Critical Assessment of Metagenome Interpretation Enters the Second Round

by Andreas Bremges, Alice C. McHardy
Published 2018-07-01

Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic.

by Susanne Reimering, Sebastian Muñoz, Alice C McHardy
Published 2020-02-01

A probabilistic model to recover individual genomes from metagenomes

by Johannes Dröge, Alexander Schönhuth, Alice C. McHardy
Published 2017-05-01

PTree: pattern-based, stochastic search for maximum parsimony phylogenies

by Ivan Gregor, Lars Steinbrück, Alice C. McHardy
Published 2013-06-01

The PARA-suite: PAR-CLIP specific sequence read simulation and processing

by Andreas Kloetgen, Arndt Borkhardt, Jessica I. Hoell, Alice C. McHardy
Published 2016-10-01

PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes

by Ivan Gregor, Johannes Dröge, Melanie Schirmer, Christopher Quince, Alice C. McHardy
Published 2016-02-01

Characterisation of a stable laboratory co-culture of acidophilic nanoorganisms

by Susanne Krause, Andreas Bremges, Philipp C. Münch, Alice C. McHardy, Johannes Gescher
Published 2017-06-01

Assessing taxonomic metagenome profilers with OPAL

by Fernando Meyer, Andreas Bremges, Peter Belmann, Stefan Janssen, Alice C. McHardy, David Koslicki
Published 2019-03-01

From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer

by Aaron Weimann, Kyra Mooren, Jeremy Frank, Phillip B. Pope, Andreas Bremges, Alice C. McHardy, Nicola Segata
Published 2016-12-01

Evolutionary Stabilization of Cooperative Toxin Production through a Bacterium-Plasmid-Phage Interplay

by Stefanie Spriewald, Eva Stadler, Burkhard A. Hense, Philipp C. Münch, Alice C. McHardy, Anna S. Weiss, Nancy Obeng, Johannes Müller, Bärbel Stecher
Published 2020-07-01

Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci.

by Phillip B Pope, Alasdair K Mackenzie, Ivan Gregor, Wendy Smith, Monica A Sundset, Alice C McHardy, Mark Morrison, Vincent G H Eijsink
Published 2012-01-01

An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome

by Till R. Lesker, Abilash C. Durairaj, Eric J.C. Gálvez, Ilias Lagkouvardos, John F. Baines, Thomas Clavel, Alexander Sczyrba, Alice C. McHardy, Till Strowig
Published 2020-03-01

YBX1 Indirectly Targets Heterochromatin-Repressed Inflammatory Response-Related Apoptosis Genes through Regulating CBX5 mRNA

by Andreas Kloetgen, Sujitha Duggimpudi, Konstantin Schuschel, Kebria Hezaveh, Daniel Picard, Heiner Schaal, Marc Remke, Jan-Henning Klusmann, Arndt Borkhardt, Alice C. McHardy, Jessica I. Hoell
Published 2020-06-01

CAMISIM: simulating metagenomes and microbial communities

by Adrian Fritz, Peter Hofmann, Stephan Majda, Eik Dahms, Johannes Dröge, Jessika Fiedler, Till R. Lesker, Peter Belmann, Matthew Z. DeMaere, Aaron E. Darling, Alexander Sczyrba, Andreas Bremges, Alice C. McHardy
Published 2019-02-01

Predicting antimicrobial resistance in Pseudomonas aeruginosa with machine learning‐enabled molecular diagnostics

by Ariane Khaledi, Aaron Weimann, Monika Schniederjans, Ehsaneddin Asgari, Tzu‐Hao Kuo, Antonio Oliver, Gabriel Cabot, Axel Kola, Petra Gastmeier, Michael Hogardt, Daniel Jonas, Mohammad RK Mofrad, Andreas Bremges, Alice C McHardy, Susanne Häussler
Published 2020-03-01

High-throughput miRNA and mRNA sequencing of paired colorectal normal, tumor and metastasis tissues and bioinformatic modeling of miRNA-1 therapeutic applications.

by Christina Röhr, Martin Kerick, Axel Fischer, Alexander Kühn, Karl Kashofer, Bernd Timmermann, Andriani Daskalaki, Thomas Meinel, Dmitriy Drichel, Stefan T Börno, Anja Nowka, Sylvia Krobitsch, Alice C McHardy, Christina Kratsch, Tim Becker, Andrea Wunderlich, Christian Barmeyer, Christian Viertler, Kurt Zatloukal, Christoph Wierling, Hans Lehrach, Michal R Schweiger
Published 2013-01-01

Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi

by Stéphane Hacquard, Barbara Kracher, Kei Hiruma, Philipp C. Münch, Ruben Garrido-Oter, Michael R. Thon, Aaron Weimann, Ulrike Damm, Jean-Félix Dallery, Matthieu Hainaut, Bernard Henrissat, Olivier Lespinet, Soledad Sacristán, Emiel Ver Loren van Themaat, Eric Kemen, Alice C. McHardy, Paul Schulze-Lefert, Richard J. O’Connell
Published 2016-05-01

Erratum: Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi

by Stéphane Hacquard, Barbara Kracher, Kei Hiruma, Philipp C. Münch, Ruben Garrido-Oter, Michael R. Thon, Aaron Weimann, Ulrike Damm, Jean-Félix Dallery, Matthieu Hainaut, Bernard Henrissat, Olivier Lespinet, Soledad Sacristán, Emiel Ver Loren van Themaat, Eric Kemen, Alice C. McHardy, Paul Schulze-Lefert, Richard J. O’Connell
Published 2016-09-01

Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes

by Irena Maus, Andreas Bremges, Yvonne Stolze, Sarah Hahnke, Katharina G. Cibis, Daniela E. Koeck, Yong S. Kim, Jana Kreubel, Julia Hassa, Daniel Wibberg, Aaron Weimann, Sandra Off, Robbin Stantscheff, Vladimir V. Zverlov, Wolfgang H. Schwarz, Helmut König, Wolfgang Liebl, Paul Scherer, Alice C. McHardy, Alexander Sczyrba, Michael Klocke, Alfred Pühler, Andreas Schlüter
Published 2017-11-01

Eleven grand challenges in single-cell data science

by David Lähnemann, Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie C. Hicks, Mark D. Robinson, Catalina A. Vallejos, Kieran R. Campbell, Niko Beerenwinkel, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M. Keizer, Indu Khatri, Szymon M. Kielbasa, Jan O. Korbel, Alexey M. Kozlov, Tzu-Hao Kuo, Boudewijn P.F. Lelieveldt, Ion I. Mandoiu, John C. Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Lukasz Raczkowski, Marcel Reinders, Jeroen de Ridder, Antoine-Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alex Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth
Published 2020-02-01