Search Results - "Münch, Philipp C."

Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley by Bulgarelli, Davide, Garrido-Oter, Ruben, Münch, Philipp C., Weiman, Aaron, Dröge, Johannes, Pan, Yao, McHardy, Alice C., Schulze-Lefert, Paul

“…The microbial communities inhabiting the root interior of healthy plants, as well as the rhizosphere, which consists of soil particles firmly attached to…”
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Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi by Hacquard, Stéphane, Kracher, Barbara, Hiruma, Kei, Münch, Philipp C., Garrido-Oter, Ruben, Thon, Michael R., Weimann, Aaron, Damm, Ulrike, Dallery, Jean-Félix, Hainaut, Matthieu, Henrissat, Bernard, Lespinet, Olivier, Sacristán, Soledad, Ver Loren van Themaat, Emiel, Kemen, Eric, McHardy, Alice C., Schulze-Lefert, Paul, O’Connell, Richard J.

“…The sessile nature of plants forced them to evolve mechanisms to prioritize their responses to simultaneous stresses, including colonization by microbes or…”
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Reproducible Colonization of Germ-Free Mice With the Oligo-Mouse-Microbiota in Different Animal Facilities by Eberl, Claudia, Ring, Diana, Münch, Philipp C, Beutler, Markus, Basic, Marijana, Slack, Emma Caroline, Schwarzer, Martin, Srutkova, Dagmar, Lange, Anna, Frick, Julia S, Bleich, André, Stecher, Bärbel

“…The Oligo-Mouse-Microbiota (OMM ) is a recently developed synthetic bacterial community for functional microbiome research in mouse models (Brugiroux et al.,…”
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Transcriptome-wide analysis uncovers the targets of the RNA-binding protein MSI2 and effects of MSI2's RNA-binding activity on IL-6 signaling by Duggimpudi, Sujitha, Kloetgen, Andreas, Maney, Sathish Kumar, Münch, Philipp C., Hezaveh, Kebria, Shaykhalishahi, Hamed, Hoyer, Wolfgang, McHardy, Alice C., Lang, Philipp A., Borkhardt, Arndt, Hoell, Jessica I.

“…The RNA-binding protein Musashi 2 (MSI2) has emerged as an important regulator in cancer initiation, progression, and drug resistance. Translocations and…”
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Characterisation of a stable laboratory co-culture of acidophilic nanoorganisms by Krause, Susanne, Bremges, Andreas, Münch, Philipp C., McHardy, Alice C., Gescher, Johannes

“…This study describes the laboratory cultivation of ARMAN (Archaeal Richmond Mine Acidophilic Nanoorganisms). After 2.5 years of successive transfers in an…”
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Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life by Vatanen, Tommi, Plichta, Damian R., Somani, Juhi, Münch, Philipp C., Arthur, Timothy D., Hall, Andrew Brantley, Rudolf, Sabine, Oakeley, Edward J., Ke, Xiaobo, Young, Rachel A., Haiser, Henry J., Kolde, Raivo, Yassour, Moran, Luopajärvi, Kristiina, Siljander, Heli, Virtanen, Suvi M., Ilonen, Jorma, Uibo, Raivo, Tillmann, Vallo, Mokurov, Sergei, Dorshakova, Natalya, Porter, Jeffrey A., McHardy, Alice C., Lähdesmäki, Harri, Vlamakis, Hera, Huttenhower, Curtis, Knip, Mikael, Xavier, Ramnik J.

“…The human gut microbiome matures towards the adult composition during the first years of life and is implicated in early immune development. Here, we…”
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Evolutionary Stabilization of Cooperative Toxin Production through a Bacterium-Plasmid-Phage Interplay by Spriewald, Stefanie, Stadler, Eva, Hense, Burkhard A., Münch, Philipp C., McHardy, Alice C., Weiss, Anna S., Obeng, Nancy, Müller, Johannes, Stecher, Bärbel

“…Bacteria are excellent model organisms to study mechanisms of social evolution. The production of public goods, e.g., toxin release by cell lysis in clonal…”
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A self-supervised deep learning method for data-efficient training in genomics by Gündüz, Hüseyin Anil, Binder, Martin, To, Xiao-Yin, Mreches, René, Bischl, Bernd, McHardy, Alice C., Münch, Philipp C., Rezaei, Mina

“…Deep learning in bioinformatics is often limited to problems where extensive amounts of labeled data are available for supervised classification. By exploiting…”
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Author Correction: Optimized model architectures for deep learning on genomic data by Gündüz, Hüseyin Anil, Mreches, René, Moosbauer, Julia, Robertson, Gary, To, Xiao-Yin, Franzosa, Eric A., Huttenhower, Curtis, Rezaei, Mina, McHardy, Alice C., Bischl, Bernd, Münch, Philipp C., Binder, Martin

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Optimized model architectures for deep learning on genomic data by Gündüz, Hüseyin Anil, Mreches, René, Moosbauer, Julia, Robertson, Gary, To, Xiao-Yin, Franzosa, Eric A., Huttenhower, Curtis, Rezaei, Mina, McHardy, Alice C., Bischl, Bernd, Münch, Philipp C., Binder, Martin

“…The success of deep learning in various applications depends on task-specific architecture design choices, including the types, hyperparameters, and number of…”
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Erratum: Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi by Hacquard, Stéphane, Kracher, Barbara, Hiruma, Kei, Münch, Philipp C., Garrido-Oter, Ruben, Thon, Michael R., Weimann, Aaron, Damm, Ulrike, Dallery, Jean-Félix, Hainaut, Matthieu, Henrissat, Bernard, Lespinet, Olivier, Sacristán, Soledad, van Themaat, Emiel Ver Loren, Kemen, Eric, McHardy, Alice C., Schulze-Lefert, Paul, O’Connell, Richard J.

“…Nature Communications 7 Article number:11362 (2016); Published 6 May 2016; Updated 29 September 2016. The HTML version of this Article previously published…”
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Functional overlap of the Arabidopsis leaf and root microbiota by Bai, Yang, Müller, Daniel B., Srinivas, Girish, Garrido-Oter, Ruben, Potthoff, Eva, Rott, Matthias, Dombrowski, Nina, Münch, Philipp C., Spaepen, Stijn, Remus-Emsermann, Mitja, Hüttel, Bruno, McHardy, Alice C., Vorholt, Julia A., Schulze-Lefert, Paul

“…Roots and leaves of healthy plants host taxonomically structured bacterial assemblies, and members of these communities contribute to plant growth and health…”
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Rapid and accurate identification of ribosomal RNA sequences via deep learning by Deng, Zhi-Luo, Münch, Philipp C, Mreches, René, McHardy, Alice C

“…Abstract Advances in transcriptomic and translatomic techniques enable in-depth studies of RNA activity profiles and RNA-based regulatory mechanisms. Ribosomal…”
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Identification of Natural CRISPR Systems and Targets in the Human Microbiome by Münch, Philipp C., Franzosa, Eric A., Stecher, Bärbel, McHardy, Alice C., Huttenhower, Curtis

“…Many bacteria resist invasive DNA by incorporating sequences into CRISPR loci, which enable sequence-specific degradation. CRISPR systems have been well…”
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In vitro interaction network of a synthetic gut bacterial community by Weiss, Anna S., Burrichter, Anna G., Durai Raj, Abilash Chakravarthy, von Strempel, Alexandra, Meng, Chen, Kleigrewe, Karin, Münch, Philipp C., Rössler, Luis, Huber, Claudia, Eisenreich, Wolfgang, Jochum, Lara M., Göing, Stephanie, Jung, Kirsten, Lincetto, Chiara, Hübner, Johannes, Marinos, Georgios, Zimmermann, Johannes, Kaleta, Christoph, Sanchez, Alvaro, Stecher, Bärbel

“…A key challenge in microbiome research is to predict the functionality of microbial communities based on community membership and (meta)-genomic data. As…”
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Strain Identification and Quantitative Analysis in Microbial Communities by Ghazi, Andrew R., Münch, Philipp C., Chen, Di, Jensen, Jordan, Huttenhower, Curtis

“…[Display omitted] •Defining and identifying strains in microbial communities.•Methods for profiling strains from metagenomic sequencing by reference or…”
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Pulsed antibiotic treatments of gnotobiotic mice manifest in complex bacterial community dynamics and resistance effects by Münch, Philipp C., Eberl, Claudia, Woelfel, Simon, Ring, Diana, Fritz, Adrian, Herp, Simone, Lade, Iris, Geffers, Robert, Franzosa, Eric A., Huttenhower, Curtis, McHardy, Alice C., Stecher, Bärbel

“…Bacteria can evolve to withstand a wide range of antibiotics (ABs) by using various resistance mechanisms. How ABs affect the ecology of the gut microbiome is…”
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Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium by Brugiroux, Sandrine, Beutler, Markus, Pfann, Carina, Garzetti, Debora, Ruscheweyh, Hans-Joachim, Ring, Diana, Diehl, Manuel, Herp, Simone, Lötscher, Yvonne, Hussain, Saib, Bunk, Boyke, Pukall, Rüdiger, Huson, Daniel H., Münch, Philipp C., McHardy, Alice C., McCoy, Kathy D., Macpherson, Andrew J., Loy, Alexander, Clavel, Thomas, Berry, David, Stecher, Bärbel

“…Protection against enteric infections, also termed colonization resistance, results from mutualistic interactions of the host and its indigenous microbes. The…”
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Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes by Hu, Kaixin, Meyer, Fernando, Deng, Zhi-Luo, Asgari, Ehsaneddin, Kuo, Tzu-Hao, Münch, Philipp C, McHardy, Alice C

“…The advent of rapid whole-genome sequencing has created new opportunities for computational prediction of antimicrobial resistance (AMR) phenotypes from…”
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DiTaxa: nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection by Asgari, Ehsaneddin, Münch, Philipp C, Lesker, Till R, McHardy, Alice C, Mofrad, Mohammad R K

“…Abstract Summary Identifying distinctive taxa for micro-biome-related diseases is considered key to the establishment of diagnosis and therapy options in…”
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