Research Detail:

Bioinformatics and Computational Biology

Summary not available

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» Research Groups:

» Related Faculties:
Dr. Md. Saidur Rahman
Dr. Masud Hasan
Dr. M. Sohel Rahman
Dr. Md. Shohrab Hossain
Dr. Md. Shamsuzzoha Bayzid
Md. Mostofa Ali Patwary
Dr. S. M. Farhad
Dr. Atif Hasan Rahman
Johra Muhammad Moosa
Dr. Rezwana Reaz
Shashata Sawmya
Nishat Anjum Bristy

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» Recent Publications:
1. 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(223), , 2020. [paper link]
2. 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]
3. Sumaiya Iqbal, David Hoksza, Eduardo PĂ©rez-Palma, Patrick May, Jakob B Jespersen, Shehab Sarar Ahmed, Zaara Rifat, Henrike O Heyne, M. Sohel Rahman, Jeffrey R Cottrell, Florence F Wagner, Mark J Daly, Arthur J Campbell, Dennis Lal, MISCAST: MIssense variant to protein StruCture Analysis web SuiTe, Nucleic Acids Research, , , 2020. [paper link]
4. Zaara Rifat, Shehab Ahmed, Map of Genetically Constrained Regions in Human Intrinsically Disordered Proteins, Biophysical Journal, 118, , 2019. [paper link]
5. 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]
6. A. H. Rahman, Ingilief Hallgrimsdottir, Michael Eisen, Lior Pachter, Association mapping from sequencing reads using k-mers, eLife, 7(e32920), , 2018.
7. Sumit Tarafder, Md. Toukir Ahmed, Sumaiya Iqbal, Md Tamjidul Hoque, M. Sohel Rahman, RBSURFpred: Modeling Protein Accessible Surface Area in Real and Binary Space using Regularized and Optimized Regression, Journal of Theoretical Biology, , To Appear, 2018. [paper link]
8. Md Mahfuzer Rahman, Ratul Sharker, Sajib Biswas, M. Sohel Rahman, HaVec: An Efficient de Bruijn Graph Construction Algorithm for Genome Assembly, International Journal of Genomics, 2017, 6120980, 2017. [paper link]
9. Md. Zahangir Alam, S. M. Niaz Arifin, Hasan Mohammad Al-Amin, Mohammad Shafiul Alam, M. Sohel Rahman, A spatial agent-based model of Anopheles vagus for malaria epidemiology: examining the impact of vector control interventions, BMC Malaria Journal, 16, 432, 2017. [paper link]
10. Md. Khaledur Rahman, M. Sohel Rahman, CRISPRpred: A flexible and efficient tool for sgRNAs on-target activity prediction in CRISPR/Cas9 systems, PLOS One, 12(8), e0181943, 2017. [paper link]
11. Farshid Rayhan, Sajid Ahmed, Swakkhar Shatabda, Dewan Farid, Zaynab Mousavian, Abdollah Dehzangi, M. Sohel Rahman, iDTI-ESBoost: Identification of Drug Target Interaction Using Evolutionary and Structural Features with Boosting, Scientific Reports, 7, 17731, 2017. [paper link]
12. Johra Muhammad Moosa, Rameen Shakur, M. Kaykobad, M. Sohel Rahman, Gene selection for cancer classification with the help of bees, BMC Medical Genomics, 9(S2), , 2016.
13. F. T. Zohora, M. Sohel Rahman, "An efficient algorithm to detect common ancestor genes for non-overlapping inversion and applications.", Theoretical Computer Science, , , 2016.
14. 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(186), 1-8, 2016. [paper link]
15. Sumaiya Iqbal, Avdesh Mishra, Md Tamjidul Hoque, Improved prediction of accessible surface area results in efficient energy function application, Journal of Theoretical Biology, 380, 380 - 391, 2015.
16. Sumaiya Iqbal, M. Kaykobad, M. Sohel Rahman, Solving the multi-objective Vehicle Routing Problem with Soft Time Windows with the help of bees, Swarm and Evolutionary Computation, 24(-), 50-64, 2015.
17. S.M.N. Arifin, R.R Arifin, D.A. Pitts, M. Sohel Rahman, Sara Nowreen, G.R. Madey, F.H. Collins, Landscape Epidemiology Modeling Using an Agent-Based Model and a Geographic Information System, Land, 4(2), 378-412, 2015.
18. Md. Khaledur Rahman, M. Sohel Rahman, Prefix and suffix transreversals on binary and ternary strings, Journal of Discrete Algorithms, 33, 160-170, 2015.
19. Kishwar Shafin, Kazi Lutful Kabir, Iffatur Ridwan, Tasmiah Tamzid Anannya, Rashid Saadman Karim, Mohammad Mozammel Hoque, M. Sohel Rahman, Impact of Heuristics in Clustering Large Biological Networks, Computational Biology and Chemistry, 59, 28-36, 2015.
20. Ahammed Ullah, Nasif Ahmed, Subrata Dey Pappu, Swakkhar Shatabda, A. Z. M. Dayem Ullah, M. Sohel Rahman, Efficient conformational space exploration in ab initio protein folding simulation, Royal Society Open Science, 2, 150238, 2015.
21. F. T. Zohora, M. Sohel Rahman, Application of Consensus String Matching in the Diagnosis of Allelic Heterogeneity Involving Transposition Mutation, International Journal of Data Mining and Bioinformatics, , , 2015.
22. Effat Farhana, M. Sohel Rahman, Constrained sequence analysis algorithms in computational biology, Information Sciences, 295, 247-257, 2015.
23. Dipan Shaw, A. S. Islam, M. Sohel Rahman, Masud Hasan, Protein folding in HP model on hexagonal lattices with diagonals, BMC Bioinformatics, 15(S-2), S7, 2014.
24. A. H. Rahman, Lior Pachter, CGAL: computing genome assembly likelihoods, Genome Biology, 14(R8), , 2013.
25. M.T.I Aumi, M.T. Moosa, M. Sohel Rahman, Pattern Matching in Indeterminate and Arc-Annotated Sequences, Recent Patents on DNA and Gene Sequences, 7(2), 96-104, 2013.
26. Deen Mohammad Abdullah, Wali Md Abdullah, M. Sohel Rahman, Improving the Performance of a Genome Sorting Algorithm with Inverted Block-Interchange, Journal of Computers, 8(5), 1119-1126, 2013.
27. Amit Kumar Dutta, Masud Hasan, M. Sohel Rahman, Prefix transpositions on binary and ternary strings, Information Processing Letters, 113(8), 265-270, 2013.
28. Sammi Abida Salma, Md. Saidur Rahman, Md. Iqbal Hossain, Triangle-Free Outerplanar 3-Graphs are Pairwise Compatibility Graphs, Journal of Graph Algorithms and Applications (JGAA), 17(2), 81-102, 2013.
29. Muhammad Rashed Alam, M. Sohel Rahman, The substring inclusion constraint longest common subsequence problem can be solved in quadratic time, Journal of Discrete Algorithms, 17, 67-73, 2012.
30. J.S. Firoz, Masud Hasan, A. Z. Khan, M. Sohel Rahman, The 1.375 Approximation Algorithm for Sorting by Transpositions Can Run in $O(nlog n)$ Time, Journal of Computational Biology, 18(8), 1007-1011, 2011.
31. A. H. Rahman, Swakkhar Shatabda, Masud Hasan, An approximation algorithm for sorting by reversals and transpositions, Journal of Discrete Algorithms, 6(3), 449-457, 2008.
32. A. S. Islam, M. Sohel Rahman, On the protein folding problem in 2D-triangular lattices, Algorithms for Molecular Biology, 8(30), , 0000.
33. Saad Maznur, Mohammad Shaown, Mahmuda Naznin, Tanvir R. Faisal, Perception Thresholding for Noise Removal in Micrographs of Cellular Tissues Obtained from Fluorescence Microscopy, IMECE, American Society of Mechanical Engineers (ASME), Pittsburgh, USA, , 1-6, 2018. [paper link]
34. M. A. R. Azim, Mohimenul Mahi, M. Sohel Rahman, A simple, fast, filter-based algorithm for circular sequence comparison, WALCOM, , 12, 2018.
35. Marjan Ferdousi, Suraiya Tairin, Sttayajit Podder, A. B. M. Alim Al Islam, Mahmuda Naznin, Finding Hierarchical Network Model in Insulin Production Process, 8th IEEE Workshop of Multicore and Multithreaded Algorithms and Applications (M2A2), co-located with IEEE HPCC, Bangkok, Thailand, , 8, 2017. [paper link]
36. Dipan Shaw, A. S. Islam, Shuvasish Karmaker, M. Sohel Rahman, Approximation Algorithms for Three Dimensional Protein Folding, WALCOM, , 274-285, 2016.
37. Md. Iqbal Hossain, Md. Saidur Rahman, A necessary condition and a sufficient condition for pairwise compatibility graphs, WALCOM 2016, , 107-113, 2016.
38. Sumaiya Iqbal, Md Nasrul Islam, Md Tamjidul Hoque, Improved protein disorder predictor by smoothing output, 17th International Conference on Computer and Information Technology (ICCIT),, , 110 - 115, 2014.
39. F. T. Zohora, M. Sohel Rahman, Application of Consensus String Matching in the Diagnosis of Allelic Heterogeneity, International Symposium on Bioinformatics Research and Applications (ISBRA 2014), , , 2014.
40. S.M. Ferdous, M. Sohel Rahman, Solving the Minimum Common String Partition Problem with the Help of Ants, International Conference on Swarm Intelligence (LNCS 7929), , 306-313, 2013.
41. S. K. K. Santu, S. Rahman, Saikat Chakraborty , M. Sohel Rahman, PIssGA: An ultra fast meta-heuristic approach to solve protein inference problem, 16th International Conference on Computer and Information Technology (ICCIT), , , 2013.
42. S. Mehnaz, M. Sohel Rahman, Pairwise Compatibility Graphs Revisited, ICIEV, , , 2013.
43. E. Farhana, M. Sohel Rahman, Efficient Algorithm for Restricted LCS Problem, 4th International Conference on Bioinformatics and Computational Biology (BiCOB), , 51-56, 2012.
44. Mahfuza Sharmin, M. Afrin, M. Sohel Rahman, Local Search Techniques for Placing Unique Restriction Sites in Synthetic Genomes, 4th International Conference on Bioinformatics and Computational Biology (BiCOB), , 13-18, 2012.
45. J. S. Firoz, M. Sohel Rahman, T. K. Saha, Bee Algorithms for Solving DNA Fragment Assembly Problem with Noisy and Noiseless data, GECCO, , , 2012.
46. J. S. Firoz, Masud Hasan, A. Z. Khan, M. Sohel Rahman, The 1.375 Approximation Algorithm for Sorting by Transpositions Can Run in O(nlogn) Time (Conference, WALCOM, , , 2010.
47. 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.
48. R. Paul, M.S. Nasif , S. M. Farhad, Fingerprint Recognition by Chain Coded String Matching Technique, Information and Communication Technology (ICICT07), , , 2007.