Computer Science

Dr Effirul Ramlan

PhD

Contact Details

Lecturer Above The Bar
E: Effirul.Ramlan@universityofgalway.ie

Biography

Dr Effirul Ramlan is a recently appointed Lecturer (Above the Bar) at the school of Computer Science, University of Galway. Previously, he was a Genuity Science (Ireland) Lecturer at UCD School of Medicine, a Lecturer in Data Analytics at Ulster University (2019 - 2021) and a Senior Lecturer at the Department of Artificial Intelligence, University Malaya (2009 - 2019). He earned a PhD in Computer Science from the University of Southampton (2009) for computational and theoretical development of nucleic acid computers as information processors. His research focuses on the development of synthetic nucleic acid devices (DNA/RNA nano-machines) performing molecular level information processing in biological systems. He has over 20 refereed journal papers and book chapters in both the life sciences and computer science journals. He has received research support as PI for projects from various funding institutions over the past decade.

Research Interests

As a scientist in the field of biological computing, my research focuses on developing DNA-RNA nano-machines that perform complex molecular-level information processing in biological systems. Through my work, I have pioneered novel molecular fabrication and programming techniques to create self-organised biomolecular computers. My work explores the potential of unconventional computation models that are strikingly different from conventional silicon-based computation, offering new avenues for future scientific applications (e.g.,amorphous computation for theranostic).

I have also developed a range of computational tools for bioinformatics, with a focus on structural and sequence annotation and analysis. Through the application of these tools, I have been able to explore new insights into the structural and functional characteristics of biomolecules, contributing to the broader scientific understanding of biological systems. I'm also involved in Evolutionary optimisation and bio-inspired algorithms.

Moreover, I have been actively involved in evolutionary optimisation and bio-inspired algorithm, and the adaptation of artificial intelligence approaches (specifically machine learning - i.e., deep learning and reinforcement learning) to facilitate a wide range of research activities in life sciences. By bridging the gap between the world of computer science and life science, my work has the potential to unlock novel insights and discoveries in critical areas such as drug discovery, medical image analysis, and disease diagnosis, among others.

Research Themes:

Biological computing (e.g. DNA/RNA nano-machines and bio-molecular computers),
Bio-inspired optimisation (e.g., evolutionary algorithm and random methods), and
Bioinformatics (e.g., prediction / design tools, post-genomic pipelines and algorithms)

Peer Reviewed Journals

	Year	Publication
	(2021)	'Machine learning in stem cells research: application for biosafety and bioefficacy assessment' Zaman, Wan Safwani Wan Kamarul and Karman, Salmah Bt and Ramlan, Effirul Ikhwan and Tukimin, Siti Nurainie Bt and Ahmad, Mohd Yazed B (2021) 'Machine learning in stem cells research: application for biosafety and bioefficacy assessment'. IEEE Access, 9 :25926-25945 [Details]
	(2021)	'Regulation of Glycine Cleavage and Detoxification by a Highly Conserved Glycine Riboswitch in Burkholderia spp' Munyati-Othman, Noor and Appasamy, Sri D and Damiri, Nadzirah and Emrizal, Reeki and Alipiah, Norfarrah Mohamed and Ramlan, Effirul Ikhwan and Firdaus-Raih, Mohd (2021) 'Regulation of Glycine Cleavage and Detoxification by a Highly Conserved Glycine Riboswitch in Burkholderia spp'. Current Microbiology, 78 (8):2943-2955 [Details]
	(2019)	'The Anglerfish algorithm: a derivation of randomized incremental construction technique for solving the traveling salesman problem' Pook, Mei F and Ramlan, Effirul I (2019) 'The Anglerfish algorithm: a derivation of randomized incremental construction technique for solving the traveling salesman problem'. Evolutionary Intelligence, 12 (1):11-20 [Details]
	(2018)	'PDPSO: the fusion of primal-dual interior point method and particle swarm optimization algorithm' Dada, Emmanuel Gbenga and Ramlan, Effirul Ikhwan (2018) 'PDPSO: the fusion of primal-dual interior point method and particle swarm optimization algorithm'. Malaysian Journal of Computer Science, 31 (1):17-34 [Details]
	(2016)	'An analysis of simple computational strategies to facilitate the design of functional molecular information processors' Lee, Yiling and Roslan, Rozieffa and Azizan, Shariza and Firdaus-Raih, Mohd and Ramlan, Effirul I (2016) 'An analysis of simple computational strategies to facilitate the design of functional molecular information processors'. BMC bioinformatics, 17 (1):1-13 [Details]
	(2016)	'Self-assembly programming of DNA polyominoes' San Ong, Hui and Syafiq-Rahim, Mohd and Kasim, Noor Hayaty Abu and Firdaus-Raih, Mohd and Ramlan, Effirul Ikhwan (2016) 'Self-assembly programming of DNA polyominoes'. Journal of Biotechnology, 236 :141-151 [Details]
	(2016)	'Understanding the limitations of particle swarm algorithm for dynamic optimization tasks: A survey towards the singularity of PSO for swarm robotic applications' Gbenga, Dada Emmanuel and Ramlan, Effirul Ikhwan (2016) 'Understanding the limitations of particle swarm algorithm for dynamic optimization tasks: A survey towards the singularity of PSO for swarm robotic applications'. ACM Computing Surveys (CSUR), 49 (1):1-25 [Details]
	(2015)	'DNA tetrominoes: the construction of DNA nanostructures using self-organised heterogeneous deoxyribonucleic acids shapes' Ong, Hui San and Rahim, Mohd Syafiq and Firdaus-Raih, Mohd and Ramlan, Effirul Ikhwan (2015) 'DNA tetrominoes: the construction of DNA nanostructures using self-organised heterogeneous deoxyribonucleic acids shapes'. Plos one, 10 (8) [Details]
	(2014)	'Eye Corners Detection using HAAR Cascade Classifiers in Controlled Environment' Asi, Salina Mohd and Ismail, Nor Hidayah and Ahmad, Roshahida and Ramlan, EI and Rahman, Zainal Arif Abdul (2014) 'Eye Corners Detection using HAAR Cascade Classifiers in Controlled Environment'. Journal of Engineering and Technology (JET), 5 (1):69-76 [Details]
	(2014)	'Automatic craniofacial anthropometry landmarks detection and measurements for the orbital region' Asi, Salina Mohd and Ismail, Nor Hidayah and Ahmad, Roshahida and Ramlan, Effirul Ikhwan and Rahman, Zainal Arif Abdul (2014) 'Automatic craniofacial anthropometry landmarks detection and measurements for the orbital region'. Procedia Computer Science, 42 :372-377 [Details]
	(2013)	'In-silico design of computational nucleic acids for molecular information processing' Ramlan, Effirul Ikhwan and Zauner, Klaus-Peter (2013) 'In-silico design of computational nucleic acids for molecular information processing'. Journal of Cheminformatics, 5 (1):1-15 [Details]
	(2013)	'Comparative sequence and structure analysis reveals the conservation and diversity of nucleotide positions and their associated tertiary interactions in the riboswitches' Appasamy, Sri D and Ramlan, Effirul Ikhwan and Firdaus-Raih, Mohd (2013) 'Comparative sequence and structure analysis reveals the conservation and diversity of nucleotide positions and their associated tertiary interactions in the riboswitches'. PLoS One, 8 (9) [Details]
	(2011)	'Design of interacting multi-stable nucleic acids for molecular information processing' Ramlan, Effirul I and Zauner, Klaus-Peter (2011) 'Design of interacting multi-stable nucleic acids for molecular information processing'. Biosystems, 105 (1):14-24 [Details]
	(2007)	'Nucleic acid enzymes: the fusion of self-assembly and conformational computing' Ramlan, Effirul I and Zauner, Klaus-Peter (2007) 'Nucleic acid enzymes: the fusion of self-assembly and conformational computing'. Unconventional Computing 2007, :68-94 [Details]

Book Chapters

	Year	Publication
	(2018)	'Engineering of Supramolecular RNA Structures' Ramlan, E and Firdaus-Raih, Mohd (2018) 'Engineering of Supramolecular RNA Structures' In: :535-545 Elsevier. [Details]

Conference Publications

	Year	Publication
	(2022)	*International Conference on Soft Computing \& Machine Intelligence* Ahmed, Salman and Singh, Muskaan and Doherty, Brendan and Ramlan, Effirul and Harkin, Kathryn and Coyle, Damien (2022) AI for Information Technology Operation (AIOps): A review of IT Incident Risk Prediction International Conference on Soft Computing \& Machine Intelligence [Details]
	(2022)	*ISCMI 2022 conference proceedings* Ahmed, Salman and Singh, Muskaan and Doherty, Brendan and Ramlan, Effirul Ikhwan and Harkin, Kathryn and Coyle, Damien (2022) Multiple Severity-Level classifications for IT Incident Risk Prediction ISCMI 2022 conference proceedings [Details]
	(2015)	*AIP Conference Proceedings* Munyati-Othman, Noor and Fatah, Ahmad Luqman Abdul and Piji, Mohd Al Akmarul Fizree Bin Md and Ramlan, Effirul Ikhwan and Raih, Mohd Firdaus (2015) Identification and cloning of four riboswitches from Burkholderia pseudomallei strain K96243 AIP Conference Proceedings [Details]
	(2015)	*3rd Int'l Conference on Advances in Engineering Sciences \& Applied Mathematics (ICAESAMâ€™2015), London (UK)* Dada, Emmanuel Gbenga and Ramlan, Effirul Ikhwan (2015) Primal-dual interior point method particle swarm optimization (pdipmPSO) algorithm 3rd Int'l Conference on Advances in Engineering Sciences \& Applied Mathematics (ICAESAMâ€™2015), London (UK) , pp.117-124 [Details]
	(2015)	*2015 Second International Conference on Computing Technology and Information Management (ICCTIM)* Dada, Emmanuel Gbenga and Ramlan, Effirul Ikhwan (2015) A hybrid primal-dual-PSO (pdipmPSO) algorithm for swarm robotics flocking strategy 2015 Second International Conference on Computing Technology and Information Management (ICCTIM) , pp.93-98 [Details]
	(2003)	*Proceedings. National Power Engineering Conference, 2003. PECon 2003* Rahimullah, BN Sheikh and Ramlan, EI and Rahman, TK Abdul (2003) Evolutionary approach for solving economic dispatch in power system Proceedings. National Power Engineering Conference, 2003. PECon 2003 , pp.32-36 [Details]

Employment

Employer	Position	From / To
Malaysia Genome Institute (MGI)	Director of Research	01-MAR-17 / 31-MAR-19
University College Dublin	Genuity Science (Ireland) Lecturer (Genomics Data Science)	01-APR-21 / 31-OCT-22
Ulster University	Lecturer in Data Analytics	01-MAY-19 / 31-MAR-21
Universiti Malaya	Senior Lecturer (Artificial Intelligence)	01-NOV-05 / 30-APR-19