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Nature Communications, ISSN 2041-1723, 12/2018, Volume 9, Issue 1, pp. 4949 - 10
Journal Article
Biophysical Journal, ISSN 0006-3495, 02/2017, Volume 112, Issue 3, p. 427
  Energy landscape theory, developed in the context of protein folding, provides, to our knowledge, a new perspective on chromosome architecture. We review... 
Bioenergetics | Protein folding | Cell division | Genetics | Biophysics | Chromosomes
Journal Article
Journal of the American Chemical Society, ISSN 0002-7863, 11/2019
Journal Article
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 02/2017, Volume 114, Issue 6, p. 1287
  The heterogeneous elastoplastic deformation of structural glasses is explored using the framework of the random first-order transition theory of the glass... 
Deformation | Theory | Glass | Shear strength | Strain rate
Journal Article
Biophysical Journal, ISSN 0006-3495, 01/2015, Volume 108, Issue 2, pp. 537a - 537a
Journal Article
The Journal of Physical Chemistry B, ISSN 1520-6106, 10/2013, Volume 117, Issue 42, pp. 12672 - 12675
Journal Article
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 04/2017, Volume 114, Issue 17, p. 4406
Huntington's disease (HD) is a neurodegenerative disease caused by an abnormal expansion in the polyglutamine (polyQ) track of the Huntingtin (HTT) protein.... 
Huntingtons disease | Animal models | Energy use | Huntingtin | Computational neuroscience | Animal memory | Fragments | Agglomeration | Polyglutamine diseases | Huntington's disease | Free energy | Fragmentation | Proteins | Oligomers | Associative memory | Extrapolation | Rodents | Computer applications | Amyloid | Polyproline | Trinucleotide repeat diseases
Journal Article
Biophysical Journal, ISSN 0006-3495, 02/2018, Volume 114, Issue 3, pp. 597a - 597a
Journal Article
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 05/2015, Volume 112, Issue 19, p. 6062
  Chromosome conformation capture experiments provide a rich set of data concerning the spatial organization of the genome. We use these data along with a... 
Bioenergetics | Microscopy | Genomes | Entropy | Chromosomes
Journal Article
BMC Systems Biology, 01/2018, Volume 12, Issue 1, pp. 1 - 11
Abstract Background Transfection of NF κB synthetic decoy Oligodeoxynucleotides (ODNs) has been proposed as a promising therapeutic strategy for a variety of... 
Therapeutic efficacy | Systems pharmacology | Systems biology | NF ΚB synthetic decoy ODNs | NF κB synthetic decoy ODNs
Journal Article
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 07/2018, Volume 115, Issue 30, p. 7753
The nucleus of a eukaryotic cell is a nonequilibrium system where chromatin is subjected to active processes that continuously rearrange it over the cell’s... 
Viscoelasticity | Chromatin | Computer simulation | Architecture | Spatial discrimination | Molecular dynamics | Genomes | Equilibrium | Loci | Proteins | Eukaryotes | Dynamic tests | Energy | Coherence | Life cycle engineering | Nuclei (cytology) | Diffusion | Chromosomes | Life cycles
Journal Article
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 05/2016, Volume 113, Issue 18, p. 5006
  Aplysia cytoplasmic polyadenylation element binding (CPEB) protein, a translational regulator that recruits mRNAs and facilitates translation, has been shown... 
Proteins | Molecules | Catalysis | Ribonucleic acid--RNA | Binding sites
Journal Article
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 07/2014, Volume 111, Issue 28, p. 10185
  Stem cell differentiation has been viewed as coming from transitions between attractors on an epigenetic landscape that governs the dynamics of a regulatory... 
Molecules | Stem cells | Gene expression | Deoxyribonucleic acid--DNA
Journal Article
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 07/2014, Volume 111, Issue 28, p. 10185
  Stem cell differentiation has been viewed as coming from transitions between attractors on an epigenetic landscape that governs the dynamics of a regulatory... 
Genes | Stem cells | Gene expression | Deoxyribonucleic acid--DNA
Journal Article
Nature Physics, ISSN 1745-2473, 03/2015, Volume 11, Issue 3, pp. 287 - 287
Journal Article
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 11/2017, Volume 114, Issue 46, p. 12126
Inside the cell nucleus, genomes fold into organized structures that are characteristic of cell type. Here, we show that this chromatin architecture can be... 
Chromatin | Immunoprecipitation | Architecture | Fluorescence | Genomes | Entropy | Marking | Experiments | Nuclei | Loci | Annotations | Neural networks | Phase separation | Fluorescence in situ hybridization | Predictions | Epigenetics | Biomarkers | Nuclei (cytology) | Mathematical models | Gene mapping | Chromosomes | Maximum entropy | Deoxyribonucleic acid--DNA
Journal Article
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 10/2016, Volume 113, Issue 42, p. 11835
  A predictive coarse-grained protein force field [associative memory, water-mediated, structure, and energy model for molecular dynamics (AWSEM)-MD] is used... 
Proteins | Molecules | Energy | Hydrogen bonds | Simulation | Sampling
Journal Article
Biophysical Journal, ISSN 0006-3495, 2011, Volume 100, Issue 3, pp. 5a - 5a
Journal Article
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 02/2014, Volume 111, Issue 6, p. 2391
  The digital nature of genes combined with the associated low copy numbers of proteins regulating them is a significant source of stochasticity, which affects... 
Proteins | Phenomenology | Genes | Genetics | Stochastic models | Experiments | Oscillators
Journal Article
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