Research Detail:

Bioinformatics and Computational Biology

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

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» Recent Publications:
1. AliHaisamMuhammadRafid, toufikuzzaman, mrahman, msrahman, CRISPRpred(SEQ): A Sequence-Based Method for sgRNA On Target Activity Prediction Using Traditional Machine Learning, BMC Bioinformatics, 21(223), , 2020. [paper link]
2. MostofaRafidUddin, SazanMahbub, mrahman, bayzid, SAINT: Self-Attention Augmented Inception-Inside-Inception Network Improves Protein Secondary Structure Prediction, Bioinformatics, , , 2020. [paper link]
3. sumaiya, DavidHoksza, EduardoPérez-Palma, PatrickMay, JakobBJespersen, shehab, ZaaraRifat, HenrikeOHeyne, msrahman, JeffreyRCottrell, FlorenceFWagner, MarkJDaly, ArthurJCampbell, DennisLal, MISCAST: MIssense variant to protein StruCture Analysis web SuiTe, Nucleic Acids Research, , , 2020. [paper link]
4. ZaaraRifat, ShehabAhmed, Map of Genetically Constrained Regions in Human Intrinsically Disordered Proteins, Biophysical Journal, 118, , 2019. [paper link]
5. mrahman, Md.KhaledurRahman, kaykobad, msrahman, 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. atif, IngiliefHallgrimsdottir, MichaelEisen, LiorPachter, Association mapping from sequencing reads using k-mers, eLife, 7(e32920), , 2018.
7. SumitTarafder, Md.ToukirAhmed, sumaiya, MdTamjidulHoque, msrahman, 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. MdMahfuzerRahman, RatulSharker, SajibBiswas, msrahman, HaVec: An Efficient de Bruijn Graph Construction Algorithm for Genome Assembly, International Journal of Genomics, 2017, 6120980, 2017. [paper link]
9. Md.ZahangirAlam, S.M.NiazArifin, HasanMohammadAl-Amin, MohammadShafiulAlam, msrahman, 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.KhaledurRahman, msrahman, 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. FarshidRayhan, SajidAhmed, SwakkharShatabda, DewanFarid, ZaynabMousavian, AbdollahDehzangi, msrahman, iDTI-ESBoost: Identification of Drug Target Interaction Using Evolutionary and Structural Features with Boosting, Scientific Reports, 7, 17731, 2017. [paper link]
12. johramoosa, RameenShakur, kaykobad, msrahman, Gene selection for cancer classification with the help of bees, BMC Medical Genomics, 9(S2), , 2016.
13. fatema, msrahman, "An efficient algorithm to detect common ancestor genes for non-overlapping inversion and applications.", Theoretical Computer Science, , , 2016.
14. mrahman, AliAlatabbi, TanverAthar, MaximeCrochemore, msrahman, 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, AvdeshMishra, MdTamjidulHoque, Improved prediction of accessible surface area results in efficient energy function application, Journal of Theoretical Biology, 380, 380 - 391, 2015.
16. sumaiya, kaykobad, msrahman, 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.RArifin, D.A.Pitts, msrahman, SaraNowreen, 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.KhaledurRahman, msrahman, Prefix and suffix transreversals on binary and ternary strings, Journal of Discrete Algorithms, 33, 160-170, 2015.
19. KishwarShafin, KaziLutfulKabir, IffaturRidwan, TasmiahTamzidAnannya, RashidSaadmanKarim, MohammadMozammelHoque, msrahman, Impact of Heuristics in Clustering Large Biological Networks, Computational Biology and Chemistry, 59, 28-36, 2015.
20. AhammedUllah, NasifAhmed, SubrataDeyPappu, SwakkharShatabda, A.Z.M.DayemUllah, msrahman, Efficient conformational space exploration in ab initio protein folding simulation, Royal Society Open Science, 2, 150238, 2015.
21. fatema, msrahman, Application of Consensus String Matching in the Diagnosis of Allelic Heterogeneity Involving Transposition Mutation, International Journal of Data Mining and Bioinformatics, , , 2015.
22. EffatFarhana, msrahman, Constrained sequence analysis algorithms in computational biology, Information Sciences, 295, 247-257, 2015.
23. DipanShaw, sohansayed, msrahman, masudhasan, Protein folding in HP model on hexagonal lattices with diagonals, BMC Bioinformatics, 15(S-2), S7, 2014.
24. atif, LiorPachter, CGAL: computing genome assembly likelihoods, Genome Biology, 14(R8), , 2013.
25. M.T.IAumi, M.T.Moosa, msrahman, Pattern Matching in Indeterminate and Arc-Annotated Sequences, Recent Patents on DNA and Gene Sequences, 7(2), 96-104, 2013.
26. DeenMohammadAbdullah, WaliMdAbdullah, msrahman, Improving the Performance of a Genome Sorting Algorithm with Inverted Block-Interchange, Journal of Computers, 8(5), 1119-1126, 2013.
27. AmitKumarDutta, masudhasan, msrahman, Prefix transpositions on binary and ternary strings, Information Processing Letters, 113(8), 265-270, 2013.
28. SammiAbidaSalma, saidurrahman, Md.IqbalHossain, Triangle-Free Outerplanar 3-Graphs are Pairwise Compatibility Graphs, Journal of Graph Algorithms and Applications (JGAA), 17(2), 81-102, 2013.
29. MuhammadRashedAlam, msrahman, 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, masudhasan, A.Z.Khan, msrahman, 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. atif, SwakkharShatabda, masudhasan, An approximation algorithm for sorting by reversals and transpositions, Journal of Discrete Algorithms, 6(3), 449-457, 2008.
32. sohansayed, msrahman, On the protein folding problem in 2D-triangular lattices, Algorithms for Molecular Biology, 8(30), , 0000.
33. SaadMaznur, MohammadShaown, mahmudanaznin, TanvirR.Faisal, Perception Thresholding for Noise Removal in Micrographs of Cellular Tissues Obtained from Fluorescence Microscopy, IMECE, American Society of Mechanical Engineers (ASME), , 1-6, 2018.
34. aashik, MohimenulMahi, msrahman, A simple, fast, filter-based algorithm for circular sequence comparison, WALCOM, , 12, 2018.
35. MarjanFerdousi, SuraiyaTairin, SttayajitPodder, razi, mahmudanaznin, Finding Hierarchical Network Model in Insulin Production Process, 8th IEEE Workshop of Multicore and Multithreaded Algorithms and Applications (M2A2), co-located with IEEE HPCC, , 8, 2017.
36. DipanShaw, sohansayed, ShuvasishKarmaker, msrahman, Approximation Algorithms for Three Dimensional Protein Folding, WALCOM, , 274-285, 2016.
37. Md.IqbalHossain, saidurrahman, A necessary condition and a sufficient condition for pairwise compatibility graphs, WALCOM 2016, , 107-113, 2016.
38. sumaiya, MdNasrulIslam, MdTamjidulHoque, Improved protein disorder predictor by smoothing output, 17th International Conference on Computer and Information Technology (ICCIT),, , 110 - 115, 2014.
39. fatema, msrahman, 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, msrahman, Solving the Minimum Common String Partition Problem with the Help of Ants, International Conference on Swarm Intelligence (LNCS 7929), , 306-313, 2013.
41. kantishubhra, sunnysajjad, SaikatChakraborty, msrahman, PIssGA: An ultra fast meta-heuristic approach to solve protein inference problem, 16th International Conference on Computer and Information Technology (ICCIT), , , 2013.
42. shagufta_mehnaz, msrahman, Pairwise Compatibility Graphs Revisited, ICIEV, , , 2013.
43. E.Farhana, msrahman, Efficient Algorithm for Restricted LCS Problem, 4th International Conference on Bioinformatics and Computational Biology (BiCOB), , 51-56, 2012.
44. mahfuza, M.Afrin, msrahman, 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, msrahman, T.K.Saha, Bee Algorithms for Solving DNA Fragment Assembly Problem with Noisy and Noiseless data, GECCO, , , 2012.
46. J.S.Firoz, masudhasan, A.Z.Khan, msrahman, The 1.375 Approximation Algorithm for Sorting by Transpositions Can Run in O(nlogn) Time (Conference, WALCOM, , , 2010.
47. mahfuza, R.Yeasmin, masudhasan, A.Rahman, msrahman, Pancake Flipping with Two Spatulas, ISCO 2010 Proceedings: Electronic Notes in Discrete Mathematics, , 231-238, 2010.
48. R.Paul, M.S.Nasif, smfarhad, Fingerprint Recognition by Chain Coded String Matching Technique, Information and Communication Technology (ICICT07), , , 2007.