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[Peer Reviewed Articles] [Listings/Genome Announcements/Abstracts]
[Feature articles/Op-Eds] [Books / Book Chapters]
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| Peer-reviewed Journal Articles |
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See latest publications list on Google Scholar.
See latest publications list on ORCID.
The list below stops at 2018 and is no longer updated.
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| 2018 |
Siuk-Mun Ng, Xin-Wei Lee, Mohd-Noor Mat-Isa, Mohd Afiq Aizat-Juhari, Jumaat Haji Adam, Rahmah Mohamed, Kiew-Lian Wan, Mohd Firdaus-Raih*. 2018. Comparative analysis of nucleus-encoded plastid-targeting proteins in Rafflesia cantleyi against photosynthetic and non-photosynthetic representatives reveals orthologous systems with potentially divergent functions. Scientific Reports, 8:17258. doi:10.1038/s41598-018-35173-1
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Izwan Bharudin, Mohd Faizal Abu Bakar, Noor Haza Fazlin Hashim, Mohd Noor Mat Isa, Halimah Alias, Mohd Firdaus-Raih, Rosli Md. Illias, Nazalan Najimudin, Nor Muhammad Mahadi, Farah Diba Abu Bakar, Abdul Munir Abdul Murad. 2018. Unravelling the adaptation strategies employed by Glaciozyma antarctica PI12 on Antarctic sea ice. Marine Environmental Research, doi.org/10.1016/j.marenvres.2018.03.007
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Mohd Firdaus-Raih*, Noor Haza Fazlin Hashim, Izwan Bharudin, Mohd Faizal Abu Bakar, Kie Kyon Huang, Halimah Alias, Bernard K.B. Lee, Mohd Noor Mat Isa, Shuhaila Mat-Sharani, Suhaila Sulaiman, Lih Jinq Tay, Radziah Zolkefli, Yusuf Muhammad Noor, Douglas Sie Nguong Law, Siti Hamidah Abdul Rahman, Rosli Md-Illias, Farah Diba Abu Bakar, Nazalan Najimudin, Abdul Munir Abdul Murad, Nor Muhammad Mahadi. 2018. The Glaciozyma antarctica genome reveals an array of systems that provide sustained responses towards temperature variations in a persistently cold habitat. PLOS ONE, (1): e0189947.
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| 2017 |
Hirzahida Mohd-Padil, Nadzirah Damiri, Suhaila Sulaiman, Shiao-Fei Chai, Sheila Nathan, Mohd Firdaus-Raih*. 2017. Identification of sRNA mediated responses to nutrient depletion in Burkholderia pseudomallei. Scientific Reports, 7: 17173.
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Kuang-Lim Chan, Rozana Rosli, Tatiana V. Tatarinova, Michael Hogan, Mohd Firdaus-Raih, Eng-Ti Leslie Low. 2017. Seqping: gene prediction pipeline for plant genomes using self-training gene models and transcriptomic data. BMC Bioinformatics, 18
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Kuang-Lim Chan, Tatiana V. Tatarinova, Rozana Rosli, Nadzirah Amiruddin, Norazah Azizi,
Mohd Amin Ab Halim, Nik Shazana Nik Mohd Sanusi, Nagappan Jayanthi, Petr Ponomarenko, Martin Triska, Victor Solovyev, Mohd Firdaus-Raih, Ravigadevi Sambanthamurthi, Denis Murphy and Eng-Ti Leslie Low. 2017. Evidence-based gene models for structural and functional annotations of the oil palm genome. Biology Direct. 12:21. 10.1186/s13062-017-0191-4
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| 2016 |
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Xin-Wei Lee, Mohd-Noor Mat-Isa, Nur-Atiqah Mohd-Elias, Mohd Afiq Aizat-Juhari, Hoe-Han Goh, Paul H. Dear, Keng-See Chow, Jumaat Haji Adam, Rahmah Mohamed, Mohd Firdaus-Raih, Kiew-Lian Wan. 2016. Perigone Lobe Transcriptome Analysis Provides Insights into Rafflesia cantleyi Flower Development. PLOS ONE, Vol 11 (12) e0167958.
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Yiling Lee, Rozieffa Roslan, Shariza Azizan, Mohd Firdaus-Raih*, Effirul I. Ramlan. 2016. An analysis of simple computational strategies to facilitate the design of functional molecular information processors. BMC Bioinformatics, Vol 17(1), 438.
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H. San Ong, M. Syafiq-Rahim, N.H.A. Kasim, Mohd Firdaus-Raih, Effirul I. Ramlan. 2016. Self-assembly programming of DNA polyominoes. Journal of Biotechnology, Vol 236, 141-151
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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
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| 2015 |
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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.
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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
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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
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| 2014 |
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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
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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
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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
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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
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| 2013 |
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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
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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
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| 2012 |
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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
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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
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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
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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
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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-W386 . doi: 10.1093/nar/gks401. HTML PDF.
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| 2011 |
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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
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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
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2003-2010
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Mohd Firdaus Raih. 2008. Computational approaches for investigating RNA three-dimensional structures. M. J. Bioch. and Mol. Biol., 16 (2).
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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