1. Messenger RNA and microRNA profiling during early mouse EB formation

    Gene Expression Patterns 11(5):334 (2011)

    Highlights ► We look at messenger RNA and microRNA expression during embryoid body formation. ► Both show large-scale changes in expression. ► Genes involved in stem cell differentiation change the most. ► MicroRNA target prediction reveals widespread regulation mediated by microRNAs. ...
  2. MiR-221 influences effector functions and actin cytoskeleton in mast cells.

    PLoS ONE 6(10):e26133 (2011) PMID 22022537 PMCID PMC3192147

    Mast cells have essential effector and immunoregulatory functions in IgE-associated allergic disorders and certain innate and adaptive immune responses, but the role of miRNAs in regulating mast cell functions is almost completely unexplored. To examine the role of the activation-induced miRNA m...
  3. Messenger RNA and microRNA profiling during early mouse EB formation.

    Gene Expression Patterns 11(5-6):334 (2011) PMID 21440681

    Embryonic stem (ES) cells can be induced to differentiate into embryoid bodies (EBs) in a synchronised manner when plated at a fixed density in hanging drops. This differentiation procedure mimics post-implantation development in mouse embryos and also serves as the starting point of protocols u...
  4. Messenger RNA and microRNA profiling during early mouse EB formation

    Gene Expression Patterns 11(5):334 (2011) PMID 21440681

    Highlights ► We look at messenger RNA and microRNA expression during embryoid body formation. ► Both show large-scale changes in expression. ► Genes involved in stem cell differentiation change the most. ► MicroRNA target prediction reveals widespread regulation mediated by microRNAs. ...
  5. MiR-221 influences effector functions and actin cytoskeleton in mast cells.

    PLoS ONE 6(10):e26133 (2011) PMID 22022537 PMCID PMC3192147

    Mast cells have essential effector and immunoregulatory functions in IgE-associated allergic disorders and certain innate and adaptive immune responses, but the role of miRNAs in regulating mast cell functions is almost completely unexplored. To examine the role of the activation-induced miRNA m...
  6. miRBase: tools for microRNA genomics.

    Nucleic Acids Research 36(Database issue):D154 (2008) PMID 17991681 PMCID PMC2238936

    miRBase is the central online repository for microRNA (miRNA) nomenclature, sequence data, annotation and target prediction. The current release (10.0) contains 5071 miRNA loci from 58 species, expressing 5922 distinct mature miRNA sequences: a growth of over 2000 sequences in the past 2 years. ...
  7. miRBase: tools for microRNA genomics.

    Nucleic Acids Research 36(Database issue):D154 (2008) PMID 17991681 PMCID PMC2238936

    miRBase is the central online repository for microRNA (miRNA) nomenclature, sequence data, annotation and target prediction. The current release (10.0) contains 5071 miRNA loci from 58 species, expressing 5922 distinct mature miRNA sequences: a growth of over 2000 sequences in the past 2 years. ...
  8. Genomic analysis of human microRNA transcripts.

    PNAS 104(45):17719 (2007) PMID 17965236 PMCID PMC2077053

    MicroRNAs (miRNAs) are important genetic regulators of development, differentiation, growth, and metabolism. The mammalian genome encodes approximately 500 known miRNA genes. Approximately 50% are expressed from non-protein-coding transcripts, whereas the rest are located mostly in the introns o...
  9. Genomic analysis of human microRNA transcripts.

    PNAS 104(45):17719 (2007) PMID 17965236 PMCID PMC2077053

    MicroRNAs (miRNAs) are important genetic regulators of development, differentiation, growth, and metabolism. The mammalian genome encodes approximately 500 known miRNA genes. Approximately 50% are expressed from non-protein-coding transcripts, whereas the rest are located mostly in the introns o...
  10. FRalanyzer: a tool for functional analysis of fold-recognition sequence-structure alignments.

    Nucleic Acids Research 35(Web Server issue):W499 (2007) PMID 17537819 PMCID PMC1933221

    We describe FRalanyzer (Fold Recognition alignment analyzer), a new web tool to visually inspect sequence-structure alignments in order to predict functionally important residues in a query sequence of unknown function. This tool is aimed at helping to infer functional relationships between a qu...
  11. FRalanyzer: a tool for functional analysis of fold-recognition sequence-structure alignments.

    Nucleic Acids Research 35(Web Server issue):W499 (2007) PMID 17537819 PMCID PMC1933221

    We describe FRalanyzer (Fold Recognition alignment analyzer), a new web tool to visually inspect sequence-structure alignments in order to predict functionally important residues in a query sequence of unknown function. This tool is aimed at helping to infer functional relationships between a qu...
  12. Structural and functional insights into Mimivirus ORFans.

    BMC Genomics 8:115 (2007) PMID 17490476 PMCID PMC1876218

    Mimivirus isolated from A. polyphaga is the largest virus discovered so far. It is unique among all the viruses in having genes related to translation, DNA repair and replication which bear close homology to eukaryotic genes. Nevertheless, only a small fraction of the proteins (33%) encoded in t...
  13. Structural and functional insights into Mimivirus ORFans.

    BMC Genomics 8:115 (2007) PMID 17490476 PMCID PMC1876218

    Mimivirus isolated from A. polyphaga is the largest virus discovered so far. It is unique among all the viruses in having genes related to translation, DNA repair and replication which bear close homology to eukaryotic genes. Nevertheless, only a small fraction of the proteins (33%) encoded in t...
  14. Meta-DP: domain prediction meta-server.

    Bioinformatics 21(12):2917 (2005) PMID 15840708

    Meta-DP, a domain prediction meta-server provides a simple interface to predict domains in a given protein sequence using a number of domain prediction methods. The Meta-DP is a convenient resource because through accessing a single site, users automatically obtain the results of the various dom...
  15. A putative novel alpha/beta hydrolase ORFan family in Bacillus.

    FEBS Letters 579(14):3175 (2005) PMID 15922334

    A large number of sequences in each newly sequenced genome correspond to lineage and species-specific proteins, also known as ORFans. Amongst these ORFans, a large number are sequences with unknown structures and functions. We have identified a family of sequences, annotated as hypothetical prot...
  16. A putative novel alpha/beta hydrolase ORFan family in Bacillus.

    FEBS Letters 579(14):3175 (2005) PMID 15922334

    A large number of sequences in each newly sequenced genome correspond to lineage and species-specific proteins, also known as ORFans. Amongst these ORFans, a large number are sequences with unknown structures and functions. We have identified a family of sequences, annotated as hypothetical prot...
  17. A putative novel alpha/beta hydrolase ORFan family inBacillus

    FEBS Letters 579(14):3175 (2005)

    A large number of sequences in each newly sequenced genome correspond to lineage and species-specific proteins, also known as ORFans. Amongst these ORFans, a large number are sequences with unknown structures and functions. We have identified a family of sequences, annotated as hypothetical...
  18. A putative novel alpha/beta hydrolase ORFan family inBacillus

    FEBS Letters 579(14):3175 (2005)

    A large number of sequences in each newly sequenced genome correspond to lineage and species-specific proteins, also known as ORFans. Amongst these ORFans, a large number are sequences with unknown structures and functions. We have identified a family of sequences, annotated as hypothetical...