For Alexander Shlyakhter's page, please go here.
Ilya Shlyakhter's page
Welcome to my (bare-bones) homepage!
Email me at 
.
Address: 75 Ames St Rm 6111, Cambridge, MA 02142
PGP key: 260343BB
I'm a computational biologist at the Broad Institute.
If you have a PDF viewer,
you can look at my resume.
Short letters on varied subjects: here
Papers:
- J. Vitti, S. Gosai, I. Shlyakhter, R. Tewhey, S. Reilly, P. C. Sabeti. Identification and characterization of adaptive
regulatory variation in diverse human populations. (in preparation).
- The 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature, 526(7571):68–74, Oct. 2015
- I. Shlyakhter, P. C. Sabeti, and S. F. Schaffner. Cosi2: An efficient simulator of exact and approximate coalescent
with selection. Bioinformatics (Oxford, England), 30(23):3427–3429, Dec. 2014
- E. K. Karlsson, J. B. Harris, S. Tabrizi, A. Rahman, I. Shlyakhter, N. Patterson, C. O’Dushlaine, S. F. Schaffner,
S. Gupta, F. Chowdhury, A. Sheikh, O. S. Shin, C. Ellis, C. E. Becker, L. M. Stuart, S. B. Calderwood, E. T.
Ryan, F. Qadri, P. C. Sabeti, and R. C. Larocque. Natural selection in a bangladeshi population from the
cholera-endemic ganges river delta. Science Translational Medicine, 5(192):192ra86, July 2013
- S. R. Grossman*, K. G. Andersen*, I. Shlyakhter*, S. Tabrizi*, S. Winnicki, A. Yen, D. J. Park, D. Griesemer, E. K.
Karlsson, S. H. Wong, M. Cabili, R. A. Adegbola, R. N. K. Bamezai, A. V. S. Hill, F. O. Vannberg, J. L. Rinn,
1000 Genomes Project, E. S. Lander, S. F. Schaffner, and P. C. Sabeti. Identifying recent adaptations in
large-scale genomic data. Cell, 152(4):703–713, Feb. 2013
- K. G. Andersen, I. Shylakhter, S. Tabrizi, S. R. Grossman, C. T. Happi, and P. C. Sabeti. Genome-wide scans
provide evidence for positive selection of genes implicated in Lassa fever. Philosophical Transactions of
the Royal Society of London. Series B, Biological Sciences, 367(1590):868–877, Mar. 2012
- D. Van Tyne, D. J. Park, S. F. Schaffner, D. E. Neafsey, E. Angelino, J. F. Cortese, K. G. Barnes, D. M. Rosen, A. K.
Lukens, R. F. Daniels, D. A. Milner, C. A. Johnson, I. Shlyakhter, and eighteen others. Identification and
functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum.
PLoS genetics, 7(4):e1001383, Apr. 2011
- S. Grossman*, I. Shlyakhter*, E. K. Karlsson, E. H. Byrne, S. Morales, G. Frieden, E. Hostetter, E. Angelino, M. Garber, O. Zuk, E. S. Lander, S. F. Schaffner, P. C. Sabeti. A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection. Science 12 February 2010:
Vol. 327. no. 5967.
- International HapMap 3 Consortium. Integrating Common and Rare Genetic Variation in Diverse Human
Populations. Nature, 467(7311):52–58, Sep. 2010
- I. Maccallum, D. Przybylski, S. Gnerre, J. Burton, I. Shlyakhter, A. Gnirke, J. Malek, K. McKernan, S. Ranade,
T. P. Shea, L. Williams, S. Young, C. Nusbaum, and D. B. Jaffe. ALLPATHS 2: Small genomes assembled
accurately and with high continuity from short paired reads. Genome Biology, 10(10):R103, 2009
- J. Butler, I. MacCallum, M. Kleber, I. A. Shlyakhter, M. K. Belmonte, E. S. Lander, C. Nusbaum, and D. B. Jaffe.
ALLPATHS: De novo assembly of whole-genome shotgun microreads. Genome Research, 18(5):810–820,
May 2008
- A. Zaks, Z. Yang, I. Shlyakhter, F. Ivancic, S. Cadambi, M. K. Ganai, A. Gupta, and P. Ashar. Bitwidth Reduction
via Symbolic Interval Analysis for Software Model Checking. IEEE Transactions on Computer-Aided Design
of Integrated Circuits and Systems, 27(8):1513–1517, Aug. 2008
- I. Shlyakhter. Generating effective symmetry-breaking predicates for search problems ( Discrete Applied Mathematics, special issue on satisfiability, vol. 155 no. 12, 15 June 2007, pp. 1539-1548, doi:10.1016/j.dam.2005.10.018
)
- F. Ivancic, I. Shlyakhter, A. Gupta, M. K. Ganai, V. Kahlon, C. Wang, Z. Yang. Model Checking C Programs Using F-Soft (invited tutorial). ICCD 2005
- F. Ivancic, Z. Yang, M.K. Ganai, A. Gupta, I. Shlyakhter, P. Ashar. F-Soft: Software Verification Platform (tool paper). CAV 2005.
- I. Shlyakhter, R. Seater, D. Jackson, M. Sridharan, M. Taghdiri. Debugging Overconstrained Declarative Models Using Unsatisfiable Cores, ASE 2003 (best paper award).
- I. Shlyakhter, M. Sridharan, R. Seater, D. Jackson. Exploiting Subformula Sharing in Automatic Analysis of Quantified Formulas. Sixth International Conference on Theory and Applications of Satisfiability Testing (SAT 2003), S. Margherita Ligure - Portofino ( Italy), May 2003 (poster).
- S. Khurshid, D. Marinov, I. Shlyakhter, D. Jackson. A Case for Efficient Solution Enumeration. Sixth International Conference on Theory and Applications of Satisfiability Testing (SAT 2003), S. Margherita Ligure - Portofino ( Italy), May 2003.
- A Micromodularity Mechanism, by Daniel Jackson, Ilya Shlyakhter and Manu Sridharan.
Proc. ACM SIGSOFT Conf. Foundations of Software Engineering/European Software Engineering Conference (FSE/ESEC '01), Vienna, September 2001.
- Alcoa: the Alloy Constraint Analyzer, by Daniel Jackson, Ian Schechter and Ilya Shlyakhter.
Proc. International Conference on Software Engineering, Limerick, Ireland, June 2000
- Reconstructing 3D Tree Models from Instrumented Photographs,
by Ilya Shlyakhter, Max Rozenoer, Julie Dorsey, and Seth Teller. IEEE Computer Graphics and Applications, 21(3): 53-61, May/June 2001.
- "Estimating uncertainty in physical measurements, observational and environmental studies: Lessons from trends in nuclear data", A.I. Shlyakhter, I. Shlyakhter, C.L. Broido and R. Wilson. In: Proceed. ISUMA '93 Second International Symposium on Uncertainty Modeling and Analysis, IEEE Computer Society Press (1993), pp. 310-317
- An Empirical Examination of Factors Influencing Prediction of Carcinogenic Hazard Across Species, G.M. Gray, P. Li, I. Shlyakhter, R. Wilson, Regulatory Toxicology and Pharmacology, 22 283-291 (1995).
- Some earlier work related to SAT solvers: a progress bar for measuring
progress of search, and a parallelization framework for SAT solvers.
- Area exam paper: a review of modern SAT techniques.
Links:
Related work: