Skmer: assembly-free and alignment-free sample identification using genome skims S Sarmashghi, K Bohmann, MT P Gilbert, V Bafna, S Mirarab Genome biology 20 (1), 1-20, 2019 | 97 | 2019 |
APPLES: scalable distance-based phylogenetic placement with or without alignments M Balaban, S Sarmashghi, S Mirarab Systematic Biology 69 (3), 566-578, 2020 | 64 | 2020 |
Cancer aneuploidies are shaped primarily by effects on tumour fitness J Shih, S Sarmashghi, N Zhakula-Kostadinova, S Zhang, Y Georgis, ... Nature 619 (7971), 793-800, 2023 | 32 | 2023 |
Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT S Sarmashghi, M Balaban, E Rachtman, B Touri, S Mirarab, V Bafna PLoS computational biology 17 (11), e1009449, 2021 | 26 | 2021 |
Computing the statistical significance of overlap between genome annotations with iStat S Sarmashghi, V Bafna Cell systems 8 (6), 523-529. e4, 2019 | 7 | 2019 |
Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling E Rachtman, S Sarmashghi, V Bafna, S Mirarab Cell systems 13 (10), 817-829. e3, 2022 | 4 | 2022 |
Uncertainty quantification using subsampling for assembly-free estimates of genomic distance and phylogenetic relationships E Rachtman, S Sarmashghi, V Bafna, S Mirarab International Conference on Research in Computational Molecular Biology, 366-368, 2022 | 3 | 2022 |
Fastvifi: fast and accurate detection of (hybrid) viral DNA and RNA S Javadzadeh, U Rajkumar, N Nguyen, S Sarmashghi, J Luebeck, ... NAR Genomics and Bioinformatics 4 (2), lqac032, 2022 | 2 | 2022 |
Statistical and Algorithmic Methods to Analyze Genome Sequencing Data S Sarmashghi University of California, San Diego, 2021 | | 2021 |
Assembly-free and alignment-free sample identification using genome skims S Sarmashghi, K Bohmann, MTP Gilbert, V Bafna, S Mirarab bioRxiv, 230409, 2018 | | 2018 |
Novel statistical methods to leverage low-coverage whole-genome sequencing data in biodiversity studies S Sarmashghi, M Balaban, E Rachtman, S Mirarab, V Bafna 2020 ESA Annual Meeting (August 3-6), 0 | | |