selected publications
-
academic article
- Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. 2023
- Additional file 1 of Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox 2021
- Additional file 1 of Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox 2021
- Additional file 2 of Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox 2021
- Additional file 2 of Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox 2021
- Additional file 3 of Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox 2021
- Additional file 3 of Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox 2021
- Diversity within species: interpreting strains in microbiomes 2020
- Polarization of microbial communities between competitive and cooperative metabolism 2020
- Statin therapy is associated with lower prevalence of gut microbiota dysbiosis 2020
- THE CLINICAL EFFECT OF PROBIOTIC-CONTAINING PRODUCT ON HEALTH INDICATORS AMONG A POPULATION OF CENTRAL ASIA 2020
- THE CLINICAL EFFECT OF PROBIOTIC-CONTAINING PRODUCT ON HEALTH INDICATORS AMONG A POPULATION OF CENTRAL ASIA 2020
- Tara Oceans: towards global ocean ecosystems biology 2020
- Author Correction: Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation 2019
- Disentangling the impact of environmental and phylogenetic constraints on prokaryotic strain diversity 2019
- Extensive transmission of microbes along the gastrointestinal tract 2019
- Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features 2019
- Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer 2019
- Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation 2019
- Microbial abundance, activity and population genomic profiling with mOTUs2 2019
- NFDI4Microbiome - Poster for the NFDI Conference 2019
- NFDI4Microbiome - Poster for the NFDI Conference 2019
- NFDI4Microbiome: extended abstract for the NFDI conference 2019
- STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets 2019
- A computational framework to integrate high-throughput ‘-omics’ datasets for the identification of potential mechanistic links 2018
- Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline 2018
- Minimum Information about an Uncultivated Virus Genome (MIUViG) 2018
- NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language 2018
- Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies 2018
- Quantifying compartment‐associated variations of protein abundance in proteomics data 2018
- Recovery of gut microbiota of healthy adults following antibiotic exposure 2018
- “Extensive Transmission of Microbes along the Gastrointestinal Tract” 2018
- Subspecies in the global human gut microbiome 2017
-
article
- 4DXpress: a database for cross-species expression pattern comparisons
- A 15q24 microdeletion in transient myeloproliferative disease (TMD) and acute megakaryoblastic leukaemia (AMKL) implicates PML and SUMO3 in the leukaemogenesis of TMD/AMKL
- A Computational Screen for Type I Polyketide Synthases in Metagenomics Shotgun Data
- A HYBRID PROTEIN KINASE-RNASE IN AN INTERFERON-INDUCED PATHWAY
- A Holistic Approach to Marine Eco-Systems Biology
- A LARGE DOMAIN COMMON TO SPERM RECEPTORS (ZP2 AND ZP3) AND TGF-BETA TYPE-III RECEPTOR
- A MODULE OF THE DNAJ HEAT-SHOCK PROTEINS FOUND IN MALARIA PARASITES
- A Molecular Study of Microbe Transfer between Distant Environments
- A NOVEL RNA-BINDING MOTIF IN OMNIPOTENT SUPPRESSORS OF TRANSLATION TERMINATION, RIBOSOMAL-PROTEINS AND A RIBOSOME MODIFICATION ENZYME
- A Nitrile Hydratase in the Eukaryote Monosiga brevicollis
- A P-LOOP-LIKE MOTH IN A WIDESPREAD ATP PYROPHOSPHATASE DOMAIN - IMPLICATIONS FOR THE EVOLUTION OF SEQUENCE MOTIFS AND ENZYME-ACTIVITY
- A Phylogeny-Based benchmarking test for orthology inference reveals the limitations of Function-Based validation
- A complex prediction: three-dimensional model of the yeast exosome
- A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens
- A faecal microbiota signature with high specificity for pancreatic cancer
- A fair comparison
- A genome-wide survey of human pseudogenes
- A human gut microbial gene catalogue established by metagenomic sequencing
- A latrophilin/CL-1-like GPS domain in polycystin-1
- A lipid-binding domain in Wnt: a case of mistaken identity?
- A method and server for predicting damaging missense mutations
- A network of conserved co-occurring motifs for the regulation of alternative splicing
- A new family of carbon-nitrogen hydrolases.
- A novel class of RanGTP binding proteins
- A novel transactivation domain in parkin.
- A phosphotyrosine interaction domain
- A protocol for the systematic and quantitative measurement of protein-lipid interactions using the liposome-microarray-based assay.
- A putative nucleic acid-binding domain in Bloom's and Werner's syndrome helicases
- A quantitative liposome microarray to systematically characterize protein-lipid interactions
- A side effect resource to capture phenotypic effects of drugs
- A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae
- A temporal map of transcription factor activity: Mef2 directly regulates at all stages of muscle target genes development
- A trefoil domain in the major rabbit zona pellucida protein.
- A versatile structural domain analysis server using profile weight matrices
- AMOP, a protein module aternativelly spliced in cancer cells
- AN ADHESIVE DOMAIN DETECTED IN FUNCTIONALLY DIVERSE RECEPTORS
- AN ATPASE DOMAIN COMMON TO PROKARYOTIC CELL-CYCLE PROTEINS, SUGAR KINASES, ACTIN, AND HSP70 HEAT-SHOCK PROTEINS
- AN EXPANDING FAMILY OF HELICASES WITHIN THE DEAD/H SUPERFAMILY
- AQUA: automated quality improvement for multiple sequence alignments
- ASTD: The Alternative Splicing and Transcript Diversity database
- Accurate and universal delineation of prokaryotic species.
- Aligning Sequences
- Alternative splicing and evolution
- Alternative splicing and genome complexity
- Alternative splicing of human genes - more the rule than the exception?
- An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum
- An integrated catalog of reference genes in the human gut microbiome.
- Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs
- Ancient animal microRNAs and the evolution of tissue identity
- Ancient duplication of DNA polymerase inferred from analysis of complete bacterial genomes
- Ancient duplication of DNA polymerase inferred from analysis of complete bacterial genomes.
- Annotation of the M. tuberculosis Hypothetical Orfeome: Adding Functional Information to More than Half of the Uncharacterized Proteins
- Anopheles gambiae pilot gene discovery project: Identification of mosquito innate immunity genes from expressed sequence tags generated from immune-competent cell lines
- Applying motif and profile searches.
- ArrayProspector: a web resource of functional associations inferred from microarray expression data
- Assessing systems properties of yeast mitochondria through an interaction map of the organelle
- Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data
- Association of genes to genetically inherited diseases using data mining
- Associative database of protein sequences.
- Automated annotation of GPI anchor sites: case study C-elegans
- Automated extraction of information in molecular biology
- BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments
- BSD: a novel domain in transcription factors and synapse-associated proteins
- Bacterial antisense RNAs are mainly the product of transcriptional noise.
- BioSapiens: a European network for integrated genome annotation
- Biochemistry - Not comparable, but complementary
- Bioinformatics in the post-sequence era
- CASH - a beta-helix domain widespread among carbohydrate-binding proteins
- CHALLENGING TIMES FOR BIOINFORMATICS
- CHARACTERIZATION OF A NOVEL PROTEIN-BINDING MODULE - THE WW DOMAIN
- COMPLEMENT COMPONENTS CLR/CLS, BONE MORPHOGENIC PROTEIN-1 AND XENOPUS-LAEVIS DEVELOPMENTALLY REGULATED PROTEIN UVS.2 SHARE COMMON REPEATS
- Cell type-specific nuclear pores: A case in point for context-dependent stoichiometry of molecular machines
- 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 Setting.
- Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding.
- Characterization of targeting domains by sequence analysis: glycogen-binding domains in protein phosphatases
- Characterization of the mammalian YAP (Yes-associated protein) gene and its role in defining a novel protein module, the WW domain.
- Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time of flight mass spectrometry and BLAST homology searching
- Circular reasoning rather than cyclic expression
- Classification and quantification of bacteriophage taxa in human gut metagenomes
- Cloning of a gene from Bacillus cereus with homology to the mreB gene from Escherichia coli.
- Co-evolution of transcriptional and posttranslational cell-cycle regulation
- Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing.
- Comments on "Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication"
- Common exon duplication in animals and its role in alternative splicing
- Comparative analysis of environmental sequences: potential and challenges
- Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages
- Comparative assessment of large-scale data sets of protein-protein interactions.
- Comparative genome analysis of the mollicutes
- Comparative genome analysis: exploiting the context of genes to infer evolution and predict function
- Comparative genome and proteome analysis of anopheles gambiae and Drosophila melanogaster
- Comparative genomic analysis in the region of a major Plasmodium-refractoriness locus of Anopheles gambiae
- Comparative metagenomics of microbial communities
- Comparison of ARM and HEAT protein repeats
- Comparison of computational methods for the identification of cell cycle-regulated genes
- Comparison of computational methods for the identification of cell cycle-regulated genes (vol 21, pg 1164, 2005)
- Complex genomic rearrangements lead to novel primate gene function
- Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III.
- Computational Analysis of Modular Protein Architectures
- Computational characterization of multiple Gag-like human proteins
- Computational eco-systems biology in Tara Oceans: translating data into knowledge.
- Conformational stability studies of the pleckstrin DEP domain: definition of the domain boundaries
- Conservation of gene co-regulation in prokaryotes and eukaryotes
- Conservation of gene order: a fingerprint of proteins that physically interact
- Consistency of genome-based methods in measuring Metazoan evolution
- Consistent mutational paths predict eukaryotic thermostability
- Convergent evolution of similar enzymatic function on different protein folds: the hexokinase, ribokinase, and galactokinase families of sugar kinases.
- Country-specific antibiotic use practices impact the human gut resistome.
- Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium
- Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton.
- Cytoplasmic signalling domains: the next generation
- DDT - a novel domain in different transcription and chromosome remodeling factors
- DROSOPHILA KELCH MOTIF IS DERIVED FROM A COMMON ENZYME FOLD
- Deciphering a global network of functionally associated post-translational modifications
- Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium.
- Detection of coding microsatellite frameshift mutations in DNA mismatch repair-deficient mouse intestinal tumors.
- Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children.
- Differential genome analysis applied to the species-specific features of Helicobacter pylori
- Differential genome display.
- Discovering Functional Novelty in Metagenomes: Examples from Light-Mediated Processes
- Discovery and validation of the antimetastatic activity of citalopram in colorectal cancer.
- Discovery, scoring and utilization of human single nucleotide polymorphisms: a multidisciplinary problem.
- Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.
- Divergent evolution of a beta/alpha-barrel subclass: detection of numerous phosphate-binding sites by motif search.
- Domain organization of Mac-2 binding protein and its oligomerization to linear and ring-like structures
- Domains in plexins: links to integrins and transcription factors
- Dot Plot
- Drug discovery in the age of systems biology: the rise of computational approaches for data integration
- Drug target identification using side-effect similarity
- Drug-Induced Regulation of Target Expression
- Durable coexistence of donor and recipient strains after fecal microbiota transplantation.
- DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data
- Dynamic complex formation during the yeast cell cycle
- ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins.
- EPIDERMAL GROWTH FACTOR-LIKE MODULES
- EST analysis online: WWW tools for detection of SNPs and alternative splice forms
- EST comparison indicates 38% of human mRNAs contain possible alternative splice forms
- ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data.
- EXOPOLYPHOSPHATE PHOSPHATASE AND GUANOSINE PENTAPHOSPHATE PHOSPHATASE BELONG TO THE SUGAR KINASE ACTIN HSP-70 SUPERFAMILY
- EXPLORING THE MYCOPLASMA-CAPRICOLUM GENOME - A MINIMAL CELL REVEALS ITS PHYSIOLOGY
- Energy efficiency trade-offs drive nucleotide usage in transcribed regions.
- Enhanced function annotations for Drosophila serine proteases: A case study for systematic annotation of multi-member gene families
- Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics.
- Enterotypes of the human gut microbiome
- Enterotypes of the human gut microbiome (vol 473, pg 174, 2011)
- Enterotypes of the human gut microbiome (vol 473, pg 174, 2011)
- Environments shape the nucleotide composition of genomes
- Estimating rates of alternative splicing in mammals and invertebrates - Reply
- Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer
- Eukaryotic translation elongation factor 1 gamma contains a glutathione transferase domain--study of a diverse, ancient protein superfamily using motif search and structural modeling.
- Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries
- Evolution and functional cross-talk of protein post-translational modifications.
- Evolution and regulation of cellular periodic processes: a role for paralogues
- Evolution of biomolecular networks - lessons from metabolic and protein interactions
- Evolution of domain families
- Evolution of new protein function: recombinational enhancer Fis originated by horizontal gene transfer from the transcriptional regulator NtrC
- Evolution of prokaryotic gene order: genome rearrangements in closely related species
- Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages
- Evolution of tuf genes: ancient duplication, differential loss and gene conversion
- Exon shuffling and other ways of module exchange - Comment
- Experimental characterization of the human non-sequence-specific nucleic acid interactome.
- Exploitation of gene context
- Exploring MEDLINE abstracts with XplorMed
- Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes.
- Extraction of regulatory gene/protein networks from Medline
- Extraction of transcript diversity from scientific literature
- FMN OR DNA-BINDING
- FROM GENOME SEQUENCES TO PROTEIN FUNCTION
- Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper
- Fibronectin type III modules in the receptor phosphatase CD45 and tapeworm antigens.
- Frame: detection of genomic sequencing errors
- Frameshift mutations in coding repeats of protein tyrosine phosphatase genes in colorectal tumors with microsatellite instability
- Frameshift peptide-derived T-cell epitopes: a source of novel tumor-specific antigens
- Friedreich's ataxia protein: Phylogenetic evidence for mitochondrial dysfunction
- Function prediction and protein networks
- Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species
- Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes
- Functional genomic analysis of cell division in C-elegans using RNAi of genes on chromosome III
- Functional motifs
- Functional organization of the yeast proteome by systematic analysis of protein complexes
- GRAM, a novel domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins
- GUNC: Detection of Chimerism and Contamination in Prokaryotic Genomes
- Gap Penalty
- Gene annotation from scientific literature using mappings between keyword systems
- Gene context conservation of a higher order than operons
- Gene expression profiling of the rat superior olivary complex using serial analysis of gene expression
- Gene families: The taxonomy of protein paralogs and chimeras
- Generation and annotation of the DNA sequences of human chromosomes 2 and 4
- Genome and protein evolution in eukaryotes
- Genome and proteome informatics - Editorial overview
- Genome evolution - gene fusion versus gene fission
- Genome evolution reveals biochemical networks and functional modules
- Genome maps 8. Building gene families. Wall chart.
- Genome organization: Teamed up for transcription
- Genome sequence of the Brown Norway rat yields insights into mammalian evolution
- Genome speak
- Genome-wide experimental determination of barriers to horizontal gene transfer
- Genomes in flux: The evolution of archaeal and proteobacterial gene content
- Genomic variation landscape of the human gut microbiome
- Get the most out of your metagenome: computational analysis of environmental sequence data
- Global analysis of bacterial transcription factors to predict cellular target processes
- Global genetic capacity for mixotrophy in marine picocyanobacteria.
- Go hunting in sequence databases but watch out for the traps
- Gut Microbiota Linked to Sexual Preference and HIV Infection.
- HEAT REPEATS IN THE HUNTINGTONS-DISEASE PROTEIN
- HGBASE: a database of SNPs and other variations in and around human genes
- HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources
- HUNDREDS OF ANKYRIN-LIKE REPEATS IN FUNCTIONALLY DIVERSE PROTEINS - MOBILE MODULES THAT CROSS PHYLA HORIZONTALLY
- Heat shock protein-90-alpha, a prolactin-STAT5 target gene identified in breast cancer cells, is involved in apoptosis regulation
- High-resolution transcription atlas of the mitotic cell cycle in budding yeast
- Histone Deacetylase Inhibitors (HDACi) Cause the Selective Depletion of Bromodomain Containing Proteins (BCPs).
- Homology among (beta alpha)(8) barrels: Implications for the evolution of metabolic pathways
- Homology-based fold predictions for Mycoplasma genitalium proteins
- Homology-based functional proteomics by mass spectrometry: Application to the Xenopus microtubule-associated proteome
- Homology-based gene prediction using neural nets
- Homology-based method for identification of protein repeats using statistical significance estimates
- Human monogenic disease genes have frequently functionally redundant paralogs.
- Human non-synonymous SNPs: server and survey
- Identical variant TSG101 transcripts in soft tissue sarcomas and various non-neoplastic tissues
- Identical variant TSG101 transcripts in soft tissue sarcomas and various non-neoplastic tissues.
- Identification and analysis of evolutionarily cohesive functional modules in protein networks
- Identification and analysis of genes and pseudogenes within duplicated regions in the human and mouse genomes
- Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.
- Identification and characterization of UEV3, a human cDNA with similarities to inactive E2 ubiquitin-conjugating enzymes
- Identification and mutation analysis of the complete gene for Chediak-Higashi syndrome
- Identification of residues within the SHC phosphotyrosine binding/phosphotyrosine interaction domain crucial for phosphopeptide interaction.
- Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis
- Identifying Single Copy Orthologs in Metazoa
- Immunity-related genes and gene families in Anopheles gambiae
- Impact of Genome Reduction on Bacterial Metabolism and Its Regulation
- Impact of selection, mutation rate and genetic drift on human genetic variation
- Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism.
- In situ structural analysis of the human nuclear pore complex.
- Increase of functional diversity by alternative splicing
- Indel
- Individual variation in protein-coding sequences of human genome
- Information extraction from full text scientific articles: Where are the keywords?
- Initial sequence of the chimpanzee genome and comparison with the human genome
- Initial sequencing and analysis of the human genome
- Initial sequencing and comparative analysis of the mouse genome
- Insight into Structure and Assembly of the Nuclear Pore Complex by Utilizing the Genome of a Eukaryotic Thermophile
- Insights into social insects from the genome of the honeybee Apis mellifera
- Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats.
- Integration of genome data and protein structures: prediction of protein folds, protein interactions and 'molecular phenotypes' of single nucleotide polymorphisms
- Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances.
- Inter-individual differences in the gene content of human gut bacterial species.
- InterPro in 2011: new developments in the family and domain prediction database
- InterPro, progress and status in 2005
- InterPro: an integrated documentation resource for protein families, domains and functional sites.
- InterPro: the integrative protein signature database
- Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation
- Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy
- Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees.
- Internal repeats in the BRCA2 protein sequence
- Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children.
- Inversions and the dynamics of eukaryotic gene order
- Is there biological research beyond Systems Biology? A comparative analysis of terms
- KEGG Atlas mapping for global analysis of metabolic pathways
- L27, a novel heterodimerization domain in receptor targeting proteins Lin-2 and Lin-7
- LSAT: learning about alternative transcripts in MEDLINE
- Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes
- Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?
- Large-scale prediction of drug-target relationships
- Linear Motif Atlas for Phosphorylation-Dependent Signaling
- Lipid Cooperativity as a General Membrane-Recruitment Principle for PH Domains.
- Literature mining for the biologist: from information retrieval to biological discovery
- LotuS: an efficient and user-friendly OTU processing pipeline.
- Luminal signalling links cell communication to tissue architecture during organogenesis.
- MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit
- MOLECULAR MODELING OF THE NORRIE DISEASE PROTEIN PREDICTS A CYSTINE KNOT GROWTH-FACTOR TERTIARY STRUCTURE
- MRNA degradation by miRNAs and GW182 requires both CCR4 : NOT deadenylase and DCP1 : DCP2 decapping complexes
- Measuring genome evolution
- Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions.
- Meconium Microbiome of Very Preterm Infants across Germany
- Medusa: a simple tool for interaction graph analysis
- Merging extracellular domains: Fold prediction for laminin G-like and amino-terminal thrombospondin-like modules based on homology to pentraxins
- Metabolic dependencies drive species co-occurrence in diverse microbial communities.
- Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli
- Metabolites: a helping hand for pathway evolution?
- Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities
- Metagenomic insights into the human gut resistome and the forces that shape it
- Metagenomic species profiling using universal phylogenetic marker genes.
- Microbiome and metabolome features of the cardiometabolic disease spectrum
- Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox
- Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine-learning toolbox
- Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat.
- Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
- Mobile modules and motifs
- Molecular characterization of a cDNA encoding functional human CLK4 kinase and localization to chromosome 4q35
- More than 1,000 putative new human signalling proteins revealed by EST data mining.
- More von Willebrand factor type A domains? Sequence similarities with malaria thrombospondin-related anonymous protein, dihydropyridine-sensitive calcium channel and inter-alpha-trypsin inhibitor.
- NAIL - Network Analysis Interface for Linking HMMER results
- NEAT: a domain duplicated in genes near the components of a putative Fe3+ siderophore transporter from Gram-positive pathogenic bacteria.
- NetworKIN: a resource for exploring cellular phosphorylation networks
- Network Neighbors of Drug Targets Contribute to Drug Side-Effect Similarity
- New developments in the InterPro database
- No Sec7-homology domain in guanine-nucleotide-exchange factors that act on Ras and Rho
- Non-orthologous gene displacement
- Non-random retention of protein-coding overlapping genes in Metazoa
- Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets
- Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways
- Novel drug candidates for the treatment of metastatic colorectal cancer through global inverse gene-expression profiling.
- Novel protein domains and repeats in Drosophila melanogaster: Insights into structure, function, and evolution
- OGEE: an online gene essentiality database
- ON ALPHA-HELICES TERMINATED BY GLYCINE .1. IDENTIFICATION OF COMMON STRUCTURAL FEATURES
- ON ALPHA-HELICES TERMINATED BY GLYCINE .2. RECOGNITION BY SEQUENCE PATTERNS
- Ocean plankton. Determinants of community structure in the global plankton interactome.
- Ocean plankton. Environmental characteristics of Agulhas rings affect interocean plankton transport.
- Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean.
- Ocean plankton. Patterns and ecological drivers of ocean viral communities.
- Ocean plankton. Structure and function of the global ocean microbiome.
- On the classification of modular proteins
- Ontologies in Quantitative Biology: A Basis for Comparison, Integration, and Discovery
- Open science resources for the discovery and analysis of Tara Oceans data.
- Operon structure and cotranslational subunit association direct protein assembly in bacteria.
- Opsins and clusters of sensory G-protein-coupled receptors in the sea urchin genome
- Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes
- Orthology prediction methods: A quality assessment using curated protein families
- PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
- PROKARYOTIC MEMBERS OF A NEW FAMILY OF PUTATIVE HELICASES WITH SIMILARITY TO TRANSCRIPTION ACTIVATOR SNF2
- PROPOSED ACQUISITION OF AN ANIMAL PROTEIN DOMAIN BY BACTERIA
- PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.
- PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins
- Palindromic repetitive DNA elements with coding potential in Methanocaldococcus jannaschii
- Pathogenesis of DNA repair-deficient cancers: a statistical meta-analysis of putative Real Common Target genes
- Pathway alignment: application to the comparative analysis of glycolytic enzymes
- Phospholipases A2 and Wnts are unlikely to share a common ancestor.
- Plankton networks driving carbon export in the oligotrophic ocean.
- Pleckstrin's repeat performance: A novel domain in G-protein signaling?
- Pleckstrin's repeat performance: a novel domain in G-protein signaling?
- Polarization of microbial communities between competitive and cooperative metabolism
- Positionally cloned human disease genes: Patterns of evolutionary conservation and functional motifs
- Post-translational GPI lipid anchor modification of proteins in kingdoms of life: analysis of protein sequence data from complete genomes
- Potential of fecal microbiota for early-stage detection of colorectal cancer.
- Powers and pitfalls in sequence analysis: The 70% hurdle
- Predicting biological networks from genomic data
- Predicting function: From genes to genomes and back
- Predicting functions from protein sequences - where are the bottlenecks?
- Predicting protein cellular localization using a domain projection method
- Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences
- Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours
- Prediction of Drug Combinations by Integrating Molecular and Pharmacological Data
- Prediction of deleterious human alleles
- Prediction of effective genome size in metagenomic samples
- Prediction of nonsynonymous single nucleotide polymorphisms in human disease-associated genes
- Prediction of potential GPI-modification sites in proprotein sequences
- Prediction of structural domains of TAP reveals details of its interaction with p15 and nucleoporins
- Preface
- Protein annotation: detective work for function prediction
- Protein coding potential of retroviruses and other transposable elements in vertebrate genomes
- Protein disorder prediction: Implications for structural proteomics
- Protein domain analysis in the era of complete genomes
- Protein families in multicellular organisms
- Protein function space: viewing the limits or limited by our view?
- Protein interaction networks from yeast to human
- Protein sequence motifs
- Proteome Organization in a Genome-Reduced Bacterium
- Proteome survey reveals modularity of the yeast cell machinery
- Quantification of insect genome divergence
- Quantifying environmental adaptation of metabolic pathways in metagenomics
- Quantitative assessment of protein function prediction from metagenomics shotgun sequences
- Quantitative phylogenetic assessment of microbial communities in diverse environments
- Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.
- Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences.
- READY FOR A MOTIF SUBMISSION - A PROPOSED CHECKLIST
- RECOGNITION OF DIFFERENT NUCLEOTIDE-BINDING SITES IN PRIMARY STRUCTURES USING A PROPERTY-PATTERN APPROACH
- RECOGNITION OF FUNCTIONAL REGIONS IN PRIMARY STRUCTURES USING A SET OF PROPERTY PATTERNS
- REF, an evolutionarily conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export
- RanBP2/Nup358 provides a major binding site for NXF1-p15 dimers at the nuclear pore complex and functions in nuclear mRNA export
- Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames
- Recent improvements to the SMART domain-based sequence annotation resource
- Richness of human gut microbiome correlates with metabolic markers.
- Role for urea in nitrification by polar marine Archaea
- SAM as a protein interaction domain involved in developmental regulation.
- SEQUENCE SIMILARITIES BETWEEN TRYPTOPHAN SYNTHASE-BETA SUBUNIT AND OTHER PYRIDOXAL-PHOSPHATE-DEPENDENT ENZYMES
- SHOT: a web server for the construction of genome phylogenies
- SMART 4.0: towards genomic data integration
- SMART 5: domains in the context of genomes and networks
- SMART 6: recent updates and new developments
- SMART 7: recent updates to the protein domain annotation resource
- SMART, a simple modular architecture research tool: Identification of signaling domains
- SMART: a web-based tool for the study of genetically mobile domains
- SMART: identification and annotation of domains from signalling and extracellular protein sequences
- SMART: recent updates, new developments and status in 2015.
- SNP frequencies in human genes - an excess of rare alleles and differing modes of selection
- SPG20 is mutated in Troyer syndrome, an hereditary spastic paraplegia
- SPRY domains in ryanodine receptors (Ca2+-release channels)
- STITCH 2: an interaction network database for small molecules and proteins
- STITCH 3: zooming in on protein-chemical interactions
- STITCH 4: integration of protein-chemical interactions with user data
- STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.
- STITCH: interaction networks of chemicals and proteins
- STRING 7 - recent developments in the integration and prediction of protein interactions
- STRING 8-a global view on proteins and their functional interactions in 630 organisms
- STRING v10: protein-protein interaction networks, integrated over the tree of life.
- STRING v9.1: protein-protein interaction networks, with increased coverage and integration
- STRING: a database of predicted functional associations between proteins
- STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene
- STRING: known and predicted protein-protein associations, integrated and transferred across organisms
- Secreted fringe-like signaling molecules may be glycosyltransferases
- SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology
- Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution
- Self-organizing hierarchic networks for pattern recognition in protein sequence.
- Sequence Analysis
- Sequence analysis of multidomain proteins: past perspectives and future directions.
- Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
- Sequence properties of GPI-anchored proteins near the omega-site: constraints for the polypeptide binding site of the putative transamidase
- Sequence-based factors influencing the expression of heterologous genes in the yeast Pichia pastoris - A comparative view on 79 human genes
- Sequence-based feature prediction and annotation of proteins
- Sequences and topology - Deriving biological knowledge from genomic sequences
- Sequences and topology - Genes and structures in context - Editorial overview
- Shared components of protein complexes-versatile building blocks or biochemical artefacts?
- Shuffled domains in extracellular proteins
- Similar gene expression profiles do not imply similar tissue functions
- Sircah: a tool for the detection and visualization of alternative transcripts
- SmashCell: a software framework for the analysis of single-cell amplified genome sequences
- SmashCommunity: a metagenomic annotation and analysis tool
- Solution structure of the receptor tyrosine kinase EphB2 SAM domain and identification of two distinct homotypic interaction sites.
- Spatiotemporal variation of mammalian protein complex stoichiometries.
- Sperm-egg binding protein or proto-oncogene?
- Splicing factors stimulate polyadenylation via USEs at non-canonical 3 ' end formation signals
- Spore number control and breeding in Saccharomyces cerevisiae: a key role for a self-organizing system
- Spray drying plants for manufacture of dustless powders - A technical note
- Standardized benchmarking in the quest for orthologs.
- Structural analysis of protein-ligand interactions: the binding of endogenous compounds and of synthetic drugs
- Structural genomics of human proteins - target selection and generation of a public catalogue of expression clones
- Structural similarity to bridge sequence space: Finding new families on the bridges
- Structure and distribution of modules in extracellular proteins.
- Structure-based assembly of protein complexes in yeast
- SuperTarget and Matador: resources for exploring drug-target relationships
- Systematic association of genes to phenotypes by genome and literature mining
- Systematic discovery of analogous enzymes in thiamin biosynthesis
- Systematic discovery of in vivo phosphorylation networks
- Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches
- Systematic identification of genes with coding microsatellites mutated in DNA mismatch repair-deficient cancer cells
- Systematic identification of novel protein domain families associated with nuclear functions
- Systematic identification of proteins that elicit drug side effects.
- Systems microbiology - Timeline - Molecular eco-systems biology: towards an understanding of community function
- TAP (NXF1) belongs to a multigene family of putative RNA export factors with a conserved modular architecture
- THE CUB DOMAIN - A WIDESPREAD MODULE IN DEVELOPMENTALLY-REGULATED PROTEINS
- THE CYTIDYLYLTRANSFERASE SUPERFAMILY - IDENTIFICATION OF THE NUCLEOTIDE-BINDING SITE AND FOLD PREDICTION
- THE IMMUNOGLOBULIN FOLD - STRUCTURAL CLASSIFICATION, SEQUENCE PATTERNS AND COMMON CORE
- THE MODULAR ARCHITECTURE OF A NEW FAMILY OF GROWTH-REGULATORS RELATED TO CONNECTIVE-TISSUE GROWTH-FACTOR
- THE MODULAR ARCHITECTURE OF VERTEBRATE COLLAGENS
- THE MODULAR STRUCTURE OF NIFU PROTEINS
- THE WW DOMAIN - A SIGNALING SITE IN DYSTROPHIN
- TRACING THE SPREAD OF FIBRONECTIN TYPE-III DOMAINS IN BACTERIAL GLYCOHYDROLASES
- Tara Oceans. Tara Oceans studies plankton at planetary scale. Introduction.
- Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing
- Temporal and technical variability of human gut metagenomes.
- The Combination of X-Ray Crystallography and Cryo-Electron Microscopy Provides Insight into the Overall Architecture of the Dodecameric Rvb1/Rvb2 Complex.
- The DNA sequence of human chromosome 7
- The Ecoresponsive Genome of Daphnia pulex
- The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.
- The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources
- The InterPro Database, 2003 brings increased coverage and new features
- The InterPro protein families database: the classification resource after 15 years.
- The KIND module: a putative signalling domain evolved from the C lobe of the protein kinase fold
- The SEA module: a new extracellular domain associated with O-glycosylation.
- The SIDER database of drugs and side effects.
- The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
- The Spir actin organizers are involved in vesicle transport processes
- The Tenth Asia Pacific Bioinformatics Conference (APBC 2012) INTRODUCTION
- The WHy domain mediates the response to desiccation in plants and bacteria
- The black-pearl gene of Drosophila defines a novel conserved protein family and is required for larval growth and survival
- The draft sequences - Filling in the gaps
- The exploration of network motifs as potential drug targets from post-translational regulatory networks.
- The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans
- The genome of the model beetle and pest Tribolium castaneum
- The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract
- The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract (vol 99, pg 14422, 2002)
- The genome sequence of the malaria mosquito Anopheles gambiae
- The human genome: Genes, pseudogenes, and variation on chromosome 7
- The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates
- The identification of a conserved domain in both spartin and spastin, mutated in hereditary spastic paraplegia
- The identification of functional modules from the genomic association of genes
- The mahogany protein is a receptor involved in suppression of obesity.
- The microbiome explored: recent insights and future challenges
- The p150-Spir protein provides a link between c-Jun N-terminal kinase function and actin reorganization
- The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly
- The protein phosphatase 2C (PP2C) superfamily: detection of bacterial homologues.
- The rhodanese/Cdc25 phosphatase superfamily - Sequence-structure-function relations
- The three-dimensional structure of the HRDC domain and implications for the Werner and Bloom syndrome proteins
- The way we write - Country-specific variations of the English language in the biomedical literature
- Toward automatic reconstruction of a highly resolved tree of life
- Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data
- Towards Cellular Systems in 4D
- Towards a structural basis of human non-synonymous single nucleotide polymorphisms
- Towards detection of orthologues in sequence databases
- Towards the biogeography of prokaryotic genes
- Transcription start site associated RNAs in bacteria
- Transcriptome Complexity in a Genome-Reduced Bacterium
- Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer
- Update of the G2D tool for prioritization of gene candidates to inherited diseases
- Update on XplorMed: a web server for exploring scientific literature
- Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism
- Utilizing the gut microbiome in decompensated cirrhosis and acute-on-chronic liver failure
- Variation and evolution of the citric acid cycle: a genomic perspective
- Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii
- Very-KIND is a novel nervous system specific guanine nucleotide exchange factor for Ras GTPases
- Visualizing translation dynamics at atomic detail inside a bacterial cell
- WHATS IN A GENOME
- Wanted: subcellular localization of proteins based on sequence
- XplorMed: a tool for exploring MEDLINE abstracts
- Younger Genes Are Less Likely to Be Essential than Older Genes, and Duplicates Are Less Likely to Be Essential than Singletons of the Same Age
- [Metagenomics of the intestinal microbiota: potential applications].
- eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.
- eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations
- eggNOG v3.0: Orthologous groups covering 1133 organisms at 41 different taxonomic ranges
- eggNOG v4.0: nested orthology inference across 3686 organisms
- eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
- eggNOG: automated construction and annotation of orthologous groups of genes
- iPath2.0: interactive pathway explorer
- iPath: interactive exploration of biochemical pathways and networks