Sarah J. Berkemer

Assistant Professor
Marie-Curie Fellow
Ecole Polytechnique
Paris, France

Contact Information

bsarah at bioinf dot uni-leipzig dot de


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), 2021.

Street Name Data as a Reflection of Migration and Settlement History.
Sarah J. Berkemer, Peter F. Stadler. MDPI Urban Sci. 2020, 4(4), 74, 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. 2020.

Compositional Properties of Alignments.
Sarah J. Berkemer, Christian Höner zu Siederdissen, Peter F. Stadler. Mathematics in Computer Science, 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, 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, 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, 2020.

Algebraic Dynamic Programming on Trees
Sarah J. Berkemer, Christian Höner zu Siederdissen, Peter F. Stadler. MDPI Algorithms, 2017

SMORE: Synteny Modulator Of Repetitive Elements.
Sarah J. Berkemer, Anne Hoffmann, Cameron R. A. Murray, Peter F. Stadler, MDPI Life, 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), 2017

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., 2016.

Processed Small RNAs in Archaea and BHB Elements
Sarah J. Berkemer, Master thesis, University of Leipzig, 2015. (pdf file)

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., 2015.

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. 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.

Cograph Editing: An Approach to Adjust the Orthology Relation for the Reconstruction of Phylogenetic Trees
Sarah Berkemer, Bachelor thesis, Saarland University, 2012. (zip directory with pdf and code.)


Mini Workshop on Algebraic Dynamic Programming 2019
Leipzig, Germany

Winter Workshop on Complex Systems 2019
Zakopane, Poland

CAS Conference: Molecular Origins of Life 2018
Munich, Germany

Computational Approaches to RNA Structure and Function 2018
Benasque, Spain

Dagstuhl Seminar: Algorithmic Chemoinformatics 2017
Wadern, Germany

RNA Computational Biology 2016
Hinxton, UK

Brasilian Symposium on Bioinformatics (BSB) 2014
ISCB-Latin America, Belo Horizonte, Brazil.

IWBBio 2014
University of Granada, Granada, Spain.

Hal8 2013
Universität Leipzig, Leipzig, Germany.

Yearly Conferences

Bioinformatics Leipzig, Doubice, Czech Republic.

TBI Vienna, Bled, Slovenia.

Special Commitments

Complex Systems Summer School 2018
Santa Fe Institute for Complex Systems, Santa Fe, NM, USA

JSPS Summer Program 2017
2 months research stay at Earth-Life-Science Institute, Tokyo Institute of Technology, Tokyo, Japan

Google Summer of Code 2014
Here you can find the GSoC website and here my GSoC blog.

Member of the Computer Science students' representative council at University of Leipzig
04/2014 - 03/2015

Member of the Computer Science students' representative council at Saarland University
07/2011 - 06/2012

Jugger trainer
For more information see our webpage or our facebook page.

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