AI-Driven Antimicrobial Peptide Discovery: Mining and Generation
Summary
preprint
AEMB: efficient abundance estimation for metagenomic binning
Summary
preprint
AI-Driven Antimicrobial Peptide Discovery
Published by
Accounts of Chemical Research
Summary
journal-article
argNorm: normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO)
Published by
Bioinformatics
Summary
journal-article
A census of hidden and discoverable microbial diversity beyond genome-centric approaches
Summary
preprint
A catalog of small proteins from the global microbiome
Published by
Nature Communications
Summary
journal-article
Discovery of antimicrobial peptides in the global microbiome with machine learning
Published by
Cell
Summary
journal-article
Challenges in computational discovery of bioactive peptides in 'omics data
Published by
Proteomics
Summary
journal-article
Challenges in computational discovery of bioactive peptides in ’omics data
Published by
PROTEOMICS
Summary
journal-article
A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer
Published by
Nature Ecology and Evolution
Summary
journal-article
A global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer
Published by
Nature Ecology & Evolution
Summary
journal-article
For long-term sustainable software in bioinformatics
Published by
PLoS Computational Biology
Summary
journal-article
For long-term sustainable software in bioinformatics
Published by
PLOS Computational Biology
Summary
journal-article
Functional and evolutionary significance of unknown genes from uncultivated taxa
Published by
Nature
Summary
journal-article
Ubiquity of inverted ’gelatinous’ ecosystem pyramids in the global ocean
Summary
preprint
Quest for Orthologs in the Era of Biodiversity Genomics
Published by
Genome Biology and Evolution
Summary
journal-article
Quest for Orthologs in the Era of Biodiversity Genomics
Published by
Genome Biology and Evolution
Summary
journal-article
argNorm: Normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO)
Summary
report
A catalog of small proteins from the global microbiome
Published by
Nature Communications
Summary
journal-article
Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide
Published by
Nature Communications
Summary
journal-article
SPIRE: a Searchable, Planetary-scale mIcrobiome REsource
Summary
other
Towards monitoring of antimicrobial resistance in the environment
Published by
Environment International
Summary
journal-article
ResFinderFG v2.0
Published by
Nucleic Acids Research
Summary
journal-article
A catalogue of small proteins from the global microbiome
Summary
preprint
SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing
Summary
preprint
ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics
Published by
Nucleic Acids Research
Summary
journal-article
SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing
Published by
Bioinformatics
Summary
journal-article
ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics
Published by
Nucleic Acids Research
Summary
journal-article
Microbially Produced Imidazole Propionate Is Associated With Heart Failure and Mortality
Published by
JACC: Heart Failure
Summary
journal-article
SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing
Published by
Bioinformatics
Summary
journal-article
SemiBin2
Published by
Bioinformatics
Summary
journal-article
SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing
Published by
bioRxiv
Summary
other
Software testing in microbial bioinformatics: a call to action
Published by
Microbial Genomics
Summary
journal-article
ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics
Summary
preprint
ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics
Published by
bioRxiv
Summary
other
Microbiome and metabolome features of the cardiometabolic disease spectrum
Published by
Nature Medicine
Summary
journal-article
A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments
Published by
Nature Communications
Summary
journal-article
A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments
Published by
Nature Communications
Summary
journal-article
A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments
Published by
Nature Communications
Summary
journal-article
metaMIC: reference-free misassembly identification and correction of de novo metagenomic assemblies
Published by
Genome Biology
Summary
journal-article
metaMIC: reference-free misassembly identification and correction of de novo metagenomic assemblies
Published by
Genome Biology
Summary
journal-article
EXPERT: transfer learning-enabled context-aware microbial community classification
Published by
Briefings in Bioinformatics
Summary
journal-article
EXPERT: transfer learning-enabled context-aware microbial community classification
Published by
Briefings in Bioinformatics
Summary
journal-article
Drivers and determinants of strain dynamics following fecal microbiota transplantation
Published by
Nature Medicine
Summary
journal-article
Drivers and determinants of strain dynamics following fecal microbiota transplantation
Published by
Nature Medicine
Summary
journal-article
Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes
Published by
Nucleic Acids Research
Summary
journal-article
Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes
Published by
Nucleic Acids Research
Summary
journal-article
Microbiome and metabolome features of the cardiometabolic disease spectrum
Published by
Nature Medicine
Summary
journal-article
Towards the biogeography of prokaryotic genes
Published by
Nature
Summary
journal-article
Towards the biogeography of prokaryotic genes
Published by
Nature
Summary
journal-article
Towards the biogeography of prokaryotic genes
Published by
Nature
Summary
journal-article
Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide with implications for heart and kidney disorders
Published by
medRxiv
Summary
other
Functional and evolutionary significance of unknown genes from uncultivated taxa
Published by
bioRxiv
Summary
other
Impairment of gut microbial biotin metabolism and host biotin status in severe obesity
Published by
Gut
Summary
journal-article
Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: Effect of biotin and prebiotic supplementation on improved metabolism
Published by
Gut
Summary
journal-article
Software testing in microbial bioinformatics
Published by
Microbial Genomics
Summary
journal-article
Software testing in microbial bioinformatics: a call to action
Published by
Microbial Genomics
Summary
journal-article
Metagenomic assessment of the global diversity and distribution of bacteria and fungi
Published by
Environmental Microbiology
Summary
journal-article
Combinatorial, additive and dose-dependent drug–microbiome associations
Published by
Nature
Summary
journal-article
Metagenomic assessment of the global diversity and distribution of bacteria and fungi
Published by
Environmental Microbiology
Summary
journal-article
EXPERT: Transfer Learning-enabled context-aware microbial source tracking
Published by
bioRxiv
Summary
other
metaMIC: Reference-free Misassembly Identification and Correction of de novo metagenomic assemblies
Published by
bioRxiv
Summary
other
GUNC: detection of chimerism and contamination in prokaryotic genomes
Published by
Genome Biology
Summary
journal-article
GUNC: detection of chimerism and contamination in prokaryotic genomes
Published by
Genome Biology
Summary
journal-article
Drivers and Determinants of Strain Dynamics Following Faecal Microbiota Transplantation
Summary
other
Drivers and determinants of strain dynamics following faecal microbiota transplantation
Published by
bioRxiv
Summary
other
SemiBin: Incorporating information from reference genomes with semi-supervised deep learning leads to better metagenomic assembled genomes (MAGs)
Summary
other
SemiBin: Incorporating information from reference genomes with semi-supervised deep learning leads to better metagenomic assembled genomes (MAGs)
Published by
bioRxiv
Summary
other
Combinatorial, additive and dose-dependent drug-microbiome associations
Published by
Nature
Summary
journal-article
Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology
Published by
Nature Communications
Summary
journal-article
Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology
Published by
Nature Communications
Summary
journal-article
Voices of the new generation
Published by
Nature Reviews Molecular Cell Biology
Summary
journal-article
Voices of the new generation: science in a state of benign confusion
Published by
Nature Reviews Molecular Cell Biology
Summary
journal-article
Voices of the new generation: science in a state of benign confusion
Published by
Nature Reviews Molecular Cell Biology
Summary
journal-article
Statin therapy is associated with lower prevalence of gut microbiota dysbiosis
Published by
Nature
Summary
journal-article
Statin therapy is associated with lower prevalence of gut microbiota dysbiosis
Published by
Nature
Summary
journal-article
Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity
Published by
The ISME Journal
Summary
journal-article
Metagenomic assessment of the global diversity and distribution of bacteria and fungi.
Published by
Environmental microbiology
Summary
journal-article
Macrel: Antimicrobial peptide screening in genomes and metagenomes
Published by
PeerJ
Summary
journal-article
ProGenomes2: An improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes
Published by
Nucleic Acids Research
Summary
journal-article
Macrel: antimicrobial peptide screening in genomes and metagenomes
Published by
PeerJ
Summary
journal-article
Macrel: Antimicrobial peptide screening in genomes and metagenomes
Published by
PeerJ
Summary
journal-article
ProGenomes2: An improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes
Published by
Nucleic Acids Research
Summary
journal-article
Macrel: antimicrobial peptide screening in genomes and metagenomes
Published by
PeerJ
Summary
journal-article
GUNC: Detection of Chimerism and Contamination in Prokaryotic Genomes
Summary
preprint
GUNC: Detection of Chimerism and Contamination in Prokaryotic Genomes
Published by
bioRxiv
Summary
other
Author Correction
Published by
Nature Communications
Summary
other
Author Correction: Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology (Nature Communications, (2020), 11, 1, (5881), 10.1038/s41467-020-19589-w)
Published by
Nature Communications
Summary
journal-article
Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome
Published by
Cell
Summary
journal-article
MACREL: antimicrobial peptide screening in genomes and metagenomes
Summary
preprint
MACREL: Antimicrobial peptide screening in genomes and metagenomes
Published by
bioRxiv
Summary
other
Microbial abundance, activity and population genomic profiling with mOTUs2
Published by
Nature Communications
Summary
journal-article
Microbial abundance, activity and population genomic profiling with mOTUs2
Published by
Nature Communications
Summary
journal-article
Microbial abundance, activity and population genomic profiling with mOTUs2
Published by
Nature Communications
Summary
journal-article
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language
Published by
Microbiome
Summary
journal-article
NG-meta-profiler
Published by
Microbiome
Summary
journal-article
NG-meta-profiler: Fast processing of metagenomes using NGLess, a domain-specific language
Published by
Microbiome
Summary
journal-article
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language
Published by
Microbiome
Summary
journal-article
Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome
Published by
Cell
Summary
journal-article
Global Trends in Marine Plankton Diversity across Kingdoms of Life
Published by
Cell
Summary
journal-article
Global Trends in Marine Plankton Diversity across Kingdoms of Life
Published by
Cell
Summary
journal-article
Disentangling the impact of environmental and phylogenetic constraints on prokaryotic strain diversity
Summary
other
Disentangling the impact of environmental and phylogenetic constraints on prokaryotic strain diversity
Published by
bioRxiv
Summary
other
Protocolo de avaliação clínica audiológica para crianças com microcefalia v1
Summary
preprint
Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer
Published by
Nature Medicine
Summary
journal-article
Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer
Published by
Nature Medicine
Summary
journal-article
Community-Level Responses to Iron Availability in Open Ocean Plankton Ecosystems
Published by
Global Biogeochemical Cycles
Summary
journal-article
Community-Level Responses to Iron Availability in Open Ocean Plankton Ecosystems
Published by
Global Biogeochemical Cycles
Summary
journal-article
Extensive transmission of microbes along the gastrointestinal tract
Published by
eLife
Summary
journal-article
Extensive transmission of microbes along the gastrointestinal tract
Published by
eLife
Summary
journal-article
Extensive transmission of microbes along the gastrointestinal tract
Published by
eLife
Summary
journal-article
Large expert-curated database for benchmarking document similarity detection in biomedical literature search
Published by
Database
Summary
journal-article
Structured Literature Image Finder: Parsing Text and Figures in Biomedical Literature
Published by
SSRN
Summary
other
NG-meta-profiler: Fast processing of metagenomes using NGLess, a domain-specific language
Published by
bioRxiv
Summary
other
Recovery of gut microbiota of healthy adults following antibiotic exposure
Published by
Nature Microbiology
Summary
journal-article
Recovery of gut microbiota of healthy adults following antibiotic exposure
Published by
Nature Microbiology
Summary
journal-article
Structure and function of the global topsoil microbiome
Published by
Nature
Summary
journal-article
Structure and function of the global topsoil microbiome.
Published by
Nature
Summary
journal-article
Structure and function of the global topsoil microbiome
Published by
Nature
Summary
journal-article
“Extensive Transmission of Microbes along the Gastrointestinal Tract”
Summary
other
Similarity of the dog and human gut microbiomes in gene content and response to diet
Published by
Microbiome
Summary
journal-article
Similarity of the dog and human gut microbiomes in gene content and response to diet
Published by
Microbiome
Summary
journal-article
Similarity of the dog and human gut microbiomes in gene content and response to diet
Published by
Microbiome
Summary
journal-article
Selective maternal seeding and environment shape the human gut microbiome
Published by
Genome Research
Summary
journal-article
Selective maternal seeding and environment shape the human gut microbiome
Published by
Genome Research
Summary
journal-article
Selective maternal seeding and environment shape the human gut microbiome
Published by
Genome Research
Summary
journal-article
“Extensive Transmission of Microbes along the Gastrointestinal Tract”
Published by
bioRxiv
Summary
other
“Extensive Transmission of Microbes along the Gastrointestinal Tract”
Summary
other
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language
Summary
other
metaSNV: A tool for metagenomic strain level analysis
Published by
PLoS ONE
Summary
journal-article
Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naive Parkinson's disease patients
Published by
Genome Medicine
Summary
journal-article
Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients.
Summary
journal-article
Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson's disease patients
Published by
Genome Medicine
Summary
journal-article
Jug: Software for Parallel Reproducible Computation in Python
Published by
Journal of Open Research Software
Summary
journal-article
Subspecies in the global human gut microbiome
Published by
Molecular Systems Biology
Summary
journal-article
Subspecies in the global human gut microbiome
Published by
Molecular Systems Biology
Summary
journal-article
Subspecies in the global human gut microbiome
Published by
Molecular Systems Biology
Summary
journal-article
Towards standards for human fecal sample processing in metagenomic studies
Published by
Nature Biotechnology
Summary
journal-article
Towards standards for human fecal sample processing in metagenomic studies.
Published by
Nature biotechnology
Summary
journal-article
Towards standards for human fecal sample processing in metagenomic studies
Published by
Nature Biotechnology
Summary
journal-article
Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes
Published by
eLife
Summary
journal-article
Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes
Published by
eLife
Summary
journal-article
Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes
Published by
eLife
Summary
journal-article
Quantitative 3D-imaging for cell biology and ecology of environmental microbial eukaryotes
Published by
eLife
Summary
journal-article
Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper
Published by
Molecular Biology and Evolution
Summary
journal-article
Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper.
Summary
journal-article
Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper
Published by
Molecular Biology and Evolution
Summary
journal-article
metaSNV: A tool for metagenomic strain level analysis
Published by
PLoS ONE
Summary
journal-article
metaSNV: A tool for metagenomic strain level analysis
Published by
PLOS ONE
Summary
journal-article
Plankton networks driving carbon export in the oligotrophic ocean
Published by
Nature
Summary
journal-article
Plankton networks driving carbon export in the oligotrophic ocean.
Summary
journal-article
Plankton networks driving carbon export in the oligotrophic ocean
Published by
Nature
Summary
journal-article
MOCAT2: A metagenomic assembly, annotation and profiling framework
Published by
Bioinformatics
Summary
journal-article
MOCAT2: a metagenomic assembly, annotation and profiling framework.
Summary
journal-article
MOCAT2: A metagenomic assembly, annotation and profiling framework
Published by
Bioinformatics
Summary
journal-article
Gene expression changes in the salivary glands of Anopheles coluzzii elicited by Plasmodium berghei infection.
Summary
journal-article
Gene expression changes in the salivary glands of Anopheles coluzzii elicited by Plasmodium berghei infection
Published by
Parasites and Vectors
Summary
journal-article
Gene expression changes in the salivary glands of Anopheles coluzzii elicited by Plasmodium berghei infection
Published by
Parasites and Vectors
Summary
journal-article
Structure and function of the global ocean microbiome
Published by
Science
Summary
journal-article
Ocean plankton. Structure and function of the global ocean microbiome.
Summary
journal-article
Structure and function of the global ocean microbiome
Published by
Science
Summary
journal-article
Automatic determination of NET (neutrophil extracellular traps) coverage in fluorescent microscopy images
Published by
Bioinformatics
Summary
journal-article
Automatic Determination of NET (Neutrophil Extracellular Traps) Coverage in Fluorescent Microscopy Images.
Summary
journal-article
Automatic determination of NET (neutrophil extracellular traps) coverage in fluorescent microscopy images
Published by
Bioinformatics
Summary
journal-article
Metagenomic insights into the human gut resistome and the forces that shape it
Published by
BioEssays
Summary
journal-article
Metagenomic insights into the human gut resistome and the forces that shape it.
Summary
journal-article
Trypanosoma brucei histone H1 inhibits RNA polymerase I transcription and is important for parasite fitness in vivo.
Summary
journal-article
Metagenomic insights into the human gut resistome and the forces that shape it
Published by
BioEssays
Summary
journal-article
Host-cell sensors for Plasmodium activate innate immunity against liver-stage infection
Published by
Nature Medicine
Summary
journal-article
Host-cell sensors for Plasmodium activate innate immunity against liver-stage infection.
Summary
journal-article
Host-cell sensors for Plasmodium activate innate immunity against liver-stage infection
Published by
Nature Medicine
Summary
journal-article
A community computational challenge to predict the activity of pairs of compounds
Published by
Nature Biotechnology
Summary
journal-article
A community effort to assess and improve drug sensitivity prediction algorithms
Published by
Nature Biotechnology
Summary
journal-article
Metagenomic species profiling using universal phylogenetic marker genes
Published by
Nature Methods
Summary
journal-article
Metagenomic species profiling using universal phylogenetic marker genes.
Summary
journal-article
Metagenomic species profiling using universal phylogenetic marker genes
Published by
Nature Methods
Summary
journal-article
Determining the subcellular location of new proteins from microscope images using local features
Published by
Bioinformatics
Summary
journal-article
Determining the subcellular location of new proteins from microscope images using local features.
Summary
journal-article
Determining the subcellular location of new proteins from microscope images using local features
Published by
Bioinformatics
Summary
journal-article
Mahotas: Open source software for scriptable computer vision
Summary
journal-article
Structured literature image finder
Published by
Journal of Web Semantics
Summary
journal-article
Automated image analysis for high-content screening and analysis
Published by
Journal of Biomolecular Screening
Summary
journal-article
Automated image analysis for high-content screening and analysis
Published by
Journal of Biomolecular Screening
Summary
journal-article
Structured literature image finder: Parsing text and figures in biomedical literature
Published by
Journal of Web Semantics
Summary
journal-article
Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing
Published by
Bioinformatics
Summary
journal-article
Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing
Published by
Bioinformatics
Summary
journal-article
Principles of bioimage informatics
Published by
Linking Literature, Information, and Knowledge for Biology
Summary
conference-paper
Principles of bioimage informatics: Focus on machine learning of cell patterns
Published by
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Summary
book
Structured literature image finder
Published by
Linking Literature, Information, and Knowledge for Biology
Summary
conference-paper
Structured literature image finder: Extracting information from text and images in biomedical literature
Published by
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Summary
book
Cell cycle dependence of protein subcellular location inferred from static, asynchronous images
Published by
Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009
Summary
conference-paper
Nuclear segmentation in microscope cell images: A hand-segmented dataset and comparison of algorithms
Published by
Proceedings - 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2009
Summary
conference-paper
Cell cycle dependence of protein subcellular location inferred from static, asynchronous images
Published by
Proceedings of the 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Summary
conference-paper
Cell cycle dependence of protein subcellular location inferred from static, asynchronous images.
Summary
journal-article
Nuclear segmentation in microscope cell images
Published by
Proceedings of the 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro
Summary
conference-paper
Identifying subcellular locations from images of unknown resolution
Published by
Communications in Computer and Information Science
Summary
book
An adaptive multiresolution approach to fingerprint recognition
Published by
Proceedings of the 2007 IEEE International Conference on Image Processing
Summary
conference-paper
Dotted suffix trees a structure for approximate text indexing
Published by
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Summary
book
Dotted suffix trees a structure for approximate text indexing
Published by
String Processing and Information Retrieval
Summary
conference-paper
An adaptive multiresolution approach to fingerprint recognition
Published by
Proceedings - International Conference on Image Processing, ICIP