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temperature-regulated DEAD-box RNA helicase CrhR interactome: autoregulation and photosynthesis-related transcripts.
- Published in:
- Journal of Experimental Botany, 2021, v. 72, n. 21, p. 7564, doi. 10.1093/jxb/erab416
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- Publication type:
- Article
CopomuS—Ranking Compensatory Mutations to Guide RNA-RNA Interaction Verification Experiments.
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- International Journal of Molecular Sciences, 2020, v. 21, n. 11, p. 3852, doi. 10.3390/ijms21113852
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- Publication type:
- Article
Improving CLIP-seq data analysis by incorporating transcript information.
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- BMC Genomics, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s12864-020-07297-0
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- Article
SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification.
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- BMC Bioinformatics, 2016, v. 17, p. 73, doi. 10.1186/s12859-016-1345-6
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- Publication type:
- Article
Temporospatial distribution and transcriptional profile of retinal microglia in the oxygen‐induced retinopathy mouse model.
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- Glia, 2020, v. 68, n. 9, p. 1859, doi. 10.1002/glia.23810
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- Publication type:
- Article
Clusters of mammalian conserved RNA structures in UTRs associate with RBP binding sites.
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- NAR Genomics & Bioinformatics, 2024, v. 6, n. 3, p. 1, doi. 10.1093/nargab/lqae089
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- Publication type:
- Article
Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization.
- Published in:
- Nucleic Acids Research, 2018, v. 46, n. W1, p. W11, doi. 10.1093/nar/gky504
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- Publication type:
- Article
Combinatorial ensemble miRNA target prediction of co-regulation networks with non-prediction data.
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- Nucleic Acids Research, 2017, v. 45, n. 15, p. 8745, doi. 10.1093/nar/gkx605
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- Publication type:
- Article
The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.
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- Nucleic Acids Research, 2017, v. 45, n. W1, p. W560, doi. 10.1093/nar/gkx409
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- Publication type:
- Article
IntaRNA 2.0: enhanced and customizable prediction of RNA--RNA interactions.
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- Nucleic Acids Research, 2017, v. 45, n. W1, p. W435, doi. 10.1093/nar/gkx279
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- Publication type:
- Article
Structural constraints and enzymatic promiscuity in the Cas6-dependent generation of crRNAs.
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- Nucleic Acids Research, 2017, v. 45, n. 2, p. 915, doi. 10.1093/nar/gkw786
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- Publication type:
- Article
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains.
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- Nucleic Acids Research, 2014, v. 42, n. W1, p. W119, doi. 10.1093/nar/gku359
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- Publication type:
- Article
CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems.
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- Nucleic Acids Research, 2013, v. 41, n. 17, p. 8034, doi. 10.1093/nar/gkt606
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- Publication type:
- Article
An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains.
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- Nucleic Acids Research, 2012, v. 40, n. 21, p. 10964, doi. 10.1093/nar/gks847
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- Publication type:
- Article
Characterization of CRISPR RNA processing in Clostridium thermocellum and Methanococcus maripaludis.
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- Nucleic Acids Research, 2012, v. 40, n. 19, p. 9887, doi. 10.1093/nar/gks737
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- Publication type:
- Article
CARNA—alignment of RNA structure ensembles.
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- Nucleic Acids Research, 2012, v. 40, p. W49, doi. 10.1093/nar/gks491
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- Publication type:
- Article
Global or local? Predicting secondary structure and accessibility in mRNAs.
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- Nucleic Acids Research, 2012, v. 40, n. 13, p. 5215, doi. 10.1093/nar/gks181
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- Publication type:
- Article
Global or local? Predicting secondary structure and accessibility in mRNAs.
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- Nucleic Acids Research, 2012, v. 40, n. 12, p. 5215, doi. 10.1093/nar/gks181
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- Publication type:
- Article
The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences.
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- Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W107, doi. 10.1093/nar/gkr248
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- Publication type:
- Article
Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LocARNA.
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- Nucleic Acids Research, 2010, v. 38, n. suppl_2, p. W373, doi. 10.1093/nar/gkq316
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- Publication type:
- Article
Accurate prediction of NAGNAG alternative splicing.
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- Nucleic Acids Research, 2009, v. 37, n. 11, p. 3569, doi. 10.1093/nar/gkp220
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- Publication type:
- Article
Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments.
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- Nucleic Acids Research, 2008, v. 36, n. 20, p. 6355, doi. 10.1093/nar/gkn544
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- Publication type:
- Article
BioBayesNet: a web server for feature extraction and Bayesian network modeling of biological sequence data.
- Published in:
- Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W688, doi. 10.1093/nar/gkm292
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- Publication type:
- Article
INFO-RNA—a server for fast inverse RNA folding satisfying sequence constraints.
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- Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W310, doi. 10.1093/nar/gkm218
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- Publication type:
- Article
TassDB: a database of alternative tandem splice sites.
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- Nucleic Acids Research, 2007, v. 35, p. d188, doi. 10.1093/nar/gkl762
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- Publication type:
- Article
Using RNA secondary structures to guide sequence motif finding towards single-stranded regions.
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- Nucleic Acids Research, 2006, v. 34, n. 17, p. e117, doi. 10.1093/nar/gkl544
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- Publication type:
- Article
Sequencing errors or SNPs at splice-acceptor guanines in dbSNP?
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- 2006
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- Publication type:
- Letter
Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains.
- Published in:
- Algorithms for Molecular Biology, 2020, v. 15, n. 1, p. 1, doi. 10.1186/s13015-020-00179-w
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- Publication type:
- Article
Widespread occurrence of alternative splicing at NAGNAG acceptors contributes to proteome plasticity.
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- Nature Genetics, 2004, v. 36, n. 12, p. 1255, doi. 10.1038/ng1469
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- Article
Partial RNA design.
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- Bioinformatics, 2024, v. 40, p. i437, doi. 10.1093/bioinformatics/btae222
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- Publication type:
- Article
RNA interaction format: a general data format for RNA interactions.
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- Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad665
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- Publication type:
- Article
CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection.
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- Bioinformatics, 2022, v. 38, p. ii42, doi. 10.1093/bioinformatics/btac466
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- Publication type:
- Article
Peakhood: individual site context extraction for CLIP-seq peak regions.
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- Bioinformatics, 2022, v. 38, n. 4, p. 1139, doi. 10.1093/bioinformatics/btab755
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- Publication type:
- Article
Robust and efficient single-cell Hi-C clustering with approximate k-nearest neighbor graphs.
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- Bioinformatics, 2021, v. 37, n. 22, p. 4006, doi. 10.1093/bioinformatics/btab394
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- Publication type:
- Article
SARS-CoV-2 sequence submission tool for the European Nucleotide Archive.
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- Bioinformatics, 2021, v. 37, n. 21, p. 3983, doi. 10.1093/bioinformatics/btab421
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- Publication type:
- Article
HRIBO: high-throughput analysis of bacterial ribosome profiling data.
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- Bioinformatics, 2021, v. 37, n. 14/15, p. 2061, doi. 10.1093/bioinformatics/btaa959
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- Publication type:
- Article
Scool: a new data storage format for single-cell Hi-C data.
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- Bioinformatics, 2021, v. 37, n. 14/15, p. 2053, doi. 10.1093/bioinformatics/btaa924
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- Publication type:
- Article
Casboundary: automated definition of integral Cas cassettes.
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- Bioinformatics, 2021, v. 37, n. 10, p. 1352, doi. 10.1093/bioinformatics/btaa984
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- Publication type:
- Article
pyGenomeTracks: reproducible plots for multivariate genomic datasets.
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- Bioinformatics, 2021, v. 37, n. 3, p. 422, doi. 10.1093/bioinformatics/btaa692
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- Publication type:
- Article
Unraveling the small proteome of the plant symbiont Sinorhizobium meliloti by ribosome profiling and proteogenomics.
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- MicroLife, 2023, v. 4, p. 1, doi. 10.1093/femsml/uqad012
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- Publication type:
- Article
Revealing the small proteome of Haloferax volcanii by combining ribosome profiling and small-protein optimized mass spectrometry.
- Published in:
- MicroLife, 2023, v. 4, p. 1, doi. 10.1093/femsml/uqad001
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- Publication type:
- Article
A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence.
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- MicroLife, 2020, v. 1, n. 1, p. 1, doi. 10.1093/femsml/uqaa002
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- Publication type:
- Article
GRIN3B missense mutation as an inherited risk factor for schizophrenia: whole-exome sequencing in a family with a familiar history of psychotic disorders.
- Published in:
- Genetics Research, 2017, v. 99, p. N.PAG, doi. 10.1017/S0016672316000148
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- Publication type:
- Article
An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy.
- Published in:
- GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad028
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- Publication type:
- Article
Loop detection using Hi-C data with HiCExplorer.
- Published in:
- GigaScience, 2022, v. 11, p. 1, doi. 10.1093/gigascience/giac061
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- Publication type:
- Article
RNAProt: an efficient and feature-rich RNA binding protein binding site predictor.
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- GigaScience, 2021, v. 10, n. 8, p. 1, doi. 10.1093/gigascience/giab054
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- Publication type:
- Article
StoatyDive: Evaluation and classification of peak profiles for sequencing data.
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- GigaScience, 2021, v. 10, n. 6, p. 1, doi. 10.1093/gigascience/giab045
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- Publication type:
- Article
ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data.
- Published in:
- GigaScience, 2021, v. 10, n. 2, p. 1, doi. 10.1093/gigascience/giaa158
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- Publication type:
- Article
Tool recommender system in Galaxy using deep learning.
- Published in:
- GigaScience, 2021, v. 10, n. 1, p. 1, doi. 10.1093/gigascience/giaa152
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- Publication type:
- Article
Galaxy CLIP-Explorer: a web server for CLIP-Seq data analysis.
- Published in:
- GigaScience, 2020, v. 9, n. 11, p. 1, doi. 10.1093/gigascience/giaa108
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- Publication type:
- Article