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Publications

Selected publications 

10: Ghaddar B, Blaser MJ, De S. Denoising sparse microbial signals from single-cell sequencing of mammalian host tissues. Nat Comput Sci. 2023 Sep;3(9):741-747. PMID: 37946872; PMCID: PMC10634611.

9: Ghaddar B, Biswas A, Harris C, Omary MB, Carpizo DR, Blaser MJ, De S. Tumor microbiome links cellular programs and immunity in pancreatic cancer. Cancer Cell. 2022 Oct 10;40(10):1240-1253.e5. PMID: 36220074; PMCID: PMC9556978. Research highlights in Cancer Cell and Science.

8: Ghaddar B, De S. Reconstructing physical cell interaction networks from single-cell data using Neighbor-seq. Nucleic Acids Res. 2022 Aug 12;50(14):e82. PMID: 35536255; PMCID: PMC9371920.

7: Hu X, Biswas A, Sharma A, Sarkodie H, Tran I, Pal I, De S. Mutational signatures associated with exposure to carcinogenic microplastic compounds bisphenol A and styrene oxide. NAR Cancer. 2021 Mar 1;3(1):zcab004. PMID: 33718875; PMCID: PMC7936647.

6: De S. Signatures Beyond Oncogenic Mutations in Cell-Free DNA Sequencing for Non-Invasive, Early Detection of Cancer. Front Genet. 2021 Oct 14;12:759832. PMID: 34721546; PMCID: PMC8551553.

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5: Sharma A, Merritt E, Hu X, Cruz A, Jiang C, Sarkodie H, Zhou Z, Malhotra J, Riedlinger GM, De S. Non-Genetic Intra-Tumor Heterogeneity Is a Major Predictor of Phenotypic Heterogeneity and Ongoing Evolutionary Dynamics in Lung Tumors. Cell Rep. 2019 Nov 19;29(8):2164-2174.e5. PMID: 31747591; PMCID: PMC6952742.

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4: Balaparya A, De S. Revisiting signatures of neutral tumor evolution in the light of complexity of cancer genomic data. Nat Genet. 2018 Dec;50(12):1626-1628. PMID: 30250123; PMCID: PMC6952740.

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3: Smith KS, Liu LL, Ganesan S, Michor F, De S. Nuclear topology modulates the mutational landscapes of cancer genomes. Nat Struct Mol Biol. 2017 Nov;24(11):1000-1006. PMID: 28967881; PMCID: PMC5744871.

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2: De S, Michor F. DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes. Nat Biotechnol. 2011 Nov 20;29(12):1103-8. PMID: 22101487; PMCID: PMC3923360.

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1: De S, Michor F. DNA secondary structures and epigenetic determinants of cancer genome evolution. Nat Struct Mol Biol. 2011 Jul 3;18(8):950-5. PMID: 21725294; PMCID: PMC3963273.

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All publications (Pubmed)

82. Ghaddar B, De S. Hierarchical and automated cell-type annotation and inference of cancer cell of origin with Census. Bioinformatics. 2023 Dec 1;39(12):btad714. PMID: 38011649; PMCID: PMC10713118.

81: Greendyk JD et al. Association between SMAD4 mutations and GATA6 expression in paired pancreatic ductal adenocarcinoma tumor specimens: Data from Two Independent Molecularly-

Characterized Cohorts. Biomedicines. 2023 Nov 15;11(11):3058. PMID: 38002058; PMCID: PMC10669842.

80: Ghaddar B, Blaser MJ, De S. Denoising sparse microbial signals from single-cell sequencing of mammalian host tissues. Nat Comput Sci. 2023 Sep;3(9):741-747. PMID: 37946872; PMCID: PMC10634611.

79: Dudgeon C et al. Netrin-1 feedforward mechanism promotes pancreatic cancer liver metastasis via hepatic stellate cell activation, retinoid, and ELF3 signaling.

Cell Rep. 2023 Nov 28;42(11):113369. PMID: 37922311.

78: Cararo Lopes E et al. Integrated metabolic and genetic analysis reveals distinct features of human differentiated thyroid cancer. Clin Transl Med. 2023 Jun;13(6):e1298. PMID: 37317665; PMCID: PMC10267429.

77: Ghaddar B, Biswas A, Harris C, Omary MB, Carpizo DR, Blaser MJ, De S. Tumor microbiome links cellular programs and immunity in pancreatic cancer. Cancer Cell. 2022 Oct 10;40(10):1240-1253.e5. PMID: 36220074; PMCID: PMC9556978.

76: Biswas A, Ghaddar B, Riedlinger G, De S. Inference on spatial heterogeneity in tumor microenvironment using spatial transcriptomics data. Comput Syst Oncol. 2022 Sep;2(3):e21043. PMID: 36035873; PMCID: PMC9410565.

75: Hu X, Biswas A, De S. KMT2C-deficient tumors have elevated APOBEC mutagenesis and genomic instability in multiple cancers. NAR Cancer. 2022 Jul 25;4(3):zcac023. PMID: 35898555; PMCID: PMC9310081.

74: Madison RW, Hu X, Ramanan V, Xu Z, Huang RSP, Sokol ES, Frampton GM, Schrock AB, Ali SM, Ganesan S, De S. Clustered 8-Oxo-Guanine Mutations and Oncogenic Gene Fusions in Microsatellite-Unstable Colorectal Cancer. JCO Precis Oncol. 2022 May;6:e2100477. PMID: 35584350; PMCID: PMC9200390.

73: Ghaddar B, De S. Reconstructing physical cell interaction networks from single-cell data using Neighbor-seq. Nucleic Acids Res. 2022 Aug 12;50(14):e82. PMID: 35536255; PMCID: PMC9371920.

72: De S. Signatures Beyond Oncogenic Mutations in Cell-Free DNA Sequencing for Non-Invasive, Early Detection of Cancer. Front Genet. 2021 Oct 14;12:759832. PMID: 34721546; PMCID: PMC8551553.

71: Hu X, Biswas A, Sharma A, Sarkodie H, Tran I, Pal I, De S. Mutational signatures associated with exposure to carcinogenic microplastic compounds bisphenol A and styrene oxide. NAR Cancer. 2021 Mar 1;3(1):zcab004. PMID: 33718875; PMCID: PMC7936647.

70: Biswas A, De S. Drivers of dynamic intratumor heterogeneity and phenotypic plasticity. Am J Physiol Cell Physiol. 2021 May 1;320(5):C750-C760. PMID: 33657326; PMCID: PMC8163571.

69: Markowitz P, Patel M, Groisberg R, Aisner J, Jabbour SK, De S, Ganesan S, Malhotra J. Genomic characterization of malignant pleural mesothelioma and associated clinical outcomes. Cancer Treat Res Commun. 2020;25:100232. PMID: 33166854.

68: Kanduri C, Sandve GK, Hovig E, De S, Layer RM. Editorial: Genomic Colocalization and Enrichment Analyses. Front Genet. 2021 Jan 26;11:617876. PMID: 33574832; PMCID: PMC7870795.

67: Clements KE, Schleicher EM, Thakar T, Hale A, Dhoonmoon A, Tolman NJ, Sharma A, Liang X, Imamura Kawasawa Y, Nicolae CM, Wang HG, De S, Moldovan GL. Identification of regulators of poly-ADP-ribose polymerase inhibitor response through complementary CRISPR knockout and activation screens. Nat Commun. 2020 Nov 30;11(1):6118. PMID: 33257658; PMCID: PMC7704667.

66: Qu H, Wu P, Huang Q, Yi J, Yan Z, Li K, Riedlinger GM, De S, Zhang S, Metaxas DN. Weakly Supervised Deep Nuclei Segmentation Using Partial Points Annotation in Histopathology Images. IEEE Trans Med Imaging. 2020 Nov;39(11):3655-3666. PMID: 32746112.

65: Lu H, Ye C, Liu J, Rabson AB, Verzi M, De S, Shen Z. Requirement of Bccip for the Regeneration of Intestinal Progenitors. Am J Pathol. 2021 Jan;191(1):66-78. PMID: 33039352; PMCID: PMC7857062.

64: Hu X, Xu Z, De S. Characteristics of mutational signatures of unknown etiology. NAR Cancer. 2020 Sep;2(3):zcaa026. PMID: 33015626; PMCID: PMC7520824.

63: Singh VK, Rastogi A, Hu X, Wang Y, De S. Mutational signature SBS8 predominantly arises due to late replication errors in cancer. Commun Biol. 2020 Aug 3;3(1):421. PMID: 32747711; PMCID: PMC7400754.

62: Gunnarsson EB, De S, Leder K, Foo J. Understanding the role of phenotypic switching in cancer drug resistance. J Theor Biol. 2020 Apr 7;490:110162. PMID: 31953135; PMCID: PMC7785289.

61: Markowitz P, Patel M, Groisberg R, Aisner J, Jabbour SK, De S, Ganesan S, Malhotra J. Genomic characterization of malignant pleural mesothelioma and associated clinical outcomes. Cancer Treat Res Commun. 2020;25:100232. PMID: 33166854.

60: Feng X, Lu H, Yue J, Schneider N, Liu J, Denzin LK, Chan CS, De S, Shen Z. Loss of Setd4 delays radiation-induced thymic lymphoma in mice. DNA Repair (Amst). 2020 Feb;86:102754. PMID: 31794893; PMCID: PMC6960333.

59: Sharma A, Merritt E, Hu X, Cruz A, Jiang C, Sarkodie H, Zhou Z, Malhotra J, Riedlinger GM, De S. Non-Genetic Intra-Tumor Heterogeneity Is a Major Predictor of Phenotypic Heterogeneity and Ongoing Evolutionary Dynamics in Lung Tumors. Cell Rep. 2019 Nov 19;29(8):2164-2174.e5. PMID: 31747591; PMCID: PMC6952742.

58: Liggett LA, Sharma A, De S, DeGregori J. FERMI: A Novel Method for Sensitive Detection of Rare Mutations in Somatic Tissue. G3 (Bethesda). 2019 Sep 4;9(9):2977-2987. PMID: 31352405; PMCID: PMC6723130.

57: Balaparya A, De S. Revisiting signatures of neutral tumor evolution in the light of complexity of cancer genomic data. Nat Genet. 2018 Dec;50(12):1626-1628. PMID: 30250123; PMCID: PMC6952740.

56: Rogozin IB, Pavlov YI, Goncearenco A, De S, Lada AG, Poliakov E, Panchenko AR, Cooper DN. Mutational signatures and mutable motifs in cancer genomes. Brief Bioinform. 2018 Nov 27;19(6):1085-1101. PMID: 28498882; PMCID: PMC6454500.

55: He YJ, Meghani K, Caron MC, Yang C, Ronato DA, Bian J, Sharma A, Moore J, Niraj J, Detappe A, Doench JG, Legube G, Root DE, D'Andrea AD, Drané P, De S, Konstantinopoulos PA, Masson JY, Chowdhury D. DYNLL1 binds to MRE11 to limit DNA end resection in BRCA1-deficient cells. Nature. 2018 Nov;563(7732):522-526. PMID: 30464262; PMCID: PMC7155769.

54: Coleman N, De S. Mutation Signatures Depend on Epigenomic Contexts. Trends Cancer. 2018 Oct;4(10):659-661. PMID: 30292349.

53: Vagner T, Spinelli C, Minciacchi VR, Balaj L, Zandian M, Conley A, Zijlstra A, Freeman MR, Demichelis F, De S, Posadas EM, Tanaka H, Di Vizio D. Large extracellular vesicles carry most of the tumour DNA circulating in prostate cancer patient plasma. J Extracell Vesicles. 2018 Aug 7;7(1):1505403. PMID: 30108686; PMCID: PMC6084494.

52: Ryan WK, Fernandez J, Peterson MK, Sheneman DW, Podell BK, De S, Torchia EC. Activation of S6 signaling is associated with cell survival and multinucleation in hyperplastic skin after epidermal loss of AURORA-A Kinase. Cell Death Differ. 2019 Mar;26(3):548-564. PMID: 30050055; PMCID: PMC6370802.

51: Sharma A, Jiang C, De S. Dissecting the sources of gene expression variation in a pan-cancer analysis identifies novel regulatory mutations. Nucleic Acids Res. 2018 May 18;46(9):4370-4381. PMID: 29672706; PMCID: PMC5961375.

50: Rogozin IB, Goncearenco A, Lada AG, De S, Yurchenko V, Nudelman G, Panchenko AR, Cooper DN, Pavlov YI. DNA polymerase η mutational signatures are found in a variety of different types of cancer. Cell Cycle. 2018;17(3):348-355. PMID: 29139326; PMCID: PMC5914734.

49: Smith KS, Liu LL, Ganesan S, Michor F, De S. Nuclear topology modulates the mutational landscapes of cancer genomes. Nat Struct Mol Biol. 2017 Nov;24(11):1000-1006. PMID: 28967881; PMCID: PMC5744871.

48: Yamamoto KN, Yachida S, Nakamura A, Niida A, Oshima M, De S, Rosati LM, Herman JM, Iacobuzio-Donahue CA, Haeno H. Personalized Management of Pancreatic Ductal Adenocarcinoma Patients through Computational Modeling. Cancer Res. 2017 Jun 15;77(12):3325-3335. PMID: 28381541.

47: Rogozin IB, Lada AG, Goncearenco A, Green MR, De S, Nudelman G, Panchenko AR, Koonin EV, Pavlov YI. Activation induced deaminase mutational signature overlaps with CpG methylation sites in follicular lymphoma and other cancers. Sci Rep. 2016 Dec 7;6:38133. PMID: 27924834; PMCID: PMC5141443.

46: 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. Rational design of a parthenolide-based drug regimen that selectively eradicates acute myelogenous leukemia stem cells. Erratum in: J Biol Chem. 2016 Nov 25;291(48):25280. PMID: 27888238; PMCID: PMC5122795.

45: 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. Rational Design of a Parthenolide-based Drug Regimen That Selectively Eradicates Acute Myelogenous Leukemia Stem Cells. J Biol Chem. 2016 Oct 14;291(42):21984-22000. PMID: 27573247; PMCID: PMC5063982.

44: Yadav VK, Smith KS, Flinders C, Mumenthaler SM, De S. Significance of duon mutations in cancer genomes. Sci Rep. 2016 Jun 8;6:27437. PMID: 27272679; PMCID: PMC4897603.

43: Choe KN, Nicolae CM, Constantin D, Imamura Kawasawa Y, Delgado-Diaz MR, De S, Freire R, Smits VA, Moldovan GL. HUWE1 interacts with PCNA to alleviate replication stress. EMBO Rep. 2016 Jun;17(6):874-86. PMID: 27146073; PMCID: PMC5278616.

42: Hintzsche J, Kim J, Yadav V, Amato C, Robinson SE, Seelenfreund E, Shellman Y, Wisell J, Applegate A, McCarter M, Box N, Tentler J, De S, Robinson WA, Tan AC. IMPACT: a whole-exome sequencing analysis pipeline for integrating molecular profiles with actionable therapeutics in clinical samples. J Am Med Inform Assoc. 2016 Jul;23(4):721-30. PMID: 27026619; PMCID: PMC4926746.

41: Yadav VK, DeGregori J, De S. The landscape of somatic mutations in protein coding genes in apparently benign human tissues carries signatures of relaxed purifying selection. Nucleic Acids Res. 2016 Mar 18;44(5):2075-84. PMID: 26883632; PMCID: PMC4797307.

40: Poczobutt JM, De S, Yadav VK, Nguyen TT, Li H, Sippel TR, Weiser-Evans MC, Nemenoff RA. Expression Profiling of Macrophages Reveals Multiple Populations with Distinct Biological Roles in an Immunocompetent Orthotopic Model of Lung Cancer. J Immunol. 2016 Mar 15;196(6):2847-59. PMID: 26873985; PMCID: PMC4779748.

39: Smith KS, Yadav VK, Pei S, Pollyea DA, Jordan CT, De S. SomVarIUS: somatic variant identification from unpaired tissue samples. Bioinformatics. 2016 Mar 15;32(6):808-13. PMID: 26589277.

38: Smith KS, Yadav VK, Pedersen BS, Shaknovich R, Geraci MW, Pollard KS, De S. Signatures of accelerated somatic evolution in gene promoters in multiple cancer types. Nucleic Acids Res. 2015 Jun 23;43(11):5307-17. PMID: 25934800; PMCID: PMC4477653.

37: Selmecki AM, Maruvka YE, Richmond PA, Guillet M, Shoresh N, Sorenson AL, De S, Kishony R, Michor F, Dowell R, Pellman D. Polyploidy can drive rapid adaptation in yeast. Nature. 2015 Mar 19;519(7543):349-52. PMID: 25731168; PMCID: PMC4497379.

36: Shaknovich R, De S, Michor F. Epigenetic diversity in hematopoietic neoplasms. Biochim Biophys Acta. 2014 Dec;1846(2):477-84. PMID: 25240947.

35: Podlaha O, De S, Gonen M, Michor F. Histone modifications are associated with transcript isoform diversity in normal and cancer cells. PLoS Comput Biol. 2014 Jun 5;10(6):e1003611.  PMID: 24901363; PMCID: PMC4046914.

34: Aghili L, Foo J, DeGregori J, De S. Patterns of somatically acquired amplifications and deletions in apparently normal tissues of ovarian cancer patients. Cell Rep. 2014 May 22;7(4):1310-9. PMID: 24794429; PMCID: PMC4108616.

33: Choi YE, Pan Y, Park E, Konstantinopoulos P, De S, D'Andrea A, Chowdhury D. MicroRNAs down-regulate homologous recombination in the G1 phase of cycling cells to maintain genomic stability. Elife. 2014 Apr 30;3:e02445. PMID: 24843000; PMCID: PMC4031983.

32: Nicolae CM, Aho ER, Vlahos AH, Choe KN, De S, Karras GI, Moldovan GL. The ADP-ribosyltransferase PARP10/ARTD10 interacts with proliferating cell nuclear antigen (PCNA) and is required for DNA damage tolerance. J Biol Chem. 2014 May 9;289(19):13627-37. PMID: 24695737; PMCID: PMC4036367.

31: Yadav VK, De S. An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples. Brief Bioinform. 2015 Mar;16(2):232-41. PMID: 24562872; PMCID: PMC4794615.

30: Chambwe N, Kormaksson M, Geng H, De S, Michor F, Johnson NA, Morin RD, Scott DW, Godley LA, Gascoyne RD, Melnick A, Campagne F, Shaknovich R. Variability in DNA methylation defines novel epigenetic subgroups of DLBCL associated with different clinical outcomes. Blood. 2014 Mar 13;123(11):1699-708. PMID: 24385541; PMCID: PMC3954051.

29: Pedersen BS, Yang IV, De S. CruzDB: software for annotation of genomic intervals with UCSC genome-browser database. Bioinformatics. 2013 Dec 1;29(23):3003-6. PMID: 24037212; PMCID: PMC3834799.

28: De S, Pedersen BS, Kechris K. The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment. Brief Bioinform. 2014 Nov;15(6):919-28. PMID: 23956260; PMCID: PMC4271068.

27: Pedersen BS, De S. Loss of heterozygosity preferentially occurs in early replicating regions in cancer genomes. Nucleic Acids Res. 2013 Sep;41(16):7615-24. PMID: 23793816; PMCID: PMC3763542.

26: Pedersen BS, Konstantinopoulos PA, Spillman MA, De S. Copy neutral loss of heterozygosity is more frequent in older ovarian cancer patients. Genes Chromosomes Cancer. 2013 Sep;52(9):794-801. PMID: 23716468; PMCID: PMC3767172.

25: Liu L, De S, Michor F. DNA replication timing and higher-order nuclear organization determine single-nucleotide substitution patterns in cancer genomes. Nat Commun. 2013;4:1502. PMID: 23422670; PMCID: PMC3633418.

24: De S, Shaknovich R, Riester M, Elemento O, Geng H, Kormaksson M, Jiang Y, Woolcock B, Johnson N, Polo JM, Cerchietti L, Gascoyne RD, Melnick A, Michor F. Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity. PLoS Genet. 2013;9(1):e1003137. PMID: 23326238; PMCID: PMC3542081.

23: Levy ED, De S, Teichmann SA. Cellular crowding imposes global constraints on the chemistry and evolution of proteomes. Proc Natl Acad Sci USA. 2012 Dec11;109(50):20461-6. PMID:23184996; PMCID: PMC3528536.

22: Martins FC, De S, Almendro V, Gönen M, Park SY, Blum JL, Herlihy W, Ethington G, Schnitt SJ, Tung N, Garber JE, Fetten K, Michor F, Polyak K. Evolutionary pathways in BRCA1-associated breast tumors. Cancer Discov. 2012 Jun;2(6):503-11. PMID: 22628410; PMCID: PMC3738298.

21: Podlaha O, Riester M, De S, Michor F. Evolution of the cancer genome. Trends Genet. 2012 Apr;28(4):155-63. PMID: 22342180; PMCID: PMC3711268.

20: Antolin MF, Jenkins KP, Bergstrom CT, Crespi BJ, De S, Hancock A, Hanley KA, Meagher TR, Moreno-Estrada A, Nesse RM, Omenn GS, Stearns SC. Evolution and medicine in undergraduate education: a prescription for all biology students. Evolution. 2012 Jun;66(6):1991-2006. PMID: 22671563; PMCID: PMC7202235.

19: De S, Michor F. DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes. Nat Biotechnol. 2011 Nov 20;29(12):1103-8. PMID: 22101487; PMCID: PMC3923360.

18: 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; PMCID: PMC3186332.

17: De S, Michor F. DNA secondary structures and epigenetic determinants of cancer genome evolution. Nat Struct Mol Biol. 2011 Jul 3;18(8):950-5. PMID: 21725294; PMCID: PMC3963273.

16: De S. Somatic mosaicism in healthy human tissues. Trends Genet. 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; PMCID: PMC2978686.

14: De S, Babu MM. A time-invariant principle of genome evolution. Proc Natl Acad Sci USA. 2010 Jul 20;107(29):13004-9. PMID: 20615949; PMCID: PMC2919972.

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: 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.

11: 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; PMCID: PMC2675967.

10: Watkins NA, Gusnanto A, de Bono B, De S, Miranda-Saavedra D, Hardie DL, Angenent WG, Attwood AP, Ellis PD, Erber W, Foad NS, Garner SF, Isacke CM, Jolley J, Koch K, Macaulay IC, Morley SL, Rendon A, Rice KM, Taylor N, Thijssen- Timmer DC, Tijssen MR, van der Schoot CE, Wernisch L, Winzer T, Dudbridge F, Buckley CD, Langford CF, Teichmann S, Göttgens B, Ouwehand WH; Bloodomics Consortium. A HaemAtlas: characterizing gene expression in differentiated human blood cells. Blood. 2009 May 7;113(19):e1-9. PMID: 19228925; PMCID: PMC2680378.

9: 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; PMCID: PMC2718492.

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; PMCID: PMC2686428.

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; PMCID: PMC2587479.

6: Loos RJ, Lindgren CM, Li S, et al. Nat Genet. 2008 Jun;40(6):768-75. PMID: 18454148; PMCID: PMC2669167.

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; PMCID: PMC2374701.

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, 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.

1: 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; PMCID: PMC1201154.