Dr. Atif Hasan Rahman (আতিফ হাসান রহমান)

Associate Professor

Research Area:

Bioinformatics and Computational Biology

Research Interest:

Genomics

Academic Background:

Ph.D. in Computer Science, 2015
University of California, Berkeley

B.Sc.Engg. in Computer Science and Engineering, 2007
Bangladesh University of Engineering and Technology

Selected Publications:

Tasfia Zahin, Md. Hasin Abrar, Mizanur Rahman, Tahrina Tasnim, Md. Shamsuzzoha Bayzid and Atif Rahman, An Alignment-free Method for Phylogeny Estimation using Maximum Likelihood. bioRxiv (2019): 875526.

Mahmudur Rahman Hera, Amatur Rahman and Atif Rahman, kRISP-meR: A Reference-free Guide-RNA Design Tool for CRISPR/Cas9. bioRxiv (2019): 869115.

Atif Rahman and Lior Pachter, SWALO: scaffolding with assembly likelihood optimization. bioRxiv (2016): 081786.

Atif Rahman, Ingilief Hallgrimsdottir, Michael B. Eisen and Lior Pachter, Association mapping from sequencing reads using k-mers. eLife 7 (2018): e32920.

Atif Rahman and Lior Pachter, CGAL: computing genome assembly likelihoods, Genome Biology, 14 (2013), R8.

Atif Rahman, Swakkhar Shatabda, and Masud Hasan. An approximation algorithm for sorting by reversals and transpositions. Journal of Discrete Algorithms, 6(3):449–457, Elsevier, 2008.

Journal Papers:

1.	Mursalin Habib* and Kowshic Roy* and Saem Hasan* and Atif Hasan Rahman and Md Shamsuzzoha Bayzid, Terraces in species tree inference from gene trees, BMC Ecology and Evolution, 24, 135, 2024. [paper link]
2.	Islam Rubyeat and Rahman Atif, An Alignment-Free Method for Detection of Missing Regions for Phylogenetic Analysis, Heliyon, 10, E32227, 2024.
3.	Roy Nilanjan, Kabir Acramul Haque, Zahan Nourin, Mouna Shahba Tasmiya, Chakravarty Sakshar, Rahman Atif Hasan, Md Shamsuzzoha Bayzid, Genome wide association studies on seven yield-related traits of 183 rice varieties in Bangladesh, Plant Direct, 8, e593, 2024.
4.	Saha Shoumik and Afroz Sadia and Rahman Atif Hasan, MAlign: Explainable static raw-byte based malware family classification using sequence alignment, Computers \& Security, 139, 103714, 2024.
5.	Yafi Mashrur Ahmed and Hisham Md Hasibul Husain and Grisanti Francisco and Martin James F and Rahman Atif and Samee Md Abul Hassan, scGIST: gene panel design for spatial transcriptomics with prioritized gene sets, Genome Biology, 25, 57, 2024.
6.	Tarafder Sumit and Islam Mazharul and Shatabda Swakkhar and Rahman Atif, Figbird: a probabilistic method for filling gaps in genome assemblies, Bioinformatics, 38, 3717--3724, 2022.
7.	Das Sarkar Snigdha Sarathi and Shanto Subangkar Karmaker and Rahman Masum and Islam Md Saiful and Rahman Atif Hasan and Masud Mohammad M and Ali Mohammed Eunus, BayesBeat: Reliable Atrial Fibrillation Detection from Noisy Photoplethysmography Data, Proceedings of the ACM on Interactive Mobile Wearable and Ubiquitous Technologies, 6, 1--21, 2022.
8.	Zakaria Mehrab, Jaiaid Mobin, Ibrahim Asadullah Tahmid, and Atif Rahman, Efficient association mapping from k-mers—an application in finding sex-specific sequences, Plos one, 16.000000, e0245058, 2021. [paper link]
9.	Ishrat Tanzila Farah, Muktadirul Islam, Kazi Tasnim Zinat, Atif Hasan Rahman, Shamsuzzoha Bayzid, Species tree estimation from gene trees by minimizing deep coalescence and maximizing quartet consistency: a comparative study and the presence of pseudo species tree terraces, Systematic Biology, 70, 1213--1231, 2021. [paper link]
10.	Rahman Atif and Pachter Lior, SWALO: scaffolding with assembly likelihood optimization, Nucleic acids research, 49, e117--e117, 2021.
11.	Mehrab Zakaria and Mobin Jaiaid and Tahmid Ibrahim Asadullah and Rahman Atif, Efficient association mapping from k-mers—An application in finding sex-specific sequences, Plos one, 16, e0245058, 2021.
12.	Mehrab Zakaria and Mobin Jaiaid and Tahmid Ibrahim Asadullah and Pachter Lior and Rahman Atif, Reference-free Association Mapping from Sequencing Reads Using k-mers, Bio-protocol, 10, e3815--e3815, 2020.
13.	Nayeem Muhammad Ali and Bayzid Md Shamsuzzoha and Rahman Atif Hasan and Shahriyar Rifat and Rahman M Sohel, Multiobjective Formulation of Multiple Sequence Alignment for Phylogeny Inference, IEEE Transactions on Cybernetics, 2020.
14.	Amam Siddiki, Masum Billah, Mohammad Alam, Kazi Shefaul Mulk Shawrob, Mahadia Kumkum, Sourav Saha, Muntaha Chowdhury, Atif H Rahman, Michael Stear, Mohammad KI Khan, Gous Miah, AK M. Mollah, Abdul Baten, Complete mitochondrial genome sequence of Black Bengal goat (Capra hircus), Mitochondrial DNA Part B, 4, 2121--2122, 2019. [paper link]
15.	Amam Zonaed Siddiki, Abdul Baten, Masum Billah, Mohammad Atique Ul Alam, Kazi Shefaul Mulk Shawrob, Sourav Saha, Muntaha Chowdhury, Atif Hasan Rahman, Michael Stear, Gous Miah, Mahadia Kumkum, Mohammad Sirazul Islam, Mohammad Alamgir Hossain, AKM Mollah, , The genome of the Black Bengal goat (Capra hircus), BMC research notes, 12, 1--3, 2019. [paper link]
16.	Ch Md Rakin Haider, Anindya Iqbal, Atif Hasan Rahman, M Sohel Rahman, An ensemble learning based approach for impression fraud detection in mobile advertising, Journal of Network and Computer Applications, 112, 126--141, 2018.
17.	A. H. Rahman, Ingilief Hallgrimsdottir, Michael Eisen, Lior Pachter, Association mapping from sequencing reads using k-mers, eLife, 7, 2018.
18.	Masud Hasan, Atif Hasan Rahman, Md. Khaledur Rahman, M. Sohel Rahman, Mahfuza Sharmin, Rukhsana Yeasmin, Pancake flipping and sorting permutations, Journal of Discrete Algorithms, 33, 139-149, 2015.
19.	A. H. Rahman, Lior Pachter, CGAL: computing genome assembly likelihoods, Genome Biology, 14, 2013.
20.	A. H. Rahman, Swakkhar Shatabda, Masud Hasan, An approximation algorithm for sorting by reversals and transpositions, Journal of Discrete Algorithms, 6, 449-457, 2008.

Conference Papers:

1.	Muhammad Ali Nayeem, Md Shamsuzzoha Bayzid, Atif Hasan Rahman, Rifat Shahriyar, and M Sohel Rahman, A 'phylogeny-aware' multi-objective optimization approach for computing MSA, Proceedings of the Genetic and Evolutionary Computation Conference, 577--585, 2019. [paper link]
2.	Atif Rahman, Lior Pachter, Transcript Abundance Estimation and the Laminar Packing Problem, Algorithms for Computational Biology: 6th International Conference, 203--211, 2019.
3.	Suri Dipannita Sayeed, M Sohel Rahman, Atif Rahman, On multiple longest common subsequence and common motifs with gaps, WALCOM: Algorithms and Computation: 12th International Conference, WALCOM 2018,, 207--215, 2018. [paper link]
4.	Mahfuza Sharmin, R. Yeasmin, Masud Hasan, A. Rahman, M. Sohel Rahman, Pancake Flipping with Two Spatulas, ISCO 2010 Proceedings: Electronic Notes in Discrete Mathematics, 231-238, 2010.
5.	Atif Rahman, Mahmuda Naznin, Masud Hasan, Integer Linear Programming in Designing Universal Arrays with Multiplexed Applications, International Conference on Electronics and Computer Technology, 215-218, 2009.
6.	Swakkhar Shatabda, Atif Rahman, Masud Hasan, An Approximation Algorithm for Bounded Degree Closest Phylogenetic 2nd Root Problem, Proceedings of the International MultiConference of Engineers and Computer Scientists, 1.000000, 2008.