Publications

Journal Articles

  1. Codes Correcting Erasures and Deletions for Rank Modulation
    R. Gabrys, E. Yaakobi, F. Farnoud, F. Sala, J. Bruck, and L. Dolecek, To appear in IEEE Trans. Information Theory.

  2. MetaCRAM: An Integrated Pipeline for Metagenomic Data Processing and Compression
    M. Kim, X. Zhang, J.G. Ligo, F. Farnoud, V.V. Veeravalli, and O. Milenkovic, BMC Bioinformatics, Feb. 2016.

  3. The Capacity of String-Duplication Systems (preprint)
    F. Farnoud, M. Schwartz, and J. Bruck, IEEE Trans. Information Theory, vol. 62, Feb. 2016.

  4. Bounds for Permutation Rate-Distortion (preprint)
    F. Farnoud, M. Schwartz, and J. Bruck, IEEE Trans. Information Theory, vol. 62, Feb. 2016.

  5. HyDRA: Gene Prioritization via Hybrid Distance-Score Rank Aggregation [Supplementary Data]
    M. Kim, F. Farnoud, and O. Milenkovic, Bioinformatics, 31(7):1034–1043, 2015.

  6. Approximate Sorting of Data Streams with Limited Storage
    F. Farnoud, E. Yaakobi, and J. Bruck, J. Combinatorial Optimization. Aug. 2015.

  7. An Axiomatic Approach to Constructing Distances for Rank Comparison and Aggregation [Slides]
    F. Farnoud, and O. Milenkovic, IEEE Trans. Information Theory, vol. 60, pp. 6417–6439, Oct. 2014.

  8. Multipermutation Codes in the Ulam Metric for Non-volatile Memories
    F. Farnoud and O. Milenkovic, IEEE J. Selected Areas in Communications, vol. 32, pp. 919–932, May 2014.

  9. Error-Correction in Flash Memories via Codes in the Ulam Metric
    F. Farnoud, V. Skachek, and O. Milenkovic, IEEE Trans. Information Theory, vol. 59, pp. 3003–3020, May 2013.

  10. Sorting of Permutations by Cost-Constrained Transpositions
    F. Farnoud and O. Milenkovic, IEEE Trans. Information Theory, vol. 58, pp. 3–23, Jan. 2012.

  11. On the Multimessage Capacity Region for Undirected Ring Networks
    S.M.S.T. Yazdi, S.A. Savari, G. Kramer, K. Carlson, and F. Farnoud, IEEE Trans. Information Theory, vol. 56, pp. 1930–1947, Apr. 2010.

  12. A Packet-Based Photonic Label Switching Router for a Multirate All-Optical CDMA-Based GMPLS Switch
    F. Farnoud, M. Ibrahimi, and J. Salehi, IEEE J. Sel. Topics Quantum Electron., vol. 13, pp. 1522–1530, May 2007.

Manuscripts and Submissions

  1. Estimating Mutation Rates and Sequence Age under a Stochastic Model for Tandem Duplication and Point Mutation
    F. Farnoud, M. Schwartz, and J. Bruck, In preparation.

  2. Capacity and Expressiveness of Genomic Tandem Duplication
    S. Jain, F. Farnoud, and J. Bruck, Submitted to IEEE Trans. Information Theory.

  3. Computing Similarity Distances Between Rankings
    F. Farnoud, G. J. Puleo, O. Milenkovic, and L. Su, In preparation.

Conferences

  1. On the Duplication Distance of Binary Strings
    N. Alon, J. Bruck, F. Farnoud, and S. Jain, In Proc. IEEE Int. Symp. Information Theory (ISIT), Barcelona, Spain, July 2016.

  2. Duplication-Correcting Codes for Data Storage in the DNA of Living Organisms
    S. Jain, F. Farnoud, M. Schwartz, and J. Bruck, In Proc. IEEE Int. Symp. Information Theory (ISIT), Barcelona, Spain, July 2016.

  3. The Capacity of Some Polya String Models
    O. Elishco, F. Farnoud, M. Schwartz, and J. Bruck, In Proc. IEEE Int. Symp. Information Theory (ISIT), Barcelona, Spain, July 2016.

  4. A Stochastic Model for Genomic Interspersed Duplication
    F. Farnoud, M. Schwartz, and J. Bruck, In Proc. IEEE Int. Symp. Information Theory (ISIT), Hong Kong, China, June 2015.

  5. Capacity and Expressiveness of Genomic Tandem Duplication
    S. Jain, F. Farnoud, and J. Bruck, In Proc. IEEE Int. Symp. Information Theory (ISIT), Hong Kong, China, June 2015.

  6. Reconciling Similar Sets of Data
    R. Gabrys, and F. Farnoud, In Proc. IEEE Int. Symp. Information Theory (ISIT), Hong Kong, China, June 2015.

  7. Approximate Sorting of Data Streams with Limited Storage [Slides]
    F. Farnoud, E. Yaakobi, and J. Bruck, In Proc. Computing and Combinatorics Conf. (COCOON), Atlanta, GA, Aug. 2014.

  8. The Capacity of String-Duplication Systems [Slides]
    F. Farnoud, M. Schwartz, and J. Bruck, In Proc. IEEE Int. Symp. Information Theory (ISIT), Honolulu, HI, June 2014.

  9. Bounds for Permutation Rate-Distortion
    F. Farnoud, M. Schwartz, and J. Bruck, In Proc. IEEE Int. Symp. Information Theory (ISIT), Honolulu, HI, June 2014.

  10. Multipermutation Codes in the Ulam Metric [Slides]
    F. Farnoud and O. Milenkovic, In Proc. IEEE Int. Symp. Information Theory (ISIT), Honolulu, HI, June 2014.

  11. Similarity Distances between Permutations
    L. Su, F. Farnoud, and O. Milenkovic, In Proc. IEEE Int. Symp. Information Theory (ISIT), Honolulu, HI, June 2014.

  12. Single-Deletion-Correcting Codes over Permutations
    R. Gabrys, E. Yaakobi, F. Farnoud, F. Sala, J. Bruck, and L. Dolecek, In Proc. IEEE Int. Symp. Information Theory (ISIT), Honolulu, HI, June 2014.

  13. Codes Correcting Erasures and Deletions for Rank Modulation
    R. Gabrys, E. Yaakobi, F. Farnoud, and J. Bruck, In Proc. IEEE Int. Symp. Information Theory (ISIT), Honolulu, HI, June 2014.

  14. Gene Prioritization via Weighted Kendall Rank Aggregation
    M. Kim, F. Raisali, F. Farnoud, O. Milenkovic, In Proc. IEEE Int. Workshop on Computational Advances in Multi-Sensor Adaptive Processing (CAMSAP), Saint Martin Island, Dec. 2013.

  15. MetaPar: Metagenomic Sequence Assembly via Iterative Reclassification
    M. Kim, J.G. Ligo, A. Emad, F. Farnoud, O. Milenkovic, and V.V. Veeravalli, In Proc. IEEE Global Conf. Signal and Information Processing (GlobalSIP), Dec. 2013.

  16. Aggregating Rankings with Positional Constraints
    F. Farnoud, O. Milenkovic, In Proc. IEEE Information Theory Workshop (ITW), Seville, Spain, Sep. 2013.

  17. Building Consensus via Iterative Voting
    F. Farnoud, E. Yaakobi, O. Milenkovic, and J. Bruck, In Proc. IEEE Int. Symp. Information Theory (ISIT), Istanbul, Turkey, Jul. 2013.

  18. Weighted Rank Aggregation via Relaxed Integer Programming
    F. Raisali, F. Farnoud, O. Milenkovic, In Proc. IEEE Int. Symp. Information Theory (ISIT), Istanbul, Turkey, Jul. 2013.

  19. A General Framework for Distributed Vote Aggregation
    B. Touri, F. Farnoud, A. Nedich, O. Milenkovic, In Proc. American Control Conf. (ACC), Washington, DC, Jun. 2013.

  20. Alternating Markov Chains for Distribution Estimation in the Presence of Errors
    F. Farnoud, N.P. Santhanam, and O. Milenkovic, In Proc. IEEE Int. Symp. Information Theory (ISIT), Boston, MA, Jul. 2012.

  21. Rank Modulation for Translocation Error Correction [Slides]
    F. Farnoud, V. Skachek, and O. Milenkovic, In Proc. IEEE Int. Symp. Information Theory (ISIT), Boston, MA, Jul. 2012.

  22. Nonuniform Vote Aggregation Algorithms
    F. Farnoud, B. Touri, and O. Milenkovic, In Proc. IEEE Int. Conf. Signal Processing and Communications (SPCOM), Bangalore, India, Jul. 2012.

  23. Decomposing Permutations via Cost-Constrained Transpositions
    F. Farnoud and O. Milenkovic, In Proc. IEEE Int. Symp. Information Theory (ISIT), Saint Petersburg, Russia, Jul./Aug. 2011.

  24. A Graphical Model for Computing the Minimum Cost Transposition Distance
    F. Farnoud, C.-Y. Chen, O. Milenkovic, and N. Kashyap, In Proc. IEEE Information Theory Workshop (ITW), Dublin, Ireland, Aug./Sep. 2010.

  25. Small-Sample Distribution Estimation over Sticky Channels
    F. Farnoud, O. Milenkovic, and N.P. Santhanam, In Proc. IEEE Int. Symp. Information Theory (ISIT), Jun./Jul. 2009, pp. 1125 –1129.

  26. Reliable Broadcast of Safety Messages in Vehicular Ad Hoc Networks
    F. Farnoud and S. Valaee, In Proc. IEEE INFOCOM, Rio de Janeiro, Brazil, Apr. 2009, pp. 226–234.

  27. Repetition-Based Broadcast in Vehicular Ad Hoc Networks in Rician Channel with Capture
    F. Farnoud and S. Valaee, In Proc. IEEE INFOCOM Workshops, Phoenix, AZ, Apr. 2008.

  28. Message Broadcast Using Optical Orthogonal Codes in Vehicular Communication Systems
    F. Farnoud, B. Hassanabadi, and S. Valaee, In Proc. 1st ACM Int. Workshop on Wireless Networking for Intelligent Transportation Systems, Vancouver, BC, Aug. 2007.

  29. A Multimessage Capacity Region for Undirected Ring Networks
    S. Yazdi, S. Savari, F. Farnoud, and G. Kramer, In Proc. IEEE Int. Symp. Information Theory (ISIT), Nice, France, June 2007.

Theses

  1. Distances on Rankings: from Social Choice to Flash Memories
    Ph.D. Thesis, University of Illinois at Urbana-Champaign, Urbana, IL, May 2013

  2. Reliable Broadcast of Safety Messages in Vehicular Ad hoc Networks
    M.Sc. Thesis, University of Toronto, Toronto, ON, August 2008