De Laboratory - Select Publications

  1. Ghaddar B, Blaser MJ, De S. Reliable detection of Host-Microbe Signatures in cancer using PRISM. Cancer Cell. S1535-6108(26)00046-2. (2026)
     
  2. Vijayan Selvarajan A, Kabiraj D, De S. Fragmentation-Induced Coverage Biases in Cell-Free DNA Sequencing Affect the Clinical Sensitivity of Liquid Biopsies. Commun Biol. 2026. PMID: 42443324
     
  3. Tripathi A, Ecker B, Boland P, Ghodoussipour S, Riedlinger GR, De S. Oncointerpreter.ai enables interactive, personalized summarization of cancer diagnostics data. J Am Med Inform Assoc. 2025 Jan 1;32(1):129-138. PMID: 39535891; PMCID: PMC11648722.
     
  4. 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.
     
  5. 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.
     
  6. 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.
     
  7. 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.
     
  8. 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.
     
  9. 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.
     
  10. 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.
     
  11. 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. doi: 10.1016/j.jtbi.2020.110162. Epub 2020 Jan 14. PubMed PMID: 31953135.
     
  12. 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. doi: 10.1016/j.dnarep.2019.102754. Epub 2019 Nov 25.  PubMed PMID: 31794893; PubMed Central PMCID: PMC6960333.
     
  13. 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. doi: 10.1016/j.celrep.2019.10.045. PubMed PMID: 31747591; PubMed Central PMCID: PMC6952742.
     
  14. 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. doi: 10.1534/g3.119.400438. PubMed PMID: 31352405; PubMed Central PMCID: PMC6723130.
     
  15. 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. (in press).
     
  16. 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.
     
  17. 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. (in press).
     
  18. Smith KS, Yadav VK, Pei S, Pollyea DA, Jordan CT, De S. (2016) SomVarIUS: Somatic variant identification from unpaired tissue samples. Bioinformatics. [Epub ahead of print] PMID: 26589277.
     
  19. 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 Res. 43(11):5307-17. PMID: 25934800.
     
  20. 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. Nature. 519(7543):349-52. PMID: 25731168.
     
  21. 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 Bioinformatics. 16(2):232-41. PMID: 24562872.
     
  22. Shaknovich R, De S, Michor F. (2014) Epigenetic diversity in hematopoietic neoplasms. (201 BBA - Reviews on Cancer. 1846(2):477-484. PMID: 25240947.
     
  23. 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 Reports. 7(4):1310-9. PMID: 24794429.
     
  24. 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. eLife. 3:e02445. PMID: 24843000.
     
  25. 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 tolerance. Journal of Biological Chemistry. 289(19):13627-37. PMID: 24695737.
     
  26. Podlaha O, De S, Gonen M, Michor F. (2014) Histone modifications are associated with transcript isoform diversity in normal and cancer cells. PLoS Computational Biology. 10(6):e1003611. PMID: 24901363.
     
  27. 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.
     
  28. Pedersen BS, Yang IV, De S. (2013) CruzDB: software for annotation of genomic intervals with UCSC genome-browser database. Bioinformatics. 29(23):3003-6. PMID: 24037212.
     
  29. De S, Pedersen BS, Kechris K. (2013) The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment. Briefings in Bioinformatics. [Epub ahead of print]. PMID: 23956260.
     
  30. Pedersen BS, De S. (2013) Loss of heterozygosity preferentially occurs in early replicating regions in cancer genomes. Nucleic Acids Research. 41(16):7615-24. PMID: 23793816.
     
  31. 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):794-801. PMID: 23716468.
     
  32. 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.
     
  33. 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.
     
  34. 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.
     
  35. 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.