Jaroslaw Pillardy

Curriculum Vitae

Work address

Cornell University
623 Rhodes Hall
Ithaca, NY 14853-1301
Tel. (607) 254-6333    
E-mail: jp86@cornell.edu

Home address

236 Yellow Barn Rd

Freeville, NY 13068

Tel. (607) 844-4236

Education

1996

received Ph.D. in theoretical chemistry at Warsaw University, Warsaw, Poland (Ph.D. diploma magna cum laudae). The Ph.D. was conducted under the supervision of Prof. L. Piela, Warsaw University and the thesis title was "Designation of the most stable structures by means of deformation of potential energy of interactions".
1991           

graduated from Warsaw University, Warsaw, Poland with MSc. degree in chemistry (graduation diploma magna cum laudae).

Research Experience

2004-present

Senior Research Associate and Director of Computational Biology Service Unit, Core Facilities Laboratories Center (CLC), Cornell University. Computational Biology Service Unit is Cornell University core facility for computational biology and provides research, software and hardware support for computational biology applications. Assistance in the design, implementation and parallelization of computational solutions is also provided. Research in the fields of protein structure prediction, molecular force field design and optimization. Development of computational biology suit for high performance computing (BioHPC, http://biohpc.org/).
2001-2004

Senior Research Associate, Computational Biology Service Unit, Cornell Theory Center, Cornell University. The Computational Biology Service Unit group provides research, software and hardware support for computational biology applications. Assistance in the design, implementation and parallelization of computational solutions is also provided. Research in the fields of protein structure prediction, molecular force field design and optimization, global optimization and crystal structure prediction.
1997-2001

Research Associate in Prof. H. A. Scheraga group, Chemistry Department, Cornell University, Ithaca, NY, USA. Research in the fields of protein force field design, molecular force field optimization, global optimization and crystal structure prediction.

1996-1997

Postdoctoral Associate in Prof. H. A. Scheraga group, Chemistry Department, Cornell University, Ithaca, NY, USA. Research in the field of global optimization: developing deformation-based global optimization methods.

1996-1997

Assistant Professor, Quantum Chemistry Laboratory, Chemistry Department, Warsaw University, Warsaw, Poland. Research in the field of global optimization. Teaching students: classes and supplemental lectures for undergraduate students in general, physical and inorganic chemistry.
1991-1996

Research/Teaching Assistant in Prof. L. Piela group, Quantum Chemistry Laboratory, Chemistry Department, Warsaw University, Warsaw, Poland. Research in the field of global optimization in application to Lennard-Jones atomic clusters and water clusters. Teaching students: classes and supplemental lectures for undergraduate students in general, physical and inorganic chemistry.

 Teaching Experience

 Classes and supplemental lectures in general, physical and inorganic chemistry.

 Workshops in general bioinformatics and protein structure prediction.

 Recent Professional Activities

2007 Presentation at PAG XV Conference, San Diego, CA (January 13-17). “Web Interface For Accessing Bioinformatics Tools On Parallel Windows Cluster”
2006 Organization and teaching at BTR School of Bioinformatics Ithaca, NY (November 2-8).
2004 Lecture at the SIAM Conference on Parallel Processing in Scientific Computing, San Francisco, CA (February 25-27, 2004)
”Adapting Computational Biology Tools and Algorithms for Massively Parallel Calculations”
2003 Organization and teaching at CBSU Bioinformatics Workshop New York, NY (September 18-19) and Ithaca, NY (October 1-2).
2003 Teaching at ACS PRF Summer School on Chemical Biology at Cornell University, Ithaca, NY (July 5-11, 2003)
“Introduction to web-based tools for sequence analysis”.
2003  Lecture at ClusterWorld conference, San Jose, CA (June 23-26, 2003)
“Parallel Computational Biology Tools and Applications for Windows Clusters”.
2003 Organization of Bioinformatics Workshop, New York, NY (January 23-24, 2003)
“Introduction to protein structure-based analysis”.
2002 Poster presentation at Fifth Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction Conference, Asilomar, CA (December 1-5, 2002)
“A new version of LOOPP algorithm for threading-based protein structure prediction”.
2002 Organization of CBSU Bioinformatics Workshop, Ithaca (August 8-13, 2002) :
“Homology modeling”, “Ab-initio protein structure prediction”, “Prediction of secondary structure”, “Comparing protein structures”, “Tools for constructing genome contigs: an introduction to Phred/Phrap/Consed”.
2001

Lecture at the Conference on Parallel Computing in Bimolecular Simulations, Gdansk, Poland (September 1-3, 2001) :
"Structure prediction by global optimization of a potential function: proteins, polypeptides, and crystals”
2001

Lecture at the Tenth SIAM Conference on Parallel Processing in Scientific Computing, Portsmouth, VA (March 12-14, 2001):
“Parallel Algorithms for Structure Prediction by Global Optimization of a Potential Function: Proteins, Polypeptides and Crystals”

 

List of Publications