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{"title"=>"Chromatin computation", "type"=>"journal", "authors"=>[{"first_name"=>"Barbara", "last_name"=>"Bryant", "scopus_author_id"=>"16202156300"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"doi"=>"10.1371/journal.pone.0035703", "issn"=>"19326203", "sgr"=>"84860451618", "scopus"=>"2-s2.0-84860451618", "pui"=>"364721381", "pmid"=>"22567109", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)"}, "id"=>"64b6855a-dd23-3c81-91d1-cc1e554af24e", "abstract"=>"In living cells, DNA is packaged along with protein and RNA into chromatin. Chemical modifications to nucleotides and histone proteins are added, removed and recognized by multi-functional molecular complexes. Here I define a new computational model, in which chromatin modifications are information units that can be written onto a one-dimensional string of nucleosomes, analogous to the symbols written onto cells of a Turing machine tape, and chromatin-modifying complexes are modeled as read-write rules that operate on a finite set of adjacent nucleosomes. I illustrate the use of this \"chromatin computer\" to solve an instance of the Hamiltonian path problem. I prove that chromatin computers are computationally universal--and therefore more powerful than the logic circuits often used to model transcription factor control of gene expression. Features of biological chromatin provide a rich instruction set for efficient computation of nontrivial algorithms in biological time scales. Modeling chromatin as a computer shifts how we think about chromatin function, suggests new approaches to medical intervention, and lays the groundwork for the engineering of a new class of biological computing machines.", "link"=>"http://www.mendeley.com/research/chromatin-computation", "reader_count"=>50, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Researcher"=>15, "Student > Ph. D. Student"=>13, "Student > Postgraduate"=>4, "Student > Master"=>4, "Other"=>1, "Student > Bachelor"=>5, "Professor"=>5}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Researcher"=>15, "Student > Ph. D. Student"=>13, "Student > Postgraduate"=>4, "Student > Master"=>4, "Other"=>1, "Student > Bachelor"=>5, "Professor"=>5}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>28, "Medicine and Dentistry"=>2, "Neuroscience"=>1, "Physics and Astronomy"=>2, "Chemistry"=>2, "Social Sciences"=>1, "Computer Science"=>7}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>2}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>28}, "Computer Science"=>{"Computer Science"=>7}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}}, "reader_count_by_country"=>{"United States"=>6, "Norway"=>1, "Italy"=>1, "Mexico"=>2, "Chile"=>1, "Germany"=>2}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/644817"], "description"=>"<p>Figure from Adleman 1994 (5). In the pictured directed graph, there is a unique Hamiltonian path from vertex 0 to vertex 6: 0123456.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "computer science", "mathematics"], "article_id"=>315309, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Genetics"], "users"=>["Barbara Bryant"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035703.g002", "stats"=>{"downloads"=>2, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hamiltonian_path_problem_/315309", "title"=>"Hamiltonian path problem.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-02 01:28:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/644869"], "description"=>"<p>(A) Application of a rule to the starting configuration. The chromatin tape is shown as a set of 7 nucleosomes, each with 6 writable positions. The top row shows the initial tape configuration; the bottom row shows the configuration after the application of the rule 0***** B*****------ 1-----. The leftmost position in each nucleosomes maps to a numbered vertex in the graph. The remaining 5 positions are used to determine whether each node appears exactly once in the path. This rule extends the path from 0 to 1. (B) Two path-checking rules operating sequentially on an intermediate configuration in the computation. (C) The final chromatin configuration showing the successful solution.</p>", "links"=>[], "tags"=>["chromatin", "solving", "hamiltonian"], "article_id"=>315369, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Genetics"], "users"=>["Barbara Bryant"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035703.g003", "stats"=>{"downloads"=>3, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Operation_of_a_chromatin_computer_solving_the_Hamiltonian_Path_Problem_/315369", "title"=>"Operation of a chromatin computer solving the Hamiltonian Path Problem.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-02 01:29:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/644780"], "description"=>"<p>This diagram illustrates the operation of the rule XX** BB**---- XX--. The chromatin tape is composed of nucleosomes having four writable locations. Each location can be marked with the symbol B or X. Rules in this CC operate on two adjacent nucleosomes. In the illustration of the read portion of the rule, matching to any symbol (*) is shown with an empty. An empty square in the write portion of the rule leaves the current symbol unchanged (−).</p>", "links"=>[], "tags"=>["chromatin"], "article_id"=>315277, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Genetics"], "users"=>["Barbara Bryant"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035703.g001", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Example_of_the_operation_of_a_chromatin_computer_rule_/315277", "title"=>"Example of the operation of a chromatin computer rule.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-02 01:27:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/644937"], "description"=>"<p>(A) Turing machine finite state machine with three rules that rewrite the string “xy” to “zz”. (B) The corresponding chromatin computer. The first position in each 3-position nucleosome corresponds to the location of the Turing read/write head. The second position corresponds to the state of the Turing machine. The third position corresponds to a cell on the Turing tape.</p>", "links"=>[], "tags"=>["turing", "chromatin"], "article_id"=>315434, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Genetics"], "users"=>["Barbara Bryant"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035703.g004", "stats"=>{"downloads"=>1, "page_views"=>65, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mapping_from_a_Turing_machine_to_a_chromatin_computer_/315434", "title"=>"Mapping from a Turing machine to a chromatin computer.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-02 01:30:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/331866"], "description"=>"<div><p>In living cells, DNA is packaged along with protein and RNA into chromatin. Chemical modifications to nucleotides and histone proteins are added, removed and recognized by multi-functional molecular complexes. Here I define a new computational model, in which chromatin modifications are information units that can be written onto a one-dimensional string of nucleosomes, analogous to the symbols written onto cells of a Turing machine tape, and chromatin-modifying complexes are modeled as read-write rules that operate on a finite set of adjacent nucleosomes. I illustrate the use of this “chromatin computer” to solve an instance of the Hamiltonian path problem. I prove that chromatin computers are computationally universal – and therefore more powerful than the logic circuits often used to model transcription factor control of gene expression. Features of biological chromatin provide a rich instruction set for efficient computation of nontrivial algorithms in biological time scales. Modeling chromatin as a computer shifts how we think about chromatin function, suggests new approaches to medical intervention, and lays the groundwork for the engineering of a new class of biological computing machines.</p> </div>", "links"=>[], "tags"=>["chromatin", "computation"], "article_id"=>125535, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Genetics"], "users"=>["Barbara Bryant"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035703", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Chromatin_Computation/125535", "title"=>"Chromatin Computation", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-02 01:32:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/644995"], "description"=>"<p>Biological equivalents for computational concepts in the CC model.</p>", "links"=>[], "tags"=>["equivalents", "computational", "concepts", "cc"], "article_id"=>315487, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Genetics"], "users"=>["Barbara Bryant"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0035703.t001", "stats"=>{"downloads"=>0, "page_views"=>35, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Biological_equivalents_for_computational_concepts_in_the_CC_model_/315487", "title"=>"Biological equivalents for computational concepts in the CC model.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-02 01:31:27"}

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  • {"unique-ip"=>"10", "full-text"=>"5", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"10"}
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  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"10"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"11"}
  • {"unique-ip"=>"7", "full-text"=>"8", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2016", "month"=>"12"}
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  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"5"}
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  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
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  • {"unique-ip"=>"5", "full-text"=>"6", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"5", "full-text"=>"7", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"7", "full-text"=>"6", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"15", "full-text"=>"15", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"13", "full-text"=>"12", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}

Relative Metric

{"start_date"=>"2012-01-01T00:00:00Z", "end_date"=>"2012-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Cell biology", "average_usage"=>[319, 556, 679, 785, 881, 970, 1062, 1149, 1236, 1323, 1402, 1474, 1545, 1617, 1681, 1754, 1822, 1892, 1963, 2031, 2099, 2165, 2233, 2299, 2359]}, {"subject_area"=>"/Computer and information sciences", "average_usage"=>[352, 587, 696, 809, 901, 989, 1072, 1156, 1257, 1334, 1422, 1486, 1555, 1647, 1714, 1780, 1844, 1919, 1997, 2051, 2138, 2198, 2267, 2324, 2391]}]}
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