Peer-reviewed publications
Mahmudur Rahman Hera, Paul Medvedev, David Koslicki, and Antonio Blanca, "Estimation of substitution and indel rates via k-mer statistics". Accepted to be presented in WABI-2025 in August 2025, and to be published in the proceedings.
Mahmudur Rahman Hera and David Koslicki. "Estimating similarity and distance using FracMinHash." Algorithms for Molecular Biology 20.1 (2025).
Luiz Irber, N Tessa Pierce-Ward, Mohamed Abuelanin, Harriet Alexander, Abhishek Anant, Keya Barve, Colton Baumler, Olga Botvinnik, Phillip Brooks, Daniel Dsouza, Laurent Gautier, Mahmudur Rahman Hera, Hannah Eve Houts, Lisa K Johnson, Fabian Klötzl, David Koslicki, Marisa Lim, Ricky Lim, Bradley Nelson, Ivan Ogasawara, Taylor Reiter, Camille Scott, Andreas Sjödin, Daniel Standage, S Joshua Swamidass, Connor Tiffany, Pranathi Vemuri, Erik Young, C Titus Brown (2024). "sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets." Journal of Open Source Software, 9(98), 6830.
Mahmudur Rahman Hera and David Koslicki. "Cosine Similarity Estimation Using FracMinHash: Theoretical Analysis, Safety Conditions, and Implementation." In Proceedings of Wonderful Algorithms in Bioinformatics (WABI) 2024.
Mahmudur Rahman Hera, Shaopeng Liu, Wei Wei, Judith S. Rodriguez, Chunyu Ma, and David Koslicki. "Fast, lightweight, and accurate metagenomic functional profiling using FracMinHash sketches". In Proceedings of 23rd European Conference on Computational Biology (ECCB) 2024.
Mahmudur Rahman Hera, N. Tessa Pierce-Ward, and David Koslicki, "Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash", Genome Research, 2023.
Mahmudur Rahman Hera, Amatur Rahman, Hua-Jun Hong, Li-Wen Pan, Md. Yusuf Sarwar Uddin, Nalini Venkatasubramanian, Cheng-Hsin Hsu, "An Adaptive IoT Platform on Budgeted 3G Data Plans", Elsevier Journal of Systems Architecture, 2018.
Mahmudur Rahman Hera, Amatur Rahman, Hua-Jun Hong, Pei-Hsuan Tsai, Md. Yusuf Sarwar Uddin, Nalini Venkatasubramanian, and Cheng-Hsin Hsu, "Adaptive Sensing Using Internet-of-Things with Constrained Communications". In Proceedings of Adaptive and Reflexive Middleware, ACM, Las Vegas, Nevada, USA, 2017.
Mahmudur Rahman Hera, Amatur Rahman, Afia Afrin, Md. Yusuf Sarwar Uddin, and Nalini Venkatasubramanian, "AQBox: An Air Quality Measuring Box from COTS Gas Sensors". In Proceedings of 2017 International Conference on Networking, Systems and Security (NSysS), Dhaka, Bangladesh, 2017.
Preprints
Luiz Carlos Irber, Phillip T. Brooks, Taylor E. Reiter, N. Tessa Pierce-Ward, Mahmudur Rahman Hera, David Koslicki, and C. Titus Brown. "Lightweight compositional analysis of metagenomes with FracMinHash and minimum metagenome covers." bioRxiv (2022), doi: https://doi.org/10.1101/2022.01.11.475838.
Mahmudur Rahman Hera, Amatur Rahman, and Atif Hasan Rahman, "kRISP-meR: A Reference-free Guide-RNA Design Tool for CRISPR/Cas9". bioRxiv, 2019, doi: https://doi.org/10.1101/869115.