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Dr Nasimul Noman

Lecturer

School of Elect Engineering and Computer Science

Career Summary

Biography

Nasimul Noman received his PhD degree in Frontier Informatics from the Graduate School of Frontier Sciences, University of Tokyo in 2007. He served in the Department of Computer Science and Engineering, University of Dhaka as a faculty member. He was a postdoctoral researcher in the Graduate School of Engineering, University of Tokyo with JSPS fellowship. He was working as a research fellow in the Graduate School of Information Since and Technology in University of Tokyo before he joined the University of Newcastle in 2013.

His current research focus is the application of evolutionary computation for synthesis of gene networks for systems and synthetic biology. His research interests also include development of evolutionary algorithms and their application in computational biology and bioinformatics. 

Research Expertise
My major research area is modeling, simulation, reconstruction and optimization of biological networks. I have been working with different types of deterministic and stochastic modeling, simulation and analysis of genetic networks for systems and synthetic biology. I have worked in model based reconstruction of genetic networks from gene expression data for quite long. Evolutionary algorithms are my preferred method for optimization and in silico construction of biological networks. I am fascinated by the field of Evolutionary Computation. My favorite topics are Differential Evolution, Local Search, Memetic Algorithms, Adaptive Evolutionary Algorithms and Genetic Based Machine Learning (GMBL). I have been working for long for development, analysis and application of EC. To me the application of evolutionary algorithms for solving different real world problems, particularly in computational biology and bioinformatics, is very challenging and appealing. I have active research experience in some bioinformatics research topics. The topics of bioinformatics I am interested/experienced in are protein phosphorylation and glycosylation site detection, promoter site prediction, protein secondary structure prediction, regulatory motif detection, etc. I have been working for enhancement, extension and effective utilization of machine learning algorithms for solving different problems in bioinformatics and computational biology.

Teaching Expertise
The courses I am teaching this year are: > Formal Languages and Automata > Operating Systems > Internet Communication In my previous appointments, I taught many undergraduate and graduate courses of Computer Science and Engineering. Some of the courses I taught recently are as follows: • Introduction to Bioinformatics • Compiler Design • Introduction to Circuit Analysis • Microprocessor and Assembly Language • Data Structure

Administrative Expertise
In my appointment in University of Dhaka, I have served as student adviser. Besides, I have worked in different administrative committees such as course curriculum development committee, examination coordination committee etc.

Collaborations
My current research collaborators are 1. Prof. Hitoshi Iba, University of Tokyo. 2. A/Prof. Yannic Rondelez, University of Tokyo.


Qualifications

  • PhD, University of Tokyo - Japan
  • Bachelor of Science (Computer Science), University of Dhaka - Bangladesh
  • Master of Science (Computer Science), University of Dhaka - Bangladesh

Keywords

  • Bioinformatics
  • Computational Biology
  • Computer Algorithms
  • Data Structure
  • Evolutionary Algorithms
  • Evolutionary Computation
  • Synthetic Biology
  • Systems Biology
  • Theory of Computation

Languages

  • Bengali (Fluent)

Fields of Research

CodeDescriptionPercentage
060102Bioinformatics20
060114Systems Biology40
080108Neural, Evolutionary and Fuzzy Computation40

Professional Experience

UON Appointment

DatesTitleOrganisation / Department
11/11/2014 - 14/12/2016LecturerUniversity of Newcastle
School of Elect Engineering and Computer Science
Australia

Academic appointment

DatesTitleOrganisation / Department
1/09/2012 - 1/02/2013Visiting Research FellowHarvard Medical School
Systems Biology
United States
1/03/2012 - 1/11/2013Research FellowThe University of Tokyo
School of Information Science and Technology
Japan
1/01/2012 - 1/05/2012Associate ProfessorUniversity of Dhaka
Computer Science and Engineering
Bangladesh
1/11/2009 - 1/11/2011Post Doctoral ResearcherThe University of Tokyo
School of Engineering
Japan
1/03/2007 - 1/01/2012Assistant ProfessorUniversity of Dhaka
Computer Science and Engineering
Bangladesh
1/03/2002 - 1/03/2007LecturerUniversity of Dhaka
Computer Science and Engineering
Bangladesh
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Publications

For publications that are currently unpublished or in-press, details are shown in italics.


Book (1 outputs)

YearCitationAltmetricsLink
2011Iba H, Noman N, New Frontier in Evolutionary Algorithms, World Scientific Publishing Company, London, 304 (2011) [A2]

Chapter (2 outputs)

YearCitationAltmetricsLink
2014Noman N, Palafox L, Iba H, 'Inferring Genetic Networks with a Recurrent Neural Network Model Using Differential Evolution', Springer Handbook of Bio-/Neuroinformatics, Springer, Berlin Heidelberg 355-373 (2014)
DOI10.1007/978-3-642-30574-0_22
2007Noman N, Iba H, 'Inferring Regulations in a Genomic Network from Gene Expression Profiles.', Analysis of Biological Data: A Soft Computing Approach, World Scientific 205-229 (2007)

Journal article (13 outputs)

YearCitationAltmetricsLink
2015Noman N, Monjo T, Moscato P, Iba H, 'Evolving robust gene regulatory networks.', PLoS One, 10 e0116258 (2015)
DOI10.1371/journal.pone.0116258Author URL
Co-authorsPablo Moscato
2015Peng Y, Hasegawa Y, Noman N, Iba H, 'Temperature compensation via cooperative stability in protein degradation', PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, 431 109-123 (2015)
DOI10.1016/j.physa.2015.03.002Author URL
2014Dinh QH, Noman N, Iba H, 'Oscillatory Synthetic Biological System Construction Using Interactive Evolutionary Computations', Journal of Computer Science, 10 2640-2652 (2014) [C1]
DOI10.3844/jcssp.2014.2640.2652
2013Noman N, Palafox L, Iba H, 'Evolving Genetic Networks for Synthetic Biology', NEW GENERATION COMPUTING, 31 71-88 (2013) [C1]
DOI10.1007/s00354-013-0201-8Author URL
CitationsScopus - 2Web of Science - 1
2013Palafox L, Noman N, Iba H, 'Reverse Engineering of Gene Regulatory Networks Using Dissipative Particle Swarm Optimization', IEEE TRANSACTIONS ON EVOLUTIONARY COMPUTATION, 17 577-587 (2013) [C1]
DOI10.1109/TEVC.2012.2218610Author URL
CitationsScopus - 2Web of Science - 2
2012Ibrahim M, Noman N, Iba H, 'Finding Perfect and Imperfect Biclusters from Gene Expression Data: A Heuristic and A Metaheuristic Approach.', International Journal of Applied Chemistry, 8 (2012)
2011Azad AKM, Shahid S, Noman N, Lee H, 'Prediction of plant promoters based on hexamers and random triplet pair analysis', ALGORITHMS FOR MOLECULAR BIOLOGY, 6 (2011) [C1]
DOI10.1186/1748-7188-6-19Author URL
CitationsScopus - 3Web of Science - 2
2011Noman N, Iba H, 'e Constrained differential evolution for economic dispatch with valve-point effect', International Journal of Bio-Inspired Computation, 3 346-357 (2011) [C1]
DOI10.1504/IJBIC.2011.043607
CitationsScopus - 6Web of Science - 4
2010Kabir M, Noman N, Iba H, 'Reverse engineering gene regulatory network from microarray data using linear time-variant model', BMC BIOINFORMATICS, 11 (2010) [C1]
DOI10.1186/1471-2105-11-S1-S56Author URL
CitationsScopus - 29Web of Science - 20
2010Biswas AK, Noman N, Sikder AR, 'Machine learning approach to predict protein phosphorylation sites by incorporating evolutionary information', BMC BIOINFORMATICS, 11 (2010) [C1]
DOI10.1186/1471-2105-11-273Author URL
CitationsScopus - 19Web of Science - 17
2008Noman N, Iba H, 'Accelerating differential evolution using an adaptive local search', IEEE TRANSACTIONS ON EVOLUTIONARY COMPUTATION, 12 107-125 (2008) [C2]
DOI10.1109/TEVC.2007.895272Author URL
CitationsScopus - 310Web of Science - 209
2008Noman N, Iba H, 'Differential evolution for economic load dispatch problems', ELECTRIC POWER SYSTEMS RESEARCH, 78 1322-1331 (2008) [C1]
DOI10.1016/j.epsr.2007.11.007Author URL
CitationsScopus - 153Web of Science - 110
2007Noman N, Iba H, 'Inferring gene regulatory networks using differential evolution with local search heuristics', IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 4 634-647 (2007)
DOI10.1109/TCBB.2007.1058Author URL
CitationsScopus - 63Web of Science - 52
Show 10 more journal articles

Conference (25 outputs)

YearCitationAltmetricsLink
2013Palafox LF, Noman N, Iba H, 'Extending Population Based Incremental Learning using Dirichlet Processes', 2013 IEEE Congress on Evolutionary Computation, CEC 2013, Cancun, MEXICO (2013) [E1]
DOI10.1109/CEC.2013.6557764
CitationsScopus - 1
2013Hettiarachchi DS, Noman N, Iba H, 'Messy Genetic Algorithm for evolving mathematical function evaluating variable length gene regulatory networks', 2013 IEEE Congress on Evolutionary Computation, CEC 2013, Cancun, MEXICO (2013) [E1]
DOI10.1109/CEC.2013.6557824
CitationsScopus - 1Web of Science - 1
2012Komiya K, Noman N, Iba H, 'The search for robust topologies of oscillatory gene regulatory networks by evolutionary computation', GECCO'12 - Proceedings of the 14th International Conference on Genetic and Evolutionary Computation Companion, Philadelphia, Pennsylvania, USA (2012) [E1]
DOI10.1145/2330784.2330963
CitationsScopus - 2
2012He C, Noman N, Iba H, 'An improved artificial bee colony algorithm with non-separable operator', Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Daejeon, South Korea (2012) [E1]
DOI10.1007/978-3-642-32645-5_26
2012Noman N, Palafox L, Iba H, 'On model selection criteria in reverse engineering gene networks using RNN model', Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Daejeon, South Korea (2012) [E1]
DOI10.1007/978-3-642-32645-5_20
CitationsScopus - 1
2011Noman N, Iba H, 'Solving dynamic economic dispatch problems using cellular differential evolution', 2011 IEEE Congress of Evolutionary Computation, CEC 2011, New Orleans, LA (2011) [E1]
DOI10.1109/CEC.2011.5949947
CitationsScopus - 1Web of Science - 1
2011Noman N, Bollegala D, Iba H, 'An adaptive differential evolution algorithm', 2011 IEEE Congress of Evolutionary Computation, CEC 2011, New Orleans, LA (2011) [E1]
DOI10.1109/CEC.2011.5949891
CitationsScopus - 7Web of Science - 3
2011Bollegala D, Noman N, Iba H, 'RankDE: Learning a ranking function for information retrieval using differential evolution', Genetic and Evolutionary Computation Conference, GECCO'11, Dublin, IRELAND (2011) [E1]
DOI10.1145/2001576.2001814
CitationsScopus - 1Web of Science - 1
2011Noman N, Bollegala D, Iba H, 'Differential evolution with self adaptive local search', Genetic and Evolutionary Computation Conference, GECCO'11, Dublin, IRELAND (2011) [E1]
DOI10.1145/2001576.2001725
CitationsScopus - 1
2011Vatanutanon J, Noman N, Iba H, 'Polynomial selection scheme with dynamic parameter estimation in cellular genetic algorithm', Genetic and Evolutionary Computation Conference, GECCO'11, Dublin, IRELAND (2011) [E1]
DOI10.1145/2001576.2001734
CitationsScopus - 2
2010Ibrahim M, Noman N, Iba H, 'On the complexity and completeness of robust biclustering algorithm (ROBA)', 2010 4th International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2010, Chengdu (2010) [E1]
DOI10.1109/ICBBE.2010.5518207
2010Noman N, Vatanutanon J, Iba H, 'Tuning selection pressure in differential evolution using local selection', Proceedings - 2010 2nd World Congress on Nature and Biologically Inspired Computing, NaBIC 2010, Kitakyushu; Japan (2010) [E1]
DOI10.1109/NABIC.2010.5716337
CitationsScopus - 1
2010Vatanutanon J, Noman N, Iba H, 'Polynomial selection: A new way to tune selective pressure', Proceedings - 2010 2nd World Congress on Nature and Biologically Inspired Computing, NaBIC 2010, Kitakyushu, Japan (2010) [E1]
DOI10.1109/NABIC.2010.5716313
CitationsScopus - 1
2010Mondal BS, Sarkar AK, Hasan MM, Noman N, 'Reconstruction of gene regulatory networks using differential evolution', Proceedings of 2010 13th International Conference on Computer and Information Technology, ICCIT 2010, Dhaka, Bangladesh (2010) [E1]
DOI10.1109/ICCITECHN.2010.5723898
CitationsScopus - 1
2010Hasan MM, Noman N, Iba H, 'A prior knowledge based approach to infer gene regulatory networks', ISB 2010 Proceedings - International Symposium on Biocomputing, Calicut, Kerala, India (2010) [E1]
DOI10.1145/1722024.1722069
2010Noman N, Iba H, 'Cellular differential evolution algorithm', Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Univ S Australia, Adelaide, AUSTRALIA (2010) [E1]
DOI10.1007/978-3-642-17432-2_30
CitationsScopus - 1Web of Science - 1
2010Ishiwata H, Noman N, Iba H, 'Emergence of cooperation in a bio-inspired multi-agent system', Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Univ S Australia, Adelaide, AUSTRALIA (2010) [E1]
DOI10.1007/978-3-642-17432-2_37
2006Noman N, Iba H, 'On the reconstruction of gene regulatory networks from noisy expression profiles', 2006 IEEE CONGRESS ON EVOLUTIONARY COMPUTATION, VOLS 1-6, Vancouver, CANADA (2006)
Author URL
2006Noman N, Iba H, 'Inference of genetic networks using S-system: Information criteria for model selection', GECCO 2006: GENETIC AND EVOLUTIONARY COMPUTATION CONFERENCE, VOL 1 AND 2, Seattle, WA (2006)
Author URL
CitationsScopus - 9Web of Science - 8
2006Noman N, Lba H, 'A new generation alternation model for differential evolution', GECCO 2006: Genetic and Evolutionary Computation Conference, Vol 1 and 2, Seattle, WA (2006)
Author URL
CitationsScopus - 14Web of Science - 4
2006Noman N, Iba H, 'On the reconstruction of gene regulatory networks from noisy expression profiles', 2006 IEEE Congress on Evolutionary Computation, CEC 2006 (2006)

Noise is inevitable in microarray data. The real challenge lies in identifying the biomolecular interactions in spite of the significant noise level present in the expression proflies that current technology offers. In this paper, we study the usefulness of an evolutionary approach in reverse engineering the biomolecular connections in a gene circuit from observed system dynamics that is contaminated with noise. The method uses an Information Criteria based fitness evaluation for selecting models, represented in decoupled S-system formalism, instead of the conventional Mean Squared Error (MSE) based fitness evaluation. The suitability of the method is tested in experiments of reconstructing an artificial network from gene expression profiles with varying noise levels. The proposed fitness function has been found more suitable for identifying correct network topology and for estimating the accurate parameter values compared to the existing one. © 2006 IEEE.

CitationsScopus - 4
2005Noman N, Iba H, 'Inference of gene regulatory networks using S-system and differential evolution', GECCO 2005: GENETIC AND EVOLUTIONARY COMPUTATION CONFERENCE, VOLS 1 AND 2, Washington, DC (2005)
Author URL
CitationsScopus - 22Web of Science - 16
2005Noman N, Iba H, 'Enhancing Differential Evolution performance with local search for high dimensional function optimization', GECCO 2005: GENETIC AND EVOLUTIONARY COMPUTATION CONFERENCE, VOLS 1 AND 2, Washington, DC (2005)
Author URL
CitationsScopus - 41Web of Science - 34
2005Noman N, Iba H, 'Reverse engineering genetic networks using evolutionary computation.', Genome informatics. International Conference on Genome Informatics. (2005)

This paper proposes an improved evolutionary method for constructing the underlying network structure and inferring effective kinetic parameters from the time series data of gene expression using decoupled S-system formalism. We employed Trigonometric Differential Evolution (TDE) as the optimization engine of our algorithm for capturing the dynamics in gene expression data. A more effective fitness function for attaining the sparse structure, which is the hallmark of biological networks, has been applied. Experiments on artificial genetic network show the power of the algorithm in constructing the network structure and predicting the regulatory parameters. The method is used to evaluate interactions between genes in the SOS signaling pathway in Escherichia coli using gene expression data.

CitationsScopus - 30
2004Noman N, Okada K, Hosoyama N, Iba H, 'Use of clustering to improve the layout of gene network for visualization', CEC2004: PROCEEDINGS OF THE 2004 CONGRESS ON EVOLUTIONARY COMPUTATION, VOLS 1 AND 2, Portland, OR (2004)
Author URL
Show 22 more conferences
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Grants and Funding

Summary

Number of grants2
Total funding$6,200

Click on a grant title below to expand the full details for that specific grant.


20142 grants / $6,200

New Staff Grant$5,000

Funding body: University of Newcastle - Faculty of Engineering & Built Environment

Funding bodyUniversity of Newcastle - Faculty of Engineering & Built Environment
Project TeamDoctor Nasimul Noman
SchemeNew Staff Grant
RoleLead
Funding Start2014
Funding Finish2014
GNoG1400989
Type Of FundingInternal
CategoryINTE
UONY

15th International Conference on Systems Biology, Melbourne, 14-18 September, 2014$1,200

Funding body: University of Newcastle - Faculty of Engineering & Built Environment

Funding bodyUniversity of Newcastle - Faculty of Engineering & Built Environment
Project TeamDoctor Nasimul Noman
SchemeTravel Grant
RoleLead
Funding Start2014
Funding Finish2015
GNoG1400795
Type Of FundingInternal
CategoryINTE
UONY
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Research Supervision

Current Supervision

CommencedResearch Title / Program / Supervisor Type
2014Feature Selection and Metaheuristic-based Aggregation of Recommender Systems for Image Processing Using Crowd-sourced Information and Their Potential Applications in Digital Pathology and Information-based Medicine
Computer Science, Faculty of Engineering and Built Environment
Co-Supervisor
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Dr Nasimul Noman

Position

Lecturer
School of Elect Engineering and Computer Science
Faculty of Engineering and Built Environment

Contact Details

Emailnasimul.noman@newcastle.edu.au
Phone(02) 4921 6867

Office

RoomES228
LocationCallaghan
University Drive
Callaghan, NSW 2308
Australia
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