Publications
Publications
Visualizing the localization of multigene families with GFViewer.
Authors: Chakravarty S and Lonardi S.
In review at Bioinformatics Advances.
[Tool]
Prediction of DNA Methylation with Long-Range State-Space Models.
Authors: Feng H, Chakravarty S and Lonardi S.
In review at IEEE Transactions on Computational Biology and Bioinformatics.
[GitHub]
RAmbler resolves complex repeats in human Chromosomes 8, 19, and X.
Authors: Chakravarty S, Logsdon G and Lonardi S.
Genome Research. 2025; 35(4):863-876.
[Paper]
Insights into the evolution, virulence and speciation of Babesia MO1 and Babesia divergens through multiomics analyses.
Authors: Singh P, Vydyam P, Fang T, Estrada K, Gonzalez L M, Grande R, Kumar M, Chakravarty S, Berry V, Ranwez V, Carcy B, Depoix D, Sánchez S, Cornillot E, Abel S, Ciampossin L, Lenz T, Harb O, Sánchez-Flores A, Montero E, Le Roch K G, Lonardi S and Mamoun C B.
Emerging Microbes & Infections. 2024; 13(1).
[Paper]
Genome wide association studies on seven yield-related traits of 183 rice varieties in Bangladesh.
Authors: Roy N, Kabir A H, Zahan N, Mouna S T, Chakravarty S, Rahman A H and Bayzid M S.
Plant Direct. 2024; 8(6):e593.
[Paper]
Babesia duncani multi-omics identifies virulence factors and drug targets.
Authors: Singh P, Lonardi S, Liang Q, Vydyam P, Khabirova E, Fang T, Gihaz S, Thekkiniath J, Munshi M, Abel S, Ciampossin L, Batugedara G, Gupta M, Lu X M, Lenz T, Chakravarty S, Cornillot E, Hu Y, Ma W, Gonzalez L M, Sánchez S, Estrada K, Sánchez-Flores A, Montero E, Harb O S, Le Roch K G and Mamoun C B.
Nature Microbiology. 2024; 8(6):e593.
[Paper]
Towards optimal selection of ultra-deep sequencing reads for de novo genome assembly.
Authors: Chakravarty S and Lonardi S.
In Proceedings of the 16th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (accepted at BCB '25).
[GitHub]
RAmbler: de novo genome assembly of complex repetitive regions.
Authors: Chakravarty S, Logsdon G and Lonardi S.
In Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (BCB '23).
[Paper]
A Multi-objective Metaheuristic Approach for Accurate Species Tree Estimation.
Authors: Nayeem M A, Bayzid M S, Chakravarty S, Rahman M S and Rahman M S.
IEEE 20th International Conference on Bioinformatics and Bioengineering (BIBE '20).
[Paper]
A Graph Theoretic Approach for Maximizing Target Coverage using Minimum Directional Sensors in Randomly Deployed Wireless Sensor Networks.
Authors: Sarker L, Chakravarty S and Rahman A.
5th International Conference on Networking, Systems and Security (NSysS '18).
[Paper]