Sarah J. Berkemer

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I am researcher in the AMIBio Group at LIX

and assistant professor at École Polytechnique, France.

I am affiliated scientist at  ELSI, Tokyo, Japan.

I was Marie-Curie Fellow between 2021 and 2024.

I did my PhD in Computer Science in the Bioinformatics Group at Leipzig University in Germany.

Contact

Contact me for internships, Bachelor, Master or PhD thesis (co-)supervision:

berkemer<REMOVETHIS>[{a_t}]lix.polytechnique.fr

Office 2008
LIX, Bâtiment Turing
École Polytechnique
1 rue Estienne d'Orves
91120 Palaiseau, France

Keywords:

  • RNA bioinformatics, RNA sequencing, SHAPE data analysis
  • Dynamic programming, Formal Languages, Graph theory
  • Early evolution, Archaea, Orthology
  • Data Science, Urban Development
  • Gender-sensitive genomic data analysis

Projects

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SYNORG (2024-2028)

Transcriptionally Engineered Addressable RNA solvent droplets as generalised synthetic organelles
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BATO-MOUCHE (2022-2025)

Big-City Analysis Taking OSM data to Model Urban Change
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Early Evolution of Archaea and Bacteria

originally funded by JSPS and DAAD
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RNA-RAPSODY (2021-2024)

RNA Bioinformatics by Robustness Analysis of Parameter Space Optimization for Dynamic Programming

Selected Publications

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    RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions
    Kimon Boehmer , Sarah J. Berkemer, Sebastian Will , and 1 more author
    In 24th International Workshop on Algorithms in Bioinformatics, WABI 2024, September 2-4, 2024, Royal Holloway, London, United Kingdom , 2024
    DOI
  2. paris.png
    City composition and accessibility statistics in and around Paris
    Marie-Olive Thaury , Simon Genet , Léopold Maurice , and 2 more authors
    Frontiers in Big Data, 2024
    DOI
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    A New Analysis of Archaea-Bacteria Domain Separation: Variable Phylogenetic Distance and the Tempo of Early Evolution.
    Sarah J. Berkemer, and Shawn E. McGlynn
    Molecular Biology and Evolution, 2020
    DOI
Here is a full list.