State-Transition Diagrams for Biologists
Publication Date
July 23, 2012
Journal
PLOS ONE
Authors
Hugues Bersini, David Klatzmann, Adrien Six & Véronique Thomas Vaslin
Volume
7
Issue
7
Pages
e41165
DOI
https://dx.plos.org/10.1371/journal.pone.0041165
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0041165
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/22844438
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3402529
Europe PMC
http://europepmc.org/abstract/MED/22844438
Web of Science
000306687700051
Scopus
84864267635
Mendeley
http://www.mendeley.com/research/statetransition-diagrams-biologists
Events
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Mendeley | Further Information

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/604935"], "description"=>"<p>Two sub state-transition diagrams ( and ) showing a weak dependency. The transition rates in the lower track depend on the state in the upper track.</p>", "links"=>[], "tags"=>["sub", "state-transition", "diagrams", "rates"], "article_id"=>275424, "categories"=>["Information And Computing Sciences", "Mathematics", "Genetics", "Immunology"], "users"=>["Hugues Bersini", "David Klatzmann", "Adrien Six", "Véronique Thomas-Vaslin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041165.g007", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Two_sub_state_transition_diagrams_and_showing_a_weak_dependency_The_transition_rates_in_the_lower_track_depend_on_the_state_in_the_upper_track_/275424", "title"=>"Two sub state-transition diagrams ( and ) showing a weak dependency. The transition rates in the lower track depend on the state in the upper track.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 02:05:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/604784"], "description"=>"<p>Here a DP cell can alternatively differentiate into either a SP4 or SP8 cell with respective probability and .</p>", "links"=>[], "tags"=>["state-transition", "diagram", "illustrating", "conditional"], "article_id"=>275277, "categories"=>["Information And Computing Sciences", "Mathematics", "Genetics", "Immunology"], "users"=>["Hugues Bersini", "David Klatzmann", "Adrien Six", "Véronique Thomas-Vaslin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041165.g004", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_state_transition_diagram_illustrating_a_conditional_transition_/275277", "title"=>"A state-transition diagram illustrating a conditional transition.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 02:04:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/605339"], "description"=>"<p>Although many transitions occur with parameterized rates, those related to differentiation are rule-based – making use of transition guards that refer to individual attributes. This model has no real hierarchical structure other than to conveniently specify a shared transition for SP4/SP8 cells.</p>", "links"=>[], "tags"=>["souza", "et", "depicting", "tcr-mhc", "binding", "anatomical", "compartments"], "article_id"=>275827, "categories"=>["Information And Computing Sciences", "Mathematics", "Genetics", "Immunology"], "users"=>["Hugues Bersini", "David Klatzmann", "Adrien Six", "Véronique Thomas-Vaslin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041165.g012", "stats"=>{"downloads"=>3, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Statechart_description_of_the_Souza_et_al_model_19_depicting_differentiation_proliferation_TCR_MHC_binding_and_movement_between_the_different_anatomical_compartments_of_the_thymus_/275827", "title"=>"Statechart description of the Souza et al. model [<b>19</b>] depicting differentiation, proliferation, TCR-MHC binding and movement between the different anatomical compartments of the thymus.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 02:07:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/605052"], "description"=>"<p>When entering its dividing cycle, all other transitions turn out to be impossible. This is indicated by the presence of <i>[Not cycle]</i> with labeling the compound state of dividing cell. Some of the transition rates “weakly” depend on the states where the lymphocyte is currently found in the other parallel tracks. indicates the birth rate to naive cells.</p>", "links"=>[], "tags"=>["illustrates", "parallel", "sub-state-transition", "diagrams", "immunological", "lymphocytes", "successive"], "article_id"=>275540, "categories"=>["Information And Computing Sciences", "Mathematics", "Genetics", "Immunology"], "users"=>["Hugues Bersini", "David Klatzmann", "Adrien Six", "Véronique Thomas-Vaslin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041165.g009", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_As_a_more_realistic_example_of_weak_and_strong_dependencies_the_figure_illustrates_three_parallel_sub_state_transition_diagrams_of_a_very_classical_immunological_situation_with_lymphocytes_differentiating_migrating_and_dividing_in_3_successive_stages_/275540", "title"=>"As a more realistic example of weak and strong dependencies, the figure illustrates three parallel sub-state-transition diagrams of a very classical immunological situation with lymphocytes <i>differentiating</i>, <i>migrating</i> and <i>dividing</i> (in 3 successive stages).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 02:05:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/604983"], "description"=>"<p>When the object is in state in the lower track, the transition becomes impossible. This is indicated by conditioning this transition with <i>[NOT Y]</i>.</p>", "links"=>[], "tags"=>["sub", "state-transition", "diagrams"], "article_id"=>275477, "categories"=>["Information And Computing Sciences", "Mathematics", "Genetics", "Immunology"], "users"=>["Hugues Bersini", "David Klatzmann", "Adrien Six", "Véronique Thomas-Vaslin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041165.g008", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Two_sub_state_transition_diagrams_and_showing_a_strong_dependency_/275477", "title"=>"Two sub state-transition diagrams ( and ) showing a strong dependency.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 02:05:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/604729"], "description"=>"<p>A more faithful and complete use of state-transition diagrams in the presence of origin and death states with possibility of proliferation and transit from stage A to B.</p>", "links"=>[], "tags"=>["faithful", "state-transition", "diagrams", "states", "proliferation"], "article_id"=>275222, "categories"=>["Information And Computing Sciences", "Mathematics", "Genetics", "Immunology"], "users"=>["Hugues Bersini", "David Klatzmann", "Adrien Six", "Véronique Thomas-Vaslin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041165.g003", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_more_faithful_and_complete_use_of_state_transition_diagrams_in_the_presence_of_origin_and_death_states_with_possibility_of_proliferation_and_transit_from_stage_A_to_B_/275222", "title"=>"A more faithful and complete use of state-transition diagrams in the presence of origin and death states with possibility of proliferation and transit from stage A to B.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 02:04:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/604826"], "description"=>"<p>A common transition leaving the compound state is shared by all single states although presenting different transition rates.</p>", "links"=>[], "tags"=>["state-transition", "diagram", "containing", "states"], "article_id"=>275319, "categories"=>["Information And Computing Sciences", "Mathematics", "Genetics", "Immunology"], "users"=>["Hugues Bersini", "David Klatzmann", "Adrien Six", "Véronique Thomas-Vaslin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041165.g005", "stats"=>{"downloads"=>1, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Example_of_compound_state_transition_diagram_containing_three_single_states_and_internal_transitions_/275319", "title"=>"Example of compound state-transition diagram containing three single states and internal transitions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 02:04:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/604892"], "description"=>"<p>Two fully independent sub state-transition diagrams ( and ) executing in parallel.</p>", "links"=>[], "tags"=>["sub", "state-transition", "diagrams", "executing"], "article_id"=>275381, "categories"=>["Information And Computing Sciences", "Mathematics", "Genetics", "Immunology"], "users"=>["Hugues Bersini", "David Klatzmann", "Adrien Six", "Véronique Thomas-Vaslin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041165.g006", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Two_fully_independent_sub_state_transition_diagrams_and_executing_in_parallel_/275381", "title"=>"Two fully independent sub state-transition diagrams ( and ) executing in parallel.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 02:04:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/605213"], "description"=>"<p>This diagram attempts to essentially capture the same biological information as the one contained in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041165#pone-0041165-g001\" target=\"_blank\">figure 1b</a>.</p>", "links"=>[], "tags"=>["diagram", "thomas-vaslin", "et", "thymocyte"], "article_id"=>275706, "categories"=>["Information And Computing Sciences", "Mathematics", "Genetics", "Immunology"], "users"=>["Hugues Bersini", "David Klatzmann", "Adrien Six", "Véronique Thomas-Vaslin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041165.g011", "stats"=>{"downloads"=>1, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_State_transition_diagram_of_the_Thomas_Vaslin_et_al_model_15_of_thymocyte_differentiation_/275706", "title"=>"State-transition diagram of the Thomas-Vaslin et al. model [<b>15</b>] of thymocyte differentiation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 02:06:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/605149"], "description"=>"<p>As cells transit from the cycling stage back to state , they should <i>also</i> move through the successive differentiated types - , and are three successive generations of cells. The default interpretation goes as the top-right figure but should rather be transformed into the bottom-right due to the shared labeling of the coupled transitions.</p>", "links"=>[], "tags"=>["coupled", "parallel", "differentiation"], "article_id"=>275643, "categories"=>["Information And Computing Sciences", "Mathematics", "Genetics", "Immunology"], "users"=>["Hugues Bersini", "David Klatzmann", "Adrien Six", "Véronique Thomas-Vaslin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041165.g010", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_illustration_of_a_coupled_transition_existing_in_parallel_tracks_representing_a_simple_cell_division_and_differentiation_left_/275643", "title"=>"An illustration of a coupled transition (<i>existing</i>) in parallel tracks, representing a simple cell division and differentiation (left).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 02:06:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/604676"], "description"=>"<p>A cell is being infected by a virus, an inactive gene becomes active and a thymocyte switches between differentiation stages.</p>", "links"=>[], "tags"=>["immunology", "genetics and genomics", "computer science", "mathematics"], "article_id"=>275167, "categories"=>["Information And Computing Sciences", "Mathematics", "Genetics", "Immunology"], "users"=>["Hugues Bersini", "David Klatzmann", "Adrien Six", "Véronique Thomas-Vaslin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041165.g002", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Three_classical_elementary_biological_state_transitions_/275167", "title"=>"Three classical elementary biological state transitions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 02:03:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/604600"], "description"=>"<p><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041165#pone.0041165-ThomasVaslin1\" target=\"_blank\">[15]</a> illustrating the conveyor belt model of thymocyte differentiation to be discussed later - extract from a paper by Rong and Perelson <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041165#pone.0041165-Rong1\" target=\"_blank\">[23]</a> illustrating the successive infection stages by the HIV virus.</p>", "links"=>[], "tags"=>["graphical", "illustrations", "immunological", "state-transition", "extract", "immunology", "illustrating", "successive", "thymocyte", "differentiation", "stages", "veronique", "thomas-vaslin", "et"], "article_id"=>275071, "categories"=>["Information And Computing Sciences", "Mathematics", "Genetics", "Immunology"], "users"=>["Hugues Bersini", "David Klatzmann", "Adrien Six", "Véronique Thomas-Vaslin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041165.g001", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Three_graphical_illustrations_of_immunological_knowledge_which_are_very_similar_in_spirit_to_state_transition_diagrams_extract_from_Janeway_s_classical_immunology_textbook_22_illustrating_the_successive_thymocyte_differentiation_stages_extract_from_a_pap/275071", "title"=>"Three graphical illustrations of immunological knowledge which are very similar in spirit to state-transition diagrams: extract from Janeway’s classical immunology textbook [<b>22</b>] illustrating the successive thymocyte differentiation stages - extract from a paper by Veronique Thomas-Vaslin et al.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 02:03:13"}

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Relative Metric

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