Sarah J. Berkemer

  • Assistant Professor
  • Marie-Curie Fellow
  • ELSI affiliated scientist

AMIBio Group
Laboratoire d'Informatique (LIX)
Department of Computer Science
Ecole Polytechnique
91128 Palaiseau Cedex, France

Earth-Life Science Institute
Tokyo Institute of Technology, Meguro, Tokyo, Japan


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


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

PhD in Computer Science

Bioinformatics Group
Leipzig University

Current Projects

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

MSCA funded by EU

  • Dynamic programming
  • Parameterized Optimization
  • Applications in RNA Bioinformatics

BATO-MOUCHE: Big-City Analysis Taking OSM data to Model Urban Change

funded by Hi! Paris

  • Data Science and Complex Systems
  • Urban Development
  • Analysis of open data in spatial and temporal context
Early Evolution of Archaea and Bacteria

originally funded by JSPS and DAAD



Year Title Authors Journal/Conference DOI
2023 Toward a Systematic Assessment of Sex Differences in Cystic Fibrosis Christiane Gärtner, Jörg Fallmann, Peter F. Stadler, Thorsten Kaiser, and Sarah J. Berkemer J. Pers. Med. 10.3390/jpm13060924
2023 Is Paris a good example for a X-minute city? Modeling city composition on POI data and X-minute statistics in Paris Sarah J. Berkemer, Simon Genet, Leopold Maurice, Marie-Olive Thaury, Paola Tubaro Book of Abstracts, FRCCS 2023 10.5281/zenodo.7957531
2022 Automated design of dynamic programming schemes for RNA folding with pseudoknots Bertrand Marchand, Sebastian Will, Sarah J. Berkemer, Laurent Bulteau, and Yann Ponty WABI 2022 --
2021 The Thermosynechococcus genus: wide environmental distribution, but a highly conserved genomic core. Alannah P. Prondzinsky, Sarah J. Berkemer, Lewis M. Ward, and Shawn E. McGlynn Microbes and Environments 36(2) 10.1264/jsme2.ME20138
2020 Street Name Data as a Reflection of Migration and Settlement History. Sarah J. Berkemer and Peter F. Stadler MDPI Urban Sci. 4(4), 74 10.3390/urbansci4040074
2020 Splicing endonuclease is an important player in rRNA and tRNA maturation in Archaea. Anita Marchfelder, Thandi S. Schwarz, Sarah J. Berkemer, Stephan H. Bernhart, Matthias Weiss, Sebastien Ferreira-Cerca, Peter F. Stadler Frontiers in Microbiology, 11, 2856 10.3389/fmicb.2020.594838
2020 Compositional Properties of Alignments. Sarah J. Berkemer, Christian Höner zu Siederdissen, Peter F. Stadler Mathematics in Computer Science 10.1007/s11786-020-00496-8
2020 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 10.1093/molbev/msaa089
2020 Convexity Deficit of Benzenoids Nino Bašić, Sarah J. Berkemer, Jörg Fallmann, Patrick W. Fowler, Thomas Gatter, Tomaž Pisanski, Nancy Retzlaff, Peter F. Stadler, Sara S. Zemljič Croatica Chemica Acta 10.5562/cca3602
2020 Identification of RNA 3' ends and termination sites in Haloferax volcanii Sarah J. Berkemer, Lisa-Katharina Maier, Fabian Amman, Stephan H. Bernhart, Julia Wörtz, Pascal Märkle, Friedhelm Pfeiffer, Peter F. Stadler, Anita Marchfelder RNA Biology 10.1080/15476286.2020.1723328
2017 Algebraic Dynamic Programming on Trees Sarah J. Berkemer, Christian Höner zu Siederdissen, Peter F. Stadler MDPI Algorithms 10.3390/a10040135
2017 SMORE: Synteny Modulator Of Repetitive Elements. Sarah J. Berkemer, Anne Hoffmann, Cameron R. A. Murray, Peter F. Stadler MDPI Life 10.3390/life7040042
2017 Expansion of Gene Clusters, Circular Orders, and the Shortest Hamiltonian Path Problem Sonja J. Prohaska, Sarah J. Berkemer, Fabian Gärtner, Thomas Gatter, Nancy Retzlaff, The Students of the Graphs and Biological Networks Lab 2017, Christian Höner zu Siederdissen, Peter F. Stadler Journal of Mathematical Biology (JOMB) 10.1007/s00285-017-1197-3
2016 Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies. Cristian A. Velandia-Huerto, Sarah J. Berkemer, Anne Hoffmann, Nancy Retzlaff, Liliana C. Romero-Marroqín, Maribel Hernández Rosales, Peter F. Stadler, Clara I. Bermúdez-Santana BMC Genomics 17.1. 10.1186/s12864-016-2927-4
2015 Processed Small RNAs in Archaea and BHB Elements. Sarah J. Berkemer, Christian Höner zu Siederdissen, Fabian Amman, Axel Wintsche, Sebastian Will, Sonja J. Prohaska, and Peter F. Stadler Genomics and Computational Biology 1.1. 10.18547/gcb.2015.vol1.iss1.e18
2014 Spiders can be recognized by counting their legs. Sarah J. Berkemer, Ricardo Chavez, Adrian Fritz, Marc Hellmuth, Maribel Hernández-Rosales and Peter F. Stadler Mathematics in Computer Science 9.4., 437-441. 10.1007/s11786-015-0233-1
2014 Comparative Detection of Processed Small RNAs in Archaea. Christian Höner zu Siederdissen, Sarah Berkemer, Fabian Amman, Axel Wintsche, Sebastian Will, Sonja J.Prohaska, and Peter F. Stadler IWBBIO 2014, Granada, Spain --