Computer Science Electrical

Jaroslaw Zola

Rutgers University Phone: 515-***-****

Department of Electrical & Computer Engineering Skype: jaroslaw.zola

Rutgers Discovery Informatics Institute (RDI2 ) ********.****@*******.***

96 Frelinghuysen Road, Piscataway, NJ 08854 http://www.jzola.org/

Positions

Oct 2012 present: Research Associate Professor

Department of Electrical and Computer Engineering

Rutgers Discovery Informatics Institute

Rutgers University, Piscataway, New Jersey

Aug 2010 Oct 2012: Research Assistant Professor

Department of Electrical and Computer Engineering

Iowa State University, Ames, Iowa

Jun 2006 Aug 2010: Postdoctoral Research Associate

Department of Electrical and Computer Engineering

Iowa State University, Ames, Iowa

Nov 2001 Jun 2006: Research Assistant

Institute of Computer and Information Sciences

Czestochowa University of Technology, Czestochowa, Poland

Education

2002 2005: Ph.D. in Computer Science (th se en cotutelle ).

Grenoble Institute of Technology, Grenoble, France.

Thesis: Parallel server for multiple sequence alignment.

2001 2005: Ph.D. in Computer Science.

Czestochowa University of Technology, Czestochowa, Poland.

2000: Study abroad (Computer Science, Erasmus Programme ).

Grenoble Institute of Technology, Grenoble, France.

1996 2001: M.Sc. in Computer Science.

Czestochowa University of Technology, Czestochowa, Poland.

Specialization: Software Engineering and Information Systems.

Thesis: Libraries for evolutionary programming and their application in solving combi-

natorial optimization problems (passed with distinction).

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Honors and Awards

2012: IEEE Senior Member.

2007: Best paper award nomination, ACM/IEEE Supercomputing Conference.

2002: Ph.D. scholarship award of the French government.

Research Proposals and Grants

1. Awarded: Co-PI, NSF/IIS, BIGDATA: Mid-Scale: DA: Collaborative Research: Genomes galore Core

techniques, libraries, and domain speci c languages for high-throughput DNA sequencing. Proposed

duration: 36 months. Requested starting date: 01/01/2013. PI: S. Aluru. Co-PIs: W. Feng, K. Olukotun,

P.S. Schnable, C.F. Sing, J. Zola.

2. Pending: Co-PI, NSF/CCF, AF: III: Large: Collaborative Research: Uncertainty modeling and scalable

algorithms for large biological and social networks. Proposed duration: 48 months. Requested

starting date: 06/01/2013. PI: S. Aluru. Co-PIs: M.R. Aluru, D. Bader, M. Khan, M. Marathe, T. Murali,

J. Riedy, A. Srinivasan, S. Tirthapura, R. Vuduc, A. Vullikanti, J. Zola.

3. Pending: Co-PI, NSF/CBET, Collaborative Research: CDS&E: Sculpting uid ow using a programmed

sequence of micro-pillars. Proposed duration: 36 months. Requested starting date: 08/15/2013. PI: B.

Ganapathysubramanian. Co-PIs: D. Di Carlo, J. Zola.

4. Completed: Researcher, Polonium Programme, Grid computing for solving large problems in bioinfor-

matics. Joint project: Grenoble Institute of Technology (France), Poznan University of Technology

(Poland) and Czestochowa University of Technology (Poland), 2005-2006.

5. Completed: Researcher, Laboratoire Franco-Mexicain d Informatique, Phylogenetic tree reconstruction

on large scale distributed systems and grids. Joint project: Grenoble Institute of Technology (France)

and Centro de Investigaci n Cientif ca y de Educati n Superior de Ensenada (Mexico), 2005-2006.

Publications and Talks

joint rst authors.

Journal Publications:

1. O. Nikolova, J. Zola, S. Aluru: Parallel Globally Optimal Structure Learning of Bayesian Networks, Journal

of Parallel and Distributed Computing, 2013 (under review).

2. X. Yang, J. Zola, S. Aluru: Large-Scale Metagenomic Clustering on Map-Reduce Clusters, Journal of

Bioinformatics and Computational Biology, 11(1):1340001, 2013.

3. M. Aluru, J. Zola, D. Nettleton, S. Aluru: Reverse Engineering and Analysis of Large Genome-Scale

Gene Networks, Nucleic Acids Research, 41(1), pp. e24, 2013.

Jaroslaw Zola Resume 2/7

4. A. Sarje, J. Zola, S. Aluru: Accelerating Pairwise Computations on Cell Processors, IEEE Transactions

on Parallel and Distributed Systems, 22(1), pp. 69 77, 2011.

5. X. Yu, L. Li, J. Zola, M. Aluru, H. Ye, A. Foudree, H. Guo, S. Anderson, S. Aluru, P. Liu, S. Rodermel,

Y. Yin: A Brassinosteroid Transcriptional Network Revealed by Genome-Wide Identi cation of BESI Target

Genes in Arabidopsis thaliana, Plant Journal, 65(4), pp. 634 646, 2011.

6. J. Zola, M. Aluru, A. Sarje, S. Aluru: Parallel Information-Theory-Based Construction of Genome-Wide

Gene Regulatory Networks, IEEE Transactions on Parallel and Distributed Systems, 21(12), pp. 1721 1733,

2010.

7. M. Aluru, J. Zola, A. Foudree, S.R. Rodermel: Chloroplast Photooxidation Induced Transcriptome Repro-

gramming in Arabidopsis immutans White Leaf Sectors, Plant Physiology, 150(2), pp. 904 923, 2009.

8. M. Ott, J. Zola, S. Aluru, A.D. Johnson, D. Janies, A. Stamatakis: Large Scale Phylogenetic Analysis on

Current HPC Architectures, Scienti c Programming, 16(2-3), pp. 255 270, 2008.

9. D. Trystram, G. Parmentier, J. Zola: Large Scale Multiple Sequence Alignment with Simultaneous Phy-

logeny Inference, Journal of Parallel and Distributed Computing, 66(12), pp. 1534 1545, 2006.

Peer-reviewed Conference Publications:

10. R. Nihalani, J. Zola, S. Aluru, Resolving Read Assignment Ambiguities in Metagenomic Clustering, In

Proc. of ISCA Int. Conference on Bioinformatics and Computational Biology (BICoB 2013), 2013 (in

press).

11. X. Yang, J. Zola, S. Aluru: Parallel Metagenomic Sequence Clustering via Sketching and Maximal Quasi-

Clique Enumeration on Map-Reduce Clouds, In IEEE Proc. of Int. Parallel and Distributed Processing

Symposium (IPDPS 2011), pp. 1210 1220, 2011.

12. J. Zola, A. Sarje, S. Aluru: Constructing Gene Regulatory Networks on Clusters of Cell Processors, In

IEEE Proc. of Int. Conference on Parallel Processing (ICPP 2009), pp. 108 115, 2009.

13. O. Nikolova, J. Zola, S. Aluru: Parallel Algorithm for Exact Bayesian Network Inference, In IEEE Proc. of

Int. Conference on High Performance Computing (HiPC 2009), pp. 342 349, 2009.

14. J. Zola, M. Aluru, S. Aluru: Parallel Information-Theory-Based Construction of Gene Regulatory Networks,

In Proc. of Int. Conference on High Performance Computing (HiPC 2008), LNCS vol. 5374, pp. 336 349,

2008.

15. M. Ott, J. Zola, S. Aluru, A. Stamatakis: Large Scale Maximum Likelihood-Based Phylogenetic Analysis

on the IBM BlueGene/L, In Proc. of ACM/IEEE Supercomputing Conference (SC 2007), 2007 (best paper

nalist).

16. J. Zola, X. Yang, S. Rospondek, S. Aluru: Parallel T-Co ee: A Parallel Multiple Sequence Aligner, In Proc.

of ISCA Int. Conference on Parallel and Distributed Computing and Systems (PDCS 2007), pp. 248 253,

2007.

17. J. Zola, D. Trystram, A. Tchernykh, C. Brizuela: Parallel Multiple Sequence Alignment with Local Phy-

logeny Search by Simulated Annealing. In Proc. of IEEE Int. Workshop on High Performance Computa-

tional Biology (HiCOMB 2006), 2006.

18. D. Trystram, J. Zola: Parallel Multiple Sequence Alignment with Decentralized Cache Support. In Proc.

of Int. European Conference on Parallel and Distributed Computing (Euro-Par 2005), LNCS vol. 3648,

pp. 1217 1226, 2005.

Jaroslaw Zola Resume 3/7

19. G. Parmentier, D. Trystram, J. Zola: Cache-Based Parallelization of Multiple Sequence Alignment Problem.

In Proc. of Int. European Conference on Parallel and Distributed Computing (Euro-Par 2004), LNCS

vol. 3149, pp. 1005 1012, 2004.

20. 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, 2004.

21. R. Wyrzykowski, A. Tomas, K. Karczewski, J. Zola, T. Kuczynski: Development, Administration and Use

of Eltoro Cluster. In Proc. of Pionier 2002, pp. 273 280, 2002 (in Polish).

22. J. Zola, R. Wyrzykowski: EPL-Julia, the High Performance Library for Evolutionary Computations. In

Proc. of Int. Conference on Parallel processing and Applied Mathematics (PPAM 2001), LNCS vol. 2328,

pp. 633 639, 2002.

Book Chapters:

23. J. Zola, S. Aluru: Network Inference in Systems Biology, Chapter in Encyclopedia of Parallel Computing,

D. Padua (ed.), Springer, 2011.

24. A. Sarje, J. Zola, S. Aluru: Pairwise Computations on the Cell Processor with Applications in Computa-

tional Biology, Chapter in Scienti c Computing with Multicore and Accelerators, J. Kurzak, D.A. Bader, J.

Dongarra (eds.), Chapman & Hall/CRC, 2010.

25. D. Trystram, J. Zola: Multiple Sequence Alignment and Phylogenetic Inference, Chapter in Grids for

Bioinformatics and Computational Biology, A. Zomaya, E. Talbi (eds.), John Wiley & Sons, 2007.

Invited Talks and Lectures:

1. Panelist: Big Data Standards and the Potential Long Term Bene ts for Research and Clinical Develop-

ment. Webinar organized by NGSLeaders, December 2012.

2. Invited talk: Large Scale Metagenomic Clustering. Presented at International Conference on the

Bioinformatics of Genome Regulation and Structure/Systems Biology in Novosibirsk, Russia, June 2012.

3. Three-hours tutorial: Not Too Short Introduction to Metagenomics. Presented at Czestochowa Univer-

sity of Technology, Poland, December 2011.

4. Invited talk: Computational Biology: Can We Do Without Parallel Computing? Presented at Corpora-

cion Universitaria para el Desarrollo de Internet meeting in Puebla, Mexico, April 2009.

5. Invited lectures: Introduction to Bioinformatics. and High Performance Computational Biology.

Presented at Pannon University, Hungary, May 2006.

6. Two-hours talk with Denis Trystram: Bio-Computing Today: What to Expect from Parallel and Dis-

tributed Systems? Presented at 4th Franco-Mexican School on Distributed Systems in Grenoble, France,

July 2005.

7. Seminar: Parallel Server for Large Scale Multiple Sequence Alignment. Presented at Poznan University

of Technology, Institute of Computing Science, Poland, May 2005.

8. 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.

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Teaching and Mentoring Experience

Courses:

Co-instructor: Introduction to Parallel Algorithms and Programming,

CprE/ComS 426/526, Spring 2011 and 2012,

Iowa State University, Ames, Iowa.

Instructor: Introduction to High Performance Computing,

Computer Science, Graduate Level, Spring 2006,

Czestochowa University of Technology, Czestochowa, Poland.

Instructor: Computer Languages and Programming Methods,

Computer Science, Graduate Level, Spring 2001 to 2005,

Czestochowa University of Technology, Czestochowa, Poland.

Instructor: Selected Topics in Combinatorial Optimization,

Computer Science, Undergraduate Level, Fall 2001,

Czestochowa University of Technology, Czestochowa, Poland.

Master s Degree Project Advisor:

Piotr Dziubecki, A User-Oriented Grid Portal For Large Scale Multiple Sequence Alignment,

Czestochowa University of Technology, Czestochowa, Poland, 2005-2006.

Adrian Rospondek, Parallel-*-Co ee: Parallel Implementation of 3D/T-Co ee Method,

Czestochowa University of Technology, Czestochowa, Poland, 2005-2006.

Malgorzata Sikorska, A Practical Comparison of 2PC and 3PC Mechanisms for Distributed Databases,

Czestochowa University of Technology, Czestochowa, Poland, 2005-2006.

Monika Zagala, Rational Arithmetic of High Precision for C++,

Czestochowa University of Technology, Czestochowa, Poland, 2005-2006.

K12 Outreach

Chaitanya Aluru, Research Internship in Bioinformatics and Computational Biology,

Ames High School, Iowa (Extended Learning Program), 2011-2012.

Professional Activities and A liations

Co-founder and program chair since 2005, Parallel Bio-Computing Workshop (PBC), workshop accom-

panying International Conference on Parallel Processing and Applied Mathematics (PPAM).

Program chair, IEEE International Workshop on High Performance Computational Biology (HiCOMB) 2013.

Publicity co-chair, ISCA International Conference on Bioinformatics and Computational Biology (BI-

CoB) 2013.

Jaroslaw Zola Resume 5/7

Co-organizer, IEEE Cluster 2010 workshop: Parallel Programming and Applications on Accelerator Clus-

ters (PPAAC) 2010.

Program committees:

International Conference on Parallel Processing and Applied Mathematics (PPAM) 2013

International Conference on Parallel Processing (ICPP) 2012

IEEE International Conference on Parallel and Distributed Systems (ICPADS) 2012

International Conference on the Bioinformatics of Genome Regulation and Structure/Systems Biology

(BGRS) 2012

IEEE International Workshop on High Performance Computational Biology (HiCOMB) 2008, 2011

and 2012

ISCA International Conference on Bioinformatics and Computational Biology (BICoB) 2012

Workshop on Using Emerging Parallel Architectures (WEPA) 2009, 2010 and 2012

International Conference on Contemporary Computing (IC3) 2011

ACM/IEEE Supercomputing 2008

Reviewer for:

IEEE Transactions on Parallel and Distributed Systems

Journal of Parallel and Distributed Computing

Parallel Computing

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Bioinformatics

IET Systems Biology

International Journal of Data Mining and Bioinformatics

BMC Bioinformatics

BMC Research Notes

Software: Practice and Experience

Senior member of Institute of Electrical and Electronics Engineers (IEEE).

Member of IEEE Computer Society.

Member of Association for Computing Machinery (ACM).

Member of International Society for Computational Biology (ISCB).

Technical Skills

Expert knowledge of C++ standard and generic programming paradigm.

Expert knowledge of parallel programming standards and paradigms

(MPI, Map-Reduce, OpenMP, Pthreads, Intel TBB, OpenCL, NVIDIA CUDA, IBM Cell SDK).

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Expert knowledge of Unix/Linux operating systems

(including shell programming and system administration).

Very good knowledge of parallel architectures

(clusters, multi/many-cores including GPGPUs and Cell BE).

Good knowledge of Perl and Bioperl, R and Bioconductor, Java SE, Erlang.

Open Source Software Development

CLOSET: Cloud-enabled framework based on map-reduce for large scale metagenomic data clustering.

The software handles data sets consisting of millions of reads and can be used to classify data at

di erent taxonomic levels http://www.jzola.org/closet.

TINGe: Systems biology parallel framework for gene networks inference. The software can handle

whole genome expression data, and it has been successfully used to reconstruct the largest to date

gene network of Arabidopsis thaliana http://www.jzola.org/tinge.

GeNA: Cytoscape plugin and standalone application for analysis of gene regulatory networks using

approach akin to PageRank algorithm http://www.jzola.org/tinge.

Parallel T-Co ee: Parallel multiple sequence aligner able to align thousands of sequences using T-

Co ee scoring method (more than 300 downloads, independent web interface developed by researchers

from Spain and UK) http://www.jzola.org/ptc.

Libpnorm: A C/C++ high performance library for scheduling pairwise computations on Cell processors

taking into account local memory limitations http://www.jzola.org/libpnorm.

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