**Recent Submissions**

Codes in the Damerau Distance for DNA-Based Storage, http://arxiv.org/abs/1601.06885

Balanced Permutation Codes, http://arxiv.org/abs/1601.06887

Inference of Latent Network Features via Co-Intersection Representations of Graphs, http://arxiv.org/abs/1601.06343

Weakly Mutually Uncorrelated Codes

**Topics in Rank Processing: Aggregation, Compression, Synchronization and Coding (11 papers)**

L. Su, Farzad Farnoud, O. Milenkovic: Similarity distances between permutations. ISIT 2014: 2267-2271

L. Su, O. Milenkovic: Synchronizing Rankings via Interactive Communication.

F. Farnoud, O. Milenkovic: Multipermutation codes in the Ulam metric. ISIT 2014: 2754-2758

L. Su, O. Milenkovic, “Synchronizing rankings through a noisy channel,” Asilomar conference, 2014.

L. Su, O. Milenkovic, “Reconciling Rankings through Iterative Communications,” CISS 2014.

A. Mazumdar, O. Milenkovic, “Smooth Compression of Rankings,” CISS 2014.

F. Farnoud and O. Milenkovic, “Aggregating Rankings with Positional Constraints,” Proceedings of the Information Theory Workshop (ITW), Seville, 2013.

F. Farnoud, E. Yaakobi, B. Touri, O. Milenkovic and S. Bruck, “Building Consensus via Iterative Voting,” Proceedings of the ISIT 2013, Istanbul, 2013.

F. Raisali, F. Farnoud, and O. Milenkovic, “Weighted Rank Aggregation via Relaxed Integer Programming,” Proceedings of the ISIT 2013, Istanbul, 2013.

B. Touri, F. Farnoud, O. Milenkovic, and A. Nedich, “A general framework for distributed vote aggregation,” Proceedings of the American Control Conference (ACC), 2013.

F. Farnoud, B. Touri, and O. Milenkovic, ”Nonuniform vote aggregation algorithms”, Signal Processing and Communications (SPCOM), 2012.

**Compressive Sampling (9 papers)**

W. Dai, D. Sejdinovic, and O. Milenkovic, “Compressive Sensing for Gaussian Dynamic Signals,” Proceedings of SPARS 2011, Edinburgh, Scotland, 2011.

W. Dai and O. Milenkovic, “Algorithmic Solutions for Quantized Compressive Sensing,” Proceedings of SampTA 2011, Singapore, 2011.

W. Dai, D. Sejdinovic and O. Milenkovic, “Gaussian Dynamic Compressive Sensing,” Proceedings of SampTA 2011, Singapore, 2011.

V.P. Hoa, W. Dai, and O. Milenkovic, “Compressive List-Support Recovery for Colluder Identification”, Proceedings of ICASSP, Texas, 2010.

W. Dai, H. Vin Pham, and O. Milenkovic, ”Distortion-Rate Functions for Compressive Sensing,” Proceedings of the ISIT’2009, Seul, Korea, 2009.

H. V. Pham,W. Dai, and O. Milenkovic, ”Sublinear Complexity Reconstruction Compressive Sensing via Belief Propagation,” Proceedings of the ISIT’2009, Seul, Korea, 2009.

W. Dai, H. Pham, O. Milenkovic, Distortion-Rate Functions for Quantized Compressive Sensing, Proceedings of the ITW’2009, Volos, Greece, 2009.

W. Dai and O. Milenkovic, “Sparse Weighted Euclidean Superimposed Coding for Integer Compressed Sensing” Proceedings of the CISS, Princeton, 2008.

W. Dai and O. Milenkovic, “Weighted Euclidean Superimposed Codes for Integer Compressed Sensing,” Proceedings of the ITW’08, Porto, Portugal, 2008.

**Low-Rank Matrix Completion (4 papers)**

P. Johnstone, A. Emad, O. Milenkovic and P. Moulin, RFIT: A New Algorithm for Matrix Rank Minimization, Proceedings of the Signal Processing with Adaptive Sparse Structured Representations (SPARS13), 2013.

A. Emad and O. Milenkovic, “Information Theoretic Bounds for Tensor Rank Minimization over Finite Fields,” Proceedings of the Globecom 2011, December 2011.

W. Dai, E. Kerman and O. Milenkovic, ’Low-Rank Matrix Completion with Geometric Performance Guarantees,” Proceedings of the ICASSP’2011, Prague, Czech Republic, 2011.

W. Dai and O. Milenkovic, “SET – an algorithm for consistent matrix completion,” Proceedings of the ICASSP 2010, Dallas, TX, http://arxiv.org/abs/0909.2705.

**Group Testing (4 papers)**

A. Emad, O. Milenkovic: Group testing for non-uniformly quantized adder channels. ISIT 2014: 2351-2355

A. Emad and O. Milenkovic, “Poisson Group Testing: AProbabilistic Model for Nonadaptive Streaming Boolean Compressed Sensing,” Proceedings of the ICASSP 2014, Florence, Italy.

A. Emad and O. Milenkovic, “Semi-quantitative Group Testing,” Proceedings of the ISIT, Boston, USA, 2012.

A. Emad and O. Milenkovic, “Symmetric Group Testing and Superimposed Codes,” Proceedings of the ITW’2011, Paraty, Brazil, 2011.

**Information and Coding Theory in Bioinformatics (19 papers)**

Z. Wang, T. Weissman, and O. Milenkovic, “Compression of RNA-seq expression data”, Cold Spring Harbor, Biological Data Science, November 2014.

M. Kim, J. Zhang, J. Ligo, A. Emad, V. Veeravalli, O. Milenkovic, MetaCRAM: Parallel compression of metagenomic sequences via extended Golomb codes, Cold Spring Harbor, Biological Data Science, November 2014 (**oral presentation**).

M. Kim, F. Farnoud and O. Milenkovic, “Prioritizing Disease Genes via Hybrid Rank Aggregation,” CISS 2014.

J. Ligo, M. Kim, A. Emad, O. Milenkovic, and V. Veeravali, “MCUIUC – A New Framework for Metagenomic Read Compression,” Proceedings of the ITW, ITW’13, Seville, 2013.

M. Kim, F. Raisali, F. Farnoud and O. Milenkovic, “Gene Prioritization via Weighted Kendall Rank Aggregation,” Proceedings of the Camsap, Saint Martin, 2013.

M. Kim, J. Ligo, A. Emad, F. Farndoud, O. Milenkovic and V. Veeravalli, “MetaPar: Metagenomic Sequence Assembly via Iterative Read Classification,” GlobalSip, 2013.

M. Deng, A. Emad and O. Milenkovic , “Causal Compressive Sensing for Reverse Engineering Gene Networks,” Proceedings of the SSP, SSP, Ann Arbor, 2012.

A. Emad,W. Dai and O. Milenkovic, “Protein-Protein Interaction Prediction using Non-Linear Matrix Completion Methods, Proceedings of RECOMB2011, Vancouver, Canada, March 2011.

W. Dai, O. Milenkovic, and Prasad Santhanam, ”Inferring Protein-Protein Interactions via Low-Rank Matrix Completion,” Proceedings of the ICNAAM, International Conference on Numerical Analysis and Applied Mathematics, Rhodes, Greece, September 2010.

J. Dingel, and O. Milenkovic, “Inferring Algebraic Gene Networks using Local-Decoding ,”Proceedings of the BIBE’08 Workshop on Systems Biology and Medicine, Philadelphia, November 2008.

W. Dai, M. Sheikh, O. Milenkovic, and R. Baraniuk, “New Probe Design Algorithms for Compressive Sensing DNA Microarrays,” Proceedings of the IEEE Conference on Bioinformatics and Biomedicine, BIBM, 2008.

J. Dingel and O. Milenkovic, “A List-Decoding Approach for Inferring the Dynamics of Gene Regulatory Networks,” Proceedings of the International Symposium on Information Theory, ISIT’08, Toronto, Canada, 2008.

M. Sheikh, S. Sarvotham, Olgica Milenkovic, and R. Baraniuk, “DNA array decoding from nonlinear measurements by belief propagation,” Proceedings of the IEEE Workshop on Statistical Signal Processing (SSP), Madison,Wisconsin, August 2007.

D. Huang and O. Milenkovic, “Superimposed coding for iterative detection of DNA microarray spot failures,” Proceedings of the IEEE Genetic Signal Processing and Statistics (GENSIPS) conference, 2008.

J. Dingel and O. Milenkovic, “Decoding the dynamics of gene regulatory networks under a dynamics model,” Proceedings of the Fifth International Workshop on Computational Systems Biology, Leipzig, Germany, 2008 (voted one of top three papers at the conference).

O. Milenkovic, “Constrained Coding via Context-Free Grammars with Applications to RNA Sequence Analysis,” Proceedings of the ISIT’2007.

O. Milenkovic and N. Kashyap, “Construction of DNA Codes which Avoid Secondary Structures,” Proceedings of the IEEE International Symposium on Information Theory 2005 (5 pages), Adelaide, Australia, September 2005.

O. Milenkovic, N. Kashyap, and B. Vasic, “Coding for DNA Computers Controlling Gene Expression Levels,” Invited paper, IEEE Conference on Decision and Control, CDC’2005, (6 pages) Seville, Spain, December 2005.

S. Chilappagari, O. Milenkovic, and B. Vasic, “Compression of DNA Sequences using Fractal Grammars and Integer Wavelet Transforms,” Proceedings of the Genetic Signal Processing Symposium (GENSIPS), (2 pages) Rhode Island.

O. Milenkovic and N. Kashyap, “Constructions of Codes for DNA Computing,” Proceedings of the Workshop on Coding and Cryptography, WCC’05, pp. 204-214, Bergen, Norway, March 2005.

O. Milenkovic and B. Vasic, “Information Theory Problems in Genetics,” Proceedings of the IEEE Information Theory Workshop, ITW’2004, pp. 60-64, San Antonio, October 2004.

**LDPC Codes and Iterative Decoding (18 papers)**

S. Laendner, O. Milenkovic, and J. Huber, “Characterization of Small Trapping Sets in LDPC Codes from Steiner Triple Systems,” Proceedings of the 6th International Symposium on Turbo Codes and Iterative Information Processing, Brest, France, September 2010.

T. Hehn, S. Laendner, O. Milenkovic, and J. Huber, ”Dense Error Correction via Automorphism Group Decoding,” HDD Workshop, Tel Aviv, February 2010.

W. Dai and O. Milenkovic, “Iterative Subspace Pursuit Decoding of Euclidean Superimposed Codes,” Proceedings of the TURBO CODING 2008 Symposium, Lausanne, September 2008.

A. McGregor and O. Milenkovic, “On the Hardness of Approximating Stopping and Trapping Sets,” Proceedings of the ITW’08, Lake Tahoe, 2007.

T. Hehn, S. Laendner, O. Milenkovic, and J. Huber, “The Stopping Redundancy Hierarchy of Cyclic Codes”, presented at the 44th Allerton Conference 2006 (regular paper), September 2006.

S. Laendner, T. Hehn, O. Milenkovic, and J. Huber, “When Does one Parity-Check Equation Matter?,” Proceedings of the Globecom 2006, San Fracisco, 2006.

O. Milenkovic, E. Soljanin, and P. Whiting, “Stopping and Trapping Sets in Generalized Covering Arrays,” Proceedings of the CISS’2006, March 2006.

O. Milenkovic, E. Soljanin, and P. Whiting, “Trapping Sets in Irregular LDPC Code Ensembles,” Proceedings of the ICC’2006, (6 pages), December 2005 (the paper received honorable mentioning as the runner up for the best paper award).

O. Milenkovic, E. Soljanin and P. Whiting, “Asymptotic Distributions of Combinatorial Configurations in Random Regular LDPC Code Ensembles,” presented at the 43rd Allerton Conference on Communications, Control and Computing (long paper), September-October 2005.

S. Laendner and O. Milenkovic, “Algorithmic and Combinatorial Analysis of Trapping Sets in Structured LDPC Codes,” Proceedings of the 2005 International Conference on Wireless Networks, Communications and Mobile Computing, WirelessCom 2005, (6 pages) Maui, Hawaii, June 2005.

V. Kumar and O. Milenkovic, “On Representations of Algebraic Codes Suitable for Iterative Decoding,” Proceedings of the 39th Conference on Information Sciences and Systems, CISS’2005, pp. 41, Baltimore, March 2005.

I. B. Djordjevic, O. Milenkovic, and B. Vasic, “Generalized Low-Density Parity-Check Codes for Long-Haul High-Speed Optical Communication,” Proceedings of the Optical Fiber Communication Conference and Exposition and The National Fiber Optic Engineers Conference, OFC’2005, OThW6, (2 pages), Washington D.C., March 2005.

V. Kumar and O. Milenkovic, “Unequal Error Protection LDPC Codes Based on Plotkin-Type Constructions,” Proceedings of the IEEE Global Telecommunications Conference, Globecom 2004, CT15-2, pp. 493-497, Dallas, Texas, December 2004.

D. Leyba, O. Milenkovic, D. Bennet, and N. Kashyap, “New Partition Regular Sequences and Generalized Array Codes of Large Girth,” Proceedings of the 42nd Annual Conference on Communications, Control and Computing, pp. 240-249, Allerton, IL, October 2004.

V. Kumar, O. Milenkovic, and B. Vasic, “Structured LDPC Codes over GF(2m) and Companion Matrix Based Decoding,” Proceedings of the IEEE International Symposium on Information Theory, ISIT’2004, p. 226, Chicago, June-July 2004.

O. Milenkovic, V. Kumar, and B. Vasic, “Companion Matrix Based Decoding” presented at IEEE CTW’2004, Capri (no Proceedings published).

O. Milenkovic and S. Laendner, “Analysis of the Cycle Structure of LDPC Codes Based on Latin Squares,” Proceedings of the IEEE International Conference on Communications ICC’2004, CT15-5, pp. 777-781, Paris, France, June 2004.

O. Milenkovic, K. Prakash, and B. Vasic, “Regular and Irregular LDPC Codes Based on Cycle-Invariant Difference Sets,” Proceedings of the 41st Annual Allerton Conference on Communication, Control and Computing, pp. 1700-1701, October 2003.

**Algebraic Error-Control Coding (11 papers)**

H. Kiah, G. Puleo and O. Milenkovic, “Coding for DNA-Based Storage,” submitted, ITW 2015.

V. Skachek, O. Milenkovic and A. Nedich, “Noncoherent Hybrid Network Coding,” Proceedings of the NETCOD, NETCOD, Boston, 2012.

F. Farnoud, V. Skachek and O. Milenkovic , “Rank Modulation Coding for Translocation errors,” Proceedings of the ISIT, ISIT, Boston, 2012.

F. Farnoud and O. Milenkovic, “Polarization coding for parallel channels,” Information Theory Workshop, ITA 2011, San Diego, CA.

W. Dai and O. Milenkovic, “Weighted `1 Superimposed Codes,” presented, Coding Theory Days in Saint Petersburg, October 2008.

C. Lott, O. Milenkovic, and E. Soljanin, “Hybrid ARQ: theory, state of the art and future directions,” Proceedings of the ITW’07, Bergen, Norway, 2007.

T. Hehn, O. Milenkovic, S. Laendner, and J. Huber, “Iterative Permutation Decoding and the Stopping Redundancy Hierarchy of Codes,” Proceedings of the ISIT, Nice, France, 2007.

T. Hehn, S. Laendner, J. Huber, and O. Milenkovic, “Multiple Bases Decoding of Algebraic Codes,” Proceedings of the ISIT, Nice, France, 2007.

V. Kumar and O. Milenkovic, “Improved Distance Bounds for Recursive Decoding of Reed-Muller Codes,” Proceedings of the Eighth International IEEE Symposium on Communication Theory and Applications 2005, pp. 326-331, St. Martin’s College, Ambleside, UK, July 2005.

O. Milenkovic and B. Vasic, “Asymptotic Analysis of A* Maximum Likelihood Decoding with Reliability Reordering,” Proceedings of the Information Theory Workshop, ITW’2003, pp. 316-319, Sorbone, Paris, April 2003.

O. Milenkovic and K. Compton, “A Method for Reducing the Number of Unknown Coefficients of Generalized Hamming Weight Enumerators,” Proceedings of the 2002 IEEE International Symposium on Information Theory, p. 234, Lauzanne, Switzerland, July 2002.

O. Milenkovic, “On the Generalized HammingWeight Enumerators and CosetWeight Distributions of Even, Isodual Codes ,” Proceedings of the 2001 IEEE International Symposium on Information Theory, p. 62,Washington D.C., USA, June 2001.

**Constrained Coding (5 papers)**

O. Milenkovic and B. Vasic “Power spectral density of multitrack (O,G/I) codes,” Proceedings of the IEEE Information Theory Symposium, Ulm, Germany, p. 142, July 1997.

B. Vasic and O. Milenkovic, “Cyclic Two-dimensional IT Reducing Codes,” Proceedings of the IEEE Information Theory Symposium, Ulm, Germany, p. 414, July 1997.

S. McLaughlin, O. Milenkovic, and B. Vasic, “Channel Capacity of M-aryMultitrack Runlength Limited Channels ,” Proceedings of the IEEE Information Theory Symposium, Ulm, Germany, p. 139, July 1997.

O. Milenkovic, B. Vasic, and S. Denic, “Novel M-ary (d,k) Codes,” accepted for publication in the Proceedings of the Canadian Workshop on Information Theory, Toronto, Canada, June 1997.

B.Vasic, O. Milenkovic, D.Vasic, “Channel Capacities and Spectra of Maxentropic (O,G/I) Matched-Spectral-Null Sequences,” Proceedings of the IEEE IT Workshop, (1 page) Rydzyna, Poland, 1995.

**Information Theory (5 papers)**

A. Emad and O. Milenkovic, “Compression of Noisy Signals via Information Bottlenecks,” Proceedings of ITW, Seville, 2013.

F. Farnoud, O. Milenkovic and P. Santhanam, “Patterns of Alternating Markov Chains,” Proceedings of ISIT, 2012.

S. Denic, C. Charalambous, S. Djouadi, and O. Milenkovic, “Capacity of MIMO Gaussian Channels with H1 Normed Channel Uncertainties,” Proceedings of the Canadian Workshop on Information Theory, pp. 315-318, Montreal, Canada, 2005.

O. Milenkovic and S. Denic, “Characterization of Generalized Tsallis Entropies,” Proceedings of the Canadian Workshop on Information Theory, pp. 20-23, Montreal, Canada 2005.

V. Nagarajan and O. Milenkovic, “Structured LDPC Codes over Polya Urn Model Channels,” Proceedings of the IEEE Canadian Conference on Electrical and Computer Engineering, IEEE CCECE’2004, V1-0541, pp. 543-546, Niagara Falls, May 2004.

**Theoretical Computer Science (4 papers)**

Jayadev Acharya, Hirakendu Das, Olgica Milenkovic, Alon Orlitsky, Shengjun Pan: String Reconstruction from Substring Compositions. CoRR abs/1403.2439 (2014)

F. Farnoud and O. Milenkovic, “Sorting of Permutations by Cost-Constrained Transpositions,” Proceedings of the ISIT’2011, Saint Petersburg, Russia.

F. Farnoud, C-Y. Chen, O. Milenkovic, Navin Kashyap, “A graphical model for computing the minimum cost transposition distance,” Proceedings of the ITW 2010 (Information TheoryWorkshop), Dublin 2010.

J. Acharya, Hirakendu Das, O. Milenkovic, Alon Orlitsky, and Shengjun Pan, ”On Reconstructing a Sequence from its Subsequence Compositions,” Proceedings of the ISIT’2010, Austin, Texas, 2010 (Best Student Paper Award).

O. Milenkovic, “Analysis of Combinatorial Bin Models with Application in Coding Theory,” Proceedings of the IEEE International Symposium on Information Theory, ISIT’2004, p. 273, Chicago, June-July 2004.

**VLSI Implementations of Signal Processing Algorithms (1 paper)**

V. Nagarajan, N. Jayakumar, S. Khatri and O. Milenkovic, “High Throughput VLSI Implementations of Iterative Decoders and Related Code Construction Problems,” Proceedings of the IEEE Global Telecommunications Conference, Globecom 2004, CT11-8 (5 pages), Dallas, Texas, December 2004.