Dr. Intikhab Alam

Research Associate,
School of Computer Science,
The University of Manchester,
Kilburn Building, Oxford Road,
M13 9PL Manchester, UK

E:ialamATcs.man.ac.uk

Current Research:
I 've been working as a Research Associate at The Information Management Group, The school of Computer Science at The University of Manchester. We are a team working on a project called e-fungi; an e-resource for comparative genomics of fungi. My research interests are Sequence Analyses, Comparative Genomics and Comparative Functional Genomics.

PhD Research:
During my PhD research work, I have been working on Integrative Approaches to Protein Homology Search under the supervision of Dr. Georg Fuellen and Prof. Andreas Dress at The NRW International Graduate School in Bioinformatics and Genome Research, The University of Bielefeld, Germany. During my this work I have been developing bioinformatics software applications like CHASE (Alam et, al., 2004, published in PNAS : pdf), which combines homology search methods searching proteins in protein databases and GenCHASE (Alam et, al., 2004b), which combines methods searching proteins in genomes. We presented CHASE in ECCB 2002, RECOMB 2003 (GIF) and GenCHASE in ISMB-ECCB 2004 (GIF), as posters.

CHASE (Comparative Homology Agreement Search) software is now available on request. GenCHASE (Genomic Comparative Homology Agreement SEarch) is currently under testing phase.

Publications

Published:
Alam I et.al. (2008) avaBLAST: a fast way of doing all versus all blast. CIBEC 2008 [view online ]

Soans DM and Alam I et.al., (2008) Comparative genomic analysis of plant pathogenic and saprophytic fungi reveals gene families that are potentially important for fungal pathogenesis. PLOS ONE 3(6): e2300 [view online ]

Hedeler C and Alam I et.al., (2007). e-Fungi: A Data Resource for Comparative Analysis of Fungal Genomes. BMC Genomics 2007, 8:426 [view online ]

Cornell M and Alam I et.al. (2007) Comparative genome analysis across a kingdom of eukaryotic organisms: specialization and diversification i n the Fungi. Genome Research [view online ]

Alam I et.al., (2007) A Methodology for Comparative Functional Genomics. Journal of Integrative Bioinformatics, 4(3):69, 2007. [view online ]

Alam I, Hubbard SJ, Oliver SG, Rattray M (2007). A kingdom-specific protein domain HMM library for improved annotation of fungal genomes. BMC Genomics. 2007 Apr 10;8:97. [view online ]

Shahid M, Alam I, Fuellen G (2006). Biotool2Web: creating simple Web interfaces for bioinformatics applications. Appl. Bioinformatics. 2006;5(1):63-6. [view online ]

Enjalbert B, and Alam I et.al., (2006). Role of the Hog1 stress-activated protein kinase in the global transcriptional response to stress in the fungal pathogen Candida albicans. Mol. Biol. Cell. 2006 Feb;17(2):1018-32. [view online ]

Cornell M and Alam I et.al., (2005) e-Fungi: An e-Science Infrastructure for Comparative Functional Genomics in Fungal Species. All Hands Meeting 2005. [view online ]

Alam, I., Dress, A., Rehmsmeier, M., Fuellen, G. (2004). Comparative Homology Agreement SEarch: an effective combination of homology-search methods. Proc. Nat. Acad. Sci. USA. 101 (38) 13814-19. [view online ]

Alam, I., Karim S., Riazzudin S (2000) Natural Variation among Rice Yellow Stem Borer, Scirpophaga Incertulas (Walker) and Rice Leaf folder, Cnaphalocrocis medinalis (Guenee) Populations to Bacillus thuringiensis delta-endotoxins. Pak. J. Biol. Sci. 3(8), 1285-1286, August 2000. [view online ]

Under Review / In Progress
Alam I et.al. (2007) avaBLAST: a fast way of doing all versus all blast. BMC Bioinformatics (under review)
Alam I et.al., (2007). Finding specific protein families in newly sequenced genomes using GenCHASE. (Draft ready).

Posters
Cornell M and Alam I et.al. (2005) e-Fungi: An e-Science Infrastructure for Comparative Functional Genomics in Fungal Species. Intelligent Systems for Molecular Biology ISMB 2005.
Alam I, Lorkowski S and Fuellen, G. (2004). Finding specific protein families in newly sequenced genomes using GenCHASE. Poster presented at ISMB/ECCB 31 July – August 04, 2004, Glasgow UK.
Alam I and Fuellen G. (2003). Consensus Homology Analysis and SEarch (CHASE). Poster presented at The Seventh Annual International Conference on Research in Computational Molecular Biology (RECOMB) 2003.
Alam I, Dress A and Fuellen G. (2002). Towards a Pattern-Based "Composite Homology Analysis and SEarch" (CHASE) Tool. Poster presented at the European Conference on Computational Biology (ECCB) 2002.