Myriads of protein families, and still counting

From the historical record of genome sequencing, we show that the rate of discovery of new families has remained constant over time, indicating that our knowledge of sequence space is far from complete.

• Publication year

  2003

• Venue

  Genome Biology

• Publication date

  2003-01-28

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1186/gb-2003-4-2-401PMID 12620116PMCID 151299
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• An efficient algorithm for large-scale detection of protein families.

  2002cited by this paper
• Biodiversity: Microbial genomes multiply

  2002cited by this paper
• Microbial genomes: dealing with diversity.

  2001cited by this paper
• Completeness in structural genomics

  2001cited by this paper
• Genome sequences and great expectations

  2000cited by this paper
• Erratum. Finding families for genomic ORFans

  1999cited by this paper
• One thousand families for the molecular biologist

  1992cited by this paper
• Proteins. One thousand families for the molecular biologist.

  1992cited by this paper

• CGG toolkit: Software components for computational genomics

  2023cites this paper
• Functional characterization of prokaryotic dark matter: the road so far and what lies ahead

  2022cites this paper
• Proposition of a Novel Strategy for Creation of Entirely New Proteins

  2021cites this paper
• Quantifying the taxonomic bias in enzymology

  2021cites this paper
• ActDES – a curated Actinobacterial Database for Evolutionary Studies

  2020cites this paper
• Machine learning can be used to distinguish protein families and generate new proteins belonging to those families.

  2019cites this paper
• Deciphering the role of microRNA - A step by step guide.

  2017cites this paper
• Cestode parasites release extracellular vesicles with microRNAs and immunodiagnostic protein cargo.

  2017cites this paper
• Genome-wide identification of microRNA targets in the neglected disease pathogens of the genus Echinococcus.

  2017cites this paper
• 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

  2017cites this paper
• 3'-UTR SNP rs2229611 in G6PC1 affects mRNA stability, expression and Glycogen Storage Disease type-Ia risk.

  2017cites this paper
• miRNA‐8159 is involved in TLR signaling pathway regulation after pathogen infection by direct targeting TLR13 in miiuy croaker

  2017cites this paper
• MicroRNA transcriptome analysis in chicken kidneys in response to differing virulent infectious bronchitis virus infections

  2017cites this paper
• microRNA analysis of Taenia crassiceps cysticerci under praziquantel treatment and genome-wide identification of Taenia solium miRNAs.

  2017cites this paper
• On the power and limits of sequence similarity based clustering of proteins into families

  2017cites this paper
• Increased Expression of a MicroRNA Correlates with Anthelmintic Resistance in Parasitic Nematodes

  2017cites this paper
• Small RNA‐Seq analysis reveals microRNA‐regulation of the Imd pathway during Escherichia coli infection in Drosophila

  2017cites this paper
• Computational deciphering of biotic stress associated genes in tomato (Solanum lycopersicum)

  2017cites this paper
• Landscape of RNAs in human lumbar disc degeneration

  2016cites this paper
• MiR-980 Is a Memory Suppressor MicroRNA that Regulates the Autism-Susceptibility Gene A2bp1.

  2016cites this paper
• Identifying miRNA synergistic regulatory networks in heterogeneous human data via network motifs.

  2016cites this paper
• The RNA world in the 21st century - a systems approach to finding non-coding keys to clinical questions

  2016cites this paper
• Genome Sequencing, Transcriptomics, and Proteomics

  2016cites this paper
• The Statistical Mechanics Approach to Protein Sequence Data: Beyond Contact Prediction

  2016cites this paper
• Urinary microRNAs as potential biomarkers of pesticide exposure.

  2016cites this paper
• MicroTrout: A comprehensive, genome-wide miRNA target prediction framework for rainbow trout, Oncorhynchus mykiss.

  2016cites this paper
• A Complex Genome-MicroRNA Interplay in Human Mitochondria

  2015cites this paper
• Cloning and characterization of nickel uptake regulator NUR mutants from Streptomyces coelicolor

  2015cites this paper
• Protein Family Identification using Markov Chain as Feature Extraction and Probabilistic Neural Net....

  2015cites this paper
• Computational approach for elucidating interactions of cross-species miRNAs and their targets in Flaviviruses.

  2015cites this paper
• MicroRNA Target Identification: Lessons from HypoxamiRs

  2014cites this paper
• Sequence Classification of Protein Families: Pfam and other Resources

  2013cites this paper
• Why so many unknown genes? Partitioning orphans from a representative transcriptome of the lone star tick Amblyomma americanum

  2013cites this paper
• A Complex Network of MicroRNAs Expressed in Brain and Genes Associated with Amyotrophic Lateral Sclerosis

  2013cites this paper
• Characterization of the Rainbow Trout Egg MicroRNA Transcriptome

  2012cites this paper
• Pseudorabies Virus Infected Porcine Epithelial Cell Line Generates a Diverse Set of Host MicroRNAs and a Special Cluster of Viral MicroRNAs

  2012cites this paper
• Evolutionary insights into scleractinian corals using comparative genomic hybridizations

  2012cites this paper
• Microbial Pattern Recognition Causes Distinct Functional Micro-RNA Signatures in Primary Human Monocytes

  2012cites this paper
• Screening for cancer associated MiRNAs through co-gene, co-function and co-pathway analysis

  2012cites this paper
• Cross Talk Between MicroRNA and Coding Cancer Genes

  2012cites this paper
• MicroRNAs as components of regulatory networks controlling erythropoiesis

  2012cites this paper
• The quest for an upper limit in systems biology

  2012cites this paper
• Protein-Protein Interactions as Drug Targets

  2012cites this paper
• Integrating microRNAs into a system biology approach to acute lung injury.

  2011cites this paper
• In silico structure‐activity‐relationship (SAR) models from machine learning: a review

  2011cites this paper
• Coregulation of transcription factors and microRNAs in human transcriptional regulatory network

  2011cites this paper
• Regulatory exaptation of the catabolite repression protein (Crp)-cAMP system in Pseudomonas putida.

  2011cites this paper
• Hyposensitization therapy with autologous semen in two Dutch caucasian males: beneficial effects in Postorgasmic Illness Syndrome (POIS; Part 2).

  2011cites this paper
• Mutagen-Specific Mutation Signature Determines Global microRNA Binding

  2011cites this paper
• MicroRNA evolution by arm switching

  2011cites this paper
• Upregulation of MiR-155 in Nasopharyngeal Carcinoma is Partly Driven by LMP1 and LMP2A and Downregulates a Negative Prognostic Marker JMJD1A

  2011cites this paper
• Efficient estimation of p-values for HMModeller

  2011cites this paper
• Identification of cardiovascular microRNA targetomes.

  2011cites this paper
• Quantitative Prediction of miRNA-mRNA Interaction Based on Equilibrium Concentrations

  2011cites this paper
• MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action.

  2011cites this paper
• Rapid Evolution of Coral Proteins Responsible for Interaction with the Environment

  2011cites this paper
• L’évolution modulaire des protéines : un point de vue phylogénétique

  2011cites this paper
• NAViGaTing the Micronome – Using Multiple MicroRNA Prediction Databases to Identify Signalling Pathway-Associated MicroRNAs

  2011cites this paper
• The evolutionary origin of orphan genes

  2011cites this paper
• Comparison and Integration of Target Prediction Algorithms for microRNA Studies

  2010cites this paper
• MicroRNAs target gene and signaling pathway by bioinformatics analysis in the cardiac hypertrophy.

  2010cites this paper
• Improving performance of mammalian microRNA target prediction

  2010cites this paper
• Dynamic isomiR regulation in Drosophila development.

  2010cites this paper
• In silico identification of conserved microRNAs and their target transcripts from expressed sequence tags of three earthworm species

  2010cites this paper
• Regulation of fibrinogen production by microRNAs.

  2010cites this paper
• Target mRNA abundance dilutes microRNA and siRNA activity

  2010cites this paper
• MicroRNA: Biogenesis, Function and Role in Cancer

  2010cites this paper
• Evolutionary Transients in the Rice Transcriptome

  2010cites this paper
• Sequencing delivers diminishing returns for homology detection: implications for mapping the protein universe

  2010cites this paper
• Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites

  2010cites this paper
• A two-step site and mRNA-level model for predicting microRNA targets

  2010cites this paper
• MiRNA–miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features

  2010cites this paper
• A Bayesian decision fusion approach for microRNA target prediction

  2010cites this paper
• The origin, evolution and structure of the protein world.

  2009cites this paper
• More than just orphans: are taxonomically-restricted genes important in evolution?

  2009cites this paper
• Algorithms and Performance measurements for MotifNetwork analysis programs

  2009cites this paper
• Computational prediction of amphioxus microRNA genes and their targets.

  2009cites this paper
• Identification of ionizing radiation-responsive microRNAs in the IM9 human B lymphoblastic cell line.

  2009cites this paper
• PMRD: plant microRNA database

  2009cites this paper
• A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

  2009cites this paper
• Predicting potentially functional SNPs in drug-response genes.

  2009cites this paper
• A Bayesian Approach for Identifying miRNA Targets by Combining Sequence Prediction and Expression Profiling

  2009cites this paper
• Bioinformatics : Tools and Applications

  2009cites this paper
• Protein Sequence Databases

  2009cites this paper
• Nature of the protein universe

  2009cites this paper
• Computational Prediction of Protein–Protein Interactions

  2008cites this paper
• Genomics and Phylogeny of Motor Proteins: Tools and Analyses

  2008cites this paper
• Genomic panorama of Bradyrhizobium japonicum CPAC 15, a commercial inoculant strain largely established in Brazilian soils and belonging to the same serogroup as USDA 123

  2008cites this paper
• Evolutionary Genomics: Linking Macromolecular Structure, Genomes and Biological Networks

  2008cites this paper
• The Microbial Engines That Drive Earth's Biogeochemical Cycles

  2008cites this paper
• Origins and evolution of modern biochemistry: insights from genomes and molecular structure.

  2008cites this paper
• Data Pushing: A Fly-Centric Guide to Bioinformatics Tools

  2008cites this paper
• Pfam 10 years on: 10 000 families and still growing

  2008cites this paper
• Chapter 17. Extension of endogenous primers as a tool to detect micro-RNA targets.

  2008cites this paper
• An Integrative Analysis of microRNA and mRNA Expression—A Case Study

  2008cites this paper
• Protein function space: viewing the limits or limited by our view?

  2007cites this paper
• The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families

  2007cites this paper
• The global landscape of sequence diversity

  2007cites this paper
• A computational approach to the identification of lineage-specific bacterial genes and a determination of their biological significance.

  2007cites this paper
• Protein Interaction networks and their applications to protein characterization and cancer genes prediction

  2007cites this paper