SjD Laboratory
Cancer Genomics and Systems Biology  


 Home   Research   Publications   Members   Resources   Contact

Publications

50: Yamamto K et al. (2017) Personalized Management of Pancreatic Ductal Adenocarcinoma Patients Through Computational Modeling. Cancer Research (in press).

49: De S, Ganesan S. (2017) Looking beyond drivers and passengers in cancer genome sequencing data. Annals of Oncology. [Epub ahead of print] PMID: 27998972.

48: Rogozin IB, Lada AG, Goncearenco A, Green MR, De S, Nudelman G, Panchenko AR, Koonin EV, Pavlov YI. (2016) Activation induced deaminase mutational signature overlaps with CpG methylation sites in follicular lymphoma and other cancers. Scientific Reports. 6:38133. PMID: 27924834.

47: Pei S, Minhajuddin M, D'Alessandro A, Nemkov T, Stevens BM, Adane B, Khan N, Hagen FK, Yadav VK, De S, Ashton JM, Hansen KC, Gutman JA, Pollyea DA, Crooks PA, Smith C, Jordan CT. (2016) Rational Design of a Parthenolide-based Drug Regimen that Selectively Eradicates Acute Myelogenous Leukemia Stem Cells. Journal of Biological Chemistry291(48):25280. PMID: 27573247.

46: Yadav VK, Smith KS, Flinders C, Mumenthaler SM, De S. (2016) Significance of duon mutations in cancer genomes. Scientific Reports. 6:27437. PMID: 27272679.

45: Choe K, Nicolae C, Constantin D, Kawasawa Y, Delgado-Diaz R, De S, Freire R, Smits V, and Moldovan GL. (2016) HUWE1 interacts with PCNA to alleviate replication stress. EMBO Reports. 17(6):874-86. PMID: 27146073.

44: Yadav VK, DeGregori J, De S. (2016) The landscape of somatic mutations in protein coding genes in apparently benign human tissues carries signatures of relaxed purifying selection. Nucleic Acids Res. 44(5):2075-84. PMID: 26883632.

43: Poczobutt JM, De S, Yadav VK, Nguyen TT, Li H, Sippel TR, Weiser-Evans MC, Nemenoff RA. (2016) Expression Profiling of Macrophages Reveals Multiple Populations with Distinct Biological Roles in an Immunocompetent Orthotopic Model of Lung Cancer. J Immunol. 196(6):2847-59. PMID: 26873985.

42:  Hintzsche J et al. (2016) IMPACT: Whole-exome sequencing analysis pipeline of integrating molecular profiles with actionable therapeutics in clinical samples Journal of the American Medical Informatics Association. 23(4):721-30. PMID: 27026619.

41: Smith KS, Yadav VK, Pei S, Pollyea DA, Jordan CT, De S. (2016) SomVarIUS: Somatic variant identification from unpaired tissue samples. Bioinformatics. 32(6):808-13. PMID: 26589277.

40: Smith KS, Yadav VK, Pedersen BS, Shaknovich RS, Geraci MW, Pollard KS, De S. (2015) Signatures of accelerated somatic evolution in gene promoters in multiple cancer types. Nucleic Acids Res43(11):5307-17. PMID: 25934800.

39: Selmecki A, Maruvka YE, Richmond PA, Guillet M, Shoresh N, Sorenson A, De S, Kishony R, Michor F, Dowell R, Pellman D. (2015) Polyploidy can drive rapid adaptation in yeast. Nature519(7543):349-52. PMID: 25731168.

38: Yadav VK, De S. (2015) An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples. Briefings in Bioinformatics16(2):232-41. PMID: 24562872

37: Shaknovich R, De S, Michor F. (2014) Epigenetic diversity in hematopoietic neoplasms. (201 BBA - Reviews on Cancer1846(2):477-484. PMID: 25240947.

36: Aghili L, Foo J, DeGregori J, De S. (2014) Patterns of somatically acquired amplifications and deletions in apparently normal human tissues of cancer patients. Cell Reports7(4):1310-9. PMID: 24794429

35: Choi YE, Pan Y, Park E, Konstantinopoulos PA, De S, D'Andrea AD, D Chowdhury (2014) MicroRNAs down-regulate homologous recombination in the G1 phase of cycling cells to maintain genomic stability. eLife3:e02445. PMID: 24843000

34: Nicolae CM, Aho ER, Vlahos AHS, Choe KN, De S, Karras GI, Moldovan G-L. (2014) The ADP-ribosyltransferase PARP10/ARTD10 interacts with Proliferating Cell Nuclear Antigen (PCNA) and is required for DNA damage toleranceJournal of Biological Chemistry289(19):13627-37. PMID: 24695737

34: Podlaha O, De S, Gonen M, Michor F. (2014) Histone modifications are associated  with transcript isoform diversity in normal and cancer cells. PLoS Computational Biology10(6):e1003611. PMID: 24901363

32: Chambwe N, Kormaksson M, Geng H, De S, Michor F, Johnson NA, Morin RD, Scott DW, Godley LA, Gascoyne RD, Melnick AM, Campagne F, Shaknovich R. (2014) Variability in DNA methylation defines novel epigenetic subgroups of DLBCL associated with different clinical outcomes. Blood. 123(11):1699-708. PMID: 24385541

31: Pedersen BS, Yang IV, De S. (2013) CruzDB: software for annotation of genomic intervals with UCSC genome-browser databaseBioinformatics. 29(23):3003-6. PMID: 24037212

30: De S, Pedersen BS, Kechris K. (2013) The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichmentBriefings in Bioinformatics[Epub ahead of print]. PMID: 23956260

29: Pedersen BS, De S. (2013) Loss of heterozygosity preferentially occurs in early replicating regions in cancer genomes. Nucleic Acids Research41(16):7615-24. PMID: 23793816

28: Pedersen BS, Konstantinopoulos PA, Spillman MA, De S. (2013) Copy neutral loss of heterozygosity is more frequent in older ovarian cancer patients. Genes, Chromosomes and Cancer. 52(9):794-801PMID: 23716468.

27:  De S, Ward RM. (2013) Revisiting mutagenesis in the age of high-throughput sequencing. Chapter 13. Stress-Induced Mutagenesis. 284-90. Ed. David Mittelman. Springer Publishing Company. 

26: De S, Shaknovich R, Riester M, Elemento O, Geng H, Kormaksson M et al. (2013) Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity. PLoS Genetics 9(1):e1003137. PMID: 23326238.

25: Liu L, De S, Michor F. (2013) DNA replication timing and higher-order nuclear organization determine single-nucleotide substitution patterns in cancer genomes. Nature Communications 4:1502. PMID: 23422670.

24: Levy ED, De S, Teichmann SA. (2012) Cellular crowding imposes global constraints on the chemistry and evolution of proteomes. Proc Natl Acad Sci U S A. 109(50):20461-6. PMID: 23184996


Before 2012/09

23: Martins F, De S, Almendoro V, Gonen M et al. (2012) Evolutionary Pathways in BRCA1-Associated breast tumors. Cancer Discovery. 2(6):503-11. PMID: 22628410

22: Podlaha O, Riester M, De S, Michor F. (2012) Evolution of the cancer genome. Trends Genet. 27(6):217-23. PMID: 21496937.

21: Antolin MF, Jenkins KP, Bergstrom CT, Crespi BJ, De S, Hancock A et al. (2012) Evolution and medicine in undergraduate education: a prescription for all biology students. Evolution. 66(6):1991-2006. PMID: 22671563

20: De S, Michor F. (2011) DNA secondary structures and epigenetic determinants of cancer genome evolution. Nature Structural and Molecular Biology.18(8):950-5. PMID: 21725294.

19: Shaknovich R, Cerchietti L, Tsikitas L, Kormaksson M, De S, Figueroa ME et al. (2011) DNA methyltransferase 1 and DNA methylation patterning contribute to germinal center B-cell differentiation. Blood. 118(13):3559-69. PMID: 21828137.

18: De S, Michor F. (2011) DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes. Nature Biotechnology. 29(12):1103-8. PMID: 22101487.

17: De S. (2011) Somatic mosaicism in healthy human tissues. Trends Genet.27(6):217-23. PMID: 21496937.

16: De S, Babu MM. (2010) A time-invariant principle of genome evolution. Proc Natl Acad  Sci U S A. 107(29):13004-9. PMID: 20615949.  

15: De S, Babu MM. (2010) Genomic neighbourhood and the regulation of gene expression. Curr Opin Cell Biol. 22(3) :326-33. PMID: 20493676.   

14: Weber K, De S, Kozarewa I, Turner D, Babu MM, de Bono M. (2010) Genetic changes associated with laboratory domestication of the nematode. PLoS One. 5(11):e13922. PMID: 21085631.

13: Lister A, Charoensawan V, De S, James K, Janga SC, Huppert J. (2009) Interfacing systems biology and synthetic biology. Genome Biol. 10(6):309.  PMID: 19591648

12: De S. (2008) Evolution of human genome and transcriptome. PhD Thesis (Univ. Cambridge)

11: De S, Teichmann SA, Babu MM. (2009) The impact of genomic neighborhood on the evolution of human and chimpanzee transcriptome. Genome Res. 19(5):785-94. PMID: 19233772.

10: De S. (2009) The effect of a dynamic nuclear environment on gene expression. Nature. 460(7251):15. PMID: 19571840. 

9: Watkins NA, Gusnanto A, de Bono B, De S, Miranda-Saavedra D et al. (2009) A HaemAtlas: characterizing gene expression in differentiated human blood cells. Blood. 113(19):e1-9. PMID: 19228925. 

8: De S, Lopez-Bigas N, Teichmann SA. (2008) Patterns of evolutionary constraints on genes in humans. BMC Evol Biol. 2008 PMID: 18840274.

7: Miranda-Saavedra D, De S, Trotter MW, Teichmann SA, Göttgens B. (2009) BloodExpress: a database of gene expression in mouse haematopoiesis. Nucleic Acids Res. 37(Database issue):D873-9. PMID: 18987008   

6: Loos RJ et al. (2008) Common variants near MC4R are associated with fat mass, weight and risk of obesity. Nat Genet. 40(6):768-75. PMID: 18454148. (more than 30 authors) 

5: Lopez-Bigas N, De S, Teichmann SA. (2008) Functional protein divergence in the evolution of Homo sapiens. Genome Biol. 9(2):R33. PMID: 18279504. 

4: Kindt KS, Quast KB, Giles AC, De S, Hendrey D, Nicastro I, Rankin CH, Schafer WR. (2007) Dopamine mediates context-dependent modulation of sensory plasticity in C. elegans. Neuron. 55(4):662-76. PMID: 17698017  

3: De S, Pal D, Ghosh SK. (2006) Entamoeba histolytica: computational identification of putative microRNA candidates. Exp Parasitol. 113(4):239-43. PMID: 16515787.  

2: De S, Krishnadev O, Srinivasan N, Rekha N. (2005) Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different. BMC Struct Biol. 5:15. PMID: 16105176.

1: De S, Sur K, Dasgupta S. (2005) Characterization of the nonregular regions of proteins by a contortion index. Biopolymers. 79(2):63-73. PMID: 15962279