Resume - Asif Javed

Asif Javed
8 Fieldcrest ct 518-281-2269
Cortlandt Manor, NY 10567 asif.javed08@gmail.com
http://asifj.org/
Education
Rensselaer Polytechnic Institute Troy, NY
Ph.D., Computer Science, (CGPA 4.0), December 2008
University of Illinois at Chicago Chicago, IL
M.S., Computer Engg., (CGPA 3.9, C.S. GPA 4.0), May 2004
University of Engineering and Technology, Lahore Lahore, Pakistan
B.S. in Electrical Engineering (with honors) 2000
Research Interests
Statistical and Computational Genetics, Design and Analysis of Algorithms, Bioinformatics,
Data Mining, Parallel Algorithms
Work Experience
Postdoctoral Researcher December 2008 - Present
Computational Biology Center, IBM T. J. Watson Research Yorktown, NY
Research Intern May 2008 - August 2008
Computational Biology Center, IBM T. J. Watson Research Yorktown, NY
Teaching / Research Assistant August 2004 - December 2008
Rensselaer Polytechnic Institute Troy, NY
Courses: Computer Science 1, Models of Computation, Randomized Algorithms
Teaching / Research Assistant August 2001 - May 2004
University of Illinois at Chicago Chicago, IL
Courses: Random Signal Processing, Analog Communication Circuits,
Computer Architecture, Digital Logic
Teaching Assistant August 2000 - August 2001
Lahore University of Management and Sciences Lahore, Pakistan
Courses: Discrete Mathematics, Algorithm Design, Advanced Algorithm Design
Circuits and Systems 1, Algorithms in Computational Biology
Publications
• A. Javed, M. Pybus, M. Mele, F. Utro, J. Bertranpetit, F. Calafell, L. Parida and The
Genographic Consortium IRiS: Construction of subARG network at genomic scales, under
submission.
• A. Javed, M. Mele, M. Pybus, P. Zalloua, M. Haber, D. Comas, M. Netea, O. Balanovsky,
E. Balanovska, L. Jin, Y. Yang, R.M. Pichappan, G. Arunkumar, J. Bertranpetit, F.
Calafell, L. Parida and The Genographic Consortium Recombination networks as genetic
markers: a human variation study of the Old World, under submission.
• M. Mele, A. Javed, M. Pybus, P. Zalloua, M. Haber, D. Comas, M. Netea, O. Balanovsky,
E. Balanovska, L. Jin, Y. Yang, R.M. Pichappan, G. Arunkumar, L. Parida, F. Calafell, J.

Bertranpetit and The Genographic Consortium The footprint of recombination gives a new
insight in the effective population size and the history of the Old World human populations,
under submission.
• A. Javed, P. Paschou, M.W. Mahoney, and P. Drineas, Reconstructing the genome with
PCA-correlated tSNPs, under second review.
• K. Yang, H. Zheng, Z. Qin, Y. Lu, S.E. Farina, S. Li, L. Jin, D. Li, H. Li, and The
Genographic Consortium*, Positive selection on mitochondrial M7 lineages among the
Gelong people in Hainan, Journal of Human Genetics March 2011.
• L. Parida, P.F. Palamara, A. Javed, A Minimal Descriptor of an Ancestral Recombinations
Graph, BMC Bioinformatics, APBC, Jan 2011.
• M. Haber, D.E. Platt, D.A. Badro, Y. Xue, M. El-Sibai, M.A. Bonab, S.C. Youhanna, S.
Saade, D.F. Soria-Hernanz, A. Royyuru, R.S. Wells, C. Tyler-Smith, P.A. Zalloua and The
Genographic Consortium*, Influences of history, geography, and religion on genetic
structure: the Maronites in Lebanon, Eur J Hum Genet Dec 2010.
• Z. Qin, Y. Yang, L. Kang, S. Yan, K. Cho, X. Cai, Y. Lu, H. Zheng, D. Zhu, D. Fei, S. Li,
L. Jin, H. Li and The Genographic Consortium* A mitochondrial revelation of early
human migrations to the Tibetan Plateau before and after the last glacial maximum, Am J
Phys Anthropol Dec 2010.
• P. Paschou, J. Lewis, A. Javed, P. Drineas, Ancestry informative markers for fine-scale
individual assignment to worldwide populations, J Med Genet. Dec 2010.
• M. Mele, A. Javed, F. Calafell, L. Parida, J. Bertranpetit and The Genographic
Consortium A New Method to Reconstruct Recombination Events at a Genomic Scale,
PLOS Comput Biol. Nov 2010.
• W. Haak, O. Balanovsky, J.J. Sanchez, S. Koshel, V. Zaporozhchenko, C.J. Adler, C.S. Der
Sarkissian, G. Brandt, C. Schwarz, N. Nicklisch, V. Dresely, B. Fritsch, E. Balanovska, R.
Villems, H. Meller, K.W. Alt, A. Cooper and The Genographic Consortium* Ancient
DNA from European early neolithic farmers reveals their near eastern affinities, PLOS
Biol. Nov 2010.
• A. Javed and L. Parida, Recombinomics: Population Genomics from a Recombination
Perspective, Proceedings of C3S2E, Montreal, 2010.
• L. Parida, A. Javed, M. Mele, F. Calafell, J. Bertranpetit and The Genographic
Consortium, Minimizing recombinations in consensus networks for phylogeographic studies,
BMC Bioinformatics, APBC, January 2009.
• L. Parida, A. Javed, M. Mele, and J. Bertranpetit, A case for Recombinomics, IBM
Technical Report RC24677, August, 2008.
• A. Javed and P. Paschou, Extracting tagging SNPs from genome-wide datasets, DMBI,
workshop held in conjunction with SDM, April 2007.
• P. Paschou, M.W. Mahoney, A. Javed, J.R. Kidd, A.J. Pakstis, S. Gu, K.K. Kidd, and P.
Drineas, Intra- and inter-population genotype reconstruction from tagging SNPs, Genome
Research, January 2007.
• P. Drineas, A. Javed, M. Magdon-Ismail, G. Pandurangan, R.Virrankoski, and A.
Savvides, Distance matrix reconstruction from incomplete distance information for sensor
network localization, (SECON), September 2006.
• A. Javed and A. Khokhar, Frequent pattern mining on message passing multiprocessor
systems, (DAPD), November 2004.

• A. Javed and A. Khokhar, Scalable parallel algorithm for mining frequent patterns on
message passing parallel systems, ISCA (PDCS), August 2003.
Presentations
* indicates consortium membership
◦ B. Pupacdi, A. Javed, M. J. Zaki, NSIT: Novel Sequence Identification Tool,
(abstract/program #1743/W) presented at the 60th Annual Meeting of ASHG, November
2010.
◦ A. Javed, Recombinomics, oral presentation at Structure Discovery in Biology: Motifs,
Networks & Phylogenies seminar at Schloss Dagstuhl, June 2010.
◦ A. Javed, Recombinomics, invited talk at GBB Annual Retreat at University of
Toronto, May 2010.
◦ A. Javed, M. Mele, and L. Parida, RECO project, oral presentation at Genographic
Consortium annual meeting.
◦ A. Javed, Recombinomics: recombination-based population genomics, accepted tutorial at
APBC 2010, January 2010.
◦ A. Javed, M. Mele, F. Calafell, J. Bertranpetit, and L. Parida, IRiS-detecting
recombinations for phylogenetics and more, oral presentation at Genome Informatics
meeting at CSHL, October 2009.
◦ A. Javed, and J. Bertranpetit, Recombinations-based population genomics, oral
presentation at Workshop on Algorithms in Human Population Genomics at DIMACS,
April 2009.
◦ A. Javed, Identification of Recombination’s in Sequences (IRiS), invited talk at SSE,
LUMS, Jan. 2009.
◦ P. Paschou, J. Lewis, A. Javed, and P. Drineas, Using principal components analysis to
identify candidate genes for natural selection, poster presentation at ASHG annual meeting
2008.
◦ A. Javed, Novel matrix decomposition for knowledge discovery in genomic data, white
paper presentation at Cyber-Enabled Discovery and Innovation, NSF symposium held
at RPI, Sep. 2007.
◦ A. Javed and A. Khokhar, Parallel frequent pattern mining, poster presentation in
Midwest Database Symposium April 2004.
◦ A. Javed, Parallel association rule mining using frequent-pattern tree data structure for
IEEE Lahore at LUMS, Jan. 2003.
Computer Skills
Operating Systems: Microsoft Windows, Unix, Linux
Programming Languages: C/C++, Assembly (x86 architecture), Perl
Parallel Programming: MPI 1 & 2, OpenMP
Tools: Matlab, bash shell scripting, L ATEX
Activities
• Program Committee Member, 10th International Workshop on Data Mining in
Bioinformatics, workshop held in conjunction with KDD, August 2011.

• Program Committee Member, Workshop on Biological DataMining and its Applications in
Healthcare, workshop held in conjunction with ICDM, December 2010.
• Reviewer for APBC 10,CPM 10, PSB 10 .
• Publications and web chair, CPM, June 2010.
• Publications and web chair, APBC, January 2010.
• Program Committee Member, Data Mining for Biomedical Informatics, workshop held in
conjunction with SDM, April 2008.
Awards
⋆ Received DIMACS travel grant to attend Workshop on Algorithmics in Human Population
Genomics, April 2009.
⋆ Received IPAM travel grant to attend Search and Knowledge Building for Biological
Datasets, workshop held as a part of Mathematics of Knowledge and Search Engines,
November 2007.
⋆ Received NSF travel grant to attend SECON 2006.
⋆ Senior design project, Efficient Implementation of RSA algorithm was awarded 2nd prize
among 250 students.
⋆ Received National Merit Scholarship throughout undergraduate studies.
References
- Jaume Bertranpetit, Director ICREA, and Professor Dept. of Experimental and Health
Sciences, UPF, Barcelona, Spain.
- Petros Drineas, Associate Professor, Dept. of Computer Science, Rensselaer Polytechnic
Institute, New York, USA.
- Francesc Calafell, Associate Professor Dept. of Experimental and Health Sciences, UPF,
Barcelona, Spain.