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| Biochemistry and Structural Biology |
| Cancer Biology |
| Cell, Molecular, & Developmental Biology |
| Genetics, Genomics and Bioinformatics |
| Microbiology |
| Pathobiology and Molecular Medicine |
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| Publication |
PUBMEDID |
| Yu L, Tanwar DK, Penha EDS, Wolf YI, Koonin EV, Basu MK. Grammar of proteindomain architectures. Proc Natl Acad Sci U S A. 2019 Feb 7. pii: 201814684. doi: 10.1073/pnas.1814684116. [Epub ahead of print] |
30733291 |
| Tanwar DK, Parker DJ, Gupta P, Spurlock B, Alvarez RD, Basu MK, Mitra K. Crosstalk between the mitochondrial fission protein, Drp1, and the cell cycle is identified across various cancer types and can impact survival of epithelial ovarian cancer patients. Oncotarget. 2016 Sep 13;7(37):60021-60037 |
27509055 |
| Tian R, Basu MK, Capriotti E. Computational methods and resources for the interpretation of genomic variants in cancer. BMC Genomics. 2015;16 Suppl 8:S7. doi:10.1186/1471-2164-16-S8-S7. Epub 2015 Jun 18. |
26111056 |
| Tian R, Basu MK, Capriotti E. ContrastRank: a new method for ranking putative cancer driver genes and classification of tumor samples. Bioinformatics. 2014 Sep 1;30(17):i572-8. doi: 10.1093/bioinformatics/btu466. |
25161249 |
| 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. |
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