Publikacje i Wykłady

2009

1. O. Nikolova, J. Zola, S. Aluru, A Parallel Algorithm for Exact Bayesian Network Inference, To appear in Proc. of HiPC 2009, 2009.
   
   
2. J. Zola, A. Sarje, S. Aluru, Constructing Gene Regulatory Networks on Clusters of Cell Processors, IEEE Proc. of ICPP 2009, pp. 108-115, 2009.
   
   
3. M. Aluru, J. Zola, A. Foudree, S.R. Rodermel, Chloroplast Photooxidation Induced Transcriptome Reprogramming in Arabidopsis immutans White Leaf Sectors, Plant Physiology, 150(2), pp. 904-923, 2009.
   
   

   2008

4. J. Zola, M. Aluru, S. Aluru, Parallel Information Theory Based Construction of Gene Regulatory Networks, Proc. of HiPC 2008, LNCS vol. 5374, pp. 336-349, 2008.
   
   
5. M. Ott, J. Zola, S. Aluru, A.D. Johnson, D. Janies, A. Stamatakis, Large-scale Phylogenetic Analysis on Current HPC Architectures, Scientific Programming, 16(2-3), pp. 255-270, 2008.
   
   

   2007

6. M. Ott, J. Zola, S. Aluru, A. Stamatakis, Large-scale Maximum Likelihood-based Phylogenetic Analysis on the IBM BlueGene/L, Proc. of Supercomputing 2007, 2007. (best paper finalist)
   
   
7. J. Zola, D. Trystram, Multiple Sequence Alignment and Phylogeny Inference, Chapter in Grids for Bioinformatics and Computational Biology, A. Zomaya, E. Talbi (Eds.), John Wiley & Sons, 2007.
   
   
8. J. Zola, X. Yang, S. Rospondek, S. Aluru, Parallel T-Coffee: A Parallel Multiple Sequence Aligner, Proc. of ISCA PDCS-2007, pp. 248-253, 2007.
   
   
9. P. Dziubecki, J. Zola, Grid Portal for Multiple Sequence Alignment, Computing, Multimedia and Intelligent Techniques, 3(1), pp. 33-42, 2007.
   
   

   2006

10. J. Zola, G. Parmentier, D. Trystram, Large Scale Multiple Sequence Alignment with Simultaneous Phylogeny Inference, Journal of Parallel and Distributed Computing, 66(12), pp. 1534-1545, 2006.
    
    
11. J. Zola, D. Trystram, A. Tchernykh, C. Brizuela, Parallel Multiple Sequence Alignment with Local Phylogeny Search by Simulated Annealing, IEEE Proc. of HiCOMB 2006, 2006.
    
    

    2005

12. J. Zola, D. Trystram, Parallel Multiple Sequence Alignment with Decentralized Cache Support, Proc. of Euro-Par 2005, LNCS vol. 3648, pp. 1217-1226, 2005.
    
    

    2004

13. J. Zola, CaLi - Efficient Library for Cache Implementation, IEEE Proc. of ENC 2004, pp. 415-420, 2004.
    
    
14. J. Zola, G. Parmentier, D. Trystram, Cache-based Parallelization of Multiple Sequence Alignment Problem, Proc. of Euro-Par 2004, LNCS vol. 3149, pp. 1005-1012, 2004.
    
    

    2002 - 1999

15. J. Zola, L. Lacinski, R. Wyrzykowski, An Object Oriented Library for Evolution Programs with Applications for Partitioning of Finite Element Meshes, IUTAM Symp. on Evolutionary Methods in Mechanics, Solid Mechanics and its Applications vol. 117, pp. 351-360, 2002.
    
    
16. R. Wyrzykowski, A. Tomas, K. Karczewski, J. Zola, T. Kuczynski, Development, Administration and Use of Eltoro Cluster, Proc. of Pionier 2002, pp. 273-280, 2002. (in Polish)
    
    
17. J. Zola, R. Wyrzykowski, EPL-Julia, the High-Performance Library for Evolutionary Computations, Proc. of PPAM 2001, LNCS vol. 2328, pp. 633-639, 2002.
    
    
18. J. Zola, R. Wyrzykowski, L. Lacinski, Application of Genetic Algorithm for FEM Mesh Partitioning, Advances in Multi-Agent Systems, pp. 161-171, 2001.
    
    
19. J. Zola, R. Wyrzykowski, STL Based Library for Evolutionary Programs, Proc. of The Year 2000 SGI Users' Conference, pp. 468-473, 2000.
    
    
20. J. Zola, R. Wyrzykowski, Application of Genetic Algorithm for Mesh Partitioning, Proc. of ParNum 2000, pp. 209-217, 2000.
    
    
21. J. Zola, R. Wyrzykowski, L. Lacinski, Using Genetic Algorithms for Mesh Smoothing and Partitioning, Proc. of 5th Conf. Neural Networks and Soft Computing, pp. 663-668, 2000.
    
    
22. J. Zola, R. Wyrzykowski, J. Silc, Genetic Algorithms as a Method for Finite Element Mesh Smooting, Proc. of PPAM 99, pp. 637-644, 1999.
    
    

Wykłady

1. Keynote talk: Computational Biology: Can We Do Without Parallel Computing? Presented at CUDI 2009 in Puebla, Mexico, April 2009.
   
   
2. Invited lecturer at Pannon University, Hungary, May 2006: Introduction to Bioinformatics and High Performance Computational Biology.
   
   
3. Two-hours talk with Denis Trystram: Bio-computing Today: What to expect from parallel and distributed systems. Presented at 4th Franco-Mexican School on Distributed Systems in Grenoble, France, July 2005.
   
   
4. Seminar: Parallel Server for Large Scale Multiple Sequence Alignment. Presented at Poznan University of Technology, Institute of Computing Science, Poland, May 2005. (in Polish)
   
   
5. Invited talk with Roman Wyrzykowski and Tomasz Olas: Parallel FEM Computations on PC-Based Cluster using Myrinet. Presented at Myrinet User's Group Conference in Vienna, Austria, May 2002.