Pinboard (cshalizi) https://pinboard.in/u:cshalizi/public/ recent bookmarks from cshalizi Boolean Networks as Predictive Models of Emergent Biological Behaviors 2026-04-17T03:18:43+00:00 https://www.cambridge.org/core/elements/boolean-networks-as-predictive-models-of-emergent-biological-behaviors/0D2383F0D64543A77892CEBD5C6A964B cshalizi to:NB biochemical_networks of_course_its_really_a_spin_glass books:noted downloaded https://pinboard.in/ https://pinboard.in/u:cshalizi/b:98c166445d04/ A recursive enzymatic competition network capable of multitask molecular information processing | Nature Chemistry 2025-12-10T15:44:15+00:00 https://www.nature.com/articles/s41557-025-01981-y cshalizi to:NB biochemical_networks biological_computation via:vaguery https://pinboard.in/ https://pinboard.in/u:cshalizi/b:d4b7ca5761e2/ Network Analysis as a Grand Unifier in Biomedical Data Science | Annual Reviews 2025-04-09T14:54:58+00:00 https://www.annualreviews.org/content/journals/10.1146/annurev-biodatasci-080917-013444 cshalizi to:NB network_data_analysis networks biochemical_networks via:aks https://pinboard.in/ https://pinboard.in/u:cshalizi/b:30e36c1f0a02/ The rat with the big balls and the enormous penis – how Frontiers published a paper with botched AI-generated images – Science Integrity Digest 2024-02-24T20:38:56+00:00 https://scienceintegritydigest.com/2024/02/15/the-rat-with-the-big-balls-and-enormous-penis-how-frontiers-published-a-paper-with-botched-ai-generated-images/ cshalizi funny:academic funny:malicious funny:laughing_instead_of_screaming ai_madness biochemical_networks https://pinboard.in/ https://pinboard.in/u:cshalizi/b:5fba6228b500/ Life in a carbon dioxide world 2021-04-24T20:39:46+00:00 https://www.nature.com/articles/d41586-021-00977-1 cshalizibiochemical_networks evolutionary_biology via:paul_mcauley have_read https://pinboard.in/ https://pinboard.in/u:cshalizi/b:15719c0774da/ [2104.10082] Modeling biological networks: from single gene systems to large microbial communities 2021-04-21T19:49:52+00:00 https://arxiv.org/abs/2104.10082 cshalizi to:NB biochemical_networks heavy_tails https://pinboard.in/ https://pinboard.in/u:cshalizi/b:27cd92aa49a4/ Wang , Li , Li , Huang : Network Modeling in Biology: Statistical Methods for Gene and Brain Networks 2020-12-21T14:09:31+00:00 https://projecteuclid.org/euclid.ss/1608541220 cshalizi to:NB network_data_analysis biochemical_networks neural_data_analysis gene_expression_data_analysis https://pinboard.in/ https://pinboard.in/u:cshalizi/b:a4b92635daad/ [1810.10854] Structure learning of undirected graphical models for count data 2020-11-25T14:54:04+00:00 https://arxiv.org/abs/1810.10854 cshalizi to:NB graphical_models biochemical_networks https://pinboard.in/ https://pinboard.in/u:cshalizi/b:cb5740b4e4f1/ [2011.10529] Computation capacities of a broad class of signaling networks are higher than their communication capacities 2020-11-23T17:36:13+00:00 https://arxiv.org/abs/2011.10529 cshalizi to:NB biochemical_networks robustness information_theory https://pinboard.in/ https://pinboard.in/u:cshalizi/b:b29e3e6e4e29/ [2011.06478] Master regulators as order parameters of gene expression states 2020-11-15T21:16:39+00:00 https://arxiv.org/abs/2011.06478 cshalizi to:NB biochemical_networks of_course_its_really_a_spin_glass https://pinboard.in/ https://pinboard.in/u:cshalizi/b:53d94fa460fe/ [2005.04751] Tractable nonlinear memory functions as a tool to capture and explain dynamical behaviours 2020-11-15T21:15:24+00:00 https://arxiv.org/abs/2005.04751 cshalizi to:NB dynamical_systems approximation networks biochemical_networks non-equilibrium https://pinboard.in/ https://pinboard.in/u:cshalizi/b:3dff9992307a/ [2006.03286] Opportunities at the interface of network science and metabolic modelling 2020-11-15T21:14:47+00:00 https://arxiv.org/abs/2006.03286 cshalizi to:NB biochemical_networks networks https://pinboard.in/ https://pinboard.in/u:cshalizi/b:4edb0b5767ec/ [1912.00401] Long-time asymptotics of stochastic reaction systems 2020-11-15T21:14:02+00:00 https://arxiv.org/abs/1912.00401 cshalizi to:NB stochastic_processes markov_models biochemical_networks to_read https://pinboard.in/ https://pinboard.in/u:cshalizi/b:3c8dfed1a256/ [1911.10252] Biological Regulatory Networks are Minimally Frustrated 2020-11-15T20:55:32+00:00 https://arxiv.org/abs/1911.10252 cshalizi biochemical_networks biophysics of_course_its_really_a_spin_glass in_NB https://pinboard.in/ https://pinboard.in/u:cshalizi/b:2225e103413d/ First Signals: The Evolution of Multicellular Development on JSTOR 2020-01-26T16:55:06+00:00 https://www.jstor.org/stable/j.ctt7rkfj cshalizibooks:noted downloaded developmental_biology evolutionary_biology biochemical_networks bonner.john_tyler in_NB https://pinboard.in/ https://pinboard.in/u:cshalizi/b:b02b7bb6a1f9/ Rev. Mod. Phys. 91, 045004 (2019) - Nonequilibrium physics in biology 2020-01-12T22:59:58+00:00 https://journals.aps.org/rmp/abstract/10.1103/RevModPhys.91.045004 cshalizi to:NB physics biology biophysics biochemical_networks non-equilibrium thermodynamics https://pinboard.in/ https://pinboard.in/u:cshalizi/b:fd84511c14b5/ Robert : Mathematical models of gene expression 2019-11-01T00:52:15+00:00 https://projecteuclid.org/euclid.ps/1572509200 cshalizi to:NB gene_expression_data_analysis biochemical_networks https://pinboard.in/ https://pinboard.in/u:cshalizi/b:cbd6f3a07c07/ [1909.12825] Dynamics of continuous time Markov chains with applications to stochastic reaction networks 2019-10-15T18:21:28+00:00 https://arxiv.org/abs/1909.12825 cshalizi to:NB markov_models biochemical_networks https://pinboard.in/ https://pinboard.in/u:cshalizi/b:2133a43c6e6f/ [1909.11070] Spin Glass Theory of Interacting Metabolic Networks 2019-09-26T18:06:23+00:00 https://arxiv.org/abs/1909.11070 cshalizi biochemical_networks of_course_its_really_a_spin_glass in_NB https://pinboard.in/ https://pinboard.in/u:cshalizi/b:f8e1e1e5f0c4/ [1907.09551] Cell differentiation: what have we learned in 50 years? 2019-09-15T14:43:28+00:00 https://arxiv.org/abs/1907.09551 cshalizi developmental_biology evolutionary_biology gene_regulation biochemical_networks in_NB https://pinboard.in/ https://pinboard.in/u:cshalizi/b:cde25938d027/ [1909.00038] Limit theorems for generalized density-dependent Markov chains and bursty stochastic gene regulatory networks 2019-09-04T15:28:27+00:00 https://arxiv.org/abs/1909.00038 cshalizi to:NB biochemical_networks stochastic_processes markov_models re:almost_none https://pinboard.in/ https://pinboard.in/u:cshalizi/b:ff5c3428890d/ [1909.00042] Macroscopic limits, analytical distributions, and noise structure for stochastic gene expression with coupled feedback loops 2019-09-04T15:27:35+00:00 https://arxiv.org/abs/1909.00042 cshalizi to:NB biochemical_networks gene_expression_data_analysis markov_models stochastic_processes re:almost_none https://pinboard.in/ https://pinboard.in/u:cshalizi/b:2ca8c6250ee0/ [1908.06872] A Modified Ising Model of Barabási-Albert Network with Gene-type Spins 2019-08-20T15:53:58+00:00 https://arxiv.org/abs/1908.06872 cshalizi to:NB statistical_mechanics biochemical_networks networks of_course_its_really_a_spin_glass color_me_skeptical https://pinboard.in/ https://pinboard.in/u:cshalizi/b:ccb8deafb587/ [1906.09410] A reaction network scheme which implements inference and learning for Hidden Markov Models 2019-08-20T15:27:24+00:00 https://arxiv.org/abs/1906.09410 cshalizi to:NB em_algorithm markov_models state-space_models biochemical_networks wiuf.carsten pointless_but_nonetheless_awesome biological_computers https://pinboard.in/ https://pinboard.in/u:cshalizi/b:df0502950c8a/ [1908.05483] Algebraic Coarse-Graining of Biochemical Reaction Networks 2019-08-16T20:37:29+00:00 https://arxiv.org/abs/1908.05483 cshalizi to:NB biochemical_networks algebra https://pinboard.in/ https://pinboard.in/u:cshalizi/b:2ddef55a1c35/ [1908.04642] Semigroup Models for Biochemical Reaction Networks 2019-08-16T20:37:08+00:00 https://arxiv.org/abs/1908.04642 cshalizi to:NB biochemical_networks algebra https://pinboard.in/ https://pinboard.in/u:cshalizi/b:356fc1ae5eec/ [1810.05575] Joining and decomposing reaction networks 2019-08-16T19:55:58+00:00 https://arxiv.org/abs/1810.05575 cshalizi to:NB biochemical_networks algebra dynamical_systems https://pinboard.in/ https://pinboard.in/u:cshalizi/b:20af1837520b/ [1907.09841] Coherent feedforward loops can be used to approximately compute positive log-likelihood ratio for detecting persistent signals 2019-07-24T14:14:17+00:00 https://arxiv.org/abs/1907.09841 cshalizi to:NB biochemical_networks biological_computation signal_transduction https://pinboard.in/ https://pinboard.in/u:cshalizi/b:fb722ba8b1ed/ Probabilistic switching circuits in DNA | PNAS 2018-05-07T16:41:12+00:00 http://www.pnas.org/content/115/5/903 cshalizi computation biochemical_networks biological_computers molecular_biology in_NB https://pinboard.in/ https://pinboard.in/u:cshalizi/b:0e9c878454d2/ Autocatalytic, bistable, oscillatory networks of biologically relevant organic reactions : Nature : Nature Research 2016-10-02T19:53:03+00:00 http://www.nature.com/nature/journal/v537/n7622/full/nature19776.html cshalizi to:NB biochemical_networks pattern_formation non-equilibrium chemistry physics https://pinboard.in/ https://pinboard.in/u:cshalizi/b:b32d9fb753af/ Del Vecchio, D. and Murray, R.M.: Biomolecular Feedback Systems (eBook and Hardcover). 2016-07-25T13:53:13+00:00 http://press.princeton.edu/titles/10285.html cshalizi to:NB books:noted biochemical_networks feedback biology networks https://pinboard.in/ https://pinboard.in/u:cshalizi/b:2646e721516e/ The Inner Workings of Life | Genomics Bioinformatics and Systems Biology | Cambridge University Press 2016-05-25T01:25:56+00:00 http://www.cambridge.org/us/academic/subjects/life-sciences/genomics-bioinformatics-and-systems-biology/inner-workings-life-vignettes-systems-biology?format=PB cshalizi to:NB books:noted biology biochemical_networks https://pinboard.in/ https://pinboard.in/u:cshalizi/b:313ddae53dc9/ [1605.01624] Complete integrability of information processing by biochemical reactions 2016-05-10T16:52:32+00:00 http://arxiv.org/abs/1605.01624 cshalizi to:NB biochemical_networks biology signal_transduction statistics via:vaguery https://pinboard.in/ https://pinboard.in/u:cshalizi/b:28018146d288/ [1506.00728] Network Assisted Analysis to Reveal the Genetic Basis of Autism 2015-07-14T13:43:17+00:00 http://arxiv.org/abs/1506.00728 cshalizi to:NB graphical_models biochemical_networks genetics gene_expression_data_analysis autism kith_and_kin roeder.kathryn lei.jing liu.li https://pinboard.in/ https://pinboard.in/u:cshalizi/b:14f7da5f061f/ The Strange Inevitability of Evolution - Issue 20: Creativity - Nautilus 2015-01-23T13:18:18+00:00 http://nautil.us/issue/20/creativity/the-strange-inevitability-of-evolution cshalizi evolutionary_biology biochemical_networks popular_science wagner.andreas schuster.peter have_read via:henry_farrell blogged https://pinboard.in/ https://pinboard.in/u:cshalizi/b:e5d44b3064c8/ Transplantation of prokaryotic two-component signaling pathways into mammalian cells 2014-11-05T18:31:54+00:00 http://www.pnas.org/content/111/44/15705.abstract.html cshalizi to:NB molecular_biology biochemical_networks computation https://pinboard.in/ https://pinboard.in/u:cshalizi/b:f84b9f78ee74/ Multivariate statistics and the enactment of metabolic complexity 2014-07-29T14:59:49+00:00 http://sss.sagepub.com/content/44/4/555.abstract?etoc cshalizi to:NB to_read ethnography science_as_a_social_process biochemical_networks biology statistics complexity data_analysis https://pinboard.in/ https://pinboard.in/u:cshalizi/b:944c59a7a680/ [1406.0063] Causal network inference using biochemical kinetics 2014-07-12T00:23:19+00:00 http://arxiv.org/abs/1406.0063 cshalizi to:NB biochemical_networks graphical_models statistics estimation https://pinboard.in/ https://pinboard.in/u:cshalizi/b:3071dc3df897/ [1404.1181] Irreversible thermodynamics of open chemical networks I: Emergent cycles and broken conservation laws 2014-04-20T18:25:50+00:00 http://arxiv.org/abs/1404.1181 cshalizi to:NB non-equilibrium statistical_mechanics chemistry biochemical_networks https://pinboard.in/ https://pinboard.in/u:cshalizi/b:f268f6e05b15/ [1309.0657] Human Genome Variation and the concept of Genotype Networks 2013-12-16T06:26:37+00:00 http://arxiv.org/abs/1309.0657 cshalizi to:NB gene_regulation biochemical_networks human_genetics https://pinboard.in/ https://pinboard.in/u:cshalizi/b:c2196e489e29/ Decisions on the fly in cellular sensory systems 2013-10-21T15:45:36+00:00 http://www.pnas.org/content/110/39/E3704.abstract cshalizi to:NB biochemical_networks decision_theory signal_transduction biological_computation biology https://pinboard.in/ https://pinboard.in/u:cshalizi/b:1d93863b9998/ Building Simulations from the Ground Up: Modeling and Theory in Systems Biology [JSTOR: Philosophy of Science, Vol. 80, No. 4 (October 2013), pp. 533-556] 2013-10-11T22:17:19+00:00 http://www.jstor.org/discover/10.1086/673209 cshalizi to:NB simulation biochemical_networks biology philosophy_of_science https://pinboard.in/ https://pinboard.in/u:cshalizi/b:f269e9bb94a7/ [1309.6849] Cyclic Causal Discovery from Continuous Equilibrium Data 2013-09-27T16:48:38+00:00 http://arxiv.org/abs/1309.6849 cshalizi to:NB causal_inference graphical_models statistics biochemical_networks https://pinboard.in/ https://pinboard.in/u:cshalizi/b:95094aa8a2a0/ [1309.6066] Bridging physiological and evolutionary time scales in a gene regulatory network 2013-09-26T19:53:37+00:00 http://arxiv.org/abs/1309.6066 cshalizi to:NB evolutionary_biology gene_regulation biochemical_networks bioinformatics sunflowers https://pinboard.in/ https://pinboard.in/u:cshalizi/b:df8f60743abc/ Robustness and Compensation of Information Transmission of Signaling Pathways 2013-09-03T13:35:26+00:00 http://www.sciencemag.org/content/341/6145/558.full?rss=1 cshalizi to:NB biochemical_networks biological_computation information_theory signal_transduction https://pinboard.in/ https://pinboard.in/u:cshalizi/b:ec8936a928a8/ Dynamic regulatory network controlling TH17 cell differentiation : Nature : Nature Publishing Group 2013-04-25T01:58:47+00:00 http://www.nature.com/nature/journal/v496/n7446/full/nature11981.html cshalizi to:NB biochemical_networks gene_expression_data_analysis immunology molecular_biology experimental_biology bioinformatics https://pinboard.in/ https://pinboard.in/u:cshalizi/b:cc937a6155af/ Li , Hsu , Peng , Wang : Bootstrap inference for network construction with an application to a breast cancer microarray study 2013-04-10T15:51:36+00:00 http://projecteuclid.org/DPubS?service=UI&version=1.0&verb=Display&handle=euclid.aoas/1365527204 cshalizi to:NB network_data_analysis bootstrap biochemical_networks gene_expression_data_analysis hypothesis_testing multiple_testing re:6dfb https://pinboard.in/ https://pinboard.in/u:cshalizi/b:aadf9efd17d1/ [1302.6548] Spatial partitioning improves the reliability of biochemical signaling 2013-03-05T22:32:57+00:00 http://arxiv.org/abs/1302.6548 cshalizi to:NB biochemical_networks biological_computation signal_transduction https://pinboard.in/ https://pinboard.in/u:cshalizi/b:76b0287641bf/ [1302.4772] Time-dependent information transmission in a model regulatory circuit 2013-02-21T23:41:50+00:00 http://arxiv.org/abs/1302.4772 cshalizi to:NB information_theory biological_computation kith_and_kin to_read biochemical_networks wiggins.chrisropher https://pinboard.in/ https://pinboard.in/u:cshalizi/b:43409390194c/ [1212.4450] Minimal autocatalytic networks 2012-12-19T13:33:17+00:00 http://arxiv.org/abs/1212.4450 cshalizi to:NB biochemical_networks autocatalysis self-organization evolution_of_life kith_and_kin hordijk.wim https://pinboard.in/ https://pinboard.in/u:cshalizi/b:92c1dc2b20de/ Taylor & Francis Online :: Statistical Challenges in Biological Networks - Journal of Computational and Graphical Statistics - Volume 21, Issue 4 2012-12-15T15:04:16+00:00 http://www.tandfonline.com/doi/abs/10.1080/10618600.2012.738614 cshalizi to:NB statistics network_data_analysis biochemical_networks bioinformatics https://pinboard.in/ https://pinboard.in/u:cshalizi/b:84abb1018253/ Katenka , Kolaczyk : Inference and characterization of multi-attribute networks with application to computational biology 2012-08-31T16:33:53+00:00 http://projecteuclid.org/DPubS?service=UI&version=1.0&verb=Display&handle=euclid.aoas/1346418574 cshalizi network_data_analysis statistics biochemical_networks in_NB to_read https://pinboard.in/ https://pinboard.in/u:cshalizi/b:4e39383a18e8/ [1207.5532] The compositional and evolutionary logic of metabolism 2012-07-25T02:44:56+00:00 http://arxiv.org/abs/1207.5532 cshalizi to:NB to_read biochemical_networks kith_and_kin smith.eric https://pinboard.in/ https://pinboard.in/u:cshalizi/b:64f12e4f0d45/ Multiscale factor models for molecular networks 2012-07-12T20:33:58+00:00 http://ftp.stat.duke.edu/WorkingPapers/09-10.html cshalizi to:NB factor_analysis gene_expression_data_analysis biochemical_networks statistics network_data_analysis mukherjee.sayan https://pinboard.in/ https://pinboard.in/u:cshalizi/b:ac872a942148/ Ingenious Genes: How Gene Regulation Networks Evolve to Control Ontogeny - The MIT Press 2012-07-06T14:38:34+00:00 http://mitpress.mit.edu/catalog/item/default.asp?ttype=2&tid=12757 cshalizi to:NB books:noted gene_regulation biochemical_networks evolutionary_biology evo-devo https://pinboard.in/ https://pinboard.in/u:cshalizi/b:998a260e88dd/ Programmable single-cell mammalian biocomputers : Nature : Nature Publishing Group 2012-07-05T14:19:46+00:00 http://www.nature.com/nature/journal/v487/n7405/full/nature11149.html cshalizi to:NB biochemical_networks molecular_biology experimental_biology did_someone_say_blood_music? biological_computers https://pinboard.in/ https://pinboard.in/u:cshalizi/b:b60d5a9d2002/ Gene Network Effects on Brain Microstructure and Intellectual Performance Identified in 472 Twins 2012-06-23T14:45:44+00:00 http://www.jneurosci.org/content/32/25/8732.short?rss=1 cshalizi to:NB neuroscience biochemical_networks human_genetics network_data_analysis causal_inference https://pinboard.in/ https://pinboard.in/u:cshalizi/b:da24282a2130/ [0801.0254] Design of experiments and biochemical network inference 2012-06-17T21:25:09+00:00 http://arxiv.org/abs/0801.0254 cshalizi to:NB biochemical_networks network_data_analysis gene_expression_data_analysis algebraic_statistics statistics experimental_design https://pinboard.in/ https://pinboard.in/u:cshalizi/b:19ffc658e3ac/ Protein Interaction Networks - Academic and Professional Books - Cambridge University Press 2012-04-23T13:59:02+00:00 http://www.cambridge.org/us/knowledge/isbn/item2327615/?site_locale=en_US cshalizi to:NB books:noted biochemical_networks https://pinboard.in/ https://pinboard.in/u:cshalizi/b:e6684dbe06fc/ [0704.2551] Inferring dynamic genetic networks with low order independencies 2012-03-18T18:53:18+00:00 http://arxiv.org/abs/0704.2551 cshalizi to:NB graphical_models gene_expression_data_analysis biochemical_networks statistics https://pinboard.in/ https://pinboard.in/u:cshalizi/b:2363f69da42b/ Global Network Reorganization During Dynamic Adaptations of Bacillus subtilis Metabolism 2012-03-03T16:29:22+00:00 http://www.sciencemag.org/content/335/6072/1099.abstract cshalizi to:NB to_read biochemical_networks adaptive_behavior experimental_biology re:network_differences gene_regulation https://pinboard.in/ https://pinboard.in/u:cshalizi/b:a0d1534d2e13/ [0811.2834] Quantifying evolvability in small biological networks 2012-01-23T19:04:38+00:00 http://arxiv.org/abs/0811.2834 cshalizi to:NB evolutionary_biology biochemical_networks kith_and_kin wiggins.christopher https://pinboard.in/ https://pinboard.in/u:cshalizi/b:d713e806e649/ [0811.4149] A stochastic spectral analysis of transcriptional regulatory cascades 2012-01-01T15:42:20+00:00 http://arxiv.org/abs/0811.4149 cshalizi to:NB biochemical_networks kith_and_kin wiggins.christopher https://pinboard.in/ https://pinboard.in/u:cshalizi/b:30629d2f1d09/ [1112.1047] Network Inference and Biological Dynamics 2011-12-12T16:18:14+00:00 http://arxiv.org/abs/1112.1047 cshalizi have_read biochemical_networks network_data_analysis in_NB statistics https://pinboard.in/ https://pinboard.in/u:cshalizi/b:fd258d20535d/ Phys. Rev. E 84, 051917 (2011): Nonequilibrium phase transitions in biomolecular signal transduction 2011-11-26T16:14:38+00:00 http://pre.aps.org/abstract/PRE/v84/i5/e051917 cshalizi to:NB heard_the_talk kith_and_kin signal_transduction biochemical_networks phase_transitions statistical_mechanics non-equilibrium smith.eric fontana.walter krakauer.david https://pinboard.in/ https://pinboard.in/u:cshalizi/b:5310b5a0ae5f/ [0812.2184] Protein-Interaction-Networks: More than mere modules 2011-10-12T15:43:33+00:00 http://arxiv.org/abs/0812.2184 cshalizi community_discovery biochemical_networks reichardt.joerg in_NB https://pinboard.in/ https://pinboard.in/u:cshalizi/b:d6cd8fc3b868/ [1101.4240] Information transmission in genetic regulatory networks: a review 2011-02-04T07:31:07+00:00 http://arxiv.org/abs/1101.4240 cshalizisignal_transduction gene_regulation biochemical_networks information_theory biological_computation in_NB https://pinboard.in/u:cshalizi/b:10aa75576a76/ [1012.1473] Randomizing genome-scale metabolic networks 2010-12-13T22:12:18+00:00 http://arxiv.org/abs/1012.1473 cshalizi network_data_analysis biochemical_networks https://pinboard.in/u:cshalizi/b:e217732405e5/ Statistical Mechanics of Cellular Systems and Processes - Academic and Professional Books - Cambridge University Press 2010-10-15T11:54:59+00:00 http://www.cambridge.org/9780521886086 cshalizi books:noted statistical_mechanics biology biochemical_networks https://pinboard.in/u:cshalizi/b:351be5957314/ Concurrency and Network Disassortativity 2010-09-01T15:03:51+00:00 http://www.mitpressjournals.org/doi/abs/10.1162/artl_a_00001 cshalizi graph_theory networks biochemical_networks https://pinboard.in/u:cshalizi/b:7f5274347994/