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Identifying interpretable gene-biomarker associations with functionally informed kernel-based tests in 190,000 exomes.
- Published in:
- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-32864-2
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- Publication type:
- Article
The Chloroplast RNA Binding Protein CP31A Has a Preference for mRNAs Encoding the Subunits of the Chloroplast NAD(P)H Dehydrogenase Complex and Is Required for Their Accumulation.
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- International Journal of Molecular Sciences, 2020, v. 21, n. 16, p. 5633, doi. 10.3390/ijms21165633
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- Article
Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data.
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- BMC Genomics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12864-021-07373-z
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- Article
JACUSA: site-specific identification of RNA editing events from replicate sequencing data.
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- BMC Bioinformatics, 2017, v. 18, p. 1, doi. 10.1186/s12859-016-1432-8
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- Publication type:
- Article
A computational map of the human-SARS-CoV-2 protein–RNA interactome predicted at single-nucleotide resolution.
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- NAR Genomics & Bioinformatics, 2023, v. 5, n. 1, p. 1, doi. 10.1093/nargab/lqad010
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- Publication type:
- Article
ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data.
- Published in:
- Nucleic Acids Research, 2017, v. 45, n. 19, p. 11004, doi. 10.1093/nar/gkx756
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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
RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.
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- Nucleic Acids Research, 2017, v. 45, n. 10, p. 1, doi. 10.1093/nar/gkx120
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- Publication type:
- Article
Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection.
- Published in:
- Nucleic Acids Research, 2014, v. 42, n. 19, p. 11865
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- Publication type:
- Article
COUGER—co-factors associated with uniquely-bound genomic regions.
- Published in:
- Nucleic Acids Research, 2014, v. 42, n. W1, p. W461, doi. 10.1093/nar/gku435
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- Publication type:
- Article
Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships.
- Published in:
- Nucleic Acids Research, 2009, v. 37, n. 13, p. e92, doi. 10.1093/nar/gkp423
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- Publication type:
- Article
Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction.
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- Nucleic Acids Research, 2006, v. 34, n. 20, p. 5943, doi. 10.1093/nar/gkl608
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- Publication type:
- Article
Spatio-temporal mRNA tracking in the early zebrafish embryo.
- Published in:
- Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-23834-1
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- Publication type:
- Article
Ythdf is a N6‐methyladenosine reader that modulates Fmr1 target mRNA selection and restricts axonal growth in Drosophila.
- Published in:
- EMBO Journal, 2021, v. 40, n. 4, p. 1, doi. 10.15252/embj.2020104975
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- Publication type:
- Article
MicroRNA target site identification by integrating sequence and binding information.
- Published in:
- Nature Methods, 2013, v. 10, n. 7, p. 630, doi. 10.1038/nmeth.2489
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- Publication type:
- Article
A microfluidic device and computational platform for high-throughput live imaging of gene expression.
- Published in:
- Nature Methods, 2012, v. 9, n. 11, p. 1101, doi. 10.1038/nmeth.2185
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- Publication type:
- Article
A paired-end sequencing strategy to map the complex landscape of transcription initiation.
- Published in:
- Nature Methods, 2010, v. 7, n. 7, p. 521, doi. 10.1038/nmeth.1464
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- Publication type:
- Article
Deep learning for prediction of population health costs.
- Published in:
- BMC Medical Informatics & Decision Making, 2022, v. 22, n. 1, p. 1, doi. 10.1186/s12911-021-01743-z
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- Article
Deep learning for prediction of population health costs.
- Published in:
- 2022
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- Publication type:
- journal article
Metadata-guided feature disentanglement for functional genomics.
- Published in:
- Bioinformatics, 2024, v. 40, p. ii4, doi. 10.1093/bioinformatics/btae403
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- Publication type:
- Article
The Drosophila Translational Control Element (TCE) Is Required for High-Level Transcription of Many Genes That Are Specifically Expressed in Testes.
- Published in:
- PLoS ONE, 2012, v. 7, n. 9, p. 1, doi. 10.1371/journal.pone.0045009
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- Publication type:
- Article
Assessing the Utility of Thermodynamic Features for microRNA Target Prediction under Relaxed Seed and No Conservation Requirements.
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- PLoS ONE, 2011, v. 6, n. 6, p. 1, doi. 10.1371/journal.pone.0020622
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- Publication type:
- Article
Global identification of functional microRNA-mRNA interactions in Drosophila.
- Published in:
- Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-09586-z
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- Publication type:
- Article
Purification of cross-linked RNA-protein complexes by phenol-toluol extraction.
- Published in:
- Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-019-08942-3
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- Publication type:
- Article
Determinants of promoter and enhancer transcription directionality in metazoans.
- Published in:
- Nature Communications, 2018, v. 9, p. 1, doi. 10.1038/s41467-018-06962-z
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- Publication type:
- Article
How to find genomic regions relevant for gene regulation.
- Published in:
- Medizinische Genetik, 2021, v. 33, n. 2, p. 157, doi. 10.1515/medgen-2021-2074
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- Publication type:
- Article
Spatial preferences of microRNA targets in 3' untranslated regions.
- Published in:
- BMC Genomics, 2007, v. 8, p. 152, doi. 10.1186/1471-2164-8-152
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- Publication type:
- Article
Gene expression divergence recapitulates the developmental hourglass model.
- Published in:
- Nature, 2010, v. 468, n. 7325, p. 811, doi. 10.1038/nature09634
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- Publication type:
- Article
A viral microRNA functions as an orthologue of cellular miR-155.
- Published in:
- Nature, 2007, v. 450, n. 7172, p. 1096, doi. 10.1038/nature05992
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- Publication type:
- Article
Paired-End Analysis of Transcription Start Sites in Arabidopsis Reveals Plant-Specific Promoter Signatures.
- Published in:
- Plant Cell, 2014, v. 26, n. 7, p. 2746, doi. 10.1105/tpc.114.125617
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- Publication type:
- Article
A stele-enriched gene regulatory network in the Arabidopsis root.
- Published in:
- Molecular Systems Biology, 2011, v. 7, n. 1, p. 459, doi. 10.1038/msb.2010.114
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- Publication type:
- Article
Divergent transcription and epigenetic directionality of human promoters.
- Published in:
- FEBS Journal, 2016, v. 283, n. 23, p. 4214, doi. 10.1111/febs.13747
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- Publication type:
- Article
Automatic Annotation of Spatial Expression Patterns via Sparse Bayesian Factor Models.
- Published in:
- PLoS Computational Biology, 2011, v. 7, n. 7, p. 1, doi. 10.1371/journal.pcbi.1002098
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- Publication type:
- Article
Modeling the Evolution of Regulatory Elements by Simultaneous Detection and Alignment with Phylogenetic Pair HMMs.
- Published in:
- PLoS Computational Biology, 2010, v. 6, n. 12, p. 1, doi. 10.1371/journal.pcbi.1001037
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- Publication type:
- Article
Strategies for Identifying RNA Splicing Regulatory Motifs and Predicting Alternative Splicing Events.
- Published in:
- PLoS Computational Biology, 2008, v. 4, n. 1, p. e21, doi. 10.1371/journal.pcbi.0040021
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- Publication type:
- Article
Recognition of Unknown Conserved Alternatively Spliced Exons.
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- PLoS Computational Biology, 2005, v. 1, n. 2, p. 113, doi. 10.1371/journal.pcbi.0010015
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- Publication type:
- Article
Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation.
- Published in:
- Science Immunology, 2024, v. 9, n. 94, p. 1, doi. 10.1126/sciimmunol.adi1023
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- Publication type:
- Article
Control of immediate early gene expression by CPEB4-repressor complex-mediated mRNA degradation.
- Published in:
- Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02760-5
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- Publication type:
- Article
Global target mRNA specification and regulation by the RNA-binding protein ZFP36.
- Published in:
- Genome Biology, 2014, v. 15, n. 1, p. 1, doi. 10.1186/gb-2014-15-1-r12
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- Publication type:
- Article
Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.
- Published in:
- Genome Biology, 2013, v. 14, n. 8, p. R85, doi. 10.1186/gb-2013-14-8-r85
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- Publication type:
- Article
Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity.
- Published in:
- Genome Biology, 2012, v. 13, n. 10, p. 1, doi. 10.1186/gb-2012-13-10-R88
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- Publication type:
- Article
PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data.
- Published in:
- Genome Biology, 2011, v. 12, n. 8, p. 1, doi. 10.1186/gb-2011-12-8-r79
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- Publication type:
- Article
Finding RNA structure in the unstructured RBPome.
- Published in:
- BMC Genomics, 2018, v. 19, p. 1, doi. 10.1186/s12864-018-4540-1
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- Publication type:
- Article
The Viral and Cellular MicroRNA Targetome in Lymphoblastoid Cell Lines.
- Published in:
- PLoS Pathogens, 2012, v. 8, n. 1, p. 1, doi. 10.1371/journal.ppat.1002484
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- Publication type:
- Article
Ectopic Transplastomic Expression of a Synthetic MatK Gene Leads to Cotyledon-Specific Leaf Variegation.
- Published in:
- Frontiers in Plant Science, 2018, p. N.PAG, doi. 10.3389/fpls.2018.01453
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- Publication type:
- Article
FMRP targets distinct mRNA sequence elements to regulate protein expression.
- Published in:
- Nature, 2012, v. 492, n. 7429, p. 382, doi. 10.1038/nature11737
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- Publication type:
- Article
Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition.
- Published in:
- Bioinformatics, 2001, v. 17, p. 199, doi. 10.1093/bioinformatics/17.suppl_1.s199
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- Publication type:
- Article
Interpolated Markov chains for eukaryotic promoter recognition.
- Published in:
- Bioinformatics, 1999, v. 15, n. 5, p. 362, doi. 10.1093/bioinformatics/15.5.362
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- Publication type:
- Article
Liam tackles complex multimodal single-cell data integration challenges.
- Published in:
- Nucleic Acids Research, 2024, v. 52, n. 12, p. e52, doi. 10.1093/nar/gkae409
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- Publication type:
- Article
Deciphering human ribonucleoprotein regulatory networks.
- Published in:
- Nucleic Acids Research, 2019, v. 47, n. 2, p. 570, doi. 10.1093/nar/gky1185
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- Publication type:
- Article