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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

Code Description Percentage
060102 Bioinformatics 20
060114 Systems Biology 40
080108 Neural, Evolutionary and Fuzzy Computation 40

Professional Experience

UON Appointment

Title Organisation / Department
Lecturer University of Newcastle
School of Elect Engineering and Computer Science
Australia

Academic appointment

Dates Title Organisation / Department
1/09/2012 - 1/02/2013 Visiting Research Fellow Harvard Medical School
Systems Biology
United States
1/03/2012 - 1/11/2013 Research Fellow The University of Tokyo
School of Information Science and Technology
Japan
1/01/2012 - 1/05/2012 Associate Professor University of Dhaka
Computer Science and Engineering
Bangladesh
1/11/2009 - 1/11/2011 Post Doctoral Researcher The University of Tokyo
School of Engineering
Japan
1/03/2007 - 1/01/2012 Assistant Professor University of Dhaka
Computer Science and Engineering
Bangladesh
1/03/2002 - 1/03/2007 Lecturer University 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)

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

Chapter (2 outputs)

Year Citation Altmetrics Link
2014 Noman 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)
DOI 10.1007/978-3-642-30574-0_22
2007 Noman 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 (14 outputs)

Year Citation Altmetrics Link
2015 Noman N, Monjo T, Moscato P, Iba H, 'Evolving robust gene regulatory networks.', PLoS One, 10 e0116258 (2015)
DOI 10.1371/journal.pone.0116258
Co-authors Pablo Moscato
2015 Peng 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)
DOI 10.1016/j.physa.2015.03.002
2015 Dinh HQ, Aubert N, Noman N, Fujii T, Rondelez Y, Iba H, 'An effective method for evolving reaction networks in synthetic biochemical systems', IEEE Transactions on Evolutionary Computation, 19 374-386 (2015)

In this paper, we introduce our approach for evolving reaction networks. It is an efficient derivative of the neuroevolution of augmenting topologies algorithm directed at the evo... [more]

In this paper, we introduce our approach for evolving reaction networks. It is an efficient derivative of the neuroevolution of augmenting topologies algorithm directed at the evolution of biochemical systems or molecular programs. Our method addresses the problem of meaningful crossovers between two chemical reaction networks of different topologies. It also builds on features such as speciation to speed up the search, to the point where it can deal with complete, realistic mathematical models of the biochemical processes. We demonstrate this framework by evolving credible biochemical answers to challenging autonomous molecular problems: in vitro batch oscillatory networks that match specific oscillation shapes. Our experimental results suggest that the search space is efficiently covered and that, by using crossover and preserving topological innovations, significant improvements in performance can be obtained for the automatic design of molecular programs.

DOI 10.1109/TEVC.2014.2326863
2014 Dinh QH, Noman N, Iba H, 'Oscillatory Synthetic Biological System Construction Using Interactive Evolutionary Computations', Journal of Computer Science, 10 2640-2652 (2014) [C1]
DOI 10.3844/jcssp.2014.2640.2652
2013 Noman N, Palafox L, Iba H, 'Evolving Genetic Networks for Synthetic Biology', NEW GENERATION COMPUTING, 31 71-88 (2013) [C1]
DOI 10.1007/s00354-013-0201-8
Citations Scopus - 2Web of Science - 1
2013 Palafox 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]
DOI 10.1109/TEVC.2012.2218610
Citations Scopus - 2Web of Science - 2
2012 Ibrahim 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)
2011 Azad 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]
DOI 10.1186/1748-7188-6-19
Citations Scopus - 3Web of Science - 2
2011 Noman 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]
DOI 10.1504/IJBIC.2011.043607
Citations Scopus - 6Web of Science - 4
2010 Kabir M, Noman N, Iba H, 'Reverse engineering gene regulatory network from microarray data using linear time-variant model', BMC BIOINFORMATICS, 11 (2010) [C1]
DOI 10.1186/1471-2105-11-S1-S56
Citations Scopus - 29Web of Science - 20
2010 Biswas AK, Noman N, Sikder AR, 'Machine learning approach to predict protein phosphorylation sites by incorporating evolutionary information', BMC BIOINFORMATICS, 11 (2010) [C1]
DOI 10.1186/1471-2105-11-273
Citations Scopus - 19Web of Science - 17
2008 Noman N, Iba H, 'Accelerating differential evolution using an adaptive local search', IEEE TRANSACTIONS ON EVOLUTIONARY COMPUTATION, 12 107-125 (2008) [C2]
DOI 10.1109/TEVC.2007.895272
Citations Scopus - 314Web of Science - 213
2008 Noman N, Iba H, 'Differential evolution for economic load dispatch problems', ELECTRIC POWER SYSTEMS RESEARCH, 78 1322-1331 (2008) [C1]
DOI 10.1016/j.epsr.2007.11.007
Citations Scopus - 155Web of Science - 112
2007 Noman 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)
DOI 10.1109/TCBB.2007.1058
Citations Scopus - 63Web of Science - 52
Show 11 more journal articles

Conference (25 outputs)

Year Citation Altmetrics Link
2013 Palafox 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]
DOI 10.1109/CEC.2013.6557764
Citations Scopus - 1
2013 Hettiarachchi 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]
DOI 10.1109/CEC.2013.6557824
Citations Scopus - 1Web of Science - 1
2012 Komiya 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]
DOI 10.1145/2330784.2330963
Citations Scopus - 2
2012 He 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]
DOI 10.1007/978-3-642-32645-5_26
2012 Noman 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]
DOI 10.1007/978-3-642-32645-5_20
Citations Scopus - 1
2011 Noman 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]
DOI 10.1109/CEC.2011.5949947
Citations Scopus - 1Web of Science - 1
2011 Noman N, Bollegala D, Iba H, 'An adaptive differential evolution algorithm', 2011 IEEE Congress of Evolutionary Computation, CEC 2011, New Orleans, LA (2011) [E1]
DOI 10.1109/CEC.2011.5949891
Citations Scopus - 7Web of Science - 3
2011 Bollegala 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]
DOI 10.1145/2001576.2001814
Citations Scopus - 1Web of Science - 1
2011 Noman N, Bollegala D, Iba H, 'Differential evolution with self adaptive local search', Genetic and Evolutionary Computation Conference, GECCO'11, Dublin, IRELAND (2011) [E1]
DOI 10.1145/2001576.2001725
Citations Scopus - 1
2011 Vatanutanon 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]
DOI 10.1145/2001576.2001734
Citations Scopus - 2
2010 Ibrahim 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]
DOI 10.1109/ICBBE.2010.5518207
2010 Noman 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]
DOI 10.1109/NABIC.2010.5716337
Citations Scopus - 1
2010 Vatanutanon 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]
DOI 10.1109/NABIC.2010.5716313
Citations Scopus - 1
2010 Mondal 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]
DOI 10.1109/ICCITECHN.2010.5723898
Citations Scopus - 1
2010 Hasan 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]
DOI 10.1145/1722024.1722069
2010 Noman 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]
DOI 10.1007/978-3-642-17432-2_30
Citations Scopus - 1Web of Science - 2
2010 Ishiwata 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]
DOI 10.1007/978-3-642-17432-2_37
2006 Noman 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)
2006 Noman 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)
Citations Scopus - 9Web of Science - 8
2006 Noman 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)
Citations Scopus - 14Web of Science - 4
2006 Noman 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 prof... [more]

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.

Citations Scopus - 4
2005 Noman 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)
Citations Scopus - 22Web of Science - 16
2005 Noman 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)
Citations Scopus - 41Web of Science - 37
2005 Noman 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 ... [more]

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.

Citations Scopus - 30
2004 Noman 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)
Show 22 more conferences
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Grants and Funding

Summary

Number of grants 2
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 body University of Newcastle - Faculty of Engineering & Built Environment
Project Team Doctor Nasimul Noman
Scheme New Staff Grant
Role Lead
Funding Start 2014
Funding Finish 2014
GNo G1400989
Type Of Funding Internal
Category INTE
UON Y

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

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

Funding body University of Newcastle - Faculty of Engineering & Built Environment
Project Team Doctor Nasimul Noman
Scheme Travel Grant
Role Lead
Funding Start 2014
Funding Finish 2015
GNo G1400795
Type Of Funding Internal
Category INTE
UON Y
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Research Supervision

Current Supervision

Commenced Research Title / Program / Supervisor Type
2014 Feature 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

Email nasimul.noman@newcastle.edu.au
Phone (02) 4042 0488

Office

Room ES228
Building ES Building
Location Callaghan
University Drive
Callaghan, NSW 2308
Australia
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