Publications

Additional information can be found on HAL and Google Scholar.

2024

  1. wabi_img.png
    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
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    Infrared: a declarative tree decomposition-powered framework for bioinformatics
    Hua-Ting Yao , Bertrand Marchand , Sarah J Berkemer , and 2 more authors
    Algorithms for Molecular Biology, 2024
    DOI
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    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

2023

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    Automated design of dynamic programming schemes for RNA folding with pseudoknots
    Bertrand Marchand , Sebastian Will , Sarah J. Berkemer, and 2 more authors
    Algorithms Mol. Biol., 2023
    DOI
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    Toward a Systematic Assessment of Sex Differences in Cystic Fibrosis
    Christiane Gärtner , Jörg Fallmann , Peter F. Stadler , and 2 more authors
    Journal of Personalized Medicine, 2023
    DOI
  3. logo-FRCCS.png
    Is Paris a good example for a X-minute city?
    Sarah J. Berkemer, Simon Genet , Léopold Maurice , and 2 more authors
    In FRCCS 2023 , 2023
    DOI

2022

  1. wabi_img.png
    Automated Design of Dynamic Programming Schemes for RNA Folding with Pseudoknots
    Bertrand Marchand , Sebastian Will , Sarah J. Berkemer, and 2 more authors
    In 22nd International Workshop on Algorithms in Bioinformatics, WABI 2022, September 5-7, 2022, Potsdam, Germany , 2022
    DOI

2021

  1. thermosynechococcaceae.png
    The Thermosynechococcus Genus: Wide Environmental Distribution, but a Highly Conserved Genomic Core
    Paula Prondzinsky , Sarah J. Berkemer, Lewis M. Ward , and 1 more author
    Microbes and Environments, 2021
    DOI

2020

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    Street Name Data as a Reflection of Migration and Settlement History
    Sarah J. Berkemer, and Peter F Stadler
    Urban Science, 2020
    DOI
  2. bhbscheme.png
    The splicing endonuclease is an important player in rRNA and tRNA maturation in Archaea
    Thandi S. Schwarz , Sarah J. Berkemer, Stephan H. Bernhart , and 4 more authors
    Frontiers in Microbiology., 2020
    DOI
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    Compositional Properties of Alignments
    Sarah J. Berkemer, Christian Höner Siederdissen , and Peter F. Stadler
    Mathematics in Computer Science, 2020
    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
  5. Convexity Deficit of Benzenoids.
    Nino Bašić , Sarah J. Berkemer, Jörg Fallmann , and 6 more authors
    Croatica Chemica Acta, 2020
    DOI
  6. drawing_peakcalling.png
    Identification of RNA 3’ends and termination sites in Haloferax volcanii.
    Sarah J. Berkemer, Lisa-Katharina Maier , Fabian Amman , and 6 more authors
    RNA Biology, 2020
    DOI
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    Towards Dynamic Programming on Generalized Data Structures and Applications of Dynamic Programming in Bioinformatics.
    Sarah J. Berkemer
    Universität Leipzig, Fakultät für Mathematik und Informatik , 2020
    PhD Thesis
    Link

2017

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    Algebraic Dynamic Programming on Trees.
    Sarah J. Berkemer, Christian Höner Siederdissen , and Peter F. Stadler
    MDPI Algorithms, 2017
    DOI
  2. trna-ala.png
    SMORE: Synteny Modulator Of Repetitive Elements.
    Sarah J. Berkemer, Anne Hoffmann , Cameron R. A. Murray , and 1 more author
    MDPI Life, 2017
    DOI
  3. JOMB
    Expansion of Gene Clusters, Circular Orders, and the Shortest Hamiltonian Path Problem.
    Sonja J. Prohaska , Sarah J. Berkemer, Fabian Gärtner , and 6 more authors
    Journal of Mathematical Biology (JOMB), 2017
    DOI

2016

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    Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies.
    Cristian A. Velandia-Huerto , Sarah J. Berkemer, Anne Hoffmann , and 5 more authors
    BMC Bioinformatics, 2016
    Shared first authorship.
    DOI

2015

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    Processed Small RNAs in Archaea and BHB Elements.
    Sarah J. Berkemer, Christian Höner Siederdissen , Fabian Amman , and 4 more authors
    Genomics and Computational Biology, 2015
    DOI
  2. spider
    Spiders can be recognized by counting their legs.
    Sarah J. Berkemer, Ricardo Chavez , Adrian Fritz , and 3 more authors
    Mathematics in Computer Science, 2015
    arXiv DOI

2014

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    Comparative Detection of Processed Small RNAs in Archaea.
    Christian Höner Siederdissen , Sarah J. Berkemer, Fabian Amman , and 4 more authors
    Conference proceedings of IWBBIO 2014, Granada, Spain, 2014