Publications by authors named "Daniel Doerr"

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Reconstructing rearrangement phylogenies of natural genomes.
Leonard Bohnenkämper, Jens Stoye, Daniel Doerr

Algorithms Mol Biol· June 2025

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Panacus: fast and exact pangenome growth and core size estimation.
Luca Parmigiani, Erik Garrison, Jens Stoye, Tobias Marschall, Daniel Doerr

Bioinformatics· November 2024

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Panacus: fast and exact pangenome growth and core size estimation.
Luca Parmigiani, Erik Garrison, Jens Stoye, Tobias Marschall, Daniel Doerr

bioRxiv· June 2024

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Family-Free Genome Comparison.
Marilia D V Braga, Daniel Doerr, Diego P Rubert, Jens Stoye

Methods Mol Biol· May 2024

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AGO, a Framework for the Reconstruction of Ancestral Syntenies and Gene Orders.
Evan P Cribbie, Daniel Doerr, Cedric Chauve

Methods Mol Biol· May 2024

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Training an automated circulating tumor cell classifier when the true classification is uncertain.
Afroditi Nanou, Nikolas H Stoecklein, Daniel Doerr, Christiane Driemel, Leon W M M Terstappen

PNAS Nexus· February 2024

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Correction: Constructing founder sets under allelic and non-allelic homologous recombination.
Konstantinn Bonnet, Tobias Marschall, Daniel Doerr

Algorithms Mol Biol· December 2023

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Constructing founder sets under allelic and non-allelic homologous recombination.
Konstantinn Bonnet, Tobias Marschall, Daniel Doerr

Algorithms Mol Biol· September 2023

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A draft human pangenome reference.
Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness

Nature· May 2023

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The potential of family-free rearrangements towards gene orthology inference.
Diego P Rubert, Daniel Doerr, Marília D V Braga

J Bioinform Comput Biol· December 2021

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Small parsimony for natural genomes in the DCJ-indel model.
Daniel Doerr, Cedric Chauve

J Bioinform Comput Biol· December 2021

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Computing the Rearrangement Distance of Natural Genomes.
Leonard Bohnenkämper, Marília D V Braga, Daniel Doerr, Jens Stoye

J Comput Biol· April 2021

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Active and repressed biosynthetic gene clusters have spatially distinct chromosome states.
Hans-Wilhelm Nützmann, Daniel Doerr, América Ramírez-Colmenero, Jesús Emiliano Sotelo-Fonseca, Eva Wegel

Proc Natl Acad Sci U S A· June 2020

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Horizontal Gene Transfer Phylogenetics: A Random Walk Approach.
Gur Sevillya, Daniel Doerr, Yael Lerner, Jens Stoye, Mike Steel

Mol Biol Evol· May 2020

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Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants.
Diego P Rubert, Fábio V Martinez, Jens Stoye, Daniel Doerr

BMC Genomics· April 2020

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Sequence-Based Synteny Analysis of Multiple Large Genomes.
Daniel Doerr, Bernard M E Moret

Methods Mol Biol· December 2018

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Family-Free Genome Comparison.
Daniel Doerr, Pedro Feijão, Jens Stoye

Methods Mol Biol· December 2018

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GraphTeams: a method for discovering spatial gene clusters in Hi-C sequencing data.
Tizian Schulz, Jens Stoye, Daniel Doerr

BMC Genomics· May 2018

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Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient genomes.
Nina Luhmann, Daniel Doerr, Cedric Chauve

Microb Genom· September 2017

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New Genome Similarity Measures based on Conserved Gene Adjacencies.
Daniel Doerr, Luis Antonio B Kowada, Eloi Araujo, Shachi Deshpande, Simone Dantas

J Comput Biol· June 2017

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The gene family-free median of three.
Daniel Doerr, Metin Balaban, Pedro Feijão, Cedric Chauve

Algorithms Mol Biol· May 2017

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Identifying gene clusters by discovering common intervals in indeterminate strings.
Daniel Doerr, Jens Stoye, Sebastian Böcker, Katharina Jahn

BMC Genomics· December 2015

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Orthology detection combining clustering and synteny for very large datasets.
Marcus Lechner, Maribel Hernandez-Rosales, Daniel Doerr, Nicolas Wieseke, Annelyse Thévenin

PLoS One· May 2015

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Gene family assignment-free comparative genomics.
Daniel Doerr, Annelyse Thévenin, Jens Stoye

BMC Bioinformatics· May 2013

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Stochastic errors vs. modeling errors in distance based phylogenetic reconstructions.
Daniel Doerr, Ilan Gronau, Shlomo Moran, Irad Yavneh

Algorithms Mol Biol· August 2012

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