt, B. (2007). Solving the Bottleneck Problem in Bioinformatics Computing: An Architectural Perspective. The Journal of VLSI Signal Processing Systems for Signal, Image, and Video Technology, 48(3), 185-188. DOI
Schimmler, M., Schmidt, B., Lang, H.-W., Heithecker, S. (2007). An area-efficient bit-serial integer and GF(2″) multiplier. MICROELECTRONIC ENGINEERING, 84(2), 253-259. DOI Author/Publisher URL
Schmidt, B. (2007). A survey of desktop grid applications for e-science. International Journal of Web and Grid Services, 3(3), 354-354. DOI
2006
Chen, C., and Schmidt, B. (2006). Constructing large suffix trees on a computational grid. JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING, 66(12), 1512-1523. DOI Author/Publisher URL
Liu, W., and Schmidt, B. (2006). Parallel pattern-based systems for computational biology: A case study. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 17(8), 750-763. Author/Publisher URL
LIU, W. (2006). Mapping of Hierarchical Parallel Genetic Algorithms for Protein Folding onto Computational Grids. IEICE Transactions on Information and Systems, E89-D(2), 589-596. DOI
Oliver, T., Schmidt, B., Maskell, D., et al. (2006). High-speed Multiple Sequence Alignment on a reconfigurable platform. International Journal of Bioinformatics Research and Applications, 2(4), 394-394. DOI
2005
Liu, T., and Schmidt, B. (2005). Parallel RNA secondary structure prediction using stochastic context-free grammars. CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, 17(14), 1669-1685. DOI Author/Publisher URL
Oliver, T. F., Schmidt, B., and Maskell, D. L. (2005). Reconfigurable architectures for bio-sequence database scanning on FPGAs. IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS II-EXPRESS BRIEFS, 52(12), 851-855. DOI Author/Publisher URL
Oliver, T., Schmidt, B., Nathan, D., et al. (2005). Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW. BIOINFORMATICS, 21(16), 3431-3432. DOI Author/Publisher URL
Chen, C. X., Schmidt, B. (2005). An adaptive grid implementation of DNA sequence alignment. FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE, 21(7), 988-1003. DOI Author/Publisher URL
2004
Schmidt, B., Feng, L., Laud, A., and Santoso, Y. (2004). Development of distributed bioinformatics applications with GMP. CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, 16(9), 945-959. DOI Author/Publisher URL
Schimmler *, M., Schmidt, B., and Lang ‡, H.-W. (2004). A bit-serial floating-point unit for a massively parallel system on a chip. Parallel Algorithms and Applications, 19(2-3), 79-95. DOI
2002
Schmidt, B., Schröder, H., and Schimmler, M. (2002). A hybrid architecture for bioinformatics. FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE, 18(6), 855-862. DOI Author/Publisher URL
2001
Schmidt, B., and Schröder, H. (2001). A Hybrid Architecture for Multimedia Processors. Comput. Artif. Intell., 20, 225-244.
Schmidt, B., Schröder, H., and Schimmler, M. (2001). Tomographic Image Reconstruction on the Instruction Systolic Array. Comput. Artif. Intell., 20, 27-42.
2000
Schmidt, B., and Schimmler, M. (2000). KPROC – An Instruction Systolic Architecture for Parallel Prefix Applications. Scalable Comput. Pract. Exp., 3.
1997
Schmidt, B., Schimmler, M., and Schröder, H. (1997). Morphological hough transform on the instruction systolic array. 798-806. DOI
2026
Dortmann, T., Vieth, M., and Schmidt, B. (2026). Cuckoo-GPU: Accelerating Cuckoo Filters on Modern GPUs. Author/Publisher URL
2025
Müller, A., Wichmann, A., Kallenborn, F., et al. (2025). Improved Metagenomic Analysis for All-Food-Sequencing with AFS-MetaCache2: Illumina vs. Nanopore. In openRxiv. DOI
Kallenborn, F., Dabbaghie, F., Steinegger, M., Schmidt, B. (2025). Accelign: a GPU-based Library for Accelerating Pairwise Sequence Alignment. In openRxiv. DOI
Jünger, D., Kristensen, K., Wang, Y., et al. (2025). Optimizing Bloom Filters for Modern GPU Architectures. Author/Publisher URL
Piechotta, M., Guo, W., Naarmann-de Vries, I. S., et al. (2025). QutRNA2: Robust tRNA modification discovery from Nanopore direct tRNA sequencing. In openRxiv. DOI
2024
Schmidt, B., Kallenborn, F., Wichmann, A., et al. (2024). gpuPairHMM: High-speed Pair-HMM Forward Algorithm for DNA Variant Calling on GPUs. Author/Publisher URL
Kallenborn, F., Chacon, A., Hundt, C., et al. (2024). GPU-accelerated homology search with MMseqs2. In openRxiv. DOI
2023
Schmidt, B., Kallenborn, F., Chacon, A., and Hundt, C. (2023). CUDASW++4.0: Ultra-fast GPU-based Smith-Waterman Protein Sequence Database Search. In openRxiv. DOI
Zhang, H., Song, H., Yin, Z., et al. (2023). RabbitVar: ultra-fast and accurate somatic small-variant calling on multi-core architectures. In openRxiv. DOI
2022
Xu, X., Yin, Z., Yan, L., et al. (2022). RabbitTClust: enabling fast clustering analysis of millions bacteria genomes with MinHash sketches. In openRxiv. DOI
2021
Bob, K., Teschner, D., Kemmer, T., et al. (2021). Locality-sensitive hashing enables signal classification in high-throughput mass spectrometry raw data at scale. In openRxiv. DOI
Hildebrandt, A.-K., Bob, K., Teschner, D., et al. (2021). CorCast: A Distributed Architecture for Bayesian Epidemic Nowcasting and its Application to District-Level SARS-CoV-2 Infection Numbers in Germany. In openRxiv. DOI
Kobus, R., Müller, A., Jünger, D., et al. (2021). MetaCache-GPU: Ultra-Fast Metagenomic Classification.
