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Faculty Detail    
Name MALAY KUMAR BASU
 
Campus Address WP P220 Zip 7331
Phone 205-934-5251
E-mail malay@uab.edu
Other websites http://www.malaybasu.org
http://cmb.path.uab.edu
     


Faculty Appointment(s)
Appointment Type Department Division Rank
Primary  Pathology   Pathology Informatics Assistant Professor
Secondary  Clinical & Diagnostic Sci   Biotechnology Program Assistant Professor
Center  Comprehensive Cancer Center  Comprehensive Cancer Center Assistant Professor

Graduate Biomedical Sciences Affiliations
Biochemistry and Structural Biology 
Cancer Biology 
Cell, Molecular, & Developmental Biology 
Genetics and Genomic Sciences 
Microbiology 
Pathobiology and Molecular Medicine 

Biographical Sketch 
Dr. Basu received his Ph.D. degree in Life Sciences from the Center for Cellular and Molecular Biology (CCMB), Hyderabad, India. He received his Master of Science (M.Sc.) Degree in Zoology with specialization in Cytology and Genetics from the University of Calcutta, Kolkata, India, and Master of Technology (M. Tech.) Degree in Biotechnology from Jadavpur University, Kolkata, India.

Dr. Basu finished his Postdoctoral training in the lab of Dr. Eugene Koonin at the National Center for Biotechnology Information (NCBI), National Institutes of Health (NIH) in Bethesda, Maryland. Before joining UAB, Dr. Basu was an Assistant Professor at the J. Craig Venter Institute in Rockville, Maryland.

Society Memberships
Organization Name Position Held Org Link
International Society for Computational Biology    http://www.iscb.org/ 

Research/Clinical Interest
Title
Computational Genomics and Bioinformatics
Description
Dr. Basu's research interests involve various aspects of Computational Genomics and Bioinformatics. Currently, he is investigating the role of genome architecture in evolution of various eukaryotic features, such as the origin of multicellularity and cancer. His other interests include writing software for large-scale genome analysis.

Selected Publications 
Publication PUBMEDID
Haft D.H., Selengut J.D., Richter R.A., Harkins D., Basu M.K., and Beck E. TIGRFAMS and Genome Properties in 2013. Nucleic Acids Res, 41(Database issue):D387-95. doi: 10.1093/nar/gks1234, 2013.   23197656 
Basu M. K., Selengut J. D., and Haft D. H. ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process. BMC Bioinform, 12(1):434, 2011.   22070167 
Haft D. H. and Basu M. K. Biological systems discovery in silico: radical S- adenosylmethionine protein families and their target peptides for posttranslational modification. J. Bacteriol., 193(11):2745–2755, 2011.   21478363 
Colbourne J. K., Pfrender M. E., Gilbert D., Thomas W. K, Tucker A., Oakley T. H., Tokishita S., Aerts A., Arnold G. J., Basu M. K., Bauer D. J., Cáceres C. E., Carmel L., Casola C., Choi J., Detter J. C., Dong Q., Dusheyko S., Eads B. D., Fröhlich T., Geiler-Samerotte K. A., Gerlach D., Hatcher P., Jogdeo S., Krijgsveld J., Kriventseva E. V., Kültz D., Laforsch C., Lindquist E., Lopez J., Manak J. R., Muller J., Pangilinan J., Patwardhan R. P., Pitluck S., Pritham E. J., Rechtsteiner A., Rho M., Rogozin I. B., Sakarya O., Salamov A., Schaack S., Shapiro H., Shiga Y., Skalitzky C., Smith Z., Souvorov A., Sung W., Tang Z., Tsuchiya D., Tu H., Vos H., Wang M., Wolf Y. I., Yamagata H., Yamada T., Ye Y., Shaw J. R., Andrews J., Crease T. J., Tang H., Lucas S. M., Robertson H. M., Bork P., Koonin E. V., Zdobnov E. M., Grigoriev I. V., Lynch M., and Boore J. L. The ecoresponsive genome of Daphnia pulex. Science, 331(6017):555–561, 2011.  21292972  
Haft D. H., Basu M. K., and Mitchell D. A. Expansion of ribosomally produced natural products: a nitrile hydrates’ and nif11-related precursor family. BMC Biology, 8:70, 2010.   20500830 
Rogozin I. B., Basu, M. K., Csürös M., and Koonin E. V. Analysis of rare genomic changes does not support the unikont-bikont phylogeny and suggests cyanobacterial symbiosis as the point of primary radiation of eukaryotes. Genome Biol Evol, 2009(0):99–113, 2009.   20333181 
Basu M. K., Poliakov E., and Rogozin I. B. Domain mobility in proteins: functional and evolutionary implications. Brief Bioinform., 10(3):205–16, 2009.   19151098 
Basu M. K., Rogozin I. B., and Koonin E. V. Primordial spliceosomal introns were probably U2-type. Trends Genet, 24(11):525–8, 2008.   18824272 
Basu M. K., Makalowski W., Rogozin I. B., and Koonin E. V. U12 intron positions are more strongly conserved between animals and plants than U2 intron positions. Biol Direct, 3(1):19, 2008.   18479526 
Basu M. K., Carmel L., Rogozin I. B., and Koonin E. V. Evolution of protein domain promiscuity in eukaryotes. Genome Res., 18(3):449–61, 2008.   18230802 
Basu M. K., Rogozin I. B., Deusch O., Dagan T., Martin W., and Koonin E. V. Evolutionary dynamics of introns in plastid-derived genes in plants: saturation nearly reached but slow intron gain continues. Mol Biol Evol, 25:111–9, 2008.   17974547 
Babenko V. N., Basu M. K., Kondrashov F. A., Rogozin I. B., and Koonin E. V. Signs of positive selection of somatic mutations in human cancers detected by EST sequence analysis. BMC cancer, 6:36, 2006.  16469093 
Rogozin I. B., Basu M. K, Jordan I. K., Pavlov Y. I., and Koonin E. V. APOBEC4, a new member of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases predicted by computational analysis. Cell cycle, 4:1281–5, 2005.   16082223 
Basu M. K. and Koonin E. V. Evolution of eukaryotic cysteine sulfinic acid reductase, sulfiredoxin (Srx), from bacterial chromosome partitioning protein ParB. Cell cycle, 4:947–52, 2005.   15917647 
Basu M. K. SeWeR: a customizable and integrated dynamic HTML interface to bioinformatics services. Bioinformatics, 17:577–8, 2001.  11395442 
Ray M. K., Kumar G. S., Janiyani K., Kannan K., Jagtap P., Basu M. K., and Shivaji S. Adaptation to low temperature and regulation of gene expression in Antarctic psychrotrophic bacteria. J Biosci, 23(4):423–35, 1998.   

Keywords
Genomics, bioinformatics, high-performance computing, grid computing, computational biology, evolution