Found: 31
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Benchmarking and building DNA binding affinity models using allele-specific and allele-agnostic transcription factor binding data.
- Published in:
- Genome Biology, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s13059-024-03424-2
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- Article
Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors.
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- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-31501-2
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- Article
Building accurate sequence-to-affinity models from high-throughput in vitro protein-DNA binding data using FeatureREDUCE.
- Published in:
- eLife, 2015, p. 1, doi. 10.7554/eLife.06397
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- Article
DSSR: an integrated software tool for dissecting the spatial structure of RNA.
- Published in:
- Nucleic Acids Research, 2015, v. 43, n. 21, p. 1, doi. 10.1093/nar/gkv716
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- Article
The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex.
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- Nucleic Acids Research, 2010, v. 38, n. 14, p. 4868, doi. 10.1093/nar/gkq155
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- Article
TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors.
- Published in:
- Nucleic Acids Research, 2008, v. 36, p. D125
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- Article
Prediction of protein–ligand binding affinity from sequencing data with interpretable machine learning.
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- Nature Biotechnology, 2022, v. 40, n. 10, p. 1520, doi. 10.1038/s41587-022-01307-0
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- Article
Genome-wide mapping of autonomous promoter activity in human cells.
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- Nature Biotechnology, 2017, v. 35, n. 2, p. 145, doi. 10.1038/nbt.3754
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- Article
Regulatory element detection using correlation with expression.
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- Nature Genetics, 2001, v. 27, n. 2, p. 167, doi. 10.1038/84792
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- Article
Paired Hormone Response Elements Predict Caveolin-1 as a Glucocorticoid Target Gene.
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- PLoS ONE, 2010, v. 5, n. 1, p. 1, doi. 10.1371/journal.pone.0008839
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- Article
Inferring Condition-Specific Modulation of Transcription Factor Activity in Yeast through Regulon-Based Analysis of Genomewide Expression.
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- PLoS ONE, 2008, v. 3, n. 9, p. 1, doi. 10.1371/journal.pone.0003112
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- Article
Simulations of Cellular Automata.
- Published in:
- Annals of the New York Academy of Sciences, 1998, v. 848, n. 1, p. 26, doi. 10.1111/j.1749-6632.1998.tb08955.x
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- Article
In vivo Hox binding specificity revealed by systematic changes to a single cis regulatory module.
- Published in:
- Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-11416-1
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- Article
HP1 controls genomic targeting of four novel heterochromatin proteins in Drosophila.
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- EMBO Journal, 2007, v. 26, n. 3, p. 741, doi. 10.1038/sj.emboj.7601527
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- Article
T-profiler: scoring the activity of predefined groups of genes using gene expression data.
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- Nucleic Acids Research, 2005, v. 33, n. suppl 2, p. w592, doi. 10.1093/nar/gki484
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- Publication type:
- Article
REDUCE: an online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data.
- Published in:
- Nucleic Acids Research, 2003, v. 31, n. 13, p. 3487, doi. 10.1093/nar/gkg630
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- Article
Revisiting the codon adaptation index from a whole‐genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models.
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- Nucleic Acids Research, 2003, v. 31, n. 8, p. 2242, doi. 10.1093/nar/gkg306
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- Article
A unified approach for quantifying and interpreting DNA shape readout by transcription factors.
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- Molecular Systems Biology, 2018, v. 14, n. 2, p. 1, doi. 10.15252/msb.20177902
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- Article
Identifying the genetic determinants of transcription factor activity.
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- Molecular Systems Biology, 2010, v. 6, n. 1, p. 1, doi. 10.1038/msb.2010.64
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- Article
Modeling gene expression control using Omes Law.
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- Molecular Systems Biology, 2006, v. 2, n. 1, p. E1, doi. 10.1038/msb4100055
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- Article
Identification of genes expressed in C. elegans touch receptor neurons.
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- Nature, 2002, v. 418, n. 6895, p. 331, doi. 10.1038/nature00891
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- Article
Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences.
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- Bioinformatics, 2008, v. 24, n. 13, p. i165, doi. 10.1093/bioinformatics/btn154
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- Article
Optimisation of TP53 reporters by systematic dissection of synthetic TP53 response elements.
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- Nucleic Acids Research, 2023, v. 51, n. 18, p. 9690, doi. 10.1093/nar/gkad718
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- Article
Defining the fine structure of promoter activity on a genome-wide scale with CISSECTOR.
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- Nucleic Acids Research, 2023, v. 51, n. 11, p. 5499, doi. 10.1093/nar/gkad232
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- Article
Systematic in vitro profiling of off-target affinity, cleavage and efficiency for CRISPR enzymes
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- Nucleic Acids Research, 2020, v. 48, n. 9, p. 5037, doi. 10.1093/nar/gkaa231
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- Article
Global Chromatin Domain Organization of the Drosophila Genome.
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- PLoS Genetics, 2008, v. 4, n. 3, p. 1, doi. 10.1371/journal.pgen.1000045
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- Article
Evolving insights on how cytosine methylation affects protein-DNA binding.
- Published in:
- Briefings in Functional Genomics, 2015, v. 14, n. 1, p. 61, doi. 10.1093/bfgp/elu040
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- Article
Recent progress in understanding transcription factor binding specificity.
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- Briefings in Functional Genomics, 2015, v. 14, n. 1, p. 1, doi. 10.1093/bfgp/elu050
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- Article
Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein–DNA binding.
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- Epigenetics & Chromatin, 2018, v. 11, p. 1, doi. 10.1186/s13072-018-0174-4
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- Article
Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast.
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- BMC Genomics, 2014, v. 15, n. 1, p. 1, doi. 10.1186/1471-2164-15-494
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- Article
Transcription factor regulation of eQTL activity across individuals and tissues.
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- PLoS Genetics, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pgen.1009719
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- Article