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Papers by Peer Bork

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101. Macroscale patterns of oceanic zooplankton composition and size structureScientific Reports · 2021
102. Association of the Liver and Plasma Lipidomes with the Histological Stage of Alcohol-Related Liver Disease2021
103. Coupling proteomics and metabolomics for the unsupervised identification of protein–metabolite interactions in Chaetomium thermophilumPLoS ONE · 2021
104. Recurrent Frameshift Neoantigen Vaccine Elicits Protective Immunity With Reduced Tumor Burden and Improved Overall Survival in a Lynch Syndrome Mouse ModelGastroenterology · 2021
105. Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection Clusters Based on Integrated Genomic Surveillance, Outbreak Analysis and Contact Tracing in an Urban SettingClinical Infectious Diseases · 2021
106. GUNC: detection of chimerism and contamination in prokaryotic genomesGenome biology · 2021
107. Prognostic performance of 7 biomarkers compared to liver biopsy in early alcohol-related liver diseaseJournal of Hepatology · 2021
108. Dispersal strategies shape persistence and evolution of human gut bacteriaCell Host & Microbe · 2021
109. eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale2021
110. Swarm Learning for decentralized and confidential clinical machine learningNature · 2021
111. Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communitiesCommunications Biology · 2021
112. Human and preclinical studies of the host–gut microbiome co-metabolite hippurate as a marker and mediator of metabolic healthSocio-Environmental Systems Modeling · 2021
113. Reference genome-independent taxonomic profiling of microbiomes with mOTUs32021
114. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotationNucleic Acids Research · 2021
115. Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolboxGenome biology · 2021
116. Uncharted biosynthetic potential of the ocean microbiome2021
117. Ocean-wide comparisons of mesopelagic planktonic community structures2021
118. GUNC: Detection of Chimerism and Contamination in Prokaryotic Genomes2020
119. The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement setsNucleic Acids Research · 2020
120. Metagenomic assessment of the global diversity and distribution of bacteria and fungiEnvironmental Microbiology · 2020
121. The InterPro protein families and domains database: 20 years onNucleic Acids Research · 2020
122. SMART: recent updates, new developments and status in 2020Nucleic Acids Research · 2020
123. OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell linesNucleic Acids Research · 2020
124. (Phospho)proteomic Profiling of Microsatellite Unstable CRC Cells Reveals Alterations in Nuclear Signaling and Cholesterol Metabolism Caused by Frameshift Mutation of NMD Regulator UPF3AInternational Journal of Molecular Sciences · 2020
125. Glycogen accumulation, central carbon metabolism, and aging of hematopoietic stem and progenitor cellsScientific Reports · 2020
126. Plant nutrient‐acquisition strategies drive topsoil microbiome structure and functionNew Phytologist · 2020
127. Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversityThe ISME Journal · 2020
128. Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine-learning toolbox2020
129. Polarization of microbial communities between competitive and cooperative metabolism2020
130. Dissecting the collateral damage of antibiotics on gut microbes2020
131. Microbiome Determinants and Physiological Effects of the Benzoate-Hippurate Microbial-Host Co-Metabolic Pathway2019
132. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems2019
133. Efficacy of Bifidobacterium animalis subsp. lactis (BB-12), B. infantis and Lactobacillus acidophilus (La-5) probiotics to prevent gut dysbiosis in preterm infants of 28+0–32+6 weeks of gestation: a randomised, placebo-controlled, double-blind, multicentre trial: the PRIMAL Clinical Study ProtocolSHILAP Revista de lepidopterología · 2019
134. Quantitative Proteome Landscape of the NCI-60 Cancer Cell LinesiScience · 2019
135. Global Trends in Marine Plankton Diversity across Kingdoms of LifeCell · 2019
136. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean MetatranscriptomeCell · 2019
137. proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomesNucleic Acids Research · 2019
138. Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural featuresBioinformatics · 2019
139. Profiling cellular diversity in sponges informs animal cell type and nervous system evolution2019
140. Disentangling the impact of environmental and phylogenetic constraints on prokaryotic strain diversity2019
141. NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific languageMicrobiome · 2019
142. Metabolic Architecture of the Deep Ocean Microbiome2019
143. Disentangling Genetic and Environmental Effects on the Proteotypes of IndividualsCell · 2019
144. Interactive Tree Of Life (iTOL) v4: recent updates and new developmentsNucleic Acids Research · 2019
145. Microbial abundance, activity and population genomic profiling with mOTUs2Nature Communications · 2019
146. Extensive transmission of microbes along the gastrointestinal tracteLife · 2019
147. Toward unrestricted use of public genomic dataScience · 2019
148. Antibiotics-induced monodominance of a novel gut bacterial orderGut · 2019
149. Community‐Level Responses to Iron Availability in Open Ocean Plankton EcosystemsGlobal Biogeochemical Cycles · 2019
150. “Extensive Transmission of Microbes along the Gastrointestinal Tract”2018