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Cancer aneuploidies are shaped primarily by effects on tumour fitness.
Nature. 2023 Jul;619(7971):793-800. doi: 10.1038/s41586-023-06266-3. Epub 2023 Jun 28.
Nature. 2023.
PMID: 37380777
Free PMC article.
Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling.
Rachtman E, Sarmashghi S, Bafna V, Mirarab S.
Rachtman E, et al. Among authors: sarmashghi s.
Cell Syst. 2022 Oct 19;13(10):817-829.e3. doi: 10.1016/j.cels.2022.06.007.
Cell Syst. 2022.
PMID: 36265468
Free PMC article.
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FastViFi: Fast and accurate detection of (Hybrid) Viral DNA and RNA.
Javadzadeh S, Rajkumar U, Nguyen N, Sarmashghi S, Luebeck J, Shang J, Bafna V.
Javadzadeh S, et al. Among authors: sarmashghi s.
NAR Genom Bioinform. 2022 Apr 26;4(2):lqac032. doi: 10.1093/nargab/lqac032. eCollection 2022 Jun.
NAR Genom Bioinform. 2022.
PMID: 35493723
Free PMC article.
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Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT.
Sarmashghi S, Balaban M, Rachtman E, Touri B, Mirarab S, Bafna V.
Sarmashghi S, et al.
PLoS Comput Biol. 2021 Nov 15;17(11):e1009449. doi: 10.1371/journal.pcbi.1009449. eCollection 2021 Nov.
PLoS Comput Biol. 2021.
PMID: 34780468
Free PMC article.
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APPLES: Scalable Distance-Based Phylogenetic Placement with or without Alignments.
Balaban M, Sarmashghi S, Mirarab S.
Balaban M, et al. Among authors: sarmashghi s.
Syst Biol. 2020 May 1;69(3):566-578. doi: 10.1093/sysbio/syz063.
Syst Biol. 2020.
PMID: 31545363
Free PMC article.
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Computing the Statistical Significance of Overlap between Genome Annotations with iStat.
Sarmashghi S, Bafna V.
Sarmashghi S, et al.
Cell Syst. 2019 Jun 26;8(6):523-529.e4. doi: 10.1016/j.cels.2019.05.006. Epub 2019 Jun 12.
Cell Syst. 2019.
PMID: 31202632
Free PMC article.
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Skmer: assembly-free and alignment-free sample identification using genome skims.
Sarmashghi S, Bohmann K, P Gilbert MT, Bafna V, Mirarab S.
Sarmashghi S, et al.
Genome Biol. 2019 Feb 13;20(1):34. doi: 10.1186/s13059-019-1632-4.
Genome Biol. 2019.
PMID: 30760303
Free PMC article.
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