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Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics.
Proceedings of the National Academy of Sciences of the United States of America May, 2002 | Pubmed ID: 12032281
Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome.
Genome research Sep, 2002 | Pubmed ID: 12213775
Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome.
Genome research Jun, 2003 | Pubmed ID: 12819126
Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome.
Genome research Jun, 2003 | Pubmed ID: 12819142
Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes.
Genome research Aug, 2003 | Pubmed ID: 12902380
The small RNA profile during Drosophila melanogaster development.
Developmental cell Aug, 2003 | Pubmed ID: 12919683
Identification of virus-encoded microRNAs.
Science (New York, N.Y.) Apr, 2004 | Pubmed ID: 15118162
Analysis of human immunodeficiency virus cytopathicity by using a new method for quantitating viral dynamics in cell culture.
Journal of virology Apr, 2005 | Pubmed ID: 15767404
Identification of microRNAs of the herpesvirus family.
Nature methods Apr, 2005 | Pubmed ID: 15782219
The developmental miRNA profiles of zebrafish as determined by small RNA cloning.
Genes & development Jun, 2005 | Pubmed ID: 15937218
Identification of clustered microRNAs using an ab initio prediction method.
BMC bioinformatics , 2005 | Pubmed ID: 16274478
SMASHing regulatory sites in DNA by human-mouse sequence comparisons.
Proceedings / IEEE Computer Society Bioinformatics Conference. IEEE Computer Society Bioinformatics Conference , 2003 | Pubmed ID: 16452803
Cell-type-specific signatures of microRNAs on target mRNA expression.
Proceedings of the National Academy of Sciences of the United States of America Feb, 2006 | Pubmed ID: 16477010
Virus-encoded microRNAs: novel regulators of gene expression.
Trends in microbiology Apr, 2006 | Pubmed ID: 16531046
SPA: a probabilistic algorithm for spliced alignment.
PLoS genetics Apr, 2006 | Pubmed ID: 16683023
A simple physical model predicts small exon length variations.
PLoS genetics Apr, 2006 | Pubmed ID: 16683028
The types and prevalence of alternative splice forms.
Current opinion in structural biology Jun, 2006 | Pubmed ID: 16713247
A novel class of small RNAs bind to MILI protein in mouse testes.
Nature Jul, 2006 | Pubmed ID: 16751777
Effects of Dicer and Argonaute down-regulation on mRNA levels in human HEK293 cells.
Nucleic acids research , 2006 | Pubmed ID: 16971455
Quantitative technologies establish a novel microRNA profile of chronic lymphocytic leukemia.
Blood Jun, 2007 | Pubmed ID: 17327404
Inference of miRNA targets using evolutionary conservation and pathway analysis.
BMC bioinformatics , 2007 | Pubmed ID: 17331257
Marek's disease virus type 2 (MDV-2)-encoded microRNAs show no sequence conservation with those encoded by MDV-1.
Journal of virology Jul, 2007 | Pubmed ID: 17459919
A mammalian microRNA expression atlas based on small RNA library sequencing.
Cell Jun, 2007 | Pubmed ID: 17604727
Cellular cofactors affecting hepatitis C virus infection and replication.
Proceedings of the National Academy of Sciences of the United States of America Jul, 2007 | Pubmed ID: 17616579
Regulation of human liver delta-aminolevulinic acid synthase by bile acids.
Hepatology (Baltimore, Md.) Dec, 2007 | Pubmed ID: 17975826
Strand-specific 5'-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity.
RNA (New York, N.Y.) Feb, 2008 | Pubmed ID: 18094121
Computational analysis of small RNA cloning data.
Methods (San Diego, Calif.) Jan, 2008 | Pubmed ID: 18158128
Computational analysis of full-length cDNAs reveals frequent coupling between transcriptional and splicing programs.
DNA research : an international journal for rapid publication of reports on genes and genomes Apr, 2008 | Pubmed ID: 18276623
MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells.
Nature structural & molecular biology Mar, 2008 | Pubmed ID: 18311153
Elevated expression of the miR-17-92 polycistron and miR-21 in hepadnavirus-associated hepatocellular carcinoma contributes to the malignant phenotype.
The American journal of pathology Sep, 2008 | Pubmed ID: 18688024
Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system.
PloS one , 2008 | Pubmed ID: 18776931
Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs.
RNA (New York, N.Y.) Dec, 2008 | Pubmed ID: 18978028
miRNA in situ hybridization in formaldehyde and EDC-fixed tissues.
Nature methods Feb, 2009 | Pubmed ID: 19137005
miR-375 maintains normal pancreatic alpha- and beta-cell mass.
Proceedings of the National Academy of Sciences of the United States of America Apr, 2009 | Pubmed ID: 19289822
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.
Nature genetics May, 2009 | Pubmed ID: 19377474
MirZ: an integrated microRNA expression atlas and target prediction resource.
Nucleic acids research Jul, 2009 | Pubmed ID: 19468042
Expression and processing of a small nucleolar RNA from the Epstein-Barr virus genome.
PLoS pathogens Aug, 2009 | Pubmed ID: 19680535
Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C-miRNA complexes and the degradation of miRNA targets.
Genome research Nov, 2009 | Pubmed ID: 19767416
The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing.
Human molecular genetics Apr, 2010 | Pubmed ID: 20053671
MicroRNA activity is suppressed in mouse oocytes.
Current biology : CB Feb, 2010 | Pubmed ID: 20116252
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP.
Cell Apr, 2010 | Pubmed ID: 20371350
Expression proteomics of UPF1 knockdown in HeLa cells reveals autoregulation of hnRNP A2/B1 mediated by alternative splicing resulting in nonsense-mediated mRNA decay.
BMC genomics , 2010 | Pubmed ID: 20946641
Analysis of in situ pre-mRNA targets of human splicing factor SF1 reveals a function in alternative splicing.
Nucleic acids research Mar, 2011 | Pubmed ID: 21062807
CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins.
Nucleic acids research Jan, 2011 | Pubmed ID: 21087992
Deciphering the role of RNA-binding proteins in the post-transcriptional control of gene expression.
Briefings in functional genomics Dec, 2010 | Pubmed ID: 21127008
Conserved generation of short products at piRNA loci.
BMC genomics , 2011 | Pubmed ID: 21247452
A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins.
Nature methods Jul, 2011 | Pubmed ID: 21572407
MicroRNAs 103 and 107 regulate insulin sensitivity.
Nature Jun, 2011 | Pubmed ID: 21654750
PAPD5, a noncanonical poly(A) polymerase with an unusual RNA-binding motif.
RNA (New York, N.Y.) Sep, 2011 | Pubmed ID: 21788334
MicroRNA-194 is a target of transcription factor 1 (Tcf1, HNF1α) in adult liver and controls expression of frizzled-6.
Hepatology (Baltimore, Md.) Jan, 2012 | Pubmed ID: 21887698
Kaposi's sarcoma herpesvirus microRNAs target caspase 3 and regulate apoptosis.
PLoS pathogens Dec, 2011 | Pubmed ID: 22174674
Genome-wide analysis of pre-mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length.
Cell reports Jun, 2012 | Pubmed ID: 22813749
Argonaute CLIP--a method to identify in vivo targets of miRNAs.
Methods (San Diego, Calif.) Oct, 2012 | Pubmed ID: 23022257
Dicer partners expand the repertoire of miRNA targets.
Genome biology Nov, 2012 | Pubmed ID: 23194401
A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets.
Nature methods Mar, 2013 | Pubmed ID: 23334102
Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation.
Genome research Apr, 2013 | Pubmed ID: 23335364
Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing.
Genome biology May, 2013 | Pubmed ID: 23706177
Translation-dependent displacement of UPF1 from coding sequences causes its enrichment in 3' UTRs.
Nature structural & molecular biology Aug, 2013 | Pubmed ID: 23832275
Modeling the binding specificity of the RNA-binding protein GLD-1 suggests a function of coding region-located sites in translational repression.
RNA (New York, N.Y.) Oct, 2013 | Pubmed ID: 23974436
3'-UTR poly(T/U) tract deletions and altered expression of EWSR1 are a hallmark of mismatch repair-deficient cancers.
Cancer research Jan, 2014 | Pubmed ID: 24158095
Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors.
Wiley interdisciplinary reviews. RNA Mar-Apr, 2014 | Pubmed ID: 24243805
Modulation of epigenetic regulators and cell fate decisions by miRNAs.
Epigenomics Dec, 2013 | Pubmed ID: 24283881
Timescales and bottlenecks in miRNA-dependent gene regulation.
Molecular systems biology Dec, 2013 | Pubmed ID: 24301800
Argonaute2 mediates compensatory expansion of the pancreatic β cell.
Cell metabolism Jan, 2014 | Pubmed ID: 24361012
TSSer: an automated method to identify transcription start sites in prokaryotic genomes from differential RNA sequencing data.
Bioinformatics (Oxford, England) Apr, 2014 | Pubmed ID: 24371151
Seq and CLIP through the miRNA world.
Genome biology Jan, 2014 | Pubmed ID: 24460822
ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs.
Genome research May, 2014 | Pubmed ID: 24515121
PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation): a step-by-step protocol to the transcriptome-wide identification of binding sites of RNA-binding proteins.
Methods in enzymology , 2014 | Pubmed ID: 24581442
Widespread context dependency of microRNA-mediated regulation.
Genome research Jun, 2014 | Pubmed ID: 24668909
MicroRNA-7a regulates pancreatic β cell function.
The Journal of clinical investigation Jun, 2014 | Pubmed ID: 24789908
Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.
Nucleic acids research Jul, 2014 | Pubmed ID: 24792157
Structural and functional implications of the QUA2 domain on RNA recognition by GLD-1.
Nucleic acids research Jul, 2014 | Pubmed ID: 24838563
Identification and consequences of miRNA-target interactions--beyond repression of gene expression.
Nature reviews. Genetics Sep, 2014 | Pubmed ID: 25022902
Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways.
Nucleic acids research Aug, 2014 | Pubmed ID: 25030899
Reconstitution of CPSF active in polyadenylation: recognition of the polyadenylation signal by WDR33.
Genes & development Nov, 2014 | Pubmed ID: 25301781
Global 3' UTR shortening has a limited effect on protein abundance in proliferating T cells.
Nature communications , 2014 | Pubmed ID: 25413384
miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction.
Nature chemical biology Feb, 2015 | Pubmed ID: 25531890
Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G.
Nucleic acids research Feb, 2015 | Pubmed ID: 25628353
Reflections on the RNA world.
RNA (New York, N.Y.) Apr, 2015 | Pubmed ID: 25780126
Quantifying the strength of miRNA-target interactions.
Methods (San Diego, Calif.) Sep, 2015 | Pubmed ID: 25892562
miR-184 Regulates Pancreatic β-Cell Function According to Glucose Metabolism.
The Journal of biological chemistry Aug, 2015 | Pubmed ID: 26152724
Inferring gene expression regulatory networks from high-throughput measurements.
Methods (San Diego, Calif.) Sep, 2015 | Pubmed ID: 26188125
Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data.
Genome biology Jul, 2015 | Pubmed ID: 26201343
Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans.
Genome research Nov, 2015 | Pubmed ID: 26232411
Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G.
Nucleic acids research Oct, 2015 | Pubmed ID: 26365243
Roquin recognizes a non-canonical hexaloop structure in the 3'-UTR of Ox40.
Nature communications Mar, 2016 | Pubmed ID: 27010430
An updated human snoRNAome.
Nucleic acids research Jun, 2016 | Pubmed ID: 27174936
Redesigning CLIP for efficiency, accuracy and speed.
Nature methods May, 2016 | Pubmed ID: 27243472
Corrigendum to "Quantifying the strength of miRNA-target interactions" [Methods (2015) 90-99].
Methods (San Diego, Calif.) Jul, 2016 | Pubmed ID: 27372217
A comprehensive analysis of 3' end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation.
Genome research 08, 2016 | Pubmed ID: 27382025
TUT-DIS3L2 is a mammalian surveillance pathway for aberrant structured non-coding RNAs.
The EMBO journal Oct, 2016 | Pubmed ID: 27647875
Patterns of ribosomal protein expression specify normal and malignant human cells.
Genome biology Nov, 2016 | Pubmed ID: 27884178
High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq.
Nucleic acids research Mar, 2017 | Pubmed ID: 28031372
Explicit Modeling of siRNA-Dependent On- and Off-Target Repression Improves the Interpretation of Screening Results.
Cell systems Feb, 2017 | Pubmed ID: 28215525
TFAP2A is a component of the ZEB1/2 network that regulates TGFB1-induced epithelial to mesenchymal transition.
Biology direct Apr, 2017 | Pubmed ID: 28412966
Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors.
PLoS computational biology Jul, 2017 | Pubmed ID: 28753602
The Gcn4 transcription factor reduces protein synthesis capacity and extends yeast lifespan.
Nature communications Sep, 2017 | Pubmed ID: 28878244
Markus Hafner1,
Markus Landthaler2,
Lukas Burger3,
Mohsen Khorshid3,
Jean Hausser4,
Philipp Berninger4,
Andrea Rothballer1,
Manuel Ascano1,
Anna-Carina Jungkamp2,
Mathias Munschauer2,
Alexander Ulrich1,
Greg S. Wardle1,
Scott Dewell5,
Mihaela Zavolan3,
Thomas Tuschl1
1Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Rockefeller University,
2Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine,
3, Biozentrum der Universität Basel and Swiss Institute of Bioinformatics (SIB),
4, Biozentrum der Universität Basel and Swiss Institute of Bioinformatics (SIB),
5Genomics Resource Center, Rockefeller University
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