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Shahabeddin Sarmashghi, Ph.D.

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UC San Diego, La JollaPhD12/2021Electrical and Computer Engineering
Sharif University of Technology, TehranMSc08/2015Electrical Engineering
Sharif University of Technology, TehranBSc06/2013Electrical Engineering

I am a postdoc in Beroukhim lab studying the genetic alterations underlying cancer. We develop methods to improve the characterization of copy number alterations and interpret them to understand the selective forces shaping the tumor genome. By studying the patterns of mutations across cancers, my goal is to further our knowledge about cancer-related biological pathways, and to identify new cancer vulnerabilities that can be exploited to develop novel personalized treatments in some of the hardest-to-cure cancers such as GBM.

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Rachtman E, Sarmashghi S, Bafna V, Mirarab S. Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling. Cell Syst. 2022 Oct 19; 13(10):817-829.e3. PMID: 36265468; PMCID: PMC9589918.
    Citations:    Fields:    
  2. Javadzadeh S, Rajkumar U, Nguyen N, Sarmashghi S, Luebeck J, Shang J, Bafna V. FastViFi: Fast and accurate detection of (Hybrid) Viral DNA and RNA. NAR Genom Bioinform. 2022 Jun; 4(2):lqac032. PMID: 35493723; PMCID: PMC9041341.
  3. Sarmashghi S, Balaban M, Rachtman E, Touri B, Mirarab S, Bafna V. Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT. PLoS Comput Biol. 2021 11; 17(11):e1009449. PMID: 34780468; PMCID: PMC8629397.
    Citations: 4     Fields:    Translation:HumansAnimalsCells
  4. Balaban M, Sarmashghi S, Mirarab S. APPLES: Scalable Distance-Based Phylogenetic Placement with or without Alignments. Syst Biol. 2020 05 01; 69(3):566-578. PMID: 31545363; PMCID: PMC7164367.
    Citations: 21     Fields:    Translation:Cells
  5. Sarmashghi S, Bafna V. Computing the Statistical Significance of Overlap between Genome Annotations with iStat. Cell Syst. 2019 06 26; 8(6):523-529.e4. PMID: 31202632; PMCID: PMC7200088.
    Citations: 2     Fields:    Translation:Humans
  6. Sarmashghi S, Bohmann K, P Gilbert MT, Bafna V, Mirarab S. Skmer: assembly-free and alignment-free sample identification using genome skims. Genome Biol. 2019 02 13; 20(1):34. PMID: 30760303; PMCID: PMC6374904.
    Citations: 34     Fields:    Translation:Animals
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.