Publications

Select Publications

1. Distributed Enhanced Suffix Arrays: Efficient Algorithms for Construction and Querying
   Flick, P. , Aluru, S. IPDPS 2019 (under review)
   BibTeX code

     @inproceedings{flick2019distributed,
     title = {Distributed Enhanced Suffix Arrays: Efficient Algorithms for Construction and Querying},
     author = {Flick, Patrick and Aluru, Srinivas},
     booktitle = {Parallel and Distributed Processing Symposium (IPDPS), 2019 IEEE International},
     series = {IPDPS '19 (under review)},
     year = {2019},
     github = {https://github.com/patflick/psac},
     venue = {IPDPS 2019 (under review)}
   }
   
     

2. Parallel Construction of Suffix Trees and the All-Nearest-Smaller-Values Problem
   Flick, P. , Aluru, S. IPDPS 2017
   BibTeX doi code

     @inproceedings{flick2017parallel,
     title = {Parallel Construction of Suffix Trees and the All-Nearest-Smaller-Values Problem},
     author = {Flick, Patrick and Aluru, Srinivas},
     booktitle = {Parallel and Distributed Processing Symposium (IPDPS), 2017 IEEE International},
     series = {IPDPS '17},
     pages = {12--21},
     year = {2017},
     organization = {IEEE},
     url = {https://doi.org/10.1109/IPDPS.2017.62},
     doi = {10.1109/IPDPS.2017.62},
     github = {https://github.com/patflick/psac},
     keywords = {psac},
     venue = {IPDPS 2017}
   }
   
     

3. Kmerind: A Flexible Parallel Library for K-mer Indexing of Biological Sequences on Distributed Memory Systems
   Pan, T. , Flick, P. , Jain, C. , Liu, Y. , Aluru, S. ACM BCB 2016
   BibTeX doi code

     @inproceedings{pan2016kmerind,
     author = {Pan, Tony and Flick, Patrick and Jain, Chirag and Liu, Yongchao and Aluru, Srinivas},
     title = {Kmerind: A Flexible Parallel Library for K-mer Indexing of Biological Sequences on Distributed Memory Systems},
     booktitle = {Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics},
     series = {BCB '16},
     year = {2016},
     isbn = {978-1-4503-4225-4},
     location = {Seattle, WA, USA},
     pages = {422--433},
     numpages = {12},
     url = {http://doi.acm.org/10.1145/2975167.2975211},
     doi = {10.1145/2975167.2975211},
     acmid = {2975211},
     publisher = {ACM},
     address = {New York, NY, USA},
     keywords = {MPI, SIMD, distributed computing, k-mer counting, k-mer index, next generation sequencing, parallel computing},
     github = {https://github.com/ParBLiSS/kmerind},
     venue = {ACM BCB 2016}
   }
   
     

4. Parallel Distributed Memory Construction of Suffix and Longest Common Prefix Arrays
   Flick, P. , Aluru, S. Supercomputing 2015
   BibTeX doi code SC’15 Best Student Paper

     @inproceedings{flick2015psac,
     author = {Flick, Patrick and Aluru, Srinivas},
     title = {Parallel Distributed Memory Construction of Suffix and Longest Common Prefix Arrays},
     booktitle = {Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis},
     series = {SC '15},
     year = {2015},
     isbn = {978-1-4503-3723-6},
     location = {Austin, Texas},
     pages = {16:1--16:10},
     articleno = {16},
     numpages = {10},
     url = {http://doi.acm.org/10.1145/2807591.2807609},
     doi = {10.1145/2807591.2807609},
     acmid = {2807609},
     publisher = {ACM},
     address = {New York, NY, USA},
     github = {https://github.com/patflick/psac},
     mytag = {SC'15 Best Student Paper},
     mytaglink = {http://www.sighpc.org/recognition/sc-awards},
     venue = {Supercomputing 2015},
     keywords = {psac}
   }
   
     

5. A Parallel Connectivity Algorithm for De Bruijn Graphs in Metagenomic Applications
   Flick, P. , Jain, C. , Pan, T. , Aluru, S. Supercomputing 2015
   BibTeX doi code SC’16 Awarded Results Replicated Badge

     @inproceedings{flick2015parCC,
     author = {Flick, Patrick and Jain, Chirag and Pan, Tony and Aluru, Srinivas},
     title = {A Parallel Connectivity Algorithm for De Bruijn Graphs in Metagenomic Applications},
     booktitle = {Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis},
     series = {SC '15},
     year = {2015},
     isbn = {978-1-4503-3723-6},
     location = {Austin, Texas},
     pages = {15:1--15:11},
     articleno = {15},
     numpages = {11},
     url = {http://doi.acm.org/10.1145/2807591.2807619},
     doi = {10.1145/2807591.2807619},
     acmid = {2807619},
     publisher = {ACM},
     address = {New York, NY, USA},
     keywords = {connected component labeling, de Bruijn graph, metagenomic assembly, soil microbiology},
     github = {https://github.com/cjain7/parconnect},
     mytag = {SC'16 Awarded Results Replicated Badge},
     mytaglink = {http://sc16.supercomputing.org/2016/03/16/sc16-explores-reproducibility-advanced-computing-student-competition-michela-taufer/},
     venue = {Supercomputing 2015}
   }
   
     

6. Malleable Sorting
   Flick, P. , Sanders, P. , Speck, J. IPDPS 2013
   BibTeX doi

     @inproceedings{flick2013malleable,
     author = {Flick, Patrick and Sanders, Peter and Speck, Jochen},
     title = {Malleable Sorting},
     booktitle = {Proceedings of the 2013 IEEE 27th International Symposium on Parallel and Distributed Processing},
     series = {IPDPS '13},
     year = {2013},
     isbn = {978-0-7695-4971-2},
     pages = {418--426},
     numpages = {9},
     url = {http://dx.doi.org/10.1109/IPDPS.2013.90},
     doi = {10.1109/IPDPS.2013.90},
     acmid = {2511359},
     publisher = {IEEE Computer Society},
     address = {Washington, DC, USA},
     venue = {IPDPS 2013}
   }
   
     

7. An Adaptive Parallel Algorithm for Computing Connectivity
   Jain, C. , Flick, P. , Pan, T. , Green, O. , Aluru, S. arXiv preprint
   BibTeX

     @article{jain2016adaptive,
     title = {An Adaptive Parallel Algorithm for Computing Connectivity},
     author = {Jain, Chirag and Flick, Patrick and Pan, Tony and Green, Oded and Aluru, Srinivas},
     journal = {arXiv preprint arXiv:1607.06156},
     year = {2016},
     venue = {arXiv preprint},
     url = {https://arxiv.org/abs/1607.06156}
   }
   
     

8. Analysis of human tissue-specific protein-protein interaction networks
   Flick, P. Master’s thesis, Karlsruhe Institute of Technology
   BibTeX code

     @phdthesis{flick2014analysis,
     title = {Analysis of human tissue-specific protein-protein interaction networks},
     author = {Flick, Patrick},
     year = {2014},
     school = {Master’s thesis, Karlsruhe Institute of Technology},
     url = {https://github.com/patflick/tsppi/blob/master/docs/master_thesis_tsppi.pdf?raw=true},
     github = {https://github.com/patflick/tsppi},
     venue = {Master’s thesis, Karlsruhe Institute of Technology}
   }