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Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs.
Hadi K, Yao X, Behr JM, Deshpande A, Xanthopoulakis C, Tian H, Kudman S, Rosiene J, Darmofal M, DeRose J, Mortensen R, Adney EM, Shaiber A, Gajic Z, Sigouros M, Eng K, Wala JA, Wrzeszczyński KO, Arora K, Shah M, Emde AK, Felice V, Frank MO, Darnell RB, Ghandi M, Huang F, Dewhurst S, Maciejowski J, de Lange T, Setton J, Riaz N, Reis-Filho JS, Powell S, Knowles DA, Reznik E, Mishra B, Beroukhim R, Zody MC, Robine N, Oman KM, Sanchez CA, Kuhner MK, Smith LP, Galipeau PC, Paulson TG, Reid BJ, Li X, Wilkes D, Sboner A, Mosquera JM, Elemento O, Imielinski M. Hadi K, et al. Among authors: smith lp. Cell. 2020 Oct 1;183(1):197-210.e32. doi: 10.1016/j.cell.2020.08.006. Cell. 2020. PMID: 33007263 Free PMC article.
The limits of fine-scale mapping.
Smith LP, Kuhner MK. Smith LP, et al. Genet Epidemiol. 2009 May;33(4):344-56. doi: 10.1002/gepi.20387. Genet Epidemiol. 2009. PMID: 19048633 Free PMC article.
CNValidator: validating somatic copy-number inference.
Smith LP, Yamato JA, Kuhner MK. Smith LP, et al. Bioinformatics. 2019 Aug 1;35(15):2660-2662. doi: 10.1093/bioinformatics/bty1022. Bioinformatics. 2019. PMID: 30541069 Free PMC article.
Somatic whole genome dynamics of precancer in Barrett's esophagus reveals features associated with disease progression.
Paulson TG, Galipeau PC, Oman KM, Sanchez CA, Kuhner MK, Smith LP, Hadi K, Shah M, Arora K, Shelton J, Johnson M, Corvelo A, Maley CC, Yao X, Sanghvi R, Venturini E, Emde AK, Hubert B, Imielinski M, Robine N, Reid BJ, Li X. Paulson TG, et al. Among authors: smith lp. Nat Commun. 2022 Apr 28;13(1):2300. doi: 10.1038/s41467-022-29767-7. Nat Commun. 2022. PMID: 35484108 Free PMC article.
SBML and CellML translation in antimony and JSim.
Smith LP, Butterworth E, Bassingthwaighte JB, Sauro HM. Smith LP, et al. Bioinformatics. 2014 Apr 1;30(7):903-7. doi: 10.1093/bioinformatics/btt641. Epub 2013 Nov 8. Bioinformatics. 2014. PMID: 24215024 Free PMC article.
Publishing reproducible dynamic kinetic models.
Porubsky V, Smith L, Sauro HM. Porubsky V, et al. Brief Bioinform. 2021 May 20;22(3):bbaa152. doi: 10.1093/bib/bbaa152. Brief Bioinform. 2021. PMID: 32793969 Free PMC article.
phraSED-ML: A paraphrased, human-readable adaptation of SED-ML.
Choi K, Smith LP, Medley JK, Sauro HM. Choi K, et al. Among authors: smith lp. J Bioinform Comput Biol. 2016 Dec;14(6):1650035. doi: 10.1142/S0219720016500359. Epub 2016 Sep 30. J Bioinform Comput Biol. 2016. PMID: 27774871 Free PMC article.
209 results