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List of works by Peer Bork

(Phospho)proteomic Profiling of Microsatellite Unstable CRC Cells Reveals Alterations in Nuclear Signaling and Cholesterol Metabolism Caused by Frameshift Mutation of NMD Regulator UPF3A

scientific article published on 23 July 2020

20 years of the SMART protein domain annotation resource

scientific article published on 10 October 2017

4DXpress: a database for cross-species expression pattern comparisons

scientific article published on 04 October 2007

A 15q24 microdeletion in transient myeloproliferative disease (TMD) and acute megakaryoblastic leukaemia (AMKL) implicates PML and SUMO3 in the leukaemogenesis of TMD/AMKL

A P-loop-like motif in a widespread ATP pyrophosphatase domain: implications for the evolution of sequence motifs and enzyme activity.

scientific article

A Previously Undescribed Highly Prevalent Phage Identified in a Danish Enteric Virome Catalog

scientific article published on 19 October 2021

A Temporal Map of Transcription Factor Activity: Mef2 Directly Regulates Target Genes at All Stages of Muscle Development

scientific article (publication date: June 2006)

A complex prediction: three-dimensional model of the yeast exosome.

scientific article published on July 2002

A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens

scientific article

A computational framework to integrate high-throughput ‘-omics’ datasets for the identification of potential mechanistic links

A computational screen for type I polyketide synthases in metagenomics shotgun data

scientific article

A fair comparison

scientific article published in April 2014

A fast, sensitive pattern-matching approach for protein sequences

scientific article published in April 1993

A genome-wide survey of human pseudogenes

scientific article

A global ocean atlas of eukaryotic genes.

scientific article published on 25 January 2018

A holistic approach to marine eco-systems biology

scientific article

A human gut microbial gene catalogue established by metagenomic sequencing

scientific article

A hybrid protein kinase-RNase in an interferon-induced pathway?

scientific article published on 01 November 1993

A large domain common to sperm receptors (Zp2 and Zp3) and TGF-beta type III receptor

scientific article

A latrophilin/CL-1-like GPS domain in polycystin-1

scientific article (publication date: 26 August 1999)

A letter of comment

article published in 1996

A lipid-binding domain in Wnt: a case of mistaken identity?

scientific article published on 01 October 1999

A method and server for predicting damaging missense mutations

scientific article (publication date: April 2010)

A module of the DnaJ heat shock proteins found in malaria parasites

scientific article published in April 1992

A molecular study of microbe transfer between distant environments

scientific article

A network of conserved co-occurring motifs for the regulation of alternative splicing

scientific article published on 11 August 2010

A new family of carbon-nitrogen hydrolases

scientific article

A nitrile hydratase in the eukaryote Monosiga brevicollis

scientific article published in 2008

A novel RNA-binding motif in omnipotent suppressors of translation termination, ribosomal proteins and a ribosome modification enzyme?

scientific article

A novel transactivation domain in parkin

A phosphotyrosine interaction domain

scientific article published on 01 March 1995

A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation

scientific article

A protocol for the systematic and quantitative measurement of protein-lipid interactions using the liposome-microarray-based assay

scientific article published on 5 May 2016

A protocol for the update of references to scientific literature in biological databases.

scientific article published in January 2003

A putative nucleic acid-binding domain in Bloom's and Werner's syndrome helicases

scientific article published on November 1997

A quantitative liposome microarray to systematically characterize protein-lipid interactions

scientific article published on 24 November 2013

A side effect resource to capture phenotypic effects of drugs

scientific article (publication date: 19 January 2010)

A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae

scientific article

A versatile structural domain analysis server using profile weight matrices

scientific article published in March 2002

AMOP, a protein module alternatively spliced in cancer cells

scientific article published on 01 March 2002

AQUA: automated quality improvement for multiple sequence alignments

scientific article published on 19 November 2009

ASTD: The Alternative Splicing and Transcript Diversity database

scientific article

Accurate and universal delineation of prokaryotic species ⬇️

scientific article published on July 28, 2013

Alternative splicing and evolution ⬇️

scientific article published on November 1, 2003

Alternative splicing and genome complexity

scientific article

Alternative splicing of human genes: more the rule than the exception?

scientific article published in October 1999

An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins ⬇️

scientific article (publication date: 15 August 1992)

An adhesive domain detected in functionally diverse receptors

scientific article

An expanding family of helicases within the 'DEAD/H' superfamily

scientific article

An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum

scientific article published on 14 November 2014

An integrated catalog of reference genes in the human gut microbiome

scientific article

Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs

scientific article (publication date: July 2004)

Ancient animal microRNAs and the evolution of tissue identity

scientific article

Ancient duplication of DNA polymerase inferred from analysis of complete bacterial genomes

scientific article published on April 1996

Ancient duplication of DNA polymerase inferred from analysis of complete bacterial genomes

article

Annotation of the M. tuberculosis hypothetical orfeome: adding functional information to more than half of the uncharacterized proteins

scientific article

Anopheles gambiae pilot gene discovery project: identification of mosquito innate immunity genes from expressed sequence tags generated from immune-competent cell lines

scientific article published on June 2000

Antibiotics-induced monodominance of a novel gut bacterial order

scientific article published on 18 January 2019

Applying motif and profile searches

scientific article published on January 1996

Assessing systems properties of yeast mitochondria through an interaction map of the organelle

scientific article

Assessment of metagenomic assembly using simulated next generation sequencing data

scientific article

Association of genes to genetically inherited diseases using data mining

scientific article

Associative database of protein sequences

scientific article published in September 1999

Author Correction: Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology

scientific article published on 21 December 2020

Author Correction: Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation

scientific article published on 01 December 2019

Automated annotation of GPI anchor sites: case study C. elegans

scientific article published in July 2000

Automated extraction of information in molecular biology

scientific article

BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments

scientific article published on 22 March 2004

BRCA1 protein products ... Functional motifs...

scientific article published in July 1996

BSD: a novel domain in transcription factors and synapse-associated proteins

scientific article

Bacterial antisense RNAs are mainly the product of transcriptional noise

scientific article published on 4 March 2016

Bioaccumulation of therapeutic drugs by human gut bacteria

scientific article published in 2021

Bioinformatics Analysis of Functional Associations of PTMs.

scientific article published in January 2017

Bioinformatics and molecular medicine--introduction and call for papers

scientific article published on 01 January 1997

Bioinformatics in the post-sequence era.

scientific article

Biosynthetic potential of the global ocean microbiome

scientific article published in July 2022

CART-a chemical annotation retrieval toolkit

scientific article

CASH--a beta-helix domain widespread among carbohydrate-binding proteins

scientific article published in February 2002

Capturing protein communities by structural proteomics in a thermophilic eukaryote.

scientific article published on 25 July 2017

Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines

scientific article

Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline

scientific article published in Nature Communications

Challenging times for bioinformatics

scientific article published in Nature

Characterization of a novel protein-binding module--the WW domain

scientific article

Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding

scientific article published on January 2013

Characterization of targeting domains by sequence analysis: glycogen-binding domains in protein phosphatases

scientific article

Characterization of the mammalian YAP (Yes-associated protein) gene and its role in defining a novel protein module, the WW domain

scientific article

Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching

scientific article published on May 2001

Circular reasoning rather than cyclic expression

scientific article (publication date: 2008)

Classification and quantification of bacteriophage taxa in human gut metagenomes

scientific article

Cloning of a gene from Bacillus cereus with homology to the mreB gene from Escherichia coli

scientific article

Co-evolution of transcriptional and post-translational cell-cycle regulation

scientific article (publication date: 27 September 2006)

Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing.

scientific article

Comments on "Human dominant disease genes are enriched in paralogs originating from whole genome duplication".

scientific article

Common exon duplication in animals and its role in alternative splicing

scientific article

Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

article

Comparative Genome Analysis of the Mollicutes

Comparative analysis of environmental sequences: potential and challenges

scientific article

Comparative analysis of protein interaction networks

article

Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages

scientific article

Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster

scientific article (publication date: 4 October 2002)

Comparative genomic analysis in the region of a major Plasmodium-refractoriness locus of Anopheles gambiae

scientific article

Comparison of CD45 extracellular domain sequences from divergent vertebrate species suggests the conservation of three fibronectin type III domains

scientific article published in August 1996

Comparison of computational methods for the identification of cell cycle-regulated genes

scientific article (publication date: 28 October 2004)

Complement components C1r/C1s, bone morphogenic protein 1 and Xenopus laevis developmentally regulated protein UVS.2 share common repeats

scientific article

Complex genomic rearrangements lead to novel primate gene function

scientific article

Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III.

scientific article published on December 1992

Computational characterization of multiple Gag-like human proteins

scientific article published on 18 September 2006

Computational eco-systems biology in Tara Oceans: translating data into knowledge

scientific article

Computing fuzzy associations for the analysis of biological literature

scientific article published in June 2002

Conformational stability studies of the pleckstrin DEP domain: definition of the domain boundaries.

scientific article published in June 1998

Consent insufficient for data release-Response

scientific article published on 01 May 2019

Conservation of gene co-regulation in prokaryotes and eukaryotes

article

Conservation of gene order: a fingerprint of proteins that physically interact

scientific article (publication date: September 1998)

Consistency of genome-based methods in measuring Metazoan evolution

scientific article

Consistent mutational paths predict eukaryotic thermostability

scientific article

Convergent evolution of similar enzymatic function on different protein folds: the hexokinase, ribokinase, and galactokinase families of sugar kinases

scientific article

Copy number variation analysis and targeted NGS in 77 families with suspected Lynch syndrome reveals novel potential causative genes

scientific article published on 03 October 2018

Correction: LotuS: an efficient and user-friendly OTU processing pipeline.

scientific article

Correspondence

Corrigendum: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

scientific article published in Nature

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

article

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

scientific article published in February 2018

Country-specific antibiotic use practices impact the human gut resistome

scientific article published on 08 April 2013

Coupling proteomics and metabolomics for the unsupervised identification of protein-metabolite interactions in Chaetomium thermophilum

scientific article published on 09 July 2021

Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium.

scientific article published on 28 February 2012

Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome

scientific article published on 8 April 2022

Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton

scientific article

Cytoplasmic signalling domains: the next generation

scientific article

DCD - a novel plant specific domain in proteins involved in development and programmed cell death

scientific article

DDT – a novel domain in different transcription and chromosome remodeling factors

scientific article published on 01 March 2001

Deciphering a global network of functionally associated post-translational modifications

scientific article

Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

scientific article

Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium

scientific article

Detection of coding microsatellite frameshift mutations in DNA mismatch repair-deficient mouse intestinal tumors

scientific article published on 11 September 2014

Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children

scientific article published on 10 July 2015

Differential gene expression in mammary carcinoma cell lines: identification of DRIM, a new gene down-regulated in metastasis

scientific article published on May 1, 1998

Differential genome analysis applied to the species-specific features of Helicobacter pylori

scientific article published on April 1998

Differential genome display

scientific article published on 01 October 1997

Discovering functional novelty in metagenomes: examples from light-mediated processes

scientific article published on 10 October 2008

Discovery and validation of the antimetastatic activity of citalopram in colorectal cancer

scientific article published on 11 February 2015

Discovery, scoring and utilization of human single nucleotide polymorphisms: a multidisciplinary problem

Disentangling Genetic and Environmental Effects on the Proteotypes of Individuals

scientific article published on 25 April 2019

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity

scientific article published on 11 February 2020

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

scientific article published on 2 December 2015

Dispersal strategies shape persistence and evolution of human gut bacteria

publication published on 09 June 2021

Divergent evolution of a beta/alpha-barrel subclass: detection of numerous phosphate-binding sites by motif search

scientific article published on February 1995

Diversity within species: interpreting strains in microbiomes

scientific article published on 04 June 2020

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

scientific article published in July 1999

Drosophila kelch motif is derived from a common enzyme fold

scientific article

Drug discovery in the age of systems biology: the rise of computational approaches for data integration.

scientific article

Drug target identification using side-effect similarity

scientific article (publication date: 11 July 2008)

Drug-induced regulation of target expression

scientific article

Durable coexistence of donor and recipient strains after fecal microbiota transplantation.

scientific article

DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data.

scientific article

ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins

scientific article

EST analysis online: WWW tools for detection of SNPs and alternative splice forms

scientific article published in September 2000

EST comparison indicates 38% of human mRNAs contain possible alternative splice forms

scientific article published in May 2000

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data.

scientific article

Ecogenomics and biogeochemical impacts of uncultivated globally abundant ocean viruses

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

scientific article

Efficacy of Bifidobacterium longum, B. infantis and Lactobacillus acidophilus 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 Clini

scientific article published on 21 November 2019

Energy efficiency trade-offs drive nucleotide usage in transcribed regions

scientific article

Enhanced function annotations for Drosophila serine proteases: A case study for systematic annotation of multi-member gene families

scientific article (publication date: 2008)

Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics

scientific article published on 24 January 2022

Enterotypes in the landscape of gut microbial community composition.

scientific article published on 18 December 2017

Enterotypes of the human gut microbiome

scientific article

Enterotypes of the human gut microbiome

scientific article published in Nature

Environments shape the nucleotide composition of genomes

scientific article

Epidermal growth factor-like modules

article by Iain D. Campbell & Peer Bork published June 1993 in Current Opinion in Structural Biology

Erratum: Addendum: Enterotypes of the human gut microbiome

scientific article published in Nature

Erratum: Classification and quantification of bacteriophage taxa in human gut metagenomes

scholarly article by Alison S Waller et al published 24 June 2014 in The ISME Journal

Estimating rates of alternative splicing in mammals and invertebrates

article

Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer

scientific article

Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries

scientific article

Evolution and functional cross-talk of protein post-translational modifications

scientific article

Evolution and regulation of cellular periodic processes: a role for paralogues

scientific article (publication date: 19 February 2010)

Evolution of Cell Cycle Control: Same Molecular Machines, Different Regulation

scientific article (publication date: August 2007)

Evolution of biomolecular networks: lessons from metabolic and protein interactions

scientific article

Evolution of domain families

scientific article

Evolution of new protein function: recombinational enhancer Fis originated by horizontal gene transfer from the transcriptional regulator NtrC ⬇️

scientific article published on August 14, 1998

Evolution of prokaryotic gene order: genome rearrangements in closely related species

scientific article published in January 2001

Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages

scholarly article

Evolution of tuf genes: ancient duplication, differential loss and gene conversion

scientific article

Evolutionarily mobile modules in proteins.

scientific article

Exopolyphosphate phosphatase and guanosine pentaphosphate phosphatase belong to the sugar kinase/actin/hsp 70 superfamily

scientific article

Experimental characterization of the human non-sequence-specific nucleic acid interactome

scientific article

Exploitation of gene context

scientific article published in June 2000

Exploring MEDLINE abstracts with XplorMed

scientific article

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

scientific article

Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology

scientific article published on June 1995

Extensive Transmission of Microbes along the Gastrointestinal Tract

article

Extensive impact of non-antibiotic drugs on human gut bacteria

scientific article published on 19 March 2018

Extensive transmission of microbes along the gastrointestinal tract

article

Extraction of regulatory gene/protein networks from Medline

scientific article (publication date: 26 July 2005)

Extraction of transcript diversity from scientific literature

scientific article

FMN- or DNA-binding?

scientific article

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper

scientific article published on 29 April 2017

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper

article

Fibronectin type III modules in the receptor phosphatase CD45 and tapeworm antigens

scientific article published on July 1993

Filling in the gaps

scientific article published in Nature

Frame: detection of genomic sequencing errors.

scientific article published on January 1998

Frameshift mutations in coding repeats of protein tyrosine phosphatase genes in colorectal tumors with microsatellite instability

scientific article

Frameshift peptide-derived T-cell epitopes: a source of novel tumor-specific antigens

scientific article

Friedreich's ataxia protein: phylogenetic evidence for mitochondrial dysfunction

article

From genome sequences to protein function

Function prediction and protein networks

scientific article

Functional and evolutionary insights from the genomes of three parasitoid Nasonia species

scientific article

Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes

scientific article published on December 2004

Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III

scientific article (publication date: 16 November 2000)

Functional organization of the yeast proteome by systematic analysis of protein complexes

scientific article

Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

scientific article published in 2022

G2D: a tool for mining genes associated with disease

scientific article

GEAR: A database of Genomic Elements Associated with drug Resistance

scientific article published on 15 March 2017

GENOME MAPS 8: Building Gene Families

scientific article published in Science

GRAM, a novel domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins

scientific article (publication date: October 2000)

GUNC: detection of chimerism and contamination in prokaryotic genomes

scientific article published on 13 June 2021

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

scientific article published on 01 November 2019

Gene annotation from scientific literature using mappings between keyword systems

scientific article published on April 2004

Gene context conservation of a higher order than operons.

scientific article

Gene expression profiling of the rat superior olivary complex using serial analysis of gene expression

scientific article published in December 2004

GeneQuiz: a workbench for sequence analysis.

scientific article published on January 1994

Generation and annotation of the DNA sequences of human chromosomes 2 and 4

scientific article

Genome and protein evolution in eukaryotes

scientific article

Genome evolution

scientific article published on 01 January 2000

Genome evolution reveals biochemical networks and functional modules

scientific article

Genome phylogeny based on gene content

scientific article (publication date: 1999)

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

scientific article

Genome speak

scientific article published in Nature

Genome-wide experimental determination of barriers to horizontal gene transfer.

scientific article published on 18 October 2007

Genomes in Flux: The Evolution of Archaeal and Proteobacterial Gene Content ⬇️

scientific article published on January 1, 2002

Genomic variation landscape of the human gut microbiome

scientific article

Get the most out of your metagenome: computational analysis of environmental sequence data

scientific article

Global analysis of bacterial transcription factors to predict cellular target processes

scientific article published on March 2004

Global genetic capacity for mixotrophy in marine picocyanobacteria

scientific article

Glycogen accumulation, central carbon metabolism, and aging of hematopoietic stem and progenitor cells

scientific article published on 14 July 2020

Go hunting in sequence databases but watch out for the traps

scientific article published in October 1996

Gut Microbiota Linked to Sexual Preference and HIV Infection.

scientific article

Gut microbiota composition is associated with environmental landscape in honey bees.

scientific article published on 30 November 2017

Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition: a metagenomic analysis

scientific article published on 30 December 2016

HEAT repeats in the Huntington's disease protein

scientific article

HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources ⬇️

scientific article published on January 1, 2002

Heat shock protein-90-alpha, a prolactin-STAT5 target gene identified in breast cancer cells, is involved in apoptosis regulation

scientific article

High-resolution transcription atlas of the mitotic cell cycle in budding yeast

scientific article (publication date: 2010)

Histone Deacetylase Inhibitors (HDACi) Cause the Selective Depletion of Bromodomain Containing Proteins (BCPs).

scientific article published on 9 March 2015

Homology among (betaalpha)(8) barrels: implications for the evolution of metabolic pathways

scientific article (publication date: 3 November 2000)

Homology-based fold predictions for Mycoplasma genitalium proteins

scientific article

Homology-based functional proteomics by mass spectrometry: application to the Xenopus microtubule-associated proteome

scientific article published in September 2004

Homology-based gene prediction using neural nets

scientific article published in December 1998

Homology-based method for identification of protein repeats using statistical significance estimates

scientific article published in May 2000

Human gut microbes impact host serum metabolome and insulin sensitivity

scientific article

Human monogenic disease genes have frequently functionally redundant paralogs

scientific article

Human non-synonymous SNPs: server and survey

scientific article

Hundreds of ankyrin-like repeats in functionally diverse proteins: mobile modules that cross phyla horizontally?

scientific article

Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity.

scientific article published on 9 May 2019

Identical variant TSG101 transcripts in soft tissue sarcomas and various non-neoplastic tissues

scientific article published on December 1998

Identical variantTSG101 transcripts in soft tissue sarcomas and various non-neoplastic tissues

scholarly article by Frank Willeke published in December 1998

Identification and analysis of genes and pseudogenes within duplicated regions in the human and mouse genomes

scientific article

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

scientific article published on 6 July 2014

Identification and characterization of UEV3, a human cDNA with similarities to inactive E2 ubiquitin-conjugating enzymes

scientific article

Identification and mutation analysis of the complete gene for Chediak-Higashi syndrome

scientific article published on November 1996

Identification of Residues within the SHC Phosphotyrosine Binding/Phosphotyrosine Interaction Domain Crucial for Phosphopeptide Interaction

scientific article published in Journal of Biological Chemistry

Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features

scholarly article published 11 March 2019

Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features

scientific article published on 01 February 2020

Identification of tightly regulated groups of genes during Drosophila melanogaster embryogenesis

scientific article (publication date: 16 January 2007)

Identifying single copy orthologs in Metazoa

scientific article published on December 2011

Imidazole propionate is increased in diabetes and associated with dietary patterns and altered microbial ecology

scientific article published on 18 November 2020

Immunity-related genes and gene families in Anopheles gambiae

scientific article published in October 2002

Impact of genome reduction on bacterial metabolism and its regulation.

scientific article published in November 2009

Impact of selection, mutation rate and genetic drift on human genetic variation.

scientific article

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

scientific article

Increase of functional diversity by alternative splicing

scientific article

Individual variation in protein-coding sequences of human genome

scientific article

Individuality and temporal stability of the human gut microbiome.

scientific article published in January 2013

Information extraction from full text scientific articles: where are the keywords?

scientific article

Initial sequencing and analysis of the human genome

scientific article published on 15 February 2001

Initial sequencing and comparative analysis of the mouse genome

scientific article

Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile

scientific article

Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats

scientific article published on 17 September 2015

Integration of genome data and protein structures: prediction of protein folds, protein interactions and "molecular phenotypes" of single nucleotide polymorphisms

scientific article

Inter-individual differences in the gene content of human gut bacterial species

scientific article published on 21 April 2015

InterPro in 2011: new developments in the family and domain prediction database

scientific article

InterPro in 2011: new developments in the family and domain prediction database

scientific article published on 19 May 2012

InterPro in 2017-beyond protein family and domain annotations

scientific article

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

article by Alex Mitchell et al published 6 November 2018 in Nucleic Acids Research

InterPro, progress and status in 2005

scientific article

InterPro: an integrated documentation resource for protein families, domains and functional sites

scientific article

InterPro: the integrative protein signature database

scientific article

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

scientific article published on 01 July 2019

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

scientific article

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation

scientific article

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy ⬇️

scientific article published on April 5, 2011

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

scientific article

Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children

scientific article published on 26 January 2016

Inversions and the dynamics of eukaryotic gene order

scientific article

Is there biological research beyond Systems Biology? A comparative analysis of terms

scientific article published on 25 May 2005

KEGG Atlas mapping for global analysis of metabolic pathways

scientific article

L27, a novel heterodimerization domain in receptor targeting proteins Lin-2 and Lin-7.

scientific article

LSAT: learning about alternative transcripts in MEDLINE.

scientific article published on 12 January 2006

Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes

scientific article published on 01 April 2022

Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?

scientific article

Large-scale prediction of drug-target relationships

scientific article (publication date: 20 February 2008)

Lipid Cooperativity as a General Membrane-Recruitment Principle for PH Domains

scientific article published on 19 August 2015

Literature mining for the biologist: from information retrieval to biological discovery

scientific article (publication date: February 2006)

LotuS: an efficient and user-friendly OTU processing pipeline.

scientific article published on 30 September 2014

Luminal signalling links cell communication to tissue architecture during organogenesis.

scientific article

MOCAT2: a metagenomic assembly, annotation and profiling framework

scientific article

MOCAT: a metagenomics assembly and gene prediction toolkit

scientific article

MVP: a microbe-phage interaction database.

scientific article

Measuring genome evolution

scientific article (publication date: 26 May 1998)

Mechismo: predicting the mechanistic impact of mutations and modifications on molecular interactions.

scientific article

Medusa: a simple tool for interaction graph analysis

scientific article published on 27 September 2005

Merging extracellular domains: fold prediction for laminin G-like and amino-terminal thrombospondin-like modules based on homology to pentraxins

scientific article

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

scientific article published on 01 April 2019

Metabolic anchor reactions for robust biorefining

scientific article

Metabolic dependencies drive species co-occurrence in diverse microbial communities

scientific article published on 4 May 2015

Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli

scientific article published on March 1996

Metabolites: a helping hand for pathway evolution?

scientific article

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

scientific article published on 18 September 2013

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation

scientific article published on 01 April 2019

Metagenomic analysis of gut microbial communities from a Central Asian population

article

Metagenomic assessment of the global distribution of bacteria and fungi

scientific article published on 13 November 2020

Metagenomic insights into the human gut resistome and the forces that shape it.

scientific article published on 29 January 2014

Metagenomic species profiling using universal phylogenetic marker genes

scientific article

Microbial Biomarkers for Early Cancer Detection

scientific article published on 24 February 2017

Microbial abundance, activity and population genomic profiling with mOTUs2

scientific article published on 4 March 2019

Microbiome and metabolome features of the cardiometabolic disease spectrum

scientific article published on 17 February 2022

Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat

scientific article published on 3 June 2008

Minimum Information about an Uncultivated Virus Genome (MIUViG)

scientific article published on 17 December 2018

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

scientific article

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

scientific article

Molecular characterization of a cDNA encoding functional human CLK4 kinase and localization to chromosome 5q35 [correction of 4q35].

scientific article

Molecular eco-systems biology: towards an understanding of community function

scientific article published in September 2008

More than 1,000 putative new human signalling proteins revealed by EST data mining

scientific article

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Sequences and topology

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Structural similarity to bridge sequence space: finding new families on the bridges

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Systematic identification of genes with coding microsatellites mutated in DNA mismatch repair-deficient cancer cells.

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Systematic identification of novel protein domain families associated with nuclear functions

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Systematic identification of proteins that elicit drug side effects

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Tara Oceans studies plankton at planetary scale

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Tara Oceans: towards global ocean ecosystems biology

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Target-specific requirements for enhancers of decapping in miRNA-mediated gene silencing

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Temporal and technical variability of human gut metagenomes

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The CUB domain. A widespread module in developmentally regulated proteins

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The Combination of X-Ray Crystallography and Cryo-Electron Microscopy Provides Insight into the Overall Architecture of the Dodecameric Rvb1/Rvb2 Complex

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The Genome Sequence of the Malaria Mosquito Anopheles gambiae

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The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data

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The Human Gut Microbiome: From Association to Modulation

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The WHy domain mediates the response to desiccation in plants and bacteria

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eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

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eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations

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eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

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eggNOG v4.0: nested orthology inference across 3686 organisms

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eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale

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iPath2.0: interactive pathway explorer

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mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes

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metaSNV: A tool for metagenomic strain level analysis

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proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes

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proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes

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