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School of Biosciences & Biotechnology,
Faculty of Science & Technology,
Universiti Kebangsaan Malaysia,
43600 UKM Bangi

Tel: +6 03 89215961
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Faculty of Science & Technology
Centre for Postgraduate Studies
Universiti Kebangsaan Malaysia




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[Peer Reviewed Articles] [Listings/Genome Announcements/Abstracts]
[Feature articles/Op-Eds] [Books / Book Chapters]

Peer-reviewed Journal Articles
  See Google Scholar for latest publications list
Sri Devan Appasamy, Hazrina Yusof Hamdani, Effirul Ikhwan Ramlan, Mohd Firdaus-Raih. 2016. InterRNA: a database of base interactions in RNA structures. Nucleic Acids Research, Vol. 44. doi: 10.1093/nar/gkv1186. HTML PDF


Faridah Hani Mohamed Salleh, Shereena Mohd Arif, Suhaila Zainuddin, Mohd Firdaus-Raih. 2015. Reconstructing Gene Regulatory Networks from Knock-Out Data Using Gaussian Noise Model and Pearson Correlation Coefficient. Computational Biology and Chemistry.


Laziana Ahmad, Teng Loong Hung, Nor Azurah Mat Akhir, Rahmah Mohamed, Sheila Nathan and Mohd Firdaus-Raih. 2015. Characterization of Burkholderia pseudomallei protein BPSL1375 validates the putative hemolytic activity of the COG3176 N-Acyltransferase family. BMC Microbiology, 15:270. doi:10.1186/s12866-015-0604-4. HTML PDF

Hui San Ong, Mohd Syafiq Rahim, Mohd Firdaus-Raih, Effirul Ikhwan Ramlan. 2015. DNA Tetrominoes: The construction of DNA nanostructures using self-organised heterogeneous deoxyribonucleic acids shapes. PLOS ONE, 10(8): e0134520. doi:10.1371/journal.pone.0134520. HTML PDF


Sofiyah Shaibullah, Nurhikmah Mohd-Sharif, Kok-Lian Ho, Mohd Firdaus-Raih,  Sheila Nathan,  Rahmah Mohamed and  Chyan Leong Ng. 2014. Crystallization and preliminary crystallographic studies of the hypothetical protein, BPSL1038, from Burkholderia pseudomallei. Acta Crystallographica Section F – Structural Biology Communications. Vol. 70(12) p1697-1700. HTML PDF


Hui-Yeng Y Yap, Yit-Heng Chooi, Mohd Firdaus-Raih, Shin-Yee Fung, Szu-Ting Ng, Chon-Seng Tan, Nget-Hong Tan. 2014. The genome of the Tiger Milk mushroom, Lignosus rhinocerotis, provides insights into the genetic basis of its medicinal properties. BMC Genomics, 15: 635. doi:10.1186/1471-2164-15-635. HTML PDF


Yusuf Muhammad Noor, Nurul Hidayah Samsulrizal, Noor Azah Jema'on, Kheng Oon Low, Aizi Nor Mazila Ramli, Noor Izawati Alias, Siti Intan Rosdianah Damis, Siti Fatimah Zaharah Mohd Fuzi, Mohd Noor Mat Isa, Abdul Munir Abdul Murad, Mohd Firdaus Mohd Raih, Farah Diba Abu Bakar, Nazalan Najimudin, Nor Muhammad Mahadi, Rosli Md. Illias. 2014. A comparative genomic analysis of the alkalitolerant soil bacterium Bacillus lehensis G1. Gene, 545 (2): 253–261. HTML PDF


Mohd Firdaus-Raih, Hazrina Yusof Hamdani, Nurul Nadzirin, Effirul Ikhwan Ramlan, Peter Willett, Peter J. Artymiuk. 2014. COGNAC: a webserver for searching and annotating hydrogen bonded base interactions in RNA 3-dimensional structures. Nucleic Acids Research, Vol. 42. doi: 10.1093/nar/gku438. HTML PDF


Sri Devan Appasamy, Effirul Ikhwan Ramlan, Mohd Firdaus-Raih. 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): e73984. doi:10.1371/journal.pone.0073984. HTML PDF

Nurul Nadzirin, Peter Willett, Peter J. Artymiuk, Mohd Firdaus-Raih. 2013. IMAAAGINE: a webserver for the searching of hypothetical 3D amino acid side chain arrangements in the Protein Data Bank. Nucleic Acids Research, Vol. 41: W432-W440. doi: 10.1093/nar/gkt431. HTML PDF

Jia Shiun Khoo, Shiao-Fei Chai, Rahmah Mohamed, Sheila Nathan, Mohd Firdaus-Raih. 2012. Computational discovery and RT-PCR validation of novel Burkholderia conserved and Burkholderia pseudomallei unique sRNAs. BMC Genomics, 13(S7), S13. doi:10.1186/1471-2164-13-S7-S13  HTML PDF


Nurul Nadzirin, Mohd Firdaus-Raih. 2012. Proteins of Unknown Function in the Protein Data Bank (PDB): An Inventory of True Uncharacterized Proteins and Computational Tools for Their Analysis. Int. J. Mol. Sci. 13, no. 10: 12761-12772. doi:10.3390/ijms131012761. HTML PDF

Hui San Ong, Rahmah Mohamed, Mohd Firdaus-Raih. 2012. Comparative genome sequence analysis reveals the extent of diversity and conservation for glycan associated proteins in Burkholderia spp. Comparative and Functional Genomics, Vol. 2012, Article 752867 doi:10.1155/2012/752867. HTML PDF


Hazrina Yusof Hamdani, Sri Devan Appasamy, Peter Willett, Peter J. Artymiuk, Mohd Firdaus-Raih. 2012. NASSAM: a server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules. Nucleic Acids Research, Vol. 40, W35-W41. doi: 10.1093/nar/gks513.  HTML PDF 

Nurul Nadzirin, Eleanor Gardiner, Peter Willett, Peter J. Artymiuk, Mohd Firdaus-Raih. 2012. SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures. Nucleic Acids Research, Vol. 40, W380-W386doi: 10.1093/nar/gks401. HTML PDF.

Mohd Firdaus-Raih, Anne-Marie Harrison, Peter Willett, Peter J. Artymiuk. 2011. Novel base triples in RNA structures revealed by graph theoretical searching methods. BMC Bioinformatics, 12(Suppl 13). doi:10.1186/1471-2105-12-S13-S2. HTML PDF

Abimael Cruz-Migoni, Guillaume M. Hautbergue, Peter J. Artymiuk, Patrick J. Baker, Monika Bokori-Brown, Chung-Te Chang, Mark J. Dickman, Angela Essex-Lopresti, Sarah V. Harding, Nor Muhammad Mahadi, Laura E. Marshall, George W. Mobbs, Rahmah Mohamed, Sheila Nathan, Sarah A. Ngugi, Catherine Ong, Wen Fong Ooi, Lynda J. Partridge, Helen L. Phillips, M. Firdaus Raih, Sergei Ruzhenikov, Mitali Sarkar-Tyson, Svetlana E. Sedelnikova, Sophie J. Smither, Patrick Tan, Richard W. Titball, Stuart A. Wilson, David W. Rice. 2011. A Burkholderia pseudomallei toxin inhibits helicase activity of translation factor eIF4A. Science, 334 (6057): 821-824. doi: 10.1126/science.1211915. HTML PDF

Mohd Firdaus Raih. 2008. Computational approaches for investigating RNA three-dimensional structures. M. J. Bioch. and Mol. Biol., 16 (2).

Mohd Firdaus Raih, Mohd Yunus Sharum, Ahmad Fuad Hilmi Muhammad, Hafiza Aida Ahmad, Raja Murzaferi Raja Moktar, Mohd Noor Mat Isa, Nor Muhammad Mahadi, Rahmah Mohamed. 2007. Bioinformatics Tools @ NBBnet: online infrastructure for the management and analysis of biological data. Journal of Information Technology and Multimedia.

Mohd Firdaus Raih, Hafiza Aida Ahmad, Mohd Yunus Sharum, Norazah Azizi, Rahmah Mohamed. 2005. ProLysED: An integrated database and metaserver of bacterial protease systems. Applied Bioinformatics, 4 (2):147-150.

Mohd Firdaus Raih, Shandar Ahmad, Rong Zheng, Rahmah Mohamed. 2005. Solvent accessibility in native and isolated domain environments: General features and prediction of unsaturated bonds in a protein sequence. Biophysical Chemistry, 114: 63-69.

Mohd Firdaus Raih, Sahidan Senafi, Abdul Munir Murad et al. 2005. A Nationwide Biotechnology Outreach and Awareness Program for Malaysian High Schools. Electronic Journal of Biotechnology, Vol. 8 (1) April 15 2005.

Mohd Firdaus Raih, Mohd Noor Mat Isa, Ng Lip Kian, Nor Muhammad Mahadi and Rahmah Mohamed. 2005. EMASGRID – A NBBnet Grid Initiative For Bioinformatics And Computational Biology Services Infrastructure In Malaysia. Lecture Notes in Computer Science, 3370, pp117-124.

Mohd Firdaus Mohd Raih, A.T. Sailan, Z. Zamrod, M.N.Embi, Rahmah Mohamed. 2003. Predicted structure of the cytochrome C oxidase from B. pseudomallei. Electronic Journal of Biotechnology, Vol.6, Issue 1, April 15.

Mohd Firdaus Raih, Mohd Noor Mat Isa, Sharr Azni Harmin, Nor Muhammad Mahadi, Latif Ibrahim, Rahmah Mohamed. 2003. NBBnet – The National Biotechnology and Bioinformatics Network: A Malaysian Initiative Towards a National Infrastructure for Bioinformatics. Electronic Journal of Biotechnology. April 15 2003.

Feature Articles / Op-Eds
  Worthy aspirations for the Nobels - New Straits Times
Boosting role of precision medicine in Malaysia - New Straits Times
Books / Book Chapters
  The Doctor is Sick
Listings / Genome Announcements / Indexed Proceedings
  See Google Scholar for a complete and updated list


Last updated: September 2012