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HomGL--comparing genelists across species and with different accession numbers.
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- Bioinformatics, 2004, v. 20, n. 1, p. 125, doi. 10.1093/bioinformatics/btg379
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- Article
High Accuracy Classification of Developmental Toxicants by In Vitro Tests of Human Neuroepithelial and Cardiomyoblast Differentiation.
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- Cells (2073-4409), 2022, v. 11, n. 21, p. 3404, doi. 10.3390/cells11213404
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- Article
Global analysis of host tissue gene expression in the invasive front of colorectal liver metastases.
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- International Journal of Cancer, 2006, v. 118, n. 1, p. 74, doi. 10.1002/ijc.21307
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How scaffolds shape MAPK signaling: what we know and opportunities for systems approaches.
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- Frontiers in Physiology, 2013, p. 1, doi. 10.3389/fphys.2012.00475
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- Article
Early senescence and production of senescence-associated cytokines are major determinants of radioresistance in head-and-neck squamous cell carcinoma.
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- Cell Death & Disease, 2021, v. 12, n. 12, p. 1, doi. 10.1038/s41419-021-04454-5
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A compendium of ERK targets.
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- FEBS Letters, 2017, v. 591, n. 17, p. 2607, doi. 10.1002/1873-3468.12740
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- Article
Robustness of signal transduction pathways.
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- Cellular & Molecular Life Sciences, 2013, v. 70, n. 13, p. 2259, doi. 10.1007/s00018-012-1162-7
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- Article
Single-cell gene regulatory network prediction by explainable AI.
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- Nucleic Acids Research, 2023, v. 51, n. 4, p. e20, doi. 10.1093/nar/gkac1212
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- Article
Perturbation-response genes reveal signaling footprints in cancer gene expression.
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- Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-017-02391-6
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- Article
RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway.
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- Nature Communications, 2015, v. 6, n. 7, p. 7367, doi. 10.1038/ncomms8367
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- Article
Neuronal activity regulates alternative exon usage.
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- Molecular Brain, 2020, v. 13, n. 1, p. N.PAG, doi. 10.1186/s13041-020-00685-3
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- Article
Reverse engineering gene regulatory networks by modular response analysis -- a benchmark.
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- Essays in Biochemistry, 2018, v. 62, n. 4, p. 535, doi. 10.1042/EBC20180012
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- Article
Consequences of feedback in signal transduction for targeted therapies.
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- Biochemical Society Transactions, 2014, v. 42, n. 4, p. 770, doi. 10.1042/BST20140130
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- Article
Neuroblastoma signalling models unveil combination therapies targeting feedback-mediated resistance.
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- PLoS Computational Biology, 2021, v. 17, n. 11, p. 1, doi. 10.1371/journal.pcbi.1009515
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- Article
Spatial partitioning of the regulatory landscape of the X-inactivation centre.
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- Nature, 2012, v. 485, n. 7398, p. 381, doi. 10.1038/nature11049
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- Article
DNA methylation reveals distinct cells of origin for pancreatic neuroendocrine carcinomas and pancreatic neuroendocrine tumors.
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- Genome Medicine, 2022, v. 14, n. 1, p. 1, doi. 10.1186/s13073-022-01018-w
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- Article
Identification of Y-Box Binding Protein 1 As a Core Regulator of MEK/ERK Pathway-Dependent Gene Signatures in Colorectal Cancer Cells.
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- PLoS Genetics, 2010, v. 6, n. 12, p. 1, doi. 10.1371/journal.pgen.1001231
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Silence on the relevant literature and errors in implementation.
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- Nature Biotechnology, 2015, v. 33, n. 4, p. 336, doi. 10.1038/nbt.3185
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- Article
Noise Management by Molecular Networks.
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- PLoS Computational Biology, 2009, v. 5, n. 9, p. 1, doi. 10.1371/journal.pcbi.1000506
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- Article
Mathematical Modeling Identifies Inhibitors of Apoptosis as Mediators of Positive Feedback and Bistability.
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- PLoS Computational Biology, 2006, v. 2, n. 9, p. e120, doi. 10.1371/journal.pcbi.0020120
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- Article
Ultrasensitization: Switch-Like Regulation of Cellular Signaling by Transcriptional Induction.
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- PLoS Computational Biology, 2005, v. 1, n. 5, p. 405, doi. 10.1371/journal.pcbi.0010054
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- Article
Identifiability and experimental design in perturbation studies.
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- Bioinformatics, 2020, v. 36, p. i482, doi. 10.1093/bioinformatics/btaa404
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Robust network inference using response logic.
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- Bioinformatics, 2019, v. 35, n. 14, p. i634, doi. 10.1093/bioinformatics/btz326
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- Article
Modelling signalling networks from perturbation data.
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- Bioinformatics, 2018, v. 34, n. 23, p. 4079, doi. 10.1093/bioinformatics/bty473
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Comparative Network Reconstruction using mixed integer programming.
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- Bioinformatics, 2018, v. 34, n. 17, p. i997, doi. 10.1093/bioinformatics/bty616
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- Article
Classification of gene signatures for their information value and functional redundancy.
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- NPJ Systems Biology & Applications, 2018, v. 4, n. 1, p. N.PAG, doi. 10.1038/s41540-017-0038-8
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- Article
Tracking in vivo dynamics of NK cells transferred in patients undergoing stem cell transplantation.
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- European Journal of Immunology, 2014, v. 44, n. 9, p. 2822, doi. 10.1002/eji.201444586
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- Article
Genome-Wide Profiling of the Activity-Dependent Hippocampal Transcriptome.
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- PLoS ONE, 2013, v. 8, n. 10, p. 1, doi. 10.1371/journal.pone.0076903
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- Article
Development of a neural rosette formation assay (RoFA) to identify neurodevelopmental toxicants and to characterize their transcriptome disturbances.
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- Archives of Toxicology, 2020, v. 94, n. 1, p. 151, doi. 10.1007/s00204-019-02612-5
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- Article
A transcriptome-based classifier to identify developmental toxicants by stem cell testing: design, validation and optimization for histone deacetylase inhibitors.
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- Archives of Toxicology, 2015, v. 89, n. 9, p. 1599, doi. 10.1007/s00204-015-1573-y
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- Article
Profiling the MAPK/ERK dependent and independent activity regulated transcriptional programs in the murine hippocampus in vivo.
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- Scientific Reports, 2017, p. 45101, doi. 10.1038/srep45101
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- Article
Helicobacter pylori shows tropism to gastric differentiated pit cells dependent on urea chemotaxis.
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- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-33165-4
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- Article
A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data.
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- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-30177-y
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- Article
Comparison of a teratogenic transcriptomebased predictive test based on human embryonic versus inducible pluripotent stem cells.
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- Stem Cell Research & Therapy, 2016, v. 7, p. 1, doi. 10.1186/s13287-016-0449-2
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- Article
Sequestration shapes the response of signal transduction cascades.
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- IUBMB Life, 2006, v. 58, n. 11, p. 659, doi. 10.1080/15216540600994340
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- Article
A systems biological approach suggests that transcriptional feedback regulation by dual-specificity phosphatase 6 shapes extracellular signal-related kinase activity in RAS-transformed fibroblasts.
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- FEBS Journal, 2009, v. 276, n. 4, p. 1024, doi. 10.1111/j.1742-4658.2008.06846.x
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- Article
Seed-based systematic discovery of specific transcription factor target genes.
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- FEBS Journal, 2008, v. 275, n. 12, p. 3178, doi. 10.1111/j.1742-4658.2008.06471.x
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- Article
Effects of sequestration on signal transduction cascades.
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- FEBS Journal, 2006, v. 273, n. 5, p. 895, doi. 10.1111/j.1742-4658.2006.05105.x
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- Article
Quantitative analysis of ultrasensitive responses.
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- FEBS Journal, 2005, v. 272, n. 16, p. 4071, doi. 10.1111/j.1742-4658.2005.04818.x
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- Article
Kinetic modeling of stem cell transcriptome dynamics to identify regulatory modules of normal and disturbed neuroectodermal differentiation.
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- Nucleic Acids Research, 2020, v. 48, n. 22, p. 12577, doi. 10.1093/nar/gkaa1089
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- Article
SPEED2: inferring upstream pathway activity from differential gene expression.
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- Nucleic Acids Research, 2020, v. 48, n. W1, p. W307, doi. 10.1093/nar/gkaa236
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- Article
Signal integration by the CYP1A1 promoter -- a quantitative study.
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- Nucleic Acids Research, 2015, v. 43, n. 11, p. 5318, doi. 10.1093/nar/gkv423
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- Article
Hypoxia-induced gene expression results from selective mRNA partitioning to the endoplasmic reticulum.
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- Nucleic Acids Research, 2015, v. 43, n. 6, p. 3219, doi. 10.1093/nar/gkv167
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- Article
Targetfinder.org: a resource for systematic discovery of transcription factor target genes.
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- Nucleic Acids Research, 2010, v. 38, n. suppl_2, p. W233, doi. 10.1093/nar/gkq374
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- Article
TransFind—predicting transcriptional regulators for gene sets.
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- Nucleic Acids Research, 2010, v. 38, n. suppl_2, p. W275, doi. 10.1093/nar/gkq438
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- Article
Discovering causal signaling pathways through gene-expression patterns.
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- Nucleic Acids Research, 2010, v. 38, n. suppl_2, p. W109, doi. 10.1093/nar/gkq424
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- Article
Analysis of impedance-based cellular growth assays.
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- Bioinformatics, 2015, v. 31, n. 16, p. 2705, doi. 10.1093/bioinformatics/btv216
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- Article
Computer-assisted curation of a human regulatory core network from the biological literature.
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- Bioinformatics, 2015, v. 31, n. 8, p. 1258, doi. 10.1093/bioinformatics/btu795
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- Article
Computer-assisted curation of a human regulatory core network from the biological literature.
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- Bioinformatics, 2015, v. 31, n. 7, p. 1258, doi. 10.1093/bioinformatics/btu795
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- Article
Stem Cell-Derived Immature Human Dorsal Root Ganglia Neurons to Identify Peripheral Neurotoxicants.
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- Stem Cells Translational Medicine, 2016, v. 5, n. 4, p. 476, doi. 10.5966/sctm.2015-0108
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- Article