… to start my own lab as an assistant professor at the Department of Medicine, University of Colorado Medical School in the fall of 2012. Our goal will be to to understand the molecular basis of genetic and epigenetic abnormalities in different cancer types, and use that knowledge to improve personalized cancer diagnostics.  We will use a variety of genomics, bioinformatics and biostatistical approaches, while working in close collaboration with bench scientists, clinicians and biostatisticians.

We will have positions for wet and dry lab postdocs and a lab technician for very motivated individuals with relavant background and training. Please feel free to write to me if you are interested. For more details see here.

2010-2012: HSPH Fellow, Dana Farber Cancer Institute and Harvard School of Public Health
2008-2010: Junior Research Fellow, King’s College, University of Cambridge, UK
2005-2008: PhD, MRC Laboratory of Molecular Biology, University of Cambridge, UK
2000-2005: BTech and MTech (Dual degree). IIT-Kharagpur, India

As a Human Frontier Science Program postdoctoral fellow at the Dana Farber Cancer Institute and Harvard School of Public Health, my research goal was to understand the role of genomic sequence context and nuclear organization in shaping the mutation landscape of cancer genomes. I have used computational and statistical techniques, and collaborated closely with bench scientists, clinician scientists and biostatisticians.

Previously, during my PhD dissertation I have worked on patterns of evolutionary constraints on genes during human evolution i.e. speciation and population differentiation. Then, as a Fellow of King’s College, I have worked on the time invariant principles of genome evolution i.e. those molecular mechanisms that operate on both the germ cell (e.g. over millions of years) and somatic cell lineages (e.g. a few years, during cancer progression).

Besides research, I’m interested in science writing for a broad audience. Some of my science articles written for the BlueSci, the Biologist, and the Biochemist would be available from the archives of respectives magazines.

2012   NCI Physical Sciences Oncology Center (PSOC) Young Investigator Award. Grant co-PI (2012-2013).
2011   NCI PSOC Young Investigator Award. Grant PI (2011-2012).
2010   Stellar abstract. PQG conference. Boston, USA.
2010   Human Frontier Science Foundation Long-term Fellowship (2010-2013).
2008   Junior Research Fellowship, King’s College, Cambridge (2008-2012). Currently on leave.
2007   First prize in the annual nationwide essay competition for conveying science to the broad
audience, organized by the Genetics Society, UK.
2007   Selected among 100 individuals from all over Europe to participate in ‘Roche continents- Youth!
Arts! Science’ at the Salzburg Festival.
2007   First prize for accessing commercial potential of a technological invention at the Tech Venture           2007 as a part of i-Team run by Cambridge University Technology & Enterprise Club.
2005   LMB Cambridge scholarship from Cambridge Commonwealth Trust.
2003   J.C.Ghosh Memorial Award for ranking first the class in Dept. of Biotechnology, IIT-Kharagpur.
2003   JNCASR Summer Research Fellowship.
2000   Qualified to appear in Indian National Physics Olympiad (INPhO’2000) through a regional level
examination. Adjudged to be in top 1% among ~20,000 students that appeared for the test and
was awarded a Certificate of Merit.
2000   Qualified to appear in Indian National Chemistry Olympiad (INChO’2000) through a regional level
examination. Adjudged to be in top 1% among ~20,000 students that appeared for the test and
was awarded a Certificate of Merit.
1999   Ranked 18 in Regional Mathematical Olympiad and represented our state, West Bengal in Indian           National Mathematical Olympiad (INMO’99). Also awarded certificate of merit.
1998   National Talent Search (NTS) Scholarship.
1998   Received certificate of merit for ranking 15th at the state-level in X-th standard board           examination.
1998   Selected as the best outgoing student of the class of 1998 in R.K. Mission Ashram High School.

21. Martins FC, De S, Almendro V et al. Evolutionary pathways in BRCA1-associated breast tumors. Cancer Discovery. 2012. 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, Ballon G, Yang SN, Weinhold N, Reimers M, Clozel T, Luttrop K, Ekstrom TJ, Frank J, Vasanthakumar A, Godley LA, Michor F, Elemento O, Melnick A. 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 (cover story for the June issue)

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. Journal club. 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. Epub 2008 Nov 4. 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.