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Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification.
- Published in:
- eLife, 2024, p. 1, doi. 10.7554/eLife.89262
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- Publication type:
- Article
An associative memory Hamiltonian model for DNA and nucleosomes.
- Published in:
- PLoS Computational Biology, 2023, v. 19, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011013
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- Publication type:
- Article
Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues.
- Published in:
- Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-35909-2
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- Article
Stochastic fluctuations promote ordered pattern formation of cells in the Notch-Delta signaling pathway.
- Published in:
- PLoS Computational Biology, 2022, v. 18, n. 7, p. 1, doi. 10.1371/journal.pcbi.1010306
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- Publication type:
- Article
Shaping the genome via lengthwise compaction, phase separation, and lamina adhesion.
- Published in:
- Nucleic Acids Research, 2022, v. 50, n. 8, p. 4258, doi. 10.1093/nar/gkac231
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- Publication type:
- Article
Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection.
- Published in:
- Molecular Biology & Evolution, 2022, v. 39, n. 5, p. 1, doi. 10.1093/molbev/msac091
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- Publication type:
- Article
DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases.
- Published in:
- Nucleic Acids Research, 2022, v. 50, n. 3, p. 1269, doi. 10.1093/nar/gkab1252
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- Publication type:
- Article
Towards decoding the coupled decision-making of metabolism and epithelial-to-mesenchymal transition in cancer.
- Published in:
- 2021
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- Publication type:
- journal article
The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome.
- Published in:
- Nucleic Acids Research, 2021, v. 49, n. D1, p. D172, doi. 10.1093/nar/gkaa818
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- Publication type:
- Article
Enhancing intracellular accumulation and target engagement of PROTACs with reversible covalent chemistry.
- Published in:
- Nature Communications, 2020, v. 11, n. 1, p. N.PAG, doi. 10.1038/s41467-020-17997-6
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- Publication type:
- Article
Drug-Tolerant Idling Melanoma Cells Exhibit Theory-Predicted Metabolic Low-Low Phenotype.
- Published in:
- Frontiers in Oncology, 2020, v. 10, p. N.PAG, doi. 10.3389/fonc.2020.01426
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- Publication type:
- Article
Modeling Chikungunya control strategies and Mayaro potential outbreak in the city of Rio de Janeiro.
- Published in:
- PLoS ONE, 2020, v. 15, n. 1, p. 1, doi. 10.1371/journal.pone.0222900
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- Publication type:
- Article
NRF2 activates a partial epithelial-mesenchymal transition and is maximally present in a hybrid epithelial/mesenchymal phenotype.
- Published in:
- Integrative Biology, 2019, v. 11, n. 6, p. 251, doi. 10.1093/intbio/zyz021
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- Publication type:
- Article
Quantifying Cancer Epithelial-Mesenchymal Plasticity and its Association with Stemness and Immune Response.
- Published in:
- Journal of Clinical Medicine, 2019, v. 8, n. 5, p. 725, doi. 10.3390/jcm8050725
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- Publication type:
- Article
Magnesium controls aptamer-expression platform switching in the SAM-I riboswitch.
- Published in:
- Nucleic Acids Research, 2019, v. 47, n. 6, p. 3158, doi. 10.1093/nar/gky1311
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- Publication type:
- Article
Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level.
- Published in:
- Biomolecules (2218-273X), 2019, v. 9, n. 2, p. 77, doi. 10.3390/biom9020077
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- Publication type:
- Article
Designing bacterial signaling interactions with coevolutionary landscapes.
- Published in:
- PLoS ONE, 2018, v. 13, n. 8, p. 1, doi. 10.1371/journal.pone.0201734
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- Publication type:
- Article
RACIPE: a computational tool for modeling gene regulatory circuits using randomization.
- Published in:
- BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0594-6
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- Publication type:
- Article
A magnesium-induced triplex pre-organizes the SAM-II riboswitch.
- Published in:
- PLoS Computational Biology, 2017, v. 13, n. 3, p. 1, doi. 10.1371/journal.pcbi.1005406
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- Publication type:
- Article
Strain Mediated Adaptation Is Key for Myosin Mechanochemistry: Discovering General Rules for Motor Activity.
- Published in:
- PLoS Computational Biology, 2016, v. 12, n. 8, p. 1, doi. 10.1371/journal.pcbi.1005035
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- Publication type:
- Article
Information and redundancy in the burial folding code of globular proteins within a wide range of shapes and sizes.
- Published in:
- Proteins, 2016, v. 84, n. 4, p. 515, doi. 10.1002/prot.24998
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- Publication type:
- Article
SMOG 2: A Versatile Software Package for Generating Structure-Based Models.
- Published in:
- PLoS Computational Biology, 2016, v. 12, n. 3, p. 1, doi. 10.1371/journal.pcbi.1004794
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- Publication type:
- Article
Periodic, Quasi-periodic and Chaotic Dynamics in Simple Gene Elements with Time Delays.
- Published in:
- Scientific Reports, 2016, p. 21037, doi. 10.1038/srep21037
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- Publication type:
- Article
Constructing sequence-dependent protein models using coevolutionary information.
- Published in:
- Protein Science: A Publication of the Protein Society, 2016, v. 25, n. 1, p. 111, doi. 10.1002/pro.2758
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- Publication type:
- Article
Geometrical Frustration in Interleukin-33 Decouples the Dynamics of the Functional Element from the Folding Transition State Ensemble.
- Published in:
- PLoS ONE, 2015, v. 10, n. 12, p. 1, doi. 10.1371/journal.pone.0144067
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- Publication type:
- Article
Cancer-Related NEET Proteins Transfer 2Fe-2S Clusters to Anamorsin, a Protein Required for Cytosolic Iron-Sulfur Cluster Biogenesis.
- Published in:
- PLoS ONE, 2015, v. 10, n. 10, p. 1, doi. 10.1371/journal.pone.0139699
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- Publication type:
- Article
Dimeric interactions and complex formation using direct coevolutionary couplings.
- Published in:
- Scientific Reports, 2015, p. 13652, doi. 10.1038/srep13652
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- Publication type:
- Article
Implications of the Hybrid Epithelial/Mesenchymal Phenotype in Metastasis.
- Published in:
- Frontiers in Oncology, 2015, p. 1, doi. 10.3389/fonc.2015.00155
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- Publication type:
- Article
Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure.
- Published in:
- Proteins, 2014, v. 82, n. 7, p. 1186, doi. 10.1002/prot.24483
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- Publication type:
- Article
Pierced Lasso Bundles Are a New Class of Knot-like Motifs.
- Published in:
- PLoS Computational Biology, 2014, v. 10, n. 6, p. 1, doi. 10.1371/journal.pcbi.1003613
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- Publication type:
- Article
Knotting pathways in proteins.
- Published in:
- Biochemical Society Transactions, 2013, v. 41, n. 2, p. 523, doi. 10.1042/BST20120342
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- Publication type:
- Article
The Dominant Folding Route Minimizes Backbone Distortion in SH3.
- Published in:
- PLoS Computational Biology, 2012, v. 8, n. 11, p. 1, doi. 10.1371/journal.pcbi.1002776
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- Publication type:
- Article
Substrate-Specific Reorganization of the Conformational Ensemble of CSK Implicates Novel Modes of Kinase Function.
- Published in:
- PLoS Computational Biology, 2012, v. 8, n. 9, p. 1, doi. 10.1371/journal.pcbi.1002695
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- Publication type:
- Article
The Unique Cysteine Knot Regulates the Pleotropic Hormone Leptin.
- Published in:
- PLoS ONE, 2012, v. 7, n. 9, p. 1, doi. 10.1371/journal.pone.0045654
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- Publication type:
- Article
Folding Circular Permutants of IL-1β: Route Selection Driven by Functional Frustration.
- Published in:
- PLoS ONE, 2012, v. 7, n. 6, p. 1, doi. 10.1371/journal.pone.0038512
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- Publication type:
- Article
The role of atomic level steric effects and attractive forces in protein folding.
- Published in:
- Proteins, 2012, v. 80, n. 2, p. 362, doi. 10.1002/prot.23187
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- Publication type:
- Article
Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites.
- Published in:
- Nature, 2010, v. 468, n. 7324, p. 713, doi. 10.1038/nature09547
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- Publication type:
- Article
SMOG@ctbp: simplified deployment of structure-based models in GROMACS.
- Published in:
- Nucleic Acids Research, 2010, v. 38, n. suppl_2, p. W657, doi. 10.1093/nar/gkq498
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- Publication type:
- Article
A Stevedore's Protein Knot.
- Published in:
- PLoS Computational Biology, 2010, v. 6, n. 4, p. 1, doi. 10.1371/journal.pcbi.1000731
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- Publication type:
- Article
Robustness and generalization of structure-based models for protein folding and function.
- Published in:
- Proteins, 2009, v. 77, n. 4, p. 881, doi. 10.1002/prot.22511
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- Publication type:
- Article
An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields.
- Published in:
- Proteins, 2009, v. 75, n. 2, p. 430, doi. 10.1002/prot.22253
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- Publication type:
- Article
Equilibrium unfolding of the poly(glutamic acid)<sub>20</sub> helix.
- Published in:
- Biopolymers, 2007, v. 86, n. 3, p. 193, doi. 10.1002/bip.20719
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- Publication type:
- Article
Structure of infectious prions: stabilization by domain swapping.
- Published in:
- FASEB Journal, 2005, v. 19, n. 13, p. 1778, doi. 10.1096/fj.05-4067hyp
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- Publication type:
- Article
Understanding protein folding with energy landscape theory Part II: Quantitative aspects.
- Published in:
- Quarterly Reviews of Biophysics, 2002, v. 35, n. 3, p. 205, doi. 10.1017/S0033583502003785
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- Publication type:
- Article
Understanding protein folding with energy landscape theory Part I: Basic concepts.
- Published in:
- Quarterly Reviews of Biophysics, 2002, v. 35, n. 2, p. 111, doi. 10.1017/S0033583502003761
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- Publication type:
- Article