Assistant Professor of Medicine
University of Colorado School of Medicine
Anschutz Medical Campus
IIT-Kharagpur, India (2005); PhD: University of Cambridge, UK (2005-08); Junior Research Fellow: University of Cambridge, UK (2008-10); Postdoctoral training: Harvard University, USA (2010-12)Research areas
• Computational biology and bioinformatics
• Cancer genomics and epigenomics
The goal of our laboratory is to understand the molecular basis of genetic and epigenetic abnormalities in different cancer types, and use that knowledge to improve personalized cancer diagnostics. Analyzing genomic amplifications and deletions from nearly three thousand cancer samples, we have recently reported that data on spatial proximity of regions replicating at the same time can be used to predict the mutational landscapes of cancer genomes (De & Michor. Nature Biotech. 2011). We also found that abnormal hypomethylation near G4s-rich regions is a common signature for many SCNA breakpoint hotspots. We propose a mechanistic hypothesis that abnormal hypomethylation in genomic regions enriched for G4s acts as a mutagenic factor driving tissue-specific mutational landscapes in cancer (De & Michor. Nature Struct Mol Biol. 2011).
We are applying a variety of genomics, bioinformatics and biostatistical approaches, and working in close collaboration with bench scientists, clinicians and biostatisticians to address scientific questions in related areas.Selected awards
2012 NCI Physical Sciences Oncology Center (PSOC) Young Investigator Award. Grant co-PI.
2011 NCI PSOC Young Investigator Award. Grant PI (2011-2012).
2010 Human Frontier Science Foundation Long-term Fellowship (2010-2013).
2008 Junior Research Fellowship, King's College, Cambridge (2008-2012).
2005 LMB Cambridge scholarship from Cambridge Commonwealth Trust.
2000 Qualified to appear in Indian National Physics Olympiad (INPhO’2000).
2000 Qualified to appear in Indian National Chemistry Olympiad (INChO’2000).
1999 Qualified to appear in Indian National Mathematics Olympiad (INMO’1999).
1998 National Talent Search (NTS) Scholarship. Publications
24. Levy ED, De S, Teichmann SA. Cellular crowding imposes global constraints on the chemistry and evolution of proteomes. Proc Natl Acad Sci U S A. (in press).
23. De S, Shaknovich R, Riester M, Elemento O, Geng H, Kormaksson M et al. Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity. PLoS Genetics (in press).
22. Antolin MF, Jenkins KP, Bergstrom CT, Crespi BJ, De S, Hancock A et al. Evolution and medicine in undergraduate education: a prescription for all biology students. Evolution. 2012 Jun;66(6):1991-2006. PMID: 22671563
21. Martins FC, De S, Almendro V, Gönen M, Park SY, Blum JL et al. Evolutionary pathways in BRCA1-associated breast tumors. Cancer Discovery. 2012 Jun; 2(6):503-11. PMID: 22628410.
20. Podlaha O, Riester M, De S, Michor F. Evolution of the cancer genome. Trends in Genetics. 2012 Apr;28(4):155-63. PMID: 22342180
19: De S, Michor F. DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes. Nature Biotechnology. 2011. Nov 20;29(12):1103-8. PMID: 22101487
18: De S, Michor F. DNA secondary structures and epigenetic determinants of cancer genome evolution.Nature Structural and Molecular Biology. 2011 Jul 3;18(8):950-5. PMID: 21725294.
17: Shaknovich R, Cerchietti L, Tsikitas L, Kormaksson M, De S, Figueroa ME et al. DNA methyltransferase 1 and DNA methylation patterning contribute to germinal center B-cell differentiation. Blood. 2011 Sep 29;118(13):3559-69. PMID: 21828137.
16: De S. Somatic mosaicism in healthy human tissues. Trends in Genetics. 2011 Jun;27(6):217-23. PMID: 21496937.
15: Weber KP, De S, Kozarewa I, Turner DJ, Babu MM, de Bono M. Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans. PLoS One. 2010 Nov 11;5(11):e13922. PMID: 21085631.
14: De S, Babu MM. A time-invariant principle of genome evolution. Proc Natl Acad Sci U S A. 2010 Jul 20;107(29):13004-9. PMID: 20615949
13: De S, Babu MM. Genomic neighbourhood and the regulation of gene expression. Curr Opin Cell Biol. 2010 Jun;22(3):326-33. PMID: 20493676.
12: Lister A, Charoensawan V, De S, James K, Janga SC, Huppert J. Interfacing systems biology and synthetic biology. Genome Biol. 2009;10(6):309. PMID: 19591648.
11: De S. A biologist looks at the effect of a dynamic nuclear environment on gene expression. Nature. 2009 Jul 2;460(7251):15. PMID: 19571840.
10: De S, Teichmann SA, Babu MM. The impact of genomic neighborhood on the evolution of human and chimpanzee transcriptome. Genome Res. 2009 May;19(5):785-94. PMID: 19233772.
9: Watkins NA, Gusnanto A, de Bono B, De S, Miranda-Saavedra D et al; Bloodomics Consortium. A HaemAtlas: characterizing gene expression in differentiated human blood cells. Blood. 2009 May 7;113(19):e1-9. PMID: 19228925.
8: Miranda-Saavedra D, De S, Trotter MW, Teichmann SA, Göttgens B. BloodExpress: a database of gene expression in mouse haematopoiesis. Nucleic Acids Res. 2009 Jan;37(Database issue):D873-9. PMID: 18987008.
7: De S, Lopez-Bigas N, Teichmann SA. Patterns of evolutionary constraints on genes in humans. BMC Evol Biol. 2008 Oct 7;8:275. PMID: 18840274.
6: Loos RJ et al. Common variants near MC4R are associated with fat mass, weight and risk of obesity.Nature Genetics. 2008 Jun;40(6):768-75. PMID: 18454148.
5: Lopez-Bigas N, De S, Teichmann SA. Functional protein divergence in the evolution of Homo sapiens.Genome Biol. 2008;9(2):R33. PMID: 18279504.
4: Kindt KS, Quast KB, Giles AC, De S, Hendrey D, Nicastro I, Rankin CH, Schafer WR. Dopamine mediates context-dependent modulation of sensory plasticity in C. elegans. Neuron. 2007 Aug 16;55(4):662-76. PMID: 17698017.
3: De S, Pal D, Ghosh SK. Entamoeba histolytica: computational identification of putative microRNA candidates. Exp Parasitol. 2006 Aug;113(4):239-43. PMID: 16515787.
2: De S, Krishnadev O, Srinivasan N, Rekha N. Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different. BMC Struct Biol. 2005 Aug 16;5:15. PMID: 16105176.
1: De S, Sur K, Dasgupta S. Characterization of the nonregular regions of proteins by a contortion index. Biopolymers. 2005 Oct 5;79(2):63-73. PMID: 15962279.