Research statement

I am always excited to work on open projects in algorithmic bioinformatics. With my experience in developing algorithms and pipelines for handling big datasets, I am capable of developing scalable and intuitive solutions that assist in biological studies. My background involves enhancing storage efficiency for sequence analysis tools and facilitating faster analysis of sequencing data. I am particularly inclined towards studying sequence similarities through k-mer based approaches, error-correction in assembly, and optimizing the performance of bioinformatics tools.

Bio

I obtained my PhD from Department of Computer Science and Engineering, Pennsylvania State University on August 2023. Before joining Penn State, I obtained my Bachelor’s degree in Computer Science and Engineering from Bangladesh University of Engineering and Technology (BUET). I also served as a lecturer in the CSE department at United International University, Bangladesh. During my PhD, I was a recipient of CBIOS Trainee Fellowship (CBIOS: Computation, Bioinformatics and Statistics, an NIH funded Predoctoral Training Program).

Biological Data Science Meeting, CSHL, November 2022

CV

My most recent CV can be found here (last updated on August 25, 2023).

Publications

You can also check my publications through dblp or Google scholar.

• Compression algorithm for colored de Bruijn graphs.
  Amatur Rahman, Yoann Dufresne and Paul Medvedev
  [ paper (preprint) ]

• Assembler artifacts include misassembly because of unsafe unitigs and under-assembly because of bidirected graphs.
  Amatur Rahman and Paul Medvedev Genome Research, 32:1-8, 2022. An abstract appeared in RECOMB 2022, LNCS 13278:377–379 (Alternative title: Uncovering hidden assembly artifacts: when unitigs are not safe and bidirected graphs are not helpful.) [ paper (free version), paper (journal version) ] [talk]

• The K-mer File Format: a standardized and compact disk representation of sets of k-mers.
  Y. Dufresne, T. Lemane, P. Marijon, P. Peterlongo, A. Rahman, M. Kokot, P. Medvedev, S. Deorowicz, and R. Chikhi Bioinformatics, 2022. [ paper ]

• GPU-accelerated and pipelined methylation calling.
  Yilin Feng, Gulsum Gudukbay Akbulut, Xulong Tang, Jashwant Raj Gunasekaran, Amatur Rahman, Paul Medvedev, Mahmut Kandemir Bioinformatics Advances, Volume 2, Issue 1, 2022, [ paper ]

• Disk compression of k-mer sets.
  Amatur Rahman, Rayan Chikhi and Paul Medvedev. WABI 2020 (accepted) Algorithms for Molecular Biology, 16(10), 2021. An extended abstract appeared in WABI 2020, LIPIcs 16:1–16:18. [ full version (journal), conference ]

• Representation of k-mer sets using spectrum-preserving string sets.
  Amatur Rahman and Paul Medvedev.
  Journal of Computational Biology, 28(4):381-394, 2021. An extended abstract appeared in RECOMB 2020, LNCS 12074:152-168. (Best Paper Award) [preprint] [talk]

• kRISP-meR: A Reference-free Guide-RNA Design Tool for CRISPR/Cas9.
  Mahmudur Rahman Hera, Amatur Rahman and Atif Hasan Rahman. bioRxiv, 2019

• An Adaptive IoT Platform on Budgeted 3G Data Plans.
  Mahmudur Rahman Hera, Amatur Rahman, Hua-Jun Hong, Li-Wen Pan, Md. Yusuf Sarwar Uddin, Nalini Venkatasubramanian, Cheng-Hsin Hsu. Elsevier Journal of Systems Architecture, 2018

• Adaptive Sensing Using Internet-of-Things with Constrained Communications.
  Mahmudur Rahman Hera, Hua-Jun Hong, Amatur Rahman, Pei-Hsuan Tsai, Afia Afrin, Md. Yusuf Sarwar Uddin, Nalini Venkatasubramanian, Cheng-Hsin Hsu. In Proceedings of Adaptive and Reflexive Middleware, ACM, Las Vegas, Nevada, USA, 2017

• AQBox: An Air Quality Measuring Box from COTS Gas Sensors.
  Mahmudur Rahman Hera, Amatur Rahman, Afia Afrin, Md. Yusuf Sarwar Uddin, and Nalini Venkatasubramanian. In Proceedings of 2017 International Conference on Networking, Systems and Security (NSysS), Dhaka, Bangladesh, 2017

Softwares

• ESS-Color: a C++/snakemake based software that compresses colored de Bruijn graph
• ESS-Compress: a C++ software to compress a set of k-mers for disk storage
• UST: a C++ software to build a spectrum-preserving string set representation of a set of k-mers

Contact Info

Email : aur1111 “at” psu “dot” edu, amatur003 “at” gmail “dot” com