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Research Output

2020

How fast does the SARS-Cov-2 virus really mutate in heterogeneous populations?

Rana, V., Chien, E., Peng, J. & Milenkovic, O., Apr 27 2020, (In preparation) Cold Spring Harbor Laboratory Press, (medRxiv).

Research output: Working paper

2019

Coded Trace Reconstruction

Cheraghchi, M., Ribeiro, J., Gabrys, R. & Milenkovic, O., Aug 2019, 2019 IEEE Information Theory Workshop, ITW 2019. Institute of Electrical and Electronics Engineers Inc., 8989261. (2019 IEEE Information Theory Workshop, ITW 2019).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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

Directed Intersection Representations and the Information Content of Digraphs

Kostochka, A. V., Liu, X., Machado, R. & Milenkovic, O., Jul 2019, 2019 IEEE International Symposium on Information Theory, ISIT 2019 - Proceedings. Institute of Electrical and Electronics Engineers Inc., p. 1477-1481 5 p. 8849253. (IEEE International Symposium on Information Theory - Proceedings; vol. 2019-July).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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., Jan 1 2019, (Accepted/In press) In : Discrete Mathematics. 111627.

Research output: Contribution to journalArticle

Reconstruction and Error-Correction Codes for Polymer-Based Data Storage

Pattabiraman, S., Gabrys, R. & Milenkovic, O., Aug 2019, 2019 IEEE Information Theory Workshop, ITW 2019. Institute of Electrical and Electronics Engineers Inc., 8989171. (2019 IEEE Information Theory Workshop, ITW 2019).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Set-Codes with Small Intersections and Small Discrepancies

Gabrys, R., Dau, H., Colbourn, C. J. & Milenkovic, O., Jul 2019, 2019 IEEE International Symposium on Information Theory, ISIT 2019 - Proceedings. Institute of Electrical and Electronics Engineers Inc., p. 2359-2363 5 p. 8849651. (IEEE International Symposium on Information Theory - Proceedings; vol. 2019-July).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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., Jan 1 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

Quadratic decomposable submodular function minimization

Li, P., He, N. & Milenkovic, O., Jan 1 2018, In : Advances in Neural Information Processing Systems. 2018-December, p. 1054-1064 11 p.

Research output: Contribution to journalConference article

Query K-means Clustering and the Double Dixie Cup Problem

Eli Chien, I., Pan, C. & Milenkovic, O., Jan 1 2018, In : Advances in Neural Information Processing Systems. 2018-December, p. 6649-6658 10 p.

Research output: Contribution to journalConference article

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

Revisiting decomposable submodular function minimization with incidence relations

Li, P. & Milenkovic, O., Jan 1 2018, In : Advances in Neural Information Processing Systems. 2018-December, p. 2237-2247 11 p.

Research output: Contribution to journalConference article

Submodular hypergraphs: P-Laplacians, cheeger inequalities and spectral clustering

Li, P. & Milenkovic, O., Jan 1 2018, 35th International Conference on Machine Learning, ICML 2018. Dy, J. & Krause, A. (eds.). International Machine Learning Society (IMLS), p. 4690-4719 30 p. (35th International Conference on Machine Learning, ICML 2018; vol. 7).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Unique Reconstruction of Coded Sequences from Multiset Substring Spectra

Gabrys, R. & Milenkovic, O., Aug 15 2018, 2018 IEEE International Symposium on Information Theory, ISIT 2018. Institute of Electrical and Electronics Engineers Inc., p. 2540-2544 5 p. 8437909. (IEEE International Symposium on Information Theory - Proceedings; vol. 2018-June).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Weight Enumerators of Some Classes of Deletion Correcting Codes

Bibak, K. & Milenkovic, O., Aug 15 2018, 2018 IEEE International Symposium on Information Theory, ISIT 2018. Institute of Electrical and Electronics Engineers Inc., p. 431-435 5 p. 8437121. (IEEE International Symposium on Information Theory - Proceedings; vol. 2018-June).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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

Inhomogeneous hypergraph clustering with applications

Li, P. & Milenkovic, O., Jan 1 2017, In : Advances in Neural Information Processing Systems. 2017-December, p. 2309-2319 11 p.

Research output: Contribution to journalConference article

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

Motif clustering and overlapping clustering for social network analysis

Li, P., Dau, H., Puleo, G. & Milenkovic, O., Oct 2 2017, INFOCOM 2017 - IEEE Conference on Computer Communications. Institute of Electrical and Electronics Engineers Inc., 8056956. (Proceedings - IEEE INFOCOM).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Multiclass MinMax rank aggregation

Li, P. & Milenkovic, O., Aug 9 2017, 2017 IEEE International Symposium on Information Theory, ISIT 2017. Institute of Electrical and Electronics Engineers Inc., p. 3000-3004 5 p. 8007080. (IEEE International Symposium on Information Theory - Proceedings).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Optimal repair schemes for some families of full-length reed-solomon codes

Dau, H. & Milenkovic, O., Aug 9 2017, 2017 IEEE International Symposium on Information Theory, ISIT 2017. Institute of Electrical and Electronics Engineers Inc., p. 346-350 5 p. 8006547. (IEEE International Symposium on Information Theory - Proceedings).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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

Repairing reed-solomon codes with two erasures

Dau, H., Duursma, I. M., Kiah, H. M. & Milenkovic, O., Aug 9 2017, 2017 IEEE International Symposium on Information Theory, ISIT 2017. Institute of Electrical and Electronics Engineers Inc., p. 351-355 5 p. 8006548. (IEEE International Symposium on Information Theory - Proceedings).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

The hybrid k-deck problem: Reconstructing sequences from short and long traces

Gabrys, R. & Milenkovic, O., Aug 9 2017, 2017 IEEE International Symposium on Information Theory, ISIT 2017. Institute of Electrical and Electronics Engineers Inc., p. 1306-1310 5 p. 8006740. (IEEE International Symposium on Information Theory - Proceedings).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2016

A new correlation clustering method for cancer mutation analysis

Hou, J. P., Emad, A., Puleo, G. J., Ma, J. & Milenkovic, O., Jan 1 2016, In : Bioinformatics. 32, 24, p. 3717-3728 12 p.

Research output: Contribution to journalArticle

Open Access

Balanced permutation codes

Gabrys, R. & Milenkovic, O., Aug 10 2016, Proceedings - ISIT 2016; 2016 IEEE International Symposium on Information Theory. Institute of Electrical and Electronics Engineers Inc., p. 390-394 5 p. 7541327. (IEEE International Symposium on Information Theory - Proceedings; vol. 2016-August).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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

Codes in the damerau distance for DNA storage

Gabrys, R., Yaakobi, E. & Milenkovic, O., Aug 10 2016, Proceedings - ISIT 2016; 2016 IEEE International Symposium on Information Theory. Institute of Electrical and Electronics Engineers Inc., p. 2644-2648 5 p. 7541778. (IEEE International Symposium on Information Theory - Proceedings; vol. 2016-August).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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

Compensating for sneak currents in multi-level crosspoint resistive memories

Luo, T., Milenkovic, O. & Peleato, B., Feb 26 2016, Conference Record of the 49th Asilomar Conference on Signals, Systems and Computers, ACSSC 2015. Matthews, M. B. (ed.). IEEE Computer Society, p. 839-843 5 p. 7421253. (Conference Record - Asilomar Conference on Signals, Systems and Computers; vol. 2016-February).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Correlation clustering and biclustering with locally bounded errors

Puleo, G. J. & Milenkovic, O., Jan 1 2016, 33rd International Conference on Machine Learning, ICML 2016. Balcan, M. F. & Weinberger, K. Q. (eds.). International Machine Learning Society (IMLS), p. 1380-1388 9 p. (33rd International Conference on Machine Learning, ICML 2016; vol. 2).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Doubly threshold graphs for social network modeling

Ravanmehr, V., Bolouki, S., Puleo, G. J. & Milenkovic, O., Oct 21 2016, 2016 IEEE Information Theory Workshop, ITW 2016. Institute of Electrical and Electronics Engineers Inc., p. 231-235 5 p. 7606830. (2016 IEEE Information Theory Workshop, ITW 2016).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Inference of latent network features via co-intersection representations of graphs

Dau, S. H. & Milenkovic, O., Aug 10 2016, Proceedings - ISIT 2016; 2016 IEEE International Symposium on Information Theory. Institute of Electrical and Electronics Engineers Inc., p. 1351-1355 5 p. 7541519. (IEEE International Symposium on Information Theory - Proceedings; vol. 2016-August).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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

Weakly mutually uncorrelated codes

Hossein, S. M., Yazdi, T., Kiah, H. M. & Milenkovic, O., Aug 10 2016, Proceedings - ISIT 2016; 2016 IEEE International Symposium on Information Theory. Institute of Electrical and Electronics Engineers Inc., p. 2649-2653 5 p. 7541779. (IEEE International Symposium on Information Theory - Proceedings; vol. 2016-August).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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

Asymmetric Lee distance codes: New bounds and constructions

Gabrys, R., Kiah, H. M. & Milenkovic, O., Jun 24 2015, 2015 IEEE Information Theory Workshop, ITW 2015. Institute of Electrical and Electronics Engineers Inc., 7133171. (2015 IEEE Information Theory Workshop, ITW 2015).

Research output: Chapter in Book/Report/Conference proceedingConference contribution