Dr. Mohammad Saifur Rahman (ডঃ মোহাম্মদ সাইফুর রহমান)

Professor

Research Area:

Research Interest:

Bioinformatics, Health Informatics, Algorithms, Applied Machine Learning

Academic Background:

Ph.D in Computer Science and Engineering (2018) from BUET
M.Sc. in Computer Science and Engineering (2014) from BUET
B.Sc. in Computer Science and Engineering (2004) from BUET

Selected Publications:

Journal Papers:

1.	Sheikh Hasib Ahmed, Dibyendu Brinto Bose, Rafi Khandoker, M Saifur Rahman, StackDPP: a stacking ensemble based DNA-binding protein prediction model, BMC Bioinformatics, 25, 1-21, 2024. [paper link]
2.	Rahman Mohammad Nuwaisir and Noman Abdullah Al and Turza Abir Mohammad and Abrar Mohammed Abid and Samee Md Abul Hassan and Rahman M Saifur, ScribbleDom: using scribble-annotated histology images to identify domains in spatial transcriptomics data, Bioinformatics, 39, btad594, 2023. [paper link]
3.	Nayeem Muhammad Ali and Samudro Naser Anjum and Rahman M Saifur and Rahman M Sohel, MAMMLE: A Framework for Phylogeny Estimation Based on Multiobjective Application-aware Multiple Sequence Alignment and Maximum Likelihood Ensemble, Journal of Computational Biology, 30, 245--249, 2023. [paper link]
4.	Mim Sharmin Akter, Md Zarif-Ul-Alam, Rezwana Reaz, Md Shamsuzzoha Bayzid, and Mohammad Saifur Rahman, Quartet Fiduccia–Mattheyses revisited for larger phylogenetic studies, Bioinformatics, 39, 2023. [paper link]
5.	Abrar Mohammed Abid and Kaykobad M and Rahman M Saifur and Samee Md Abul Hassan, NoVaTeST: identifying genes with location-dependent noise variance in spatial transcriptomics data, Bioinformatics, 39, 2023. [paper link]
6.	A K M Mehedi Hasan, Ajmain Yasar Ahmed, Sazan Mahbub, M Saifur Rahman, Shamsuzzoha Bayzid, SAINT-Angle: self-attention augmented inception-inside-inception network and transfer learning improve protein backbone torsion angle prediction, Bioinformatics Advances, 3, 2023. [paper link]
7.	Jony Sheikh Saifur Rahman and Shahriyar Rifat and Rahman M Saifur and Rahman M Sohel and Alam Tanvir, Linking Tweets Towards Geo-Localized Policies: COVID-19 Perspective, MEDINFO 2021: One World, One Health--Global Partnership for Digital Innovation, 290, 709--713, 2022. [paper link]
8.	Ahmed Shehab Sarar and Rifat Zaara Tasnim and Rahman M Saifur and Rahman M Sohel, Succinylated lysine residue prediction revisited, Briefings in Bioinformatics, 24, 2022. [paper link]
9.	Sana Joydeb Kumar and Abedin Mohammad Zoynul and Rahman M Sohel and Rahman M Saifur, A novel customer churn prediction model for the telecommunication industry using data transformation methods and feature selection, Plos one, 17, e0278095, 2022. [paper link]
10.	Muhammad Ali Nayeem, Md. Shamsuzzoha Bayzid, Naser Anjum Samudro, Mohammad Saifur Rahman, and M. Sohel Rahman,, PASTA with many application-aware optimization criteria for alignment based phylogeny inference, Computational Biology and Chemistry, To appear, 2022.
11.	Zzaman Rashed Uz and Nowreen Sara and Khan Irtesam Mahmud and Islam Md and Ibtehaz Nabil and Rahman M Saifur and Zahid Anwar and Farzana Dilruba and Sharmin Afroza and Rahman M Sohel and others, A Machine Learning-based Approach for Groundwater Mapping, Natural Resources Research, 31, 281--299, 2021.
12.	Mahim Mahbub, and Zahin Wahab, Rezwana Reaz, M Saifur Rahman, and Md Shamsuzzoha Bayzid, wQFM: highly accurate genome-scale species tree estimation from weighted quartets, Bioinformatics, 37, 3734-3743, 2021. [paper link]
13.	Anjum Naser and Nabil Raian Latif and Rafi Rakibul Islam and Bayzid Shamsuzzoha and Rahman M. Saifur, CD-MAWS: An Alignment-free Phylogeny Estimation Method Using Cosine Distance on Minimal Absent Word Sets, IEEE/ACM Transactions on Computational Biology and Bioinformatics, Online, 2021. [paper link]
14.	Hoque Iram Tazim and Ibtehaz Nabil and Chakravarty Saumitra and Rahman M Saifur and Rahman M Sohel, A contour property based approach to segment nuclei in cervical cytology images, BMC Medical Imaging, 21, 1--12, 2021. [paper link]
15.	Alam Md Zahangir, Masud Mohammad M, Rahman M Saifur, Cheratta Muhsin, Nayeem Muhammad Ali and Rahman M Sohel, Feature-ranking-based ensemble classifiers for survivability prediction of intensive care unit patients using lab test data, Informatics in Medicine Unlocked, 22, 100495, 2021. [paper link]
16.	Akon, Mujtahid and Akon, Muntashir and Kabir, Mohimenul and Rahman, M Saifur and Rahman, M Sohel, ADACT: a tool for analysing dissimilarity among nucleotide and protein sequences using minimal and relative absent words, Bioinformatics, 37, 1468–1470, 2021. [paper link]
17.	Khan Junaed Younus and Khondaker Md Tawkat Islam and Hoque Iram Tazim and Al-Absi Hamada RH and Rahman Mohammad Saifur and Guler Reto and Alam Tanvir and Rahman M Sohel, Toward Preparing a Knowledge Base to Explore Potential Drugs and Biomedical Entities Related to COVID-19: Automated Computational Approach, JMIR medical informatics, 8, e21648, 2020.
18.	Shahid, Farhana and Rahman, Wasifur and Rahman, M Saifur and Purabi, Sharmin Akther and Seddiqa, Ayesha and Mostakim, Moin and Feroz, Farhan and Soron, Tanjir Rashid and Hossain, Fahmida and Khan, Nabila and others, Leveraging Free-Hand Sketches for Potential Screening of PTSD, Proceedings of the ACM on Interactive, Mobile, Wearable and Ubiquitous Technologies, 4, 1--22, 2020. [paper link]
19.	Mostofa Rafid Uddin, Sazan Mahbub, Mohammad Saifur Rahman, Md. Shamsuzzoha Bayzid, SAINT: Self-Attention Augmented Inception-Inside-Inception Network Improves Protein Secondary Structure Prediction, Bioinformatics, 2020. [paper link]
20.	Ali Haisam Muhammad Rafid, Md. Toufikuzzaman, Mohammad Saifur Rahman, M. Sohel Rahman, CRISPRpred(SEQ): A Sequence-Based Method for sgRNA On Target Activity Prediction Using Traditional Machine Learning, BMC Bioinformatics, 21, 2020. [paper link]
21.	Farhana Shahid, Wasifur Rahman, Anika Binte Islam, Nipi Paul, Nabila Khan, Mohammad Saifur Rahman, Md Munirul Haque, A. B. M. Alim Al Islam, Two Tell-tale Perspectives of PTSD: Neurobiological Abnormalities and Bayesian Regulatory Network of the Underlying Disorder in a Refugee Context, Proceedings of the ACM on Interactive, Mobile, Wearable and Ubiquitous Technologies (IMWUT), 3, 2019. [paper link]
22.	Md Zahangir Alam, Mohammad Saifur Rahman, M. Sohel Rahman, A Random Forest based predictor for medical data classification using feature ranking, Informatics in Medicine Unlocked, 15, 100180, 2019. [paper link]
23.	Nabil Ibtehaz, Mohammad Saifur Rahman, M. Sohel Rahman, VFPred: A fusion of signal processing and machine learning techniques in detecting ventricular fibrillation from ECG signals, Biomedical Signal Processing and Control, 49, 349-359, 2019. [paper link]
24.	Mohammad Saifur Rahman, Md. khaledur Rahman, Sanjay Saha, M. Kaykobad, M. Sohel Rahman, Antigenic: An improved prediction model of protective antigens, Artificial Intelligence in Medicine, 94, 28-41, 2019. [paper link]
25.	Mohammad Saifur Rahman, Swakkhar Shatabda, Sanjay Saha, M. Kaykobad, M. Sohel Rahman, DPP-PseAAC: A DNA-binding protein prediction model using Chou's general PseAAC, Journal of Theoretical Biology, 452, 22-34, 2018. [paper link]
26.	Mohammad Saifur Rahman, Md. Yusuf Sarwar Uddin, Tahmid Hasan, M. Sohel Rahman, M. Kaykobad, Using Adaptive Heartbeat Rate on Long-Lived TCP Connections, IEEE/ACM TRANSACTIONS ON NETWORKING, 26, 203-216, 2018. [paper link]
27.	Mohammad Saifur Rahman, Md. Khaledur Rahman, M. Kaykobad, M. Sohel Rahman, isGPT: An optimized model to identify sub-Golgi protein types using SVM and Random Forest based feature selection, Artificial Intelligence in Medicine, 84, 90-100, 2018. [paper link]
28.	Mohammad Saifur Rahman, Ali Alatabbi, Tanver Athar, Maxime Crochemore, M. Sohel Rahman, Absent words and the (dis)similarity analysis of DNA sequences: An Experimental Study, BMC Research Notes, 9, 1-8, 2016. [paper link]
29.	Md. Mahbubul Hasan, A. S. Islam, Mohammad Saifur Rahman, M. Sohel Rahman, Order preserving pattern matching revisited, Pattern Recognition Letters, 55, 15-21, 2015. [paper link]
30.	Asif-ul Haque, Mohammad Saifur Rahman, Mehedi Bakht, M. Kaykobad, Drawing lines by uniform packing, International journal of Computers and Graphics, 30, 207-212, 2006. [paper link]

Conference Papers:

1.	Shashata Sawmya, Arpita Saha, Sadia Tasnim, Naser Anjum, Md. Toufikuzzaman , Ali Haisam Muhamad Rafid, Mohammad Saifur Rahman, M. Sohel Rahman, and Tanvir Alam, Phylogenetic Analyses of SARS-CoV-2 Strains Reveal Its Link to the Spread of COVID-19 Across the Globe, MEDINFO 2021: One World, One Health--Global Partnership for Digital Innovation, 729--733, 2022. [paper link]
2.	M. A. Nayeem and M. S. Bayzid and S. Chakravarty and M. S. Rahman and M. S. Rahman, A Multi-objective Metaheuristic Approach for Accurate Species Tree Estimation, IEEE 20th International Conference on Bioinformatics and Bioengineering (BIBE), 79-84, 2020. [paper link]
3.	E M Wasifur Rahman Chowdhury, Mohammad Saifur Rahman, A. B. M. Alim Al Islam, M. Sohel Rahman, Salty Secret: Let us secretly salt the secret, 2017 International Conference on Networking, Systems and Security (NSysS), 115-123, 2017. [paper link]
4.	Mohammad Saifur Rahman, Md. Yusuf Sarwar Uddin, M. Sohel Rahman, M. Kaykobad, Using Adaptive Heartbeat rate on Long-lived TCP Connections, 2016 International Conference on Networking Systems and Security (NSysS 2016), 16-24, 2016. [paper link]
5.	Taslim Arefin Khan, Mainuddin Ahmad Jonas, S.M. Hasanur Rashid, Mushfequr Rahman, Mohammad Saifur Rahman, A. B. M. Alim Al Islam, Sign of Life: A System for Escalating Post-Disaster Rescue Missions in Ready-Made Garment Factories, International Conference on Networking Systems and Security (NSysS), 145-150, 2015. [paper link]
6.	Md. Mahbubul Hasan, A. S. Islam, Mohammad Saifur Rahman, M. Sohel Rahman, Order Preserving Prefix Tables, International Symposium on String Processing and Information Retrieval (SPIRE), 111-116, 2014. [paper link]
7.	Asif-ul Haque, Mohammad Saifur Rahman, Mehedi Bakht, M. Kaykobad, Drawing Lines by Uniform Packing, International Conference on Computer and Information Technology (ICCIT), 186-190, 2004.
8.	M. Kaykobad, Asif-ul Haque , Mohammad Saifur Rahman, M. Sohel Rahman, On Average Length of Cycle in a Complete Graph, International Conference on Computer and Information Technology, 47-49, 2002.