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Alternative Epigenetic States Understood in Terms of Specific Regulatory Structures.
- Published in:
- Annals of the New York Academy of Sciences, 2002, v. 981, n. 1, p. 135, doi. 10.1111/j.1749-6632.2002.tb04916.x
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- Publication type:
- Article
Genetic control of flower morphogenesis inArabidopsis thaliana: a logical analysis.
- Published in:
- Bioinformatics, 1999, v. 15, n. 7, p. 593, doi. 10.1093/bioinformatics/15.7.593
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- Publication type:
- Article
On Circuit Functionality in Boolean Networks.
- Published in:
- Bulletin of Mathematical Biology, 2013, v. 75, n. 6, p. 906, doi. 10.1007/s11538-013-9829-2
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- Publication type:
- Article
Targeting LINC00152 activates cAMP/Ca<sup>2+</sup>/ferroptosis axis and overcomes tamoxifen resistance in ER+ breast cancer.
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- Cell Death & Disease, 2024, v. 15, n. 6, p. 1, doi. 10.1038/s41419-024-06814-3
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- Publication type:
- Article
Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance.
- Published in:
- BMC Systems Biology, 2009, v. 3, p. 1, doi. 10.1186/1752-0509-3-1
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- Publication type:
- Article
Transcriptional and epigenetic signatures of zygotic genome activation during early drosophila embryogenesis.
- Published in:
- BMC Genomics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2164-14-226
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- Publication type:
- Article
Putting DNA on the map.
- Published in:
- 2006
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- Publication type:
- Book Review
MethMotif.Org 2024: a database integrating context-specific transcription factor-binding motifs with DNA methylation patterns.
- Published in:
- Nucleic Acids Research, 2024, v. 52, n. D1, p. D222, doi. 10.1093/nar/gkad894
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- Publication type:
- Article
Cooperation between T cell receptor and Toll-like receptor 5 signaling for CD4<sup>+</sup> T cell activation.
- Published in:
- Science Signaling, 2019, v. 12, n. 577, p. N.PAG, doi. 10.1126/scisignal.aar3641
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- Publication type:
- Article
The shortest path is not the one you know: application of biological network resources in precision oncology research.
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- Mutagenesis, 2015, v. 30, n. 2, p. 191, doi. 10.1093/mutage/geu078
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- Publication type:
- Article
Logical Modeling and Dynamical Analysis of Cellular Networks.
- Published in:
- Frontiers in Genetics, 2016, p. 1, doi. 10.3389/fgene.2016.00094
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- Publication type:
- Article
Graphing genes, cells and embryos.
- Published in:
- 2007
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- Publication type:
- Proceeding
Epigenomics: large scale analysis of chromatin modifications and transcription factors/genome interactions.
- Published in:
- BioEssays, 2005, v. 27, n. 11, p. 1203, doi. 10.1002/bies.20319
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- Publication type:
- Article
The genome in context: biologists and philosophers on epigenetics.
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- BioEssays, 2002, v. 24, n. 4, p. 392, doi. 10.1002/bies.10071
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- Publication type:
- Article
Modularity in development and evolution.
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- BioEssays, 2000, v. 22, n. 11, p. 1043, doi. 10.1002/1521-1878(200011)22:11<1043::AID-BIES11>3.0.CO;2-C
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- Publication type:
- Article
From global expression data to gene networks.
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- BioEssays, 1999, v. 21, n. 11, p. 895, doi. 10.1002/(SICI)1521-1878(199911)21:11<895::AID-BIES1>3.0.CO;2-F
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- Publication type:
- Article
From specific gene regulation to genomic networks: A global analysis of transcriptional...
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- BioEssays, 1998, v. 20, n. 5, p. 433, doi. 10.1002/(SICI)1521-1878(199805)20:5<433::AID-BIES10>3.0.CO;2-2
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- Publication type:
- Article
Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes.
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- PLoS Computational Biology, 2016, v. 12, n. 9, p. 1, doi. 10.1371/journal.pcbi.1005073
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- Publication type:
- Article
Setting the basis of best practices and standards for curation and annotation of logical models in biology—highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.
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- Briefings in Bioinformatics, 2021, v. 22, n. 2, p. 1848, doi. 10.1093/bib/bbaa046
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- Publication type:
- Article
Dynamical roles of biological regulatory circuits.
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- Briefings in Bioinformatics, 2007, v. 8, n. 4, p. 220, doi. 10.1093/bib/bbm028
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- Publication type:
- Article
Evaluating the Reproducibility of Single-Cell Gene Regulatory Network Inference Algorithms.
- Published in:
- Frontiers in Genetics, 2021, v. 11, p. N.PAG, doi. 10.3389/fgene.2021.617282
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- Publication type:
- Article
Postgenomics? A conference at the Max Planck Institute for the History of Science in Berlin.
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- BioScience, 1999, v. 49, n. 3, p. 223, doi. 10.1093/bioscience/49.3.223
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- Publication type:
- Article
Prediction of Mutations to Control Pathways Enabling Tumor Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial).
- Published in:
- Frontiers in Physiology, 2018, p. N.PAG, doi. 10.3389/fphys.2018.00787
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- Publication type:
- Article
Logical Modeling and Analysis of Cellular Regulatory Networks With GINsim 3.0.
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- Frontiers in Physiology, 2018, p. N.PAG, doi. 10.3389/fphys.2018.00646
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- Publication type:
- Article
The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks.
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- Frontiers in Physiology, 2018, p. N.PAG, doi. 10.3389/fphys.2018.00680
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- Publication type:
- Article
Logical modelling and analysis of the budding yeast cell cycle.
- Published in:
- BMC Bioinformatics, 2007, v. 8, p. 1, doi. 10.1186/1471-2105-8-S8-P1
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- Publication type:
- Article
Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling.
- Published in:
- PLoS Computational Biology, 2015, v. 11, n. 8, p. 1, doi. 10.1371/journal.pcbi.1004426
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- Publication type:
- Article
Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision.
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- PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003286
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- Publication type:
- Article
Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling.
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- PLoS Computational Biology, 2010, v. 6, n. 9, p. 1, doi. 10.1371/journal.pcbi.1000912
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- Publication type:
- Article
Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement.
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- PLoS Computational Biology, 2010, v. 6, n. 3, p. 1, doi. 10.1371/journal.pcbi.1000702
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- Publication type:
- Article
Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer.
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- Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-020-20430-7
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- Publication type:
- Article
Histone Chaperone SSRP1 is Essential for Wnt Signaling Pathway Activity During Osteoblast Differentiation.
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- Stem Cells, 2016, v. 34, n. 5, p. 1369, doi. 10.1002/stem.2287
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- Publication type:
- Article
Metagenome Annotation Using a Distributed Grid of Undergraduate Students.
- Published in:
- PLoS Biology, 2008, v. 6, n. 11, p. e296, doi. 10.1371/journal.pbio.0060296
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- Publication type:
- Article
C/EBPα poises B cells for rapid reprogramming into induced pluripotent stem cells.
- Published in:
- Nature, 2014, v. 506, n. 7487, p. 235, doi. 10.1038/nature12885
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- Publication type:
- Article
RSAT 2022: regulatory sequence analysis tools.
- Published in:
- Nucleic Acids Research, 2022, v. 50, n. W1, p. W670, doi. 10.1093/nar/gkac312
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- Publication type:
- Article
TFregulomeR reveals transcription factors' context-specific features and functions.
- Published in:
- Nucleic Acids Research, 2020, v. 48, n. 2, p. e10, doi. 10.1093/nar/gkz1088
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- Publication type:
- Article
MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles.
- Published in:
- Nucleic Acids Research, 2019, v. 47, n. D1, p. D145, doi. 10.1093/nar/gky1005
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- Publication type:
- Article
RSAT 2018: regulatory sequence analysis tools 20th anniversary.
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- Nucleic Acids Research, 2018, v. 46, n. W1, p. W209, doi. 10.1093/nar/gky317
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- Publication type:
- Article
RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections.
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- Nucleic Acids Research, 2017, v. 45, n. 13, p. 1, doi. 10.1093/nar/gkx314
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- Publication type:
- Article
RSAT 2015: Regulatory Sequence Analysis Tools.
- Published in:
- Nucleic Acids Research, 2015, v. 43, n. W1, p. W50, doi. 10.1093/nar/gkv362
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- Publication type:
- Article
RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets.
- Published in:
- Nucleic Acids Research, 2012, v. 40, n. 4, p. e31, doi. 10.1093/nar/gkr1104
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- Publication type:
- Article
RSAT 2011: regulatory sequence analysis tools.
- Published in:
- Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W86, doi. 10.1093/nar/gkr377
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- Publication type:
- Article
Dynamical Boolean Modeling of Immunogenic Cell Death.
- Published in:
- Frontiers in Physiology, 2020, v. 11, p. N.PAG, doi. 10.3389/fphys.2020.590479
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- Publication type:
- Article
Computational Verification of Large Logical Models—Application to the Prediction of T Cell Response to Checkpoint Inhibitors.
- Published in:
- Frontiers in Physiology, 2020, v. 11, p. N.PAG, doi. 10.3389/fphys.2020.558606
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- Publication type:
- Article
Logical model specification aided by model-checking techniques: application to the mammalian cell cycle regulation.
- Published in:
- Bioinformatics, 2016, v. 32, n. 17, p. i772, doi. 10.1093/bioinformatics/btw457
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- Publication type:
- Article
Cooperative development of logical modelling standards and tools with CoLoMoTo.
- Published in:
- Bioinformatics, 2015, v. 31, n. 7, p. 1154, doi. 10.1093/bioinformatics/btv013
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- Publication type:
- Article
CoCAS: a ChIP-on-chip analysis suite.
- Published in:
- Bioinformatics, 2009, v. 25, n. 7, p. 954, doi. 10.1093/bioinformatics/btp075
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- Publication type:
- Article
RegulonDB: a database on transcriptional regulation in Escherichia coli.
- Published in:
- Nucleic Acids Research, 1998, v. 26, n. 1, p. 55, doi. 10.1093/nar/26.1.55
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- Publication type:
- Article
Contribution of ROS and metabolic status to neonatal and adult CD8<sup>+</sup> T cell activation.
- Published in:
- PLoS ONE, 2019, v. 14, n. 12, p. 1, doi. 10.1371/journal.pone.0226388
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- Publication type:
- Article
Neonatal CD4<sup>+</sup> T cells have a characteristic transcriptome and epigenome and respond to TCR stimulation with proliferation and yet a limited immune response.
- Published in:
- Journal of Leukocyte Biology, 2024, v. 116, n. 1, p. 64, doi. 10.1093/jleuko/qiad162
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- Publication type:
- Article