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Research Output

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

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

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

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., 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., 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

Efficient rank aggregation via Lehmer codes

Li, P., Mazumdar, A. & Milenkovic, O., 2017.

Research output: Contribution to conferencePaper

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., 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