{"id":45,"date":"2016-03-18T17:27:19","date_gmt":"2016-03-18T21:27:19","guid":{"rendered":"https:\/\/sites.bu.edu\/ckmadsen\/?page_id=45"},"modified":"2018-08-24T18:11:29","modified_gmt":"2018-08-24T22:11:29","slug":"publications","status":"publish","type":"page","link":"https:\/\/sites.bu.edu\/ckmadsen\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"<h3>2018<\/h3>\n<p>\nT. Neupane, Z. Zhang, <strong>C. Madsen<\/strong>, H. Zheng, and C. J. Myers, &#8220;Approximation Techniques for Stochastic Analysis of Biological Systems,&#8221; in <span style=\"font-style: italic\">Automated Reasoning for Systems Biology and Medicine<\/span>, P. Li\u00f2 and P. Zuliani, Ed., Springer, 2018 (submitted). <br \/>    <a href=\"javascript:toggleBibtex('Neupane2018')\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Neupane2018\">@incollection{Neupane2018,\r\nAuthor = {Thakur Neupane and\r\nZhen Zhang and\r\nCurtis Madsen and\r\nHao Zheng and\r\nChris J. Myers},\r\nSeries={Computational Biology},\r\nEditor={Pietro Li\\`{o} and\r\nPaolo Zuliani},\r\nPublisher={Springer},\r\nTitle = {Approximation Techniques for Stochastic Analysis of Biological Systems},\r\nBooktitle = {Automated Reasoning for Systems Biology and Medicine},\r\nYear = {2018}\r\n}<\/pre>\n<\/p>\n<p>\n<strong>C. Madsen<\/strong>, P. Vaidyanathan, S. Sadraddini, C. Vasile, N. A. DeLateur, R. Weiss, D. Densmore, and C. Belta, &#8220;Metrics for Signal Temporal Logic Formulae,&#8221; <span style=\"font-style: italic\">IEEE Conference on Decision and Control (CDC)<\/span>, 2018 (accepted). <br \/>    <a href=\"javascript:toggleBibtex('Madsen2018')\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Madsen2018\">@inproceedings{Madsen2018,\r\nAuthor = {Curtis Madsen and\r\nPrashant Vaidyanathan and\r\nSadra Sadraddini and\r\nCristian-Ioan Vasile and\r\nNicholas A. DeLateur and\r\nRon Weiss and\r\nDouglas Densmore and\r\nCalin Belta},\r\nTitle = {Metrics for Signal Temporal Logic Formulae},\r\nBooktitle = {IEEE Conference on Decision and Control (CDC)},\r\nYear = {2018}\r\n}<\/pre>\n<\/p>\n<p>\n<a href='https:\/\/doi.org\/10.1021\/acssynbio.8b00078' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a>L. Watanabe, T. Nguyen, M. Zhang, Z. Zundel, Z. Zhang, <strong>C. Madsen<\/strong>, N. Roehner, and C. J. Myers, &#8220;iBioSim 3: A Tool for Model-Based Genetic Circuit Design,&#8221; <span style=\"font-style: italic\">ACS Synthetic Biology<\/span>, 2018. <br \/>    <a href=\"javascript:toggleBibtex('Watanabe2018')\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Watanabe2018\">@article{Watanabe2018,\r\nauthor = {Leandro Watanabe and\r\nTramy Nguyen and\r\nMichael Zhang and\r\nZach Zundel and\r\nCurtis Madsen and\r\nNicholas Roehner and\r\nChris J. Myers},\r\ntitle = {i{B}io{S}im 3: A Tool for Model-Based Genetic Circuit Design},\r\njournal = {ACS Synthetic Biology},\r\nyear = {2018},\r\ndoi = {10.1021\/acssynbio.8b00078}\r\n}<\/pre>\n<\/p>\n<p>\n<a href='https:\/\/doi.org\/10.1515\/jib-2017-0074' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a>R. S. Cox III, <strong>C. Madsen<\/strong>, J. A. McLaughlin, T. Nguyen, N. Roehner, B. Bartley, S. Bhatia, M. Bissell, K. Clancy, T. Gorochowski, R. Gr\u00fcnberg, A. Luna, N. Le Nov\u00e8re, M. R. Pocock, H. M. Sauro, J. T. Sexton, G. Stan, J. J. Tabor, C. Voigt, Z. Zundel, C. J. Myers, J. Beal, and A. Wipat, &#8220;Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0,&#8221; <span style=\"font-style: italic\">Journal of Integrative Bioinformatics<\/span>, 2018. <br \/>   <a href=\"javascript:toggleBibtex('Cox2018_2')\" title=\"show citation\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Cox2018_2\">@article{Cox2018,\r\nauthor = {Robert Sidney Cox III and\r\nCurtis Madsen and\r\nJames Alastair McLaughlin and\r\nTramy Nguyen and\r\nNicholas Roehner and\r\nBryan Bartley and\r\nSwapnil Bhatia and\r\nMichael Bissell and\r\nKevin Clancy and\r\nThomas Gorochowski and\r\nRaik Gr{\\\"{u}}nberg and\r\nAugustin Luna and\r\nNicolas Le Nov\\`{e}re and\r\nMatthew R. Pocock and\r\nHerbert M. Sauro and\r\nJohn T. Sexton and\r\nGuy-Bart Stan and\r\nJeffery J. Tabor and\r\nChris Voigt and\r\nZach Zundel and\r\nChris J. Myers and\r\nJacob Beal and\r\nAnil Wipat},\r\ntitle = {Synthetic Biology Open Language Visual {(SBOL Visual)} Version 2.0},\r\njournal = {J. Integrative Bioinformatics},\r\nyear = {2018}\r\n}<\/pre>\n<\/p>\n<p>\n<a href='https:\/\/doi.org\/10.1515\/jib-2018-0001' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a>R. S. Cox III, <strong>C. Madsen<\/strong>, J. A. McLaughlin, T. Nguyen, N. Roehner, B. Bartley, J. Beal, M. Bissell, K. Choi, K. Clancy, R. Gr\u00fcnberg, C. Macklin, G. Misirli, E. Oberortner, M. R. Pocock, M. Samineni, M. Zhang, Z. Zhang, Z. Zundel, J. H. Gennari, C. J. Myers, H. M. Sauro, and A. Wipat, &#8220;Synthetic Biology Open Language (SBOL) Version 2.2.0,&#8221; <span style=\"font-style: italic\">Journal of Integrative Bioinformatics<\/span>, 2018. <br \/>   <a href=\"javascript:toggleBibtex('Cox2018')\" title=\"show citation\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Cox2018\">@article{Cox2018,\r\nauthor = {Robert Sidney Cox III and\r\nCurtis Madsen and\r\nJames Alastair McLaughlin and\r\nTramy Nguyen and\r\nNicholas Roehner and\r\nBryan Bartley and\r\nJacob Beal and\r\nMichael Bissell and\r\nKiri Choi and\r\nKevin Clancy and\r\nRaik Gr{\\\"{u}}nberg and\r\nChris Macklin and\r\nGoksel Misirli and\r\nErnst Oberortner and\r\nMatthew R. Pocock and\r\nMeher Samineni and\r\nMichael Zhang and\r\nZhen Zhang and\r\nZach Zundel and\r\nJohn H. Gennari and\r\nChris J. Myers and\r\nHerbert M. Sauro and\r\nAnil Wipat},\r\ntitle = {Synthetic Biology Open Language {(SBOL)} Version 2.2.0},\r\njournal = {J. Integrative Bioinformatics},\r\nyear = {2018}\r\n}<\/pre>\n<\/p>\n<h3>2017<\/h3>\n<p>\n<a href='http:\/\/sbolstandard.org\/wp-content\/uploads\/2017\/10\/SBOLVisual_Specification_2_0_0.pdf' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a>R. S. Cox III, <strong>C. Madsen<\/strong>, J. A. McLaughlin, T. Nguyen, N. Roehner, A. Wipat, B. Bartley, J. Beal, S. Bhatia, M. Bissell, K. Clancy, T. Gorochowski, R. Gr\u00fcnberg, A. Luna, C. J. Myers, N. Le Nov\u00e8re, M. R. Pocock, H. M. Sauro, J. T. Sexton, G. Stan, J. J. Tabor, C. Voigt, and Z. Zundel, &#8220;Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0,&#8221; BBF RFC #115, 2017. <br \/>   <a href=\"javascript:toggleBibtex('Cox2017_2')\" title=\"show citation\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Cox2017_2\">@techreport{Cox2017,\r\nauthor = {Robert Sidney Cox III and\r\nCurtis Madsen and\r\nJames Alastair McLaughlin and\r\nTramy Nguyen and\r\nNicholas Roehner and\r\nAnil Wipat and\r\nBryan Bartley and\r\nJacob Beal and\r\nSwapnil Bhatia and\r\nMike Bissell and\r\nKevin Clancy and\r\nThomas Gorochowski and\r\nRaik Gr{\\\"{u}}nberg and\r\nAugustin Luna and\r\nChris J. Myers and\r\nNicolas Le Nov\\`{e}re and\r\nMatthew R. Pocock and\r\nHerbert M. Sauro and\r\nJohn T. Sexton and\r\nGuy-Bart Stan and\r\nJeffrey J. Tabor and\r\nChris Voigt and\r\nZach Zundel},\r\nTitle = {{S}ynthetic {B}iology {O}pen {L}anguage {V}isual ({SBOL} {V}isual) {V}ersion 2.0},\r\nKeywords = {SBOL},\r\nYear = {2017},\r\nNumber = {BBF RFC #115}\r\n}\r\n}<\/pre>\n<\/p>\n<p>\n<a href='http:\/\/sbolstandard.org\/wp-content\/uploads\/2018\/01\/BBF-RFC114-SBOL2.2.0.pdf' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a>R. S. Cox III, <strong>C. Madsen<\/strong>, J. A. McLaughlin, T. Nguyen, N. Roehner, A. Wipat, J. Beal, K. Clancy, R. Gr\u00fcnberg, C. Macklin, M. Bissell, G. Misirli, E. Oberortner, M. R. Pocock, Z. Zhang, C. Myers, M. Zhang, M. Samineni, Z. Zundel, B. Bartley, K. Choi, J. H. Gennari, and H. M. Sauro, &#8220;Synthetic Biology Open Language (SBOL) Version 2.2.0,&#8221; BBF RFC #114, 2017. <br \/>   <a href=\"javascript:toggleBibtex('Cox2017')\" title=\"show citation\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Cox2017\">@techreport{Cox2017,\r\nauthor = {Robert Sidney Cox III and\r\nCurtis Madsen and\r\nJames Alastair McLaughlin and\r\nTramy Nguyen and\r\nNicholas Roehner and\r\nAnil Wipat and\r\nJacob Beal and\r\nKevin Clancy and\r\nRaik Gr{\\\"{u}}nberg and\r\nChris Macklin and\r\nMichael Bissell and\r\nGoksel Misirli and\r\nErnst Oberortner and\r\nMatthew R. Pocock and\r\nZhen Zhang and\r\nChris Myers and\r\nMichael Zhang and\r\nMeher Samineni and\r\nZach Zundel and\r\nBryan Bartley and\r\nKiri Choi and\r\nJohn H. Gennari and\r\nHerbert M. Sauro},\r\nTitle = {{S}ynthetic {B}iology {O}pen {L}anguage ({SBOL}) {V}ersion 2.2.0},\r\nKeywords = {SBOL},\r\nYear = {2017},\r\nNumber = {BBF RFC #114}\r\n}\r\n}<\/pre>\n<\/p>\n<p>\n<a href='https:\/\/doi.org\/10.1016\/j.cbpa.2017.08.005' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a>E. Appleton, D. Densmore, <strong>C. Madsen<\/strong>, and N. Roehner, &#8220;Needs and Opportunities in Bio-Design Automation: Four Areas for Focus,&#8221; <span style=\"font-style: italic\">Current Opinion in Chemical Biology<\/span>, vol. 40, pp. 111-118, 2017. <br \/>    <a href=\"javascript:toggleBibtex('Appleton2017_2')\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Appleton2017_2\">@article{Appleton2017,\r\nauthor = {Evan Appleton and\r\nDouglas Densmore and\r\nCurtis Madsen and\r\nNicholas Roehner},\r\ntitle = \"Needs and opportunities in bio-design automation: four areas for focus\",\r\njournal = \"Current Opinion in Chemical Biology\",\r\nvolume = \"40\",\r\nnumber = \"Supplement C\",\r\npages = \"111 - 118\",\r\nyear = \"2017\",\r\nnote = \"Synthetic Biology Synthetic Biomolecules\",\r\nissn = \"1367-5931\",\r\ndoi = \"https:\/\/doi.org\/10.1016\/j.cbpa.2017.08.005\",\r\nurl = \"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S1367593117300753\"\r\n}<\/pre>\n<\/p>\n<p>\n<a href='https:\/\/doi.org\/10.1371\/journal.pone.0181965' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a>P. G. Jayathilake, P. Gupta, B. Li, <strong>C. Madsen<\/strong>, O. Oyebamiji, R. Gonz\u00e1lez-Cabaleiro, S. Rushton, B. Bridgens, D. Swailes, B. Allen, A.S. McGough, P. Zuliani, I. D. Ofiteru, D. Wilkinson, J. Chen, and T. Curtis, &#8220;A Mechanistic Individual-Based Model of Microbial Communities,&#8221; <span style=\"font-style: italic\">PLOS One<\/span>, vol. 12(8), pp. 1-26, 2017. <br \/>    <a href=\"javascript:toggleBibtex('Jayathilake2017')\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Jayathilake2017\">@article{Jayathilake2017,\r\nauthor = {Pahala Gedara Jayathilake and\r\nPrashant Gupta and\r\nBowen Li and\r\nCurtis Madsen and\r\nOluwole Oyebamiji and\r\nRebeca Gonz\\'{a}lez-Cabaleiro and\r\nSteve Rushton and\r\nBen Bridgens and\r\nDavid Swailes and\r\nBen Allen and\r\nA. Stephen McGough and\r\nPaolo Zuliani and\r\nIrina Dana Ofiteru and\r\nDarren Wilkinson and\r\nJinju Chen and\r\nTom Curtis},\r\njournal = {PLOS ONE},\r\npublisher = {Public Library of Science},\r\ntitle = {A mechanistic Individual-based Model of microbial communities},\r\nyear = {2017},\r\nmonth = {08},\r\nvolume = {12},\r\nurl = {https:\/\/doi.org\/10.1371\/journal.pone.0181965},\r\npages = {1-26},\r\nnumber = {8},\r\ndoi = {10.1371\/journal.pone.0181965}\r\n}<\/pre>\n<\/p>\n<p>\n<a href='https:\/\/doi.org\/10.1042\/BST20160347' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a>C. Myers, J. Beal, T. Gorochowski, H. Kuwahara, <strong>C. Madsen<\/strong>, J. A. McLaughlin, G. Misirli, T. Nguyen, E. Oberortner, M. Samineni, A. Wipat, M. Zhang, and Z. Zundel, &#8220;A Standard-Enabled Workflow for Synthetic Biology,&#8221; <span style=\"font-style: italic\">Biochemical Society Transactions<\/span>, vol. 45(3), pp. 793-803, 2017. <br \/><a href=\"javascript:toggleBibtex('Myers2017')\" title=\"show citation\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Myers2017\">@article{Myers2017,\r\nauthor = {Chris Myers and\r\nJacob Beal and\r\nThomas Gorochowski and\r\nHiroyuki Kuwahara and\r\nCurtis Madsen and\r\nJames Alastair McLaughlin and\r\nGoksel Misirli and\r\nTramy Nguyen and\r\nErnst Oberortner and\r\nMeher Samineni and\r\nAnil Wipat and\r\nMichael Zhang and\r\nZach Zundel}, \r\ntitle = {A standard-enabled workflow for synthetic biology},\r\nvolume = {45},\r\nnumber = {3},\r\npages = {793--803},\r\nyear = {2017},\r\ndoi = {10.1042\/BST20160347},\r\npublisher = {Portland Press Limited},\r\nissn = {0300-5127},\r\nURL = {http:\/\/www.biochemsoctrans.org\/content\/45\/3\/793},\r\neprint = {http:\/\/www.biochemsoctrans.org\/content\/45\/3\/793.full.pdf},\r\njournal = {Biochemical Society Transactions}\r\n}<\/pre>\n<\/p>\n<p>\n<a href='https:\/\/doi.org\/10.1049\/enb.2017.0001' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a>G. Misirli, <strong>C. Madsen<\/strong>, I. S. de Murieta, M. Bultelle, K. Flanagan, M. Pocock, J. Hallinan, J. A. McLaughlin, J. Clark-Casey, M. Lyne, G. Micklem, G. Stan, R. Kitney, and A. Wipat, &#8220;Constructing Synthetic Biology Workflows in the Cloud,&#8221; <span style=\"font-style: italic\">IET Engineering Biology<\/span>, vol. 1(1), pp. 61-65, 2017. <br \/><a href=\"javascript:toggleBibtex('Misirli2017')\" title=\"show citation\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Misirli2017\">@article{Misirli2017,\r\nauthor = {Goksel Misirli and\r\nCurtis Madsen and\r\nI\\~{n}aki Sainz de Murieta and\r\nMatthieu Bultelle and\r\nKeith Flanagan and\r\nMatthew Pocock and\r\nJennifer Hallinan and\r\nJames Alastair McLaughlin and\r\nJustin Clark-Casey and\r\nMike Lyne and\r\nGos Micklem and\r\nGuy-Bart Stan and\r\nRichard Kitney and\r\nAnil Wipat}, \r\njournal={Engineering Biology},\r\ntitle={Constructing synthetic biology workflows in the cloud},\r\nyear={2017},\r\nvolume={1},\r\nnumber={1},\r\npages={61-65},\r\nkeywords={bioinformatics;cloud computing;Cloud-based system;Protocol for Linking External Nodes;bioinformatics;computational workflows;synthetic biology},\r\ndoi={10.1049\/enb.2017.0001}\r\n}<\/pre>\n<\/p>\n<p>\n<a href='http:\/\/dx.doi.org\/10.1101\/cshperspect.a023978' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a>E. Appleton, <strong>C. Madsen<\/strong>, N. Roehner, and D. Densmore, &#8220;Design Automation in Synthetic Biology,&#8221; <span style=\"font-style: italic\">Cold Spring Harbor Perspectives in Biology<\/span>, 2017. <br \/>    <a href=\"javascript:toggleBibtex('Appleton2017')\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Appleton2017\">@article{Appleton2017,\r\nauthor = {Evan Appleton and\r\nCurtis Madsen and\r\nNicholas Roehner and\r\nDouglas Densmore},\r\ntitle = {Design Automation in Synthetic Biology},\r\nyear = {2017}, \r\ndoi = {10.1101\/cshperspect.a023978},\r\njournal = {Cold Spring Harbor Perspectives in Biology} \r\n}<\/pre>\n<\/p>\n<h3>2016<\/h3>\n<p>\n<a href='http:\/\/dx.doi.org\/10.2390\/biecoll-jib-2016-291' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a> J. Beal, R. S. Cox III, R. Gr\u00fcnberg, J. McLaughlin, T. Nguyen, B. Bartley, M. Bissell, K. Choi, K. Clancy, C. Macklin, <strong>C. Madsen<\/strong>, G. Misirli, E. Oberortner, M. R. Pocock, N. Roehner, M. Samineni, M. Zhang, Z. Zhang, Z. Zundel, J. H. Gennari, C. J. Myers, H. M. Sauro, and A. Wipat, &#8220;Synthetic Biology Open Language (SBOL) Version 2.1.0,&#8221; <span style=\"font-style: italic\">Journal of Integrative Bioinformatics<\/span>, vol. 13(3), 2016. <br \/>   <a href=\"javascript:toggleBibtex('Beal2016_2')\" title=\"show citation\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Beal2016_2\">@article{Beal2016,\r\nauthor = {Jacob Beal and\r\nRobert Sidney Cox III and\r\nRaik Gr{\\\"{u}}nberg and\r\nJames McLaughlin and\r\nTramy Nguyen and\r\nBryan Bartley and\r\nMichael Bissell and\r\nKiri Choi and\r\nKevin Clancy and\r\nChris Macklin and\r\nCurtis Madsen and\r\nGoksel Misirli and\r\nErnst Oberortner and\r\nMatthew R. Pocock and\r\nNicholas Roehner and\r\nMeher Samineni and\r\nMichael Zhang and\r\nZhen Zhang and\r\nZach Zundel and\r\nJohn H. Gennari and\r\nChris J. Myers and\r\nHerbert M. Sauro and\r\nAnil Wipat},\r\ntitle = {Synthetic Biology Open Language {(SBOL)} Version 2.1.0},\r\njournal = {J. Integrative Bioinformatics},\r\nvolume = {13},\r\nnumber = {3},\r\nyear = {2016},\r\nurl = {https:\/\/doi.org\/10.2390\/biecoll-jib-2016-291},\r\ndoi = {10.2390\/biecoll-jib-2016-291}\r\n}<\/pre>\n<\/p>\n<p>\n<a href='http:\/\/dx.doi.org\/1721.1\/105278' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a> J. Beal, R. S. Cox III; R. Gr\u00fcnberg, J. McLaughlin, T. Nguyen, C. Macklin, M. Bissell, <strong>C. Madsen<\/strong>, N. Roehner, E. Oberortner, G. Misirli, K. Clancy, M. R. Pocock, Z. Zhang, C. J. Myers, M. Zhang, M. Samineni, Z. Zundel, B. Bartley, K. Choi, J. H. Gennari, and H. M. Sauro, &#8220;Synthetic Biology Open Language (SBOL) Version 2.1.0,&#8221; BBF RFC #112, 2016. <br \/>   <a href=\"javascript:toggleBibtex('Beal2016')\" title=\"show citation\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Beal2016\">@techreport{Beal2016,\r\nauthor = {Jacob Beal and\r\nRobert Sidney Cox III and\r\nRaik Gr\\\"{u}nberg and\r\nJames Alastair McLaughlin and\r\nTramy Nguyen and\r\nChris Macklin and\r\nMichael Bissell and\r\nCurtis Madsen and\r\nNicholas Roehner and\r\nErnst Oberortner and\r\nGoksel Misirli and\r\nKevin Clancy and\r\nMatthew R. Pocock and\r\nZhen Zhang and\r\nChris J. Myers and\r\nMichael Zhang and\r\nMeher Samineni and\r\nZach Zundel and\r\nBryan Bartley and\r\nKiri Choi and\r\nJohn H. Gennari and\r\nHerbert M. Sauro},\r\nTitle = {{S}ynthetic {B}iology {O}pen {L}anguage ({SBOL}) {V}ersion 2.1.0},\r\nKeywords = {SBOL},\r\nYear = {2016},\r\nNumber = {BBF RFC #112},\r\ndoi = {1721.1\/105278}\r\n}\r\n}<\/pre>\n<\/p>\n<p>\n<a href='http:\/\/dx.doi.org\/10.1021\/acssynbio.5b00210' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a> <strong>C. Madsen<\/strong>, J. A. McLaughlin, G. Misirli, M. Pocock, K. Flanagan, J. Hallinan, and A. Wipat, &#8220;The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs,&#8221; <span style=\"font-style: italic\">ACS Synthetic Biology<\/span>, 2016. <br \/>   <a href=\"javascript:toggleBibtex('Madsen2016')\" title=\"show citation\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Madsen2016\">@article{Madsen2016,\r\nauthor = {Curtis Madsen and\r\nJames Alastair McLaughlin and\r\nGoksel Misirli and\r\nMatthew Pocock and\r\nKeith Flanagan and\r\nJennifer Hallinan and\r\nAnil Wipat},\r\ntitle = {The {SBOL} Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs},\r\njournal = {ACS Synthetic Biology},\r\nyear = {2016},\r\ndoi = {10.1021\/acssynbio.5b00210},\r\nURL = {http:\/\/dx.doi.org\/10.1021\/acssynbio.5b00210},\r\neprint = {http:\/\/dx.doi.org\/10.1021\/acssynbio.5b00210}\r\n}<\/pre>\n<\/p>\n<p>\n<a href='http:\/\/dx.doi.org\/10.1021\/acssynbio.5b00215' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a> N. Roehner, J. Beal, K. Clancy, B. Bartley, G. Misirli, R. Gr\u00fcnberg, E. Oberortner, M. Pocock, M. Bissell, <strong>C. Madsen<\/strong>, T. Nguyen, Z. Zhang, Z. Zundel, J. H. Gennari, A. Wipat, H. M. Sauro, and C. J. Myers, &#8220;Sharing Structure and Function in Biological Design with SBOL 2.0,&#8221; <span style=\"font-style: italic\">ACS Synthetic Biology<\/span>, 2016. <br \/>   <a href=\"javascript:toggleBibtex('Roehner2016')\" title=\"show citation\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Roehner2016\">@article{Roehner2016,\r\nauthor = {Roehner, Nicholas and\r\nBeal, Jacob and\r\nClancy, Kevin and\r\nBartley, Bryan and\r\nMisirli, Goksel and\r\nGr\\\"{u}nberg, Raik and\r\nOberortner, Ernst and\r\nPocock, Matthew and\r\nBissell, Michael and\r\nMadsen, Curtis and\r\nNguyen, Tramy and\r\nZhang, Zhen and\r\nZundel, Zach and\r\nGennari, John H. and\r\nWipat, Anil and\r\nSauro, Herbert M. and\r\nMyers, Chris J.},\r\ntitle = {Sharing Structure and Function in Biological Design with {SBOL} 2.0},\r\njournal = {ACS Synthetic Biology},\r\nyear = {2016},\r\ndoi = {10.1021\/acssynbio.5b00215},\r\nURL = {http:\/\/dx.doi.org\/10.1021\/acssynbio.5b00215},\r\neprint = {http:\/\/dx.doi.org\/10.1021\/acssynbio.5b00215}\r\n}<\/pre>\n<\/p>\n<p>\n<a href='http:\/\/dx.doi.org\/10.1021\/acssynbio.5b00244' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a> J. A. McLaughlin, M. Pocock, G. Misirli, <strong>C. Madsen<\/strong>, and A. Wipat, &#8220;VisBOL: Web-Based Tools for Synthetic Biology Design Visualization,&#8221; <span style=\"font-style: italic\">ACS Synthetic Biology<\/span>, 2016. <br \/>   <a href=\"javascript:toggleBibtex('McLaughlin2016')\" title=\"show citation\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"McLaughlin2016\">@article{McLaughlin2016,\r\nauthor = {James Alastair McLaughlin and\r\nMatthew Pocock and\r\nGoksel Misirli and\r\nCurtis Madsen and\r\nAnil Wipat},\r\ntitle = {{VisBOL}: Web-Based Tools for Synthetic Biology Design Visualization},\r\njournal = {ACS Synthetic Biology},\r\nyear = {2016},\r\ndoi = {10.1021\/acssynbio.5b00244},\r\nURL = {http:\/\/dx.doi.org\/10.1021\/acssynbio.5b00244},\r\neprint = {http:\/\/dx.doi.org\/10.1021\/acssynbio.5b00244}\r\n}<\/pre>\n<\/p>\n<p>\n<a href='http:\/\/dx.doi.org\/10.1021\/acssynbio.6b00213' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a> H. Fellermann, O. Markovitch, O. Gilfellon, <strong>C. Madsen<\/strong>, and A. Phillips, &#8220;Toward Programmable Biology,&#8221; <span style=\"font-style: italic\">ACS Synthetic Biology<\/span>, 2016. <br \/>   <a href=\"javascript:toggleBibtex('Fellermann2016')\" title=\"show citation\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Fellermann2016\">@article{Fellermann2016,\r\nauthor = {Harold Fellermann and\r\nOmer Markovitch and\r\nOwen Gilfellon and\r\nCurtis Madsen and\r\nAndrew Phillips},\r\ntitle = {Toward Programmable Biology},\r\njournal = {ACS Synthetic Biology},\r\nyear = {2016},\r\ndoi = {10.1021\/acssynbio.6b00213},\r\nURL = {http:\/\/dx.doi.org\/10.1021\/acssynbio.6b00213},\r\neprint = {http:\/\/dx.doi.org\/10.1021\/acssynbio.6b00213}\r\n}<\/pre>\n<\/p>\n<p>\n<a href='http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btv660' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a> G. Misirli, M. Cavaliere, W. Waites, M. Pocock, <strong>C. Madsen<\/strong>, O. Gilfellon, R. Honorato-Zimmer, P. Zuliani, V. Danos, and A. Wipat, &#8220;Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualisation,&#8221; <span style=\"font-style: italic\">Bioinformatics<\/span>, vol. 32, iss. 6, pp. 908-917, 2016. <br \/><a href=\"javascript:toggleBibtex('Misirli2016')\" title=\"show citation\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Misirli2016\">@article{Misirli2016,\r\nauthor = {Misirli, Goksel and\r\nCavaliere, Matteo and\r\nWaites, William and\r\nPocock, Matthew and\r\nMadsen, Curtis and\r\nGilfellon, Owen and\r\nHonorato-Zimmer, Ricardo and\r\nZuliani, Paolo and\r\nDanos, Vincent and\r\nWipat, Anil}, \r\ntitle = {Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualisation},\r\nvolume = {32},\r\nnumber = {6},\r\nyear = {2016},\r\npages = {908-917},\r\ndoi = {10.1093\/bioinformatics\/btv660},\r\nURL = {http:\/\/bioinformatics.oxfordjournals.org\/content\/early\/2015\/11\/11\/bioinformatics.btv660.abstract},\r\neprint = {http:\/\/bioinformatics.oxfordjournals.org\/content\/early\/2015\/11\/11\/bioinformatics.btv660.full.pdf+html}, \r\njournal = {Bioinformatics} \r\n}<\/pre>\n<\/p>\n<h3>2015<\/h3>\n<p>\n<a href='http:\/\/dx.doi.org\/10.1007\/978-3-319-23401-4_16' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a> <strong>C. Madsen<\/strong>, F. Shmarov, and P. Zuliani, &#8220;BioPSy: An SMT-based Tool for Guaranteed Parameter Set Synthesis of Biological Models,&#8221; <span style=\"font-style: italic\">Computational Methods in Systems Biology (CMSB)<\/span>, p. 182&#8211;194, 2015. <br \/>    <a href=\"javascript:toggleBibtex('Madsen2015_2')\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Madsen2015_2\">@inproceedings{Madsen2015,\r\nAuthor = {Curtis Madsen and\r\nFedor Shmarov and\r\nPaolo Zuliani},\r\nTitle = {BioPSy: An SMT-based Tool for Guaranteed Parameter Set Synthesis of Biological Models},\r\nBooktitle = {Computational Methods in Systems Biology (CMSB)},\r\nPages = {182--194},\r\nYear = {2015},\r\nurl = {http:\/\/dx.doi.org\/10.1007\/978-3-319-23401-4_16},\r\ndoi = {10.1007\/978-3-319-23401-4_16}\r\n}<\/pre>\n<\/p>\n<p>\n<a href='http:\/\/dx.doi.org\/10.2390\/biecoll-jib-2015-272' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a> B. Bartley, J. Beal, K. Clancy, G. Misirli, N. Roehner, E. Oberortner, M. R. Pocock, M. Bissell, <strong>C. Madsen<\/strong>, T. Nguyen, Z. Zhang, J. H. Gennari, C. J. Myers, A. Wipat, and H. M. Sauro, &#8220;Synthetic Biology Open Language (SBOL) Version 2.0.0,&#8221; <span style=\"font-style: italic\">Journal of Integrative Bioinformatics<\/span>, vol. 12(2), 2015. <br \/> <a href=\"javascript:toggleBibtex('Bartley2015_2')\" title=\"show citation\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Bartley2015_2\">@article{Bartley2015,\r\nauthor = {Bryan Bartley and\r\nJacob Beal and\r\nKevin Clancy and\r\nGoksel Misirli and\r\nNicholas Roehner and\r\nErnst Oberortner and\r\nMatthew R. Pocock and\r\nMichael Bissell and\r\nCurtis Madsen and\r\nTramy Nguyen and\r\nZhen Zhang and\r\nJohn H. Gennari and\r\nChris J. Myers and\r\nAnil Wipat and\r\nHerbert M. Sauro},\r\ntitle = {Synthetic Biology Open Language {(SBOL)} Version 2.0.0},\r\njournal = {J. Integrative Bioinformatics},\r\nvolume = {12},\r\nnumber = {2},\r\nyear = {2015},\r\nurl = {https:\/\/doi.org\/10.2390\/biecoll-jib-2015-272},\r\ndoi = {10.2390\/biecoll-jib-2015-272}\r\n}<\/pre>\n<\/p>\n<p>\n<a href='http:\/\/dx.doi.org\/1721.1\/98369' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a> B. Bartley, J. Beal, K. Clancy, G. Misirli, N. Roehner, H. M. Sauro, E. Oberortner, <strong>C. Madsen<\/strong>, M. R. Pocock, A. Wipat, T. Nguyen, Z. Zhang, C. J. Myers, J. H. Gennari, and M. Bissell, &#8220;Synthetic Biology Open Language (SBOL) Version 2.0.0,&#8221; BBF RFC #108, 2015. <br \/> <a href=\"javascript:toggleBibtex('Bartley2015')\" title=\"show citation\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Bartley2015\">@techreport{Bartley2015,\r\nAuthor = {Bartley, Bryan and\r\nBeal, Jacob and\r\nClancy, Kevin and\r\nMisirli, Goksel and\r\nRoehner, Nicholas and\r\nSauro, Herbert M. and\r\nOberortner, Ernst and\r\nMadsen, Curtis and\r\nPocock, Matthew R. and\r\nWipat, Anil and\r\nNguyen, Tramy and\r\nZhang, Zhen and\r\nMyers, Chris J. and\r\nGennari, John H. and\r\nBissell, Michael},\r\nTitle = {{S}ynthetic {B}iology {O}pen {L}anguage ({SBOL}) {V}ersion 2.0.0},\r\nKeywords = {SBOL},\r\nYear = {2015},\r\nNumber = {BBF RFC #108},\r\ndoi = {1721.1\/98369}\r\n}<\/pre>\n<\/p>\n<p>\n<a href='http:\/\/dx.doi.org\/10.1007\/978-1-4939-1878-2_11' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a> <strong>C. Madsen<\/strong>, C. J. Myers, N. Roehner, C. Winstead, and Z. Zhang, &#8220;Efficient analysis methods in synthetic biology,&#8221; in <span style=\"font-style: italic\">Computational methods in synthetic biology<\/span>, M. A. Marchisio, Ed., Springer New York, 2015, vol. 1244, pp. 217-257. <br \/>    <a href=\"javascript:toggleBibtex('Madsen2015')\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Madsen2015\">@incollection{Madsen2015,\r\nyear={2015},\r\nisbn={978-1-4939-1877-5},\r\nbooktitle={Computational Methods in Synthetic Biology},\r\nvolume={1244},\r\nseries={Methods in Molecular Biology},\r\neditor={Mario Andrea Marchisio},\r\ndoi={10.1007\/978-1-4939-1878-2_11},\r\ntitle={Efficient Analysis Methods in Synthetic Biology},\r\nurl={http:\/\/dx.doi.org\/10.1007\/978-1-4939-1878-2_11},\r\npublisher={Springer New York},\r\nkeywords={Design space exploration;\r\nSynthetic genetic circuits;\r\nStochastic model checking;\r\nStochastic simulation;\r\nSynthetic biology},\r\nauthor = {Curtis Madsen and\r\nChris J. Myers and\r\nNicholas Roehner and\r\nChris Winstead and\r\nZhen Zhang},\r\npages={217-257}\r\n}<\/pre>\n<\/p>\n<h3>2014<\/h3>\n<p>\n<a href='http:\/\/dx.doi.org\/10.1145\/2644817' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a> <strong>C. Madsen<\/strong>, Z. Zhang, N. Roehner, C. Winstead, and C. J. Myers, &#8220;Stochastic model checking of genetic circuits,&#8221; <span style=\"font-style: italic\">J. emerg. technol. comput. syst.<\/span>, vol. 11, iss. 3, p. 23:1&#8211;23:21, 2014. <br \/>    <a href=\"javascript:toggleBibtex('Madsen2014')\" title=\"show citation\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Madsen2014\">@article{Madsen2014,\r\nauthor = {Curtis Madsen and\r\nZhen Zhang and\r\nNicholas Roehner and\r\nChris Winstead and\r\nChris J. Myers},\r\ntitle = {Stochastic Model Checking of Genetic Circuits},\r\njournal = {J. Emerg. Technol. Comput. Syst.},\r\nvolume = {11},\r\nnumber = {3},\r\nmonth = dec,\r\nyear = {2014},\r\nissn = {1550-4832},\r\npages = {23:1--23:21},\r\narticleno = {23},\r\nnumpages = {21},\r\nurl = {http:\/\/doi.acm.org\/10.1145\/2644817},\r\ndoi = {10.1145\/2644817},\r\nacmid = {2644817},\r\npublisher = {ACM},\r\naddress = {New York, NY, USA},\r\nkeywords = {Markov chain analysis,\r\nStochastic model checking,\r\ncontinuous stochastic logic,\r\ndesign space exploration,\r\nsynthetic genetic circuits},\r\n}<\/pre>\n<\/p>\n<p>\n<a href='http:\/\/dx.doi.org\/10.1021\/sb500176h' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a> N. Roehner, E. Oberortner, M. Pocock, J. Beal, K. Clancy, <strong>C. Madsen<\/strong>, G. Misirli, A. Wipat, H. Sauro, and C. J. Myers, &#8220;Proposed data model for the next version of the synthetic biology open language,&#8221; <span style=\"font-style: italic\">ACS Synthetic Biology<\/span>, 2014. <br \/>   <a href=\"javascript:toggleBibtex('Roehner2014')\" title=\"show citation\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Roehner2014\">@article{Roehner2014,\r\nauthor = {Roehner, Nicholas and\r\nOberortner, Ernst and\r\nPocock, Matthew and\r\nBeal, Jacob and\r\nClancy, Kevin and\r\nMadsen, Curtis and\r\nMisirli, Goksel and\r\nWipat, Anil and\r\nSauro, Herbert and\r\nMyers, Chris J.},\r\ntitle = {Proposed Data Model for the Next Version\r\nof the Synthetic Biology Open Language},\r\njournal = {{ACS} {S}ynthetic {B}iology},\r\nyear = 2014,\r\ndoi = {10.1021\/sb500176h},\r\nURL = {http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/sb500176h},\r\neprint = {http:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/sb500176h}\r\n}<\/pre>\n<\/p>\n<h3>2012<\/h3>\n<p>\n<a href='http:\/\/dx.doi.org\/1721.1\/73909' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a> M. Galdzicki, M. L. Wilson, C. A. Rodriguez, M. R. Pocock, E. Oberortner, L. Adam, A. Adler, C. J. Anderson, J. Beal, Y. Cai, D. Chandran, D. Densmore, O. A. Drory, D. Endy, J. H. Gennari, R. Gr\u00fcnberg, T. S. Ham, N. J. Hillson, J. D. Johnson, A. Kuchinsky, M. W. Lux, <strong>C. Madsen<\/strong>, G. Misirli, C. J. Myers, C. Olguin, J. Peccoud, H. Plahar, D. Platt, N. Roehner, E. Sirin, T. F. Smith, G. Stan, A. Villalobos, A. Wipat, and H. M. Sauro, &#8220;Synthetic Biology Open Language (SBOL) Version 1.1.0,&#8221; BBF RFC #87, 2012. <br \/> <a href=\"javascript:toggleBibtex('Galdzicki2012')\" title=\"show citation\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Galdzicki2012\">@techreport{Galdzicki2012,\r\nAuthor = {Galdzicki, Michal and\r\nWilson, Mandy L. and\r\nRodriguez, Cesar A. and\r\nPocock, Matthew R. and\r\nOberortner, Ernst and\r\nAdam, Laura and\r\nAdler, Aaron and\r\nAnderson, J. Christopher and\r\nBeal, Jacob and\r\nCai, Yizhi and\r\nChandran, Deepak and\r\nDensmore, Douglas and\r\nDrory, Omri A. and\r\nEndy, Drew and\r\nGennari, John H. and\r\nGr\\\"{u}nberg, Raik and\r\nHam, Timothy S. and\r\nHillson, Nathan J. and\r\nJohnson, Jeffrey D. and\r\nKuchinsky, Allan and\r\nLux, Matthew W. and\r\nMadsen, Curtis and\r\nMisirli, Goksel and\r\nMyers, Chris J. and\r\nOlguin, Carlos and\r\nPeccoud, Jean and\r\nPlahar, Hector and\r\nPlatt, Darren and\r\nRoehner, Nicholas and\r\nSirin, Evren and\r\nSmith, Trevor F. and\r\nStan, Guy-Bart and\r\nVillalobos, Alan and\r\nWipat, Anil and\r\nSauro, Herbert M.},\r\nTitle = {{S}ynthetic {B}iology {O}pen {L}anguage ({SBOL}) {V}ersion 1.1.0},\r\nKeywords = {SBOL},\r\nYear = {2012},\r\nNumber = {BBF RFC #87},\r\ndoi = {1721.1\/73909}\r\n}<\/pre>\n<\/p>\n<p>\n<a href='http:\/\/dx.doi.org\/10.1109\/MDT.2012.2187875' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a> <strong>C. Madsen<\/strong>, C. J. Myers, T. Patterson, N. Roehner, J. T. Stevens, and C. Winstead, &#8220;Design and test of genetic circuits using iBioSim,&#8221; <span style=\"font-style: italic\">IEEE Design &amp; Test of Computers<\/span>, vol. 29, iss. 3, pp. 32-39, 2012. <br \/> <a href=\"javascript:toggleBibtex('Madsen2012_2')\" title=\"show citation\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Madsen2012_2\">@article{Madsen2012,\r\nauthor = {Curtis Madsen and\r\nChris J. Myers and\r\nTyler Patterson and\r\nNicholas Roehner and\r\nJason T. Stevens and\r\nChris Winstead},\r\ntitle = {Design and Test of Genetic Circuits Using {iBioSim}},\r\njournal = {{IEEE Design {\\&amp;} Test of Computers}},\r\nvolume = {29},\r\nnumber = {3},\r\nyear = {2012},\r\npages = {32-39},\r\ndoi = {10.1109\/MDT.2012.2187875},\r\nee = {http:\/\/dx.doi.org\/10.1109\/MDT.2012.2187875}\r\n}<\/pre>\n<\/p>\n<p>\n<a href='http:\/\/dx.doi.org\/10.1109\/CIBCB.2012.6217255' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a> <strong>C. Madsen<\/strong>, C. J. Myers, N. Roehner, C. Winstead, and Z. Zhang, &#8220;Utilizing stochastic model checking to analyze genetic circuits.,&#8221; in <span style=\"font-style: italic\">IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)<\/span>,  2012, pp. 379-386 <strong>(Best Student Paper)<\/strong>. <br \/> <a href=\"javascript:toggleBibtex('Madsen2012')\" title=\"show citation\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Madsen2012\">@inproceedings{Madsen2012,\r\nauthor = {Madsen, Curtis and\r\nMyers, Chris J. and\r\nRoehner, Nicholas and\r\nWinstead, Chris and\r\nZhang, Zhen},\r\nbooktitle = {{IEEE Symposium on Computational Intelligence\r\nin Bioinformatics and Computational Biology (CIBCB)}},\r\nee = {http:\/\/dx.doi.org\/10.1109\/CIBCB.2012.6217255},\r\ninterhash = {613357012415bdba0883eee6fe183ff6},\r\nintrahash = {c5c868dd08b7df5ea2241fbee03a618a},\r\nisbn = {978-1-4673-1190-8},\r\nkeywords = {dblp},\r\npages = {379-386},\r\ntimestamp = {2012-06-20T00:00:00.000+0200},\r\ntitle = {Utilizing stochastic model checking to analyze genetic circuits.},\r\nurl = {http:\/\/dblp.uni-trier.de\/db\/conf\/cibcb\/cibcb2012.html#MadsenMRWZ12},\r\nyear = 2012,\r\ndoi = {10.1109\/CIBCB.2012.6217255},\r\nnote = {(best student paper)}\r\n}<\/pre>\n<\/p>\n<h3>2011<\/h3>\n<p>\n<a href='http:\/\/dx.doi.org\/1721.1\/66172' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a> M. Galdzicki, M. L. Wilson, C. A. Rodriguez, L. Adam, A. Adler, C. J. Anderson, J. Beal, D. Chandran, D. Densmore, O. A. Drory, D. Endy, J. H. Gennari, R. Gr\u00fcnberg, T. S. Ham, A. Kuchinsky, M. W. Lux, <strong>C. Madsen<\/strong>, G. Misirli, C. J. Myers, J. Peccoud, H. Plahar, M. R. Pocock, N. Roehner, T. F. Smith, G. Stan, A. Villalobos, A. Wipat, and H. M. Sauro, &#8220;Synthetic Biology Open Language (SBOL) Version 1.0.0,&#8221; BBF RFC #84, 2011. <br \/> <a href=\"javascript:toggleBibtex('Galdzicki2011')\" title=\"show citation\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Galdzicki2011\">@techreport{Galdzicki2011,\r\nAuthor = {Galdzicki, Michal and\r\nWilson, Mandy L. and\r\nRodriguez, Cesar A. and\r\nAdam, Laura and\r\nAdler, Aaron and\r\nAnderson, J. Christopher and\r\nBeal, Jacob and\r\nChandran, Deepak and\r\nDensmore, Douglas and\r\nDrory, Omri A. and\r\nEndy, Drew and\r\nGennari, John H. and\r\nGr\\\"{u}nberg, Raik and\r\nHam, Timothy S. and\r\nKuchinsky, Allan and\r\nLux, Matthew W. and\r\nMadsen, Curtis and\r\nMisirli, Goksel and\r\nMyers, Chris J. and\r\nPeccoud, Jean and\r\nPlahar, Hector and\r\nPocock, Matthew R. and\r\nRoehner, Nicholas and\r\nSmith, Trevor F. and\r\nStan, Guy-Bart and\r\nVillalobos, Alan and\r\nWipat, Anil and\r\nSauro, Herbert M.},\r\nTitle = {{S}ynthetic {B}iology {O}pen {L}anguage ({SBOL}) {V}ersion 1.0.0},\r\nKeywords = {SBOL},\r\nYear = {2011},\r\nNumber = {BBF RFC #84},\r\ndoi = {1721.1\/66172}\r\n}<\/pre>\n<\/p>\n<h3>2010<\/h3>\n<p>\n<a href='http:\/\/www.intechopen.com\/books\/stochastic-control\/effecient-stochastic-simulation-to-analyze-targeted-properties-of-biological-systems' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a> H. Kuwahara, <strong>C. Madsen<\/strong>, I. Mura, C. J. Myers, A. Tejeda, and C. Winstead, &#8220;Efficient stochastic simulation to analyze targeted properties of biological systems,&#8221; in <span style=\"font-style: italic\">Stochastic control<\/span>, C. J. Myers, Ed., Sciyo, 2010, pp. 505-532. <br \/> <a href=\"javascript:toggleBibtex('Kuwahara2010')\" title=\"show citation\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Kuwahara2010\">@incollection{Kuwahara2010,\r\nauthor = {Hiroyuki Kuwahara and\r\nCurtis Madsen and\r\nIvan Mura and\r\nChris J. Myers and\r\nAbiezer Tejeda and\r\nChris Winstead},\r\ntitle = {Efficient stochastic simulation\r\nto analyze targeted properties of biological systems},\r\nbooktitle = {Stochastic Control},\r\neditor = {Chris J. Myers},\r\npublisher = {Sciyo},\r\npages = {505--532},\r\nyear = 2010\r\n}<\/pre>\n<\/p>\n<p>\n<a href='http:\/\/dx.doi.org\/10.1109\/ISCAS.2010.5537539' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a> C. Winstead, <strong>C. Madsen<\/strong>, and C. J. Myers, &#8220;iSSA: An incremental stochastic simulation algorithm for genetic circuits,&#8221; in <span style=\"font-style: italic\">International Symposium on Circuits and Systems (ISCAS)<\/span>,  2010, pp. 553-556. <br \/> <a href=\"javascript:toggleBibtex('Winstead2010')\" title=\"show citation\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Winstead2010\">@inproceedings{Winstead2010,\r\nauthor = {Chris Winstead and\r\nCurtis Madsen and\r\nChris J. Myers},\r\ntitle = {{iSSA}: {A}n incremental stochastic simulation algorithm for\r\ngenetic circuits},\r\nbooktitle = {{International Symposium on Circuits and Systems (ISCAS)}},\r\nyear = {2010},\r\npages = {553-556},\r\ndoi = {10.1109\/ISCAS.2010.5537539},\r\nee = {http:\/\/dx.doi.org\/10.1109\/ISCAS.2010.5537539}\r\n}<\/pre>\n<\/p>\n<h3>2009<\/h3>\n<p>\n<a href='http:\/\/dx.doi.org\/10.1145\/1687399.1687531' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a> C. J. Myers, N. A. Barker, H. Kuwahara, K. R. Jones, <strong>C. Madsen<\/strong>, and N. D. Nguyen, &#8220;Genetic design automation,&#8221; in <span style=\"font-style: italic\">International Conference on Computer-Aided Design (ICCAD)<\/span>,  2009, pp. 713-716. <br \/> <a href=\"javascript:toggleBibtex('Myers2009_2')\" title=\"show citation\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Myers2009_2\">@inproceedings{Myers2009,\r\nauthor = {Chris J. Myers and\r\nNathan A. Barker and\r\nHiroyuki Kuwahara and\r\nKevin R. Jones and\r\nCurtis Madsen and\r\nNam-Phuong D. Nguyen},\r\ntitle = {Genetic design automation},\r\nbooktitle = {{International Conference on Computer-Aided Design (ICCAD)}},\r\nyear = {2009},\r\npages = {713-716},\r\nee = {http:\/\/ieeexplore.ieee.org\/xpls\/abs_all.jsp?arnumber=5361217},\r\ndoi = {10.1145\/1687399.1687531}\r\n}<\/pre>\n<\/p>\n<p>\n<a href='http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btp457' class='papercite_doi' title='View document on publisher site' target='_blank'><img src='\/ckmadsen\/files\/2016\/03\/external.png' width='10' height='10' alt='[DOI]' \/><\/a> C. J. Myers, N. A. Barker, K. R. Jones, H. Kuwahara, <strong>C. Madsen<\/strong>, and N. D. Nguyen, &#8220;iBioSim: a tool for the analysis and design of genetic circuits,&#8221; <span style=\"font-style: italic\">Bioinformatics<\/span>, vol. 25, iss. 21, pp. 2848-2849, 2009. <br \/><a href=\"javascript:toggleBibtex('Myers2009')\" title=\"show citation\">[Bibtex]<\/a><\/p>\n<pre hidden id=\"Myers2009\">@article{Myers2009,\r\nauthor = {Chris J. Myers and\r\nNathan A. Barker and\r\nKevin R. Jones and\r\nHiroyuki Kuwahara and\r\nCurtis Madsen and\r\nNam-Phuong D. Nguyen},\r\ntitle = {{iBioSim}: a tool for the analysis and design of genetic circuits},\r\njournal = {Bioinformatics},\r\nvolume = {25},\r\nnumber = {21},\r\nyear = {2009},\r\npages = {2848-2849},\r\ndoi = {10.1093\/bioinformatics\/btp457},\r\nee = {http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btp457}\r\n}<\/pre>\n<\/p>\n<p><script type=\"text\/javascript\">\r\nfunction toggleBibtex(id) {\r\n  element = document.getElementById(id);\r\n  if (\"block\" != element.style.display) {\r\n    element.style.display = \"block\";\r\n  } else {\r\n    element.style.display = \"none\";\r\n  }\r\n}\r\n<\/script><\/p>\n","protected":false},"excerpt":{"rendered":"<p>2018 T. Neupane, Z. Zhang, C. Madsen, H. Zheng, and C. J. Myers, &#8220;Approximation Techniques for Stochastic Analysis of Biological Systems,&#8221; in Automated Reasoning for Systems Biology and Medicine, P. Li\u00f2 and P. Zuliani, Ed., Springer, 2018 (submitted). [Bibtex] @incollection{Neupane2018, Author = {Thakur Neupane and Zhen Zhang and Curtis Madsen and Hao Zheng and Chris [&hellip;]<\/p>\n","protected":false},"author":11553,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/sites.bu.edu\/ckmadsen\/wp-json\/wp\/v2\/pages\/45"}],"collection":[{"href":"https:\/\/sites.bu.edu\/ckmadsen\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.bu.edu\/ckmadsen\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.bu.edu\/ckmadsen\/wp-json\/wp\/v2\/users\/11553"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.bu.edu\/ckmadsen\/wp-json\/wp\/v2\/comments?post=45"}],"version-history":[{"count":50,"href":"https:\/\/sites.bu.edu\/ckmadsen\/wp-json\/wp\/v2\/pages\/45\/revisions"}],"predecessor-version":[{"id":255,"href":"https:\/\/sites.bu.edu\/ckmadsen\/wp-json\/wp\/v2\/pages\/45\/revisions\/255"}],"wp:attachment":[{"href":"https:\/\/sites.bu.edu\/ckmadsen\/wp-json\/wp\/v2\/media?parent=45"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}