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Article
2020

DNA punch cards for storing data on native DNA sequences via enzymatic nicking

Tabatabaei, S. K., Wang, B., Athreya, N. B. M., Enghiad, B., Hernandez, A. G., Fields, C. J., Leburton, J. P., Soloveichik, D., Zhao, H. & Milenkovic, O., Dec 1 2020, In : Nature communications. 11, 1, 1742.

Research output: Contribution to journalArticle

Open Access
Open Access

Motif and Hypergraph Correlation Clustering

Li, P., Puleo, G. J. & Milenkovic, O., May 2020, In : IEEE Transactions on Information Theory. 66, 5, p. 3065-3078 14 p., 8830473.

Research output: Contribution to journalArticle

Open Access
2019

Detecting topological variations of DNA at single-molecule level

Liu, K., Pan, C., Kuhn, A., Nievergelt, A. P., Fantner, G. E., Milenkovic, O. & Radenovic, A., Dec 1 2019, In : Nature communications. 10, 1, 3.

Research output: Contribution to journalArticle

Explicit formulas for the weight enumerators of some classes of deletion correcting codes

Bibak, K. & Milenkovic, O., Mar 2019, In : IEEE Transactions on Communications. 67, 3, p. 1809-1816 8 p., 8573841.

Research output: Contribution to journalArticle

On the triangle clique cover and Kt clique cover problems

Dau, H., Milenkovic, O. & Puleo, G. J., 2019, (Accepted/In press) In : Discrete Mathematics. 111627.

Research output: Contribution to journalArticle

Unique Reconstruction of Coded Strings from Multiset Substring Spectra

Gabrys, R. & Milenkovic, O., Dec 2019, In : IEEE Transactions on Information Theory. 65, 12, p. 7682-7696 15 p., 8805120.

Research output: Contribution to journalArticle

2018

ChIPWig: A random access-enabling lossless and lossy compression method for ChIP-seq data

Ravanmehr, V., Kim, M., Wang, Z. & Milenkovic, O., Mar 15 2018, In : Bioinformatics. 34, 6, p. 911-919 9 p.

Research output: Contribution to journalArticle

Codes in the Damerau Distance for Deletion and Adjacent Transposition Correction

Gabrys, R., Yaakobi, E. & Milenkovic, O., Apr 2018, In : IEEE Transactions on Information Theory. 64, 4, p. 2550-2570 21 p.

Research output: Contribution to journalArticle

Correlation Clustering and Biclustering with Locally Bounded Errors

Puleo, G. J. & Milenkovic, O., Jun 2018, In : IEEE Transactions on Information Theory. 64, 6, p. 4105-4119 15 p.

Research output: Contribution to journalArticle

Exabytes in a Test Tube: With the right coding, DNA could archive our entire civilization

Milenkovic, O., Gabrys, R., Kiah, H. M. & Yazdi, S. M. H. T., May 2018, In : IEEE Spectrum. 55, 5, p. 40-45 6 p.

Research output: Contribution to journalArticle

Maxminsum steiner systems for access balancing in distributed storage

Dau, H. & Milenkovic, O., Jan 1 2018, In : SIAM Journal on Discrete Mathematics. 32, 3, p. 1644-1671 28 p.

Research output: Contribution to journalArticle

METHCOMP: A special purpose compression platform for DNA methylation data

Peng, J., Milenkovic, O. & Ochoa, I., 2018, In : Bioinformatics. 34, 15, p. 2654-2656 3 p.

Research output: Contribution to journalArticle

Mutually uncorrelated primers for DNA-based data storage

Tabatabaei Yazdi, S. M. H., Kiah, H. M., Gabrys, R. & Milenkovic, O., Sep 2018, In : IEEE Transactions on Information Theory. 64, 9, p. 6283-6296 14 p., 8255669.

Research output: Contribution to journalArticle

Paired threshold graphs

Ravanmehr, V., Puleo, G. J., Bolouki, S. & Milenković, O., Dec 11 2018, In : Discrete Applied Mathematics. 250, p. 291-308 18 p.

Research output: Contribution to journalArticle

Repairing Reed-Solomon Codes With Multiple Erasures

Dau, H., Duursma, I. M., Kiah, H. M. & Milenkovic, O., Oct 2018, In : IEEE Transactions on Information Theory. 64, 10, p. 6567-6582 16 p., 8340062.

Research output: Contribution to journalArticle

2017

Asymmetric Lee Distance Codes for DNA-Based Storage

Gabrys, R., Kiah, H. M. & Milenkovic, O., Aug 2017, In : IEEE Transactions on Information Theory. 63, 8, p. 4982-4995 14 p., 7918539.

Research output: Contribution to journalArticle

Computing similarity distances between rankings

Farnoud (Hassanzadeh), F., Milenkovic, O., Puleo, G. J. & Su, L., Dec 11 2017, In : Discrete Applied Mathematics. 232, p. 157-175 19 p.

Research output: Contribution to journalArticle

Latent Network Features and Overlapping Community Discovery via Boolean Intersection Representations

Dau, H. & Milenkovic, O., Oct 2017, In : IEEE/ACM Transactions on Networking. 25, 5, p. 3219-3234 16 p., 8004484.

Research output: Contribution to journalArticle

Portable and Error-Free DNA-Based Data Storage

Hossein TabatabaeiYazdi, S. M., Gabrys, R. & Milenkovic, O., Dec 1 2017, In : Scientific reports. 7, 1, 5011.

Research output: Contribution to journalArticle

2016

A new correlation clustering method for cancer mutation analysis

Hou, J. P., Emad, A., Puleo, G. J., Ma, J. & Milenkovic, O., 2016, In : Bioinformatics. 32, 24, p. 3717-3728 12 p.

Research output: Contribution to journalArticle

Open Access

Code Construction and Decoding Algorithms for Semi-Quantitative Group Testing with Nonuniform Thresholds

Emad, A. & Milenkovic, O., Apr 1 2016, In : IEEE Transactions on Information Theory. 62, 4, p. 1674-1687 14 p., 7398035.

Research output: Contribution to journalArticle

Codes for DNA Sequence Profiles

Kiah, H. M., Puleo, G. J. & Milenkovic, O., Jun 2016, In : IEEE Transactions on Information Theory. 62, 6, p. 3125-3146 22 p., 7454723.

Research output: Contribution to journalArticle

Coding in 2D: Using Intentional Dispersity to Enhance the Information Capacity of Sequence-Coded Polymer Barcodes

Laure, C., Karamessini, D., Milenkovic, O., Charles, L. & Lutz, J. F., Jan 1 2016, In : Angewandte Chemie - International Edition. 55, 36, p. 10722-10725 4 p.

Research output: Contribution to journalArticle

MetaCRAM: An integrated pipeline for metagenomic taxonomy identification and compression

Kim, M., Zhang, X., Ligo, J. G., Farnoud, F., Veeravalli, V. V. & Milenkovic, O., Feb 19 2016, In : BMC bioinformatics. 17, 1, 94.

Research output: Contribution to journalArticle

SmallWig: Parallel compression of RNA-seq WIG files

Wang, Z., Weissman, T. & Milenkovic, O., Jan 15 2016, In : Bioinformatics. 32, 2, p. 173-180 8 p.

Research output: Contribution to journalArticle

Synchronization and Deduplication in Coded Distributed Storage Networks

El Rouayheb, S., Goparaju, S., Kiah, H. M. & Milenkovic, O., Oct 2016, In : IEEE/ACM Transactions on Networking. 24, 5, p. 3056-3069 14 p.

Research output: Contribution to journalArticle

2015

A Rewritable, Random-Access DNA-Based Storage System

Tabatabaei Yazdi, S. M. H., Yuan, Y., Ma, J., Zhao, H. & Milenkovic, O., Sep 18 2015, In : Scientific reports. 5, 14138.

Research output: Contribution to journalArticle

Correlation clustering with constrained cluster sizes and extended weights bounds

Puleo, G. J. & Milenkovic, O., Jan 1 2015, In : SIAM Journal on Optimization. 25, 3, p. 1857-1872 16 p.

Research output: Contribution to journalArticle

DNA-Based Storage: Trends and Methods

Yazdi, S. M. H. T., Kiah, H. M., Garcia-Ruiz, E., Ma, J., Zhao, H. & Milenkovic, O., Sep 2015, In : IEEE Transactions on Molecular, Biological, and Multi-Scale Communications. 1, 3, p. 230-248 19 p., 7423733.

Research output: Contribution to journalArticle

HyDRA: Gene prioritization via hybrid distance-score rank aggregation

Kim, M., Farnoud, F. & Milenkovic, O., Apr 1 2015, In : Bioinformatics. 31, 7, p. 1034-1043 10 p.

Research output: Contribution to journalArticle

Poisson Group Testing: A Probabilistic Model for Boolean Compressed Sensing

Emad, A. & Milenkovic, O., Aug 15 2015, In : IEEE Transactions on Signal Processing. 63, 16, p. 4396-4410 15 p., 7124525.

Research output: Contribution to journalArticle

String reconstruction from substring compositions

Acharya, J., Das, H., Milenkovic, O., Orlitsky, A. & Pan, S., Jan 1 2015, In : SIAM Journal on Discrete Mathematics. 29, 3, p. 1340-1371 32 p.

Research output: Contribution to journalArticle

2014

An axiomatic approach to constructing distances for rank comparison and aggregation

Farnoud Hassanzadeh, F. & Milenkovic, O., Oct 1 2014, In : IEEE Transactions on Information Theory. 60, 10, p. 6417-6439 23 p., 6872786.

Research output: Contribution to journalArticle

CaSPIAN: A causal compressive sensing algorithm for discovering directed interactions in gene networks

Emad, A. & Milenkovic, O., Mar 12 2014, In : PloS one. 9, 3, e90781.

Research output: Contribution to journalArticle

Multipermutation codes in the Ulam metric for nonvolatile memories

Farnoud Hassanzadeh, F. & Milenkovic, O., May 2014, In : IEEE Journal on Selected Areas in Communications. 32, 5, p. 919-932 14 p., 6804937.

Research output: Contribution to journalArticle

Semiquantitative group testing

Emad, A. & Milenkovic, O., Aug 2014, In : IEEE Transactions on Information Theory. 60, 8, p. 4614-4636 23 p., 6823721.

Research output: Contribution to journalArticle

2013

Error-correction in flash memories via codes in the ulam metric

Farnoud, F. H., Skachek, V. & Milenkovic, O., May 1 2013, In : IEEE Transactions on Information Theory. 59, 5, p. 3003-3020 18 p., 6410424.

Research output: Contribution to journalArticle

Hybrid noncoherent network coding

Skachek, V., Milenkovic, O. & Nedić, A., May 23 2013, In : IEEE Transactions on Information Theory. 59, 6, p. 3317-3331 15 p., 6423921.

Research output: Contribution to journalArticle

2012

A geometric approach to low-rank matrix completion

Dai, W., Kerman, E. & Milenkovic, O., Jan 1 2012, In : IEEE Transactions on Information Theory. 58, 1, p. 237-247 11 p., 6121985.

Research output: Contribution to journalArticle

Sorting of permutations by cost-constrained transpositions

Farnoud, F. & Milenkovic, O., Jan 1 2012, In : IEEE Transactions on Information Theory. 58, 1, p. 3-23 21 p., 6121988.

Research output: Contribution to journalArticle

Structured sublinear compressive sensing via belief propagation

Dai, W., Milenkovic, O. & Vin Pham, H., Jun 1 2012, In : Physical Communication. 5, 2, p. 76-90 15 p.

Research output: Contribution to journalArticle

2011

Information theoretical and algorithmic approaches to quantized compressive sensing

Dai, W. & Milenkovic, O., Jul 1 2011, In : IEEE Transactions on Communications. 59, 7, p. 1857-1866 10 p., 5773638.

Research output: Contribution to journalArticle

Subspace evolution and transfer (SET) for low-rank Matrix completion

Dai, W., Milenkovic, O. & Kerman, E., Jul 1 2011, In : IEEE Transactions on Signal Processing. 59, 7, p. 3120-3132 13 p., 5753950.

Research output: Contribution to journalArticle

2010

Joint statistics and MLSD in filtered incoherent high-speed fiber-optic communications

Alic, N., Karlsson, M., Skold, M., Milenkovic, O., Andrekson, P. A. & Radic, S., Jun 4 2010, In : Journal of Lightwave Technology. 28, 10, p. 1564-1572 9 p., 5418986.

Research output: Contribution to journalArticle

Multiple-bases belief-propagation decoding of high-density cyclic codes

Hehn, T., Huber, J., Milenkovic, O. & Laendner, S., Jan 1 2010, In : IEEE Transactions on Communications. 58, 1, p. 1-8 8 p., 5397887.

Research output: Contribution to journalArticle

On the hardness of approximating stopping and trapping sets

McGregor, A. & Milenkovic, O., Apr 1 2010, In : IEEE Transactions on Information Theory. 56, 4, p. 1640-1650 11 p., 5437429.

Research output: Contribution to journalArticle

2009

Compressive sensing DNA microarrays

Dai, W., Sheikh, M. A., Milenkovic, O. & Baraniuk, R. G., Feb 16 2009, In : Eurasip Journal on Bioinformatics and Systems Biology. 2009, 162824.

Research output: Contribution to journalArticle

List-decoding methods for inferring polynomials in finite dynamical gene network models

Dingel, J. & Milenkovic, O., Jun 29 2009, In : Bioinformatics. 25, 13, p. 1686-1693 8 p.

Research output: Contribution to journalArticle