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Feed-Forward Regulation of a Cell Fate Determinant by an RNA-Binding Protein Generates Asymmetry in Yeast.
- Published in:
- Genetics, 2010, v. 185, n. 2, p. 513, doi. 10.1534/genetics.110.113944
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- Article
A multi-parametric flow cytometric assay to analyze DNA–protein interactions.
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- Nucleic Acids Research, 2013, v. 41, n. 2, p. e38, doi. 10.1093/nar/gks1034
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- Article
ORegAnno: an open-access community-driven resource for regulatory annotation.
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- Nucleic Acids Research, 2008, v. 36, p. D107
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- Publication type:
- Article
STAMP: a web tool for exploring DNA-binding motif similarities.
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- Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W253, doi. 10.1093/nar/gkm272
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- Article
Embryonic stem cell-based mapping of developmental transcriptional programs.
- Published in:
- Nature Methods, 2011, v. 8, n. 12, p. 1056, doi. 10.1038/nmeth.1775
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- Article
S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types.
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- Bioinformatics, 2021, v. 37, n. 18, p. 3011, doi. 10.1093/bioinformatics/btab148
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- Publication type:
- Article
PEGR: a flexible management platform for reproducible epigenomic and genomic research.
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- Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-022-02671-5
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- Article
An interpretable bimodal neural network characterizes the sequence and preexisting chromatin predictors of induced transcription factor binding.
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- Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-020-02218-6
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- Article
Large Scale Comparison of Innate Responses to Viral and Bacterial Pathogens in Mouse and Macaque.
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- PLoS ONE, 2011, v. 6, n. 7, p. 1, doi. 10.1371/journal.pone.0022401
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- Article
The PfAP2‐G2 transcription factor is a critical regulator of gametocyte maturation.
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- Molecular Microbiology, 2021, v. 115, n. 5, p. 1005, doi. 10.1111/mmi.14676
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- Article
Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models.
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- BMC Bioinformatics, 2004, v. 5, p. 23, doi. 10.1186/1471-2105-5-23
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- Publication type:
- Article
An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding.
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- PLoS Computational Biology, 2014, v. 10, n. 3, p. 1, doi. 10.1371/journal.pcbi.1003501
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- Article
High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints.
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- PLoS Computational Biology, 2012, v. 8, n. 8, p. 1, doi. 10.1371/journal.pcbi.1002638
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- Article
DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies.
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- PLoS Computational Biology, 2007, v. 3, n. 3, p. 0578, doi. 10.1371/journal.pcbi.0030061
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- Article
Reconstructing an Ancestral Mammalian Immune Supercomplex from a Marsupial Major Histocompatibility Complex.
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- PLoS Biology, 2006, v. 4, n. 3, p. 317, doi. 10.1371/journal.pbio.0040046
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- Article
Inferring protein DNA dependencies using motif alignments and mutual information.
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- Bioinformatics, 2007, v. 23, n. 13, p. i297, doi. 10.1093/bioinformatics/btm215
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- Publication type:
- Article
Improved detection of DNA motifs using a self-organized clustering of familial binding profiles.
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- Bioinformatics, 2005, v. 21, p. i283, doi. 10.1093/bioinformatics/bti1025
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- Publication type:
- Article
Transcription factor binding site identification using the self-organizing map.
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- Bioinformatics, 2005, v. 21, n. 9, p. 1807, doi. 10.1093/bioinformatics/bti256
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- Publication type:
- Article
Improved detection of DNA motifs using a self-organized clustering of familial binding profiles.
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- Bioinformatics, 2005, v. 21, n. 1, p. i283, doi. 10.1093/bioinformatics/bti1025
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- Publication type:
- Article
Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons.
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- Nature Neuroscience, 2014, v. 17, n. 8, p. 1046, doi. 10.1038/nn.3757
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- Article
Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals.
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- Nature Neuroscience, 2013, v. 16, n. 9, p. 1191, doi. 10.1038/nn.3490
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- Publication type:
- Article
Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity.
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- Nature Neuroscience, 2013, v. 16, n. 9, p. 1219, doi. 10.1038/nn.3467
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- Publication type:
- Article
DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum.
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- Nucleic Acids Research, 2024, v. 52, n. 17, p. 10161, doi. 10.1093/nar/gkae585
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- Publication type:
- Article
Alignment and quantification of ChIP-exo crosslinking patterns reveal the spatial organization of protein–DNA complexes.
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- Nucleic Acids Research, 2020, v. 48, n. 20, p. 11215, doi. 10.1093/nar/gkaa618
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- Article
Self-Organizing Maps of Position Weight Matrices for Motif Discovery in Biological Sequences.
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- Artificial Intelligence Review, 2005, v. 24, n. 3/4, p. 397, doi. 10.1007/s10462-005-9011-9
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- Article
Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells.
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- IUBMB Life, 2020, v. 72, n. 1, p. 27, doi. 10.1002/iub.2195
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- Article
Joint inference and alignment of genome structures enables characterization of compartment-independent reorganization across cell types.
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- Epigenetics & Chromatin, 2019, v. 12, n. 1, p. N.PAG, doi. 10.1186/s13072-019-0308-3
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- Article
Direct prediction of regulatory elements from partial data without imputation.
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- PLoS Computational Biology, 2019, v. 15, n. 11, p. 1, doi. 10.1371/journal.pcbi.1007399
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- Article
Characterizing protein–DNA binding event subtypes in ChIP-exo data.
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- Bioinformatics, 2019, v. 35, n. 6, p. 903, doi. 10.1093/bioinformatics/bty703
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- Article
miniMDS: 3D structural inference from high-resolution Hi-C data.
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- Bioinformatics, 2017, v. 33, n. 14, p. i261, doi. 10.1093/bioinformatics/btx271
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- Article
Discovering homotypic binding events at high spatial resolution.
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- Bioinformatics, 2010, v. 26, n. 24, p. 3028, doi. 10.1093/bioinformatics/btq590
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- Article
Constructing and deconstructing spinal motor neurons
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- 2012
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- Abstract
Foxa2 and Pet1 Direct and Indirect Synergy Drive Serotonergic Neuronal Differentiation.
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- Frontiers in Neuroscience, 2022, v. 16, p. 1, doi. 10.3389/fnins.2022.903881
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- Article
Deconvolving sequence features that discriminate between overlapping regulatory annotations.
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- PLoS Computational Biology, 2017, v. 13, n. 10, p. 1, doi. 10.1371/journal.pcbi.1005795
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- Article