Book Chapters

73. B. Vasic, E. Kurtas, A. Kuznetsov and O. Milenkovic, Structured LDPC codes, CRC Coding and Signal Processing for Magnetic Recording, CRC Press, Eds. B. Vasic and E. Kurtas, Chapter 38, pp. 1-21, 2004.

72. B. Vasic and O. Milenkovic, Detection for Multitrack Systems, CRC Coding and Signal Processing for Magnetic Recording, CRC Press, Eds. B. Vasic and E. Kurtas, Chapter 24, pp. 1-9, 2004.

71. O. Milenkovic, The Three Faces of DNA/RNA Sequence Hybridization, Systems Bioinformatics: An Engineering Case-Based Approach, pp. 285-313, Editors G. Alterovitz and M. Ramoni, Artech House, 2007.

70. O. Milenkovic, Data Processing and Storage in Cells: An Information-Theoretic Approach, in Advances in Information Recording, Editors P. Siegel, E. Soljanin, A. van Wijngaarden, and B. Vasic, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, vol. 73, pp. 105-147, 2008.

Guest Editor in Chief – Introduction

69. O. Milenkovic, G. Alterovitz, G. Battail, R. Coleman, J. Hagenauer, S. Meyn, N. Price, M. Ramoni, I. Shmulevich, W. Szpankowski: Introduction to the special issue on information theory in molecular biology and neuroscience. IEEE Transactions on Information Theory 56(2): 649-652 (2010)

Opinion Pieces

68. Jeffrey G. Andrews, Alexandros G. Dimakis, Lara Dolecek, Michelle Effros, Muriel Médard, Olgica Milenkovic, Andrea Montanari, Sriram Vishwanath, Edmund M. Yeh, Randall Berry, Ken R. Duffy, Soheil Feizi, Saul Kato, Manolis Kellis, Stuart Licht, Jon Sorenson, Lav R. Varshney, Haris Vikalo, “A Perspective on Future Research Directions in Information Theory,” CoRR abs/1507.05941, 2015.

Cell – Voices

67. J. Ma and O. Milenkovic, Expanding the Biology Toolkit, Cell (Invited)

Journal Papers (By Topic)

Graph Theory, Networks and Machine Learning

66. P. Li, H. Dau, G. J. Puleo, O. Milenkovic, “Weighted Hypergraph Clustering and Overlapping
Clustering with Performance Guarantees,” submitted, 2016 (preliminary version to be presented at Infocom 2017 Link).

65. H. Dau, O. Milenkovic, G. J. Puleo, “On the Triangle Clique Cover and Kt Clique Cover Problems,” Link , submitted 2017.

64. H. Dau and O. Milenkovic, “Latent Network Features and Overlapping Community Discovery via Boolean Intersection Representations,” Link , IEEE/ACM Trans. Netw. 25(5): 3219-3234, 2017.

63. V. Ravanmehr, G. J. Puleo, S. Bolouki, O. Milenkovic, “Doubly-Threshold Graphs for Social Network Modeling,” Link , revised 2017.

62. F. Farnoud, O. Milenkovic, G. Puleo and L. Su, “Computing Similarity Distances Between Rankings,” Link , Discrete Applied Mathematics 232: 157-175, 2017.

61. S. ElRouyhaeb, S. Goparaju, H. Kiah and O. Milenkovic, “Synchronizing Edits in Distributed Storage Networks,” Link , IEEE/ACM Transactions on Networks, October 2016.

60. G. J. Puleo, O. Milenkovic, “Community Detection via Minimax Correlation Clustering and Biclustering,” Link, submitted 2016, revised 2017.

59. G. J. Puleo and O. Milenkovic,”Correlation Clustering with Bounded Cluster Sizes and New Weight Bounds,” SIAM Journal on Optimization 25(3): 1857-1872, 2015.

58. F. Farnoud, O. Milenkovic “An Axiomatic Approach to Constructing Distances for Rank Comparison and Aggregation,” IEEE Transactions on Information Theory, vol. 60, no. 10, pp. 6417-6439, 2014.

57. W. Dai, O. Milenkovic, and H. V. Pham, “Structured Sublinear Compressive Sensing via Belief Propagation,” Physical Communication, Special Issue on compressive sensing in communications, vol. 5, no. 2, pp. 76-90, November 2011 (online), June 2012.

56. F. Farnoud and O. Milenkovic, ”Sorting of Permutations by Cost-Constrained Transpositions,” IEEE Transactions on Information Theory, 58(1): 3-23, 2012.

55. W. Dai, E. Kerman, and O. Milenkovic, ”A Geometric Approach to Low-Rank Matrix Completion,” IEEE Transactions on Information Theory, 58(1): 237-247, 2012.

54. W. Dai, O. Milenkovic, and E. Kerman, ”Subspace Evolution and Transfer (SET) for Low-Rank Matrix Completion,” IEEE Transactions on Signal Processing, 59(7): 3120-3132, 2011.

53. W. Dai and O. Milenkovic, “A Comparative Study of Quantized Compressive Sensing Schemes,” IEEE Trans. on Communications, 59(7): 1857-1866, 2011.

52. W. Dai and O. Milenkovic, “Weighted Superimposed Codes and Constrained Integer Compressed Sensing,” IEEE Transactions on Information Theory, vol. 55, no. 5, pp. 2215-2230, May 2009.

51. W. Dai and O. Milenkovic, “Subspace Pursuit for Compressive Sensing Signal Reconstruction,” IEEE Transaction on Information Theory, vol. 55, no. 5, pp. 2230-2250, May 2009.

DNA-Based Storage

50. (New) R. Gabrys, H. M. Kiah, O. Milenkovic and H. T. Yazdi, DNA-Based Data Storage.

49. (New) S. M. Hossein Tabatabaei Yazdi, R. Gabrys, O. Milenkovic, Portable and Error-Free DNA-Based Data Storage, biorxive, Link, Nature Scientific Reports, 2017.

48. S. M. Hossein Tabatabaei Yazdi, Han Mao Kiah, Eva Ruiz Garcia, Jian Ma, Huimin Zhao, Olgica Milenkovic, DNA-Based Storage: Trends and Methods. CoRR abs/1507.01611, to appear in IEEE Transactions on Molecular, Biological and Multi-Scale Communications, 2016. Link

47. S. H. Tabatabaei Yazdi, Y. Yuan, J. Ma, H. Zhao, and O. Milenkovic, “A Rewritable, Random-Access DNA-Based Storage System,” Link , Nature Scientific Reports, 5, Article number: 14138, 2015. (Press coverage: RealClearScience, NYT, IEEE Spectrum, Nature etc.)

46. R. Gabrys, H. M. Kiah, and O. Milenkovic, “Asymmetric Lee Distance Codes for DNA-Based Storage,” Link, to appear in IEEE Transactions on Information Theory, 2017.

45. H. M. Kiah, G. J. Puleo and O. Milenkovic, “Codes for DNA Sequence Profiles,” IEEE Trans. Information Theory 62(6): 3125-3146, 2016, Link .

44. C. Laure, D. Karamessini, O. Milenkovic, L. Charles, J-F. Lutz, “Coding in 2D: Using Intentional Dispersity to Enhance the Information Capacity of Sequence-Coded Polymer Barcodes,” Angewandte Chemie, August 2016. Link (Press coverage: New Scientist.)

Coding Theory

43. (New) S. M. Hossein Tabatabaei Yazdi, Han Mao Kiah, Ryan Gabrys, Olgica Milenkovic, Mutually Uncorrelated Primers for DNA-Based Data Storage. CoRR abs/1709.05214 (2017), to appear in IEEE Transactions on Information Theory, 2018.

42. (New) H. Dau and O. Milenkovic, MaxMinSum Steiner Systems for Access-Balancing in Distributed Storage, Link, revised, 2017.

41. (New) H. Dau, I. Duursma, H. M. Kiah and O. Milenkovic, Repairing Reed-Solomon Codes from Multiple Erasures, Link, revised, 2017.

40. Ryan Gabrys, Han Mao Kiah, Olgica Milenkovic, Asymmetric Lee Distance Codes for DNA-Based Storage. IEEE Trans. Information Theory 63(8): 4982-4995, 2017.

39. R. Gabrys, E. Yaakobi, O. Milenkovic, Codes in the Damerau Distance for Deletion and Adjacent Transposition Correction, Link, to appear in IEEE Transactions on Information Theory, 2018.

38. F. Farnoud and O. Milenkovic, “Multipermutation Codes in the Ulam Metric for Nonvolatile Memories,” Journal of Selected Areas in Communications (JSAC), Special Issue on Data Storage, IEEE Journal on Selected Areas in Communications 32(5): 919-932, 2014 (Best Student Paper Award!).

37. F. Farnoud, V. Skachek and O. Milenkovic, “Error-Correction in Flash Memories via Codes in the Ulam Metric,” IEEE Transactions on Information Theory, 59(5): 3003-3020, 2013.

36. V. Skachek, O. Milenkovic and A. Nedich, “Hybrid Noncoherent Network Coding,” IEEE Transactions on Information Theory, 59(6): 3317-333, 2013.

35. A. McGregor and O. Milenkovic, “On the Hardness of Approximating Stopping and Trapping Sets,” IEEE Trans. on Information Theory, vol. 56, (4), pp. 1640 – 1650, April 2010.

34. T. Hehn, J. Huber, O. Milenkovic, and S. Laendner, “Multiple-bases belief-propagation decoding of high-density cyclic codes,” IEEE Trans. on Comm., vol. 58 , no. 1, pp. 1-8, January 2010.

33. S. Laendner, T. Hehn, O. Milenkovic, and J. Huber, “The Trapping Redundancy of Linear Block Codes”, IEEE Transaction on Information Theory, vol. 55, no. 1, pp. 53-63, January 2009.
Errata: The authors gratefully acknowledge the correction of a proof in the paper communicated by Yu Tsunoda and Yuichiro Fujiwara, which may be found at

32. T. Hehn, O. Milenkovic, S. Laendner, and J. Huber, “Permutation Decoding and the Stopping Redundancy Hierarchy of Cyclic and Extended Cyclic Codes,” IEEE Transaction on Information Theory, vol. 54, no. 12, pp. 5308-5331, December 2008.

31. O. Milenkovic, E. Soljanin, and P. Whiting, “On the Asymptotic Spectrum of Trapping Sets in Random, Regular and Irregular Code Ensembles,” IEEE Transaction on InformationTheory, Vol. 53, No. 1, pp. 39-55, January 2007.

30. S. Laendner and O. Milenkovic, “Codes Based on Latin Squares: Stopping Set, Trapping Set, and Cycle-Length Distribution Analysis,”  IEEE Transaction on Communications, Vol. 55, No. 2, pp. 303-312, February 2007.

29. V. Nagarajan, S. Laendner, O. Milenkovic, N. Jayakumar, and S. Khatri, “High-Throughput VLSI Implementations of Iterative Decoders and Related Code Construction Problems,” The Journal of VLSI Signal Processing, Vol. 49, No. 1, pp. 185-206, May 2007.

28. O. Milenkovic, N. Kashyap, and D. Leyba, “Shortened Array Codes of Large Girth,” IEEE Transactions on Information Theory, Vol. 5, No. 8, pp. 3707-3722, August 2006.

27. V. Kumar and O. Milenkovic, “Unequal Error Protection LDPC Codes based on Plotkin-Type Constructions,” IEEE Transactions on Communications, Vol. 54, No. 6, pp. 994-1005, June 2006.

26. O. Milenkovic and N. Kashyap, “On the Design of Codes for DNA Computing,” Lecture Notes in Computer Science 3969, pp. 100-119, Springer Verlag, Berlin-Heidelberg, 2006.

25. V. Kumar and O. Milenkovic, “On Graphical Representations of Algebraic Codes Suitable for Iterative Decoding,” IEEE Communications Letters, Vol. 9, No. 8, pp. 729-731, August 2005.

24. I. Djordjevic, O. Milenkovic, and B. Vasic, “Generalized LDPC Codes for Long-Haul Optical Communication Systems,” IEEE Journal of Lightwave Technology, Vol. 23, No. 5, pp. 1939-1946, May 2005.

23. O. Milenkovic, “Higher Weight and Coset Weight Enumerators of Formally Self-Dual Codes,” Designs, Codes and Cryptography, Vol. 35, No.1, pp. 89-101, April 2005.

22. O. Milenkovic, I. Djordjevic, and B. Vasic, “Block-Circulant Low-Density Parity-Check Codes for Optical Communication Systems,” IEEE Journal of Selected Topics in Quantum Electronics, Vol. 10, No.2, pp. 294-299, April 2004.

21. B. Vasic, O. Milenkovic, “Combinatorial Constructions of Low-Density Parity-Check Codes for Iterative Decoding,” IEEE Transactions on Information Theory, Vol. 50, No. 6, pp 1156-1176, June 2004.

20. O. Milenkovic, S. Coffey, K. Compton, “The Third Support Weight Enumerators of the [32,16,8] Doubly-Even, Self-Dual Codes,” IEEE Transactions on Information Theory, Vol. 49, No. 3, pp. 740-747, March 2003.

19. O. Milenkovic, B. Vasic, “Permutation (d,k) Codes: Efficient Enumerative Coding and Phrase Length Distribution Shaping”, IEEE Transactions on Information Theory, Vol. 46, No. 7, pp. 2671-2675, Nov. 2000.

18. B. Vasic, S. McLaughlin, O. Milenkovic, “Shannon Capacity of M-ary Redundant Multitrack Runlength Limited Codes”, IEEE Transactions on Information Theory, Vol. 44, No. 2, pp. 766-774, March 1998.

17. B. Vasic, O. Milenkovic, S. McLaughlin, “Power Spectral Density of Multitrack (0,G/I) codes,” IEE Electronics Letters, Vol. 33, No. 9, pp. 784-786, April 1997.

Group Testing

16. A. Emad and O. Milenkovic, “Code Construction and Decoding Algorithms for Semi-Quantitative Group Testing With Nonuniform Thresholds,” Link , IEEE Transactions on Information Theory, 62(4): 1674-1687, 2016.

15. A. Emad and O. Milenkovic, “Poisson Group Testing: A Probabilistic Model for Boolean Compressed sensing,” Link , IEEE Transactions on Signal Processing, 63 (16), pp. 4396-4410, 2015.

14. A. Emad and O. Milenkovic, “Semi-Quantitative Group Testing,” IEEE Transactions on Information Theory, Vol. 60, No. 8, pp. 4614-4636, August 2014.

Combinatorics and CS

13. J. Acharya, H. Das, O. Milenkovic, A. Orlitsky, S. Pan, “String Reconstruction from Substring Compositions,” Link , SIAM J. Discrete Math. 29(3): 1340-1371, 2015.

12. O. Milenkovic and K. Compton, “Average Case Analysis of Gosper ’s Algorithm,” Algorithmica, Vol. 43, No. 3, pp. 211-244, September 2005.

11. O. Milenkovic and K. Compton, “Probabilistic Transforms for Combinatorial Urn Models,” Combinatorics, Probability and Computing, pp. 645-675, Vol. 13, No. 4-5, July-September 2004.

Bioinformatics and Mathematical Biology

10. V. Ravanmehr, M. Kim, Z. Wang, O. Milenkovic, “ChIPWig: A Random Access-Enabling Lossless And Lossy Compression Method For ChIP-Seq Data,” Bioinformatics, 2017.

9. J. Hou, A. Emad, G. Puleo, J. Ma, and O. Milenkovic, “A New Correlation Clustering Method for Cancer Mutation Analysis,” Link Bioinformatics 32(24): 3717-3728, 2016.

8. M. Kim, J. Zhang, J. Ligo, V. Veeravalli, O. Milenkovic, “MetaCRAM: An Integrated Pipeline for Metagenomic Data Processing and Compression,” BMC Bioinformatics 17: 94, 2016.

7. Z. Wang, T. Weissman, O. Milenkovic, “smallWig: Parallel Low-Rate Compression Algorithms for RNA-seq WIG Files,” Bioinformatics 32(2): 173-180, 2016.

6. M. Kim, F. Farnoud, and O. Milenkovic, “HyDRA: Gene Prioritization via Hybrid Distance-Score Rank Aggregation,” Bioinformatics (software link), published online 2014, Bioinformatics 31(7): 1034-1043, 2015.

5. A. Emad and O. Milenkovic, “CaSPIAN: A Causal Compressive Sensing Algorithm for Discovering Directed Interactions in Gene Networks,” Plos One, March 2014 (link).

4. J. Dingel and O. Milenkovic, “List-decoding Methods for Inferring Polynomials in Finite Dynamical Gene Network Models,” Bioinformatics 25(13): 1686-1693, doi: 10.1093/bioinformatics/btp281, 2009.

3. W. Dai, M. Sheikh, O. Milenkovic, and R. Baraniuk, “Compressed Sensing DNA Microarrays,” EURASIP Journal on Bioinformatics and Systems Biology, Article ID 162824, 12 pages doi:10.1155/2009/162824, 2009.

Communication Theory

2. N. Alic, M. Karlsson, M. Skoeld, Milenkovic, P. A. Andrekson, and S. Radic, ”Joint Statistics and MLSD in Filtered Incoherent High-Speed Fiber Optic Communications,” IEEE – OSA Journal on Lightwave Technology, vol. 28, Issue 10, pp. 1564-1572, 2010.

1. B. Vasic, O. Milenkovic, S. McLaughlin, “Scrambling for Unequiprobable Signaling,” IEE Electronics Letters, Vol. 32, No. 17, pp. 1551-1552, Aug. 1996.

In Archive