See my CV .

I am a Lane Postdoctoral Fellow (Special Faculty) at the Yun William Yu Lab in the Ray and Stephanie Lane Computational Biology Department at the Carnegie Mellon University, Pittsburgh. I work on solving biological questions using computational techniques.

In spirit, I am a computational biologist with a core background in computer science. I like to apply theory and algorithms to solve challenges in biological data analysis and package my work into fast, efficient bioinformatics software.

Education

  • PhD in Computer Science and Engineering, 2025

    The Pennsylvania State University (Penn State), USA

  • MSc in Computer Science and Engineering, 2020

    Bangladesh University of Engineering and Technology (BUET), Bangladesh

  • BSc in Computer Science and Engineering, 2017

    Bangladesh University of Engineering and Technology (BUET), Bangladesh

Experience

Postdoctoral Researcher

CABM @ Rutgers

– Piscataway, NJ, USA

Publications

Peer-reviewed publications

  1. Àlex Font, Conrado Martínez, Mahmudur Rahman Hera and David Koslicki. "A Detailed Analysis of MaxGeomHash Sketches". Accepted for presentation in SISAP-2026 (Brno, Czechia).
  2. Mahmudur Rahman Hera, David Koslicki, and Conrado Martínez. "MaxGeomHash: An Algorithm for Variable-Size Random Sampling of Distinct Elements." Accepted for presentation in RECOMB-2026, invited for submission to Genome Research.
  3. Mahmudur Rahman Hera, Paul Medvedev, David Koslicki, and Antonio Blanca, "Estimation of substitution and indel rates via k-mer statistics". In Proceedings of Wonderful Algorithms in Bioinformatics (WABI) 202 5.
  4. Mahmudur Rahman Hera and David Koslicki. "Estimating similarity and distance using FracMinHash." Algorithms for Molecular Biology (AMB) 20.1 (2025).
  5. 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 (JOSS), 9(98), 6830.
  6. 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.
  7. 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.
  8. 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.
  9. 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 (JSA), 2018.
  10. 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 (ARM), ACM, Las Vegas, Nevada, USA, 2017.
  11. 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

  1. 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.
  2. 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.

Teaching

As of 2025, my teaching experience can be grouped into three stages: before 2017, 2017 to late 2020, and since 2021.

Before 2017 (undergrad days, Bangladesh)

During my undergraduate studies in Bangladesh, I completely supported myself financially by tutoring students at home and by teaching in a tutoring center called Udvash. Most my students during this time were at high-school level (in US terms). From late 2011 to late 2016, I have privately tutored more than 30 students. From mid-2012 to late 2016, I have delivered more than 1000 lectures (at least 1.5 hours long) at Udvash.

I was recognized by Udvash as a distinguished lecturer for my time and dedication there.

2017 to late 2020 (Lecturer and Teaching Asst. Professor at BUET, Bangladesh)

After graduation, I worked at Bangladesh University of Engineering and Technology (BUET) as a Lecturer for 3.5 years, and as a Teaching Assistant Professor for three months. During my tenure at BUET, I have instructed the following courses. The class size in each of these courses was 120 (±10).

  • CSE 313 - Operating Systems
  • CSE 409 - Computer Graphics
  • CSE 309 - Compilers
  • CSE 315 - Microprocessors and Microcontrollers

Since 2021 (PhD student at Penn State, USA)

In my PhD, I have worked as a TA for the following courses.

  • CMPSC 473 - Operating Systems

News (YTD)

  1. Started at Carnegie Mellon University (CMU)
  2. Paper on estimating indel rates is officially published in Algorithms for Molecular Biology (AMB)
  3. Paper for MaxGeomHash's analysis accepted for presentation in SISAP-2026 (Brno, Czechia)
  4. Accepted the Lane Fellow position at the Computational Biology Department at Carnegie Mellon University (CBD, CMU)
  5. Our proposal led by Dr. Kreimer has been awarded BMIHAI Postdoctoral Research Fellow Funding. News link.
  6. Presented paper on MaxGeomHash as a talk at RECOMB 2026 (Thessaloniki, Greece)
  7. Presented variant effect prediction work as a poster at RECOMB 2026 (Thessaloniki, Greece)
  8. Paper on estimating mutation rates is accepted in Algorithms for Molecular Biology (AMB)
  9. Presented regulatory variant effect prediction work as a poster at Biology of Genomes 2026 (CSHL, NY)
  10. Received Travel Fellowship from ISCB to attend RECOMB-2026
  11. Submitted abstract to Biology of Genomes 2026 (CSHL, NY)
  12. Paper of MaxGeomHash is accepted in RECOMB-2026

Contact

mahmudur AT psu DOT edu or mahmudhera93 AT gmail DOT com.