Philipp C. Münch
YOU?
Author Swipe
View article: Comparison of different AI systems for diagnosing sepsis, septic shock, and cardiogenic shock: a retrospective study
Comparison of different AI systems for diagnosing sepsis, septic shock, and cardiogenic shock: a retrospective study Open
Sepsis, septic shock, and cardiogenic shock are life-threatening conditions associated with high mortality rates, but differentiating them is complex because they share certain symptoms. Using the Medical Information Mart for Intensive Car…
View article: Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes
Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes Open
The advent of rapid whole-genome sequencing has created new opportunities for computational prediction of antimicrobial resistance (AMR) phenotypes from genomic data. Both rule-based and machine learning (ML) approaches have been explored …
View article: Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes
Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes Open
The advent of rapid whole-genome sequencing has created new opportunities for computational prediction of antimicrobial resistance (AMR) phenotypes from genomic data. Both rule-based and machine learning (ML) approaches have been explored …
View article: Contribution of bacterial and host factors to pathogen “blooming” in a gnotobiotic mouse model for <i>Salmonella enterica</i> serovar Typhimurium-induced enterocolitis
Contribution of bacterial and host factors to pathogen “blooming” in a gnotobiotic mouse model for <i>Salmonella enterica</i> serovar Typhimurium-induced enterocolitis Open
Inflammation has a pronounced impact on the intestinal ecosystem by driving an expansion of facultative anaerobic bacteria at the cost of obligate anaerobic microbiota. This pathogen “blooming” is also a hallmark of enteric Salmonella ente…
View article: A self-supervised deep learning method for data-efficient training in genomics
A self-supervised deep learning method for data-efficient training in genomics Open
Deep learning in bioinformatics is often limited to problems where extensive amounts of labeled data are available for supervised classification. By exploiting unlabeled data, self-supervised learning techniques can improve the performance…
View article: Neural Architecture Search for Genomic Sequence Data
Neural Architecture Search for Genomic Sequence Data Open
Deep learning has enabled outstanding progress on bioinformatics datasets and a variety of tasks, such as protein structure prediction, identification of regulatory regions, genome annotation, and interpretation of the noncoding genome. Th…
View article: Contribution of bacterial and host factors to pathogen “blooming” in a gnotobiotic mouse model for<i>Salmonella enterica</i>serovar Typhimurium-induced enterocolitis
Contribution of bacterial and host factors to pathogen “blooming” in a gnotobiotic mouse model for<i>Salmonella enterica</i>serovar Typhimurium-induced enterocolitis Open
Inflammation has a pronounced impact on the intestinal ecosystem by driving an expansion of facultative anaerobic bacteria at the cost of obligate anaerobic microbiota. This pathogen “blooming” is also a hallmark of enteric Salmonella ente…
View article: Optimized model architectures for deep learning on genomic data
Optimized model architectures for deep learning on genomic data Open
In computational biology, there is a lack of agreement on the optimal design of deep learning architectures, such as types and number of layers, often resulting in non-optimal design choices. We introduce GenomeNet-Architect, an architectu…
View article: A self-supervised deep learning method for data-efficient training in genomics
A self-supervised deep learning method for data-efficient training in genomics Open
While deep learning is frequently applied in bioinformatics, it is mostly limited to problems where huge amounts of labeled data are present to train a classifier in a supervised manner. Here, we introduce Self-GenomeNet– a method that uti…
View article: A platform for deep learning on (meta)genomic sequences
A platform for deep learning on (meta)genomic sequences Open
We describe deepG, a platform for the generation, interpretation, and application of deep learning models for sequence labeling, classification, and regression based on nucleotide sequences. Unlike other bioinformatic deep learning platfor…
View article: Rapid and accurate identification of ribosomal RNA sequences via deep learning
Rapid and accurate identification of ribosomal RNA sequences via deep learning Open
Advances in transcriptomic and translatomic techniques enable in-depth studies of RNA activity profiles and RNA-based regulatory mechanisms. Ribosomal RNA (rRNA) sequences are highly abundant among cellular RNA, but if the target sequences…
View article: Slip Detection and Control for Harvesting Machines
Slip Detection and Control for Harvesting Machines Open
This paper deals with a traction control system (TCS) for combine harvesters. Off-road vehicles typically have a lower traction efficiency compared to on-road vehicles. The rising demand for high-power agricultural machines leads to a sign…
View article: In vitro interaction network of a synthetic gut bacterial community
In vitro interaction network of a synthetic gut bacterial community Open
A key challenge in microbiome research is to predict the functionality of microbial communities based on community membership and (meta)-genomic data. As central microbiota functions are determined by bacterial community networks, it is im…
View article: APOS - Antibiotic Prophylaxis For Preventing Infectious Complications In Orthognathic Surgery: Study Protocol For A Phase III, Multicentre, Randomised, Controlled, Double Blinded, Clinical Trial With Two Parallel Study Arms
APOS - Antibiotic Prophylaxis For Preventing Infectious Complications In Orthognathic Surgery: Study Protocol For A Phase III, Multicentre, Randomised, Controlled, Double Blinded, Clinical Trial With Two Parallel Study Arms Open
Background: It is a constant debate among surgeons whether the use of prolonged postoperative antibiotics may reduce surgical site infection rates. As specific treatment guidelines are still lacking, many surgeons continue to use broad-spe…
View article: Accompanying dataset to the study "Natural CRISPR systems and targets in the human microbiome"
Accompanying dataset to the study "Natural CRISPR systems and targets in the human microbiome" Open
This repository hosts data products resulting from the CRISPR and cas gene study of the Human Microbiome Project (HMP1-II) population, consisting of spacer and repeat sequences (hmp1-II-crispr-spacers, hmp1-II-crispr-repeats) recovered fro…
View article: Evolutionary Stabilization of Cooperative Toxin Production through a Bacterium-Plasmid-Phage Interplay
Evolutionary Stabilization of Cooperative Toxin Production through a Bacterium-Plasmid-Phage Interplay Open
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 bacterial populations, is a frequently studied example of cooperative behavior. Her…
View article: Neither black nor white: do altered intestinal microbiota reflect chronic liver disease severity?
Neither black nor white: do altered intestinal microbiota reflect chronic liver disease severity? Open
In their outstanding study, Wei et al 1 compared the intestinal microbiota (IM) of well-defined autoimmune hepatitis (AIH) patients to healthy controls. They reported significantly reduced IM alpha diversity and disparate IM compositional …
View article: Evaluating assembly and variant calling software for strain-resolved analysis of large DNA viruses
Evaluating assembly and variant calling software for strain-resolved analysis of large DNA viruses Open
Infection with human cytomegalovirus (HCMV) can cause severe complications in immunocompromised individuals and congenitally infected children. Characterizing heterogeneous viral populations and their evolution by high-throughput sequencin…
View article: Evaluating assembly and variant calling software for strain-resolved analysis of large DNA-viruses
Evaluating assembly and variant calling software for strain-resolved analysis of large DNA-viruses Open
Infection with human cytomegalovirus (HCMV) can cause severe complications in immunocompromised individuals and congenitally infected children. Characterizing heterogeneous viral populations and their evolution by high-throughput sequencin…
View article: Reproducible Colonization of Germ-Free Mice With the Oligo-Mouse-Microbiota in Different Animal Facilities
Reproducible Colonization of Germ-Free Mice With the Oligo-Mouse-Microbiota in Different Animal Facilities Open
The Oligo-Mouse-Microbiota (OMM12) is a recently developed synthetic bacterial community for functional microbiome research in mouse models (Brugiroux et al., 2016). To date, the OMM12 model has been established in several germ-free mouse …
View article: DiTaxa: nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection
DiTaxa: nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection Open
Summary Identifying distinctive taxa for micro-biome-related diseases is considered key to the establishment of diagnosis and therapy options in precision medicine and imposes high demands on the accuracy of micro-biome analysis techniques…
View article: Transcriptome-wide analysis uncovers the targets of the RNA-binding protein MSI2 and effects of MSI2's RNA-binding activity on IL-6 signaling
Transcriptome-wide analysis uncovers the targets of the RNA-binding protein MSI2 and effects of MSI2's RNA-binding activity on IL-6 signaling Open
The RNA-binding protein Musashi 2 (MSI2) has emerged as an important regulator in cancer initiation, progression, and drug resistance. Translocations and deregulation of the MSI2 gene are diagnostic of certain cancers, including chronic my…
View article: Nucleotide-pair encoding of 16S rRNA sequences for host phenotype and biomarker detection
Nucleotide-pair encoding of 16S rRNA sequences for host phenotype and biomarker detection Open
Identifying combinations of taxa distinctive for microbiome-associated diseases is considered key to the establishment of diagnosis and therapy options in precision medicine and imposes high demands on accuracy of microbiome analysis techn…