The metabolome of Mexican cavefish shows a convergent signature highlighting sugar, antioxidant, and Ageing-Related metabolites
Medley, J Kyle, Persons, Jenna, Biswas, Tathagata, Olsen, Luke, Peuß, Robert, Krishnan, Jaya, Xiong, Shaolei, Rohner, Nicolas
Published in eLife (15.06.2022)
Published in eLife (15.06.2022)
Get full text
Journal Article
Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology
Medley, J Kyle, Choi, Kiri, König, Matthias, Smith, Lucian, Gu, Stanley, Hellerstein, Joseph, Sealfon, Stuart C, Sauro, Herbert M
Published in PLoS computational biology (01.06.2018)
Published in PLoS computational biology (01.06.2018)
Get full text
Journal Article
A compiler for biological networks on silicon chips
Medley, J. Kyle, Teo, Jonathan, Woo, Sung Sik, Hellerstein, Joseph, Sarpeshkar, Rahul, Sauro, Herbert M
Published in PLoS computational biology (01.09.2020)
Published in PLoS computational biology (01.09.2020)
Get full text
Journal Article
Tellurium: An extensible python-based modeling environment for systems and synthetic biology
Choi, Kiri, Medley, J. Kyle, König, Matthias, Stocking, Kaylene, Smith, Lucian, Gu, Stanley, Sauro, Herbert M.
Published in BioSystems (01.09.2018)
Published in BioSystems (01.09.2018)
Get full text
Journal Article
Synthetic Biology: Engineering Living Systems from Biophysical Principles
Bartley, Bryan A., Kim, Kyung, Medley, J. Kyle, Sauro, Herbert M.
Published in Biophysical journal (28.03.2017)
Published in Biophysical journal (28.03.2017)
Get full text
Journal Article
libRoadRunner: a high performance SBML simulation and analysis library
Somogyi, Endre T, Bouteiller, Jean-Marie, Glazier, James A, König, Matthias, Medley, J Kyle, Swat, Maciej H, Sauro, Herbert M
Published in Bioinformatics (15.10.2015)
Published in Bioinformatics (15.10.2015)
Get full text
Journal Article
Metabolic reprogramming underlies cavefish muscular endurance despite loss of muscle mass and contractility
Olsen, Luke, Levy, Michaella, Medley, J Kyle, Hassan, Huzaifa, Miller, Brandon, Alexander, Richard, Wilcock, Emma, Yi, Kexi, Florens, Laurence, Weaver, Kyle, McKinney, Sean A, Peuß, Robert, Persons, Jenna, Kenzior, Alexander, Maldonado, Ernesto, Delventhal, Kym, Gluesenkamp, Andrew, Mager, Edward, Coughlin, David, Rohner, Nicolas
Published in Proceedings of the National Academy of Sciences - PNAS (31.01.2023)
Published in Proceedings of the National Academy of Sciences - PNAS (31.01.2023)
Get full text
Journal Article
Guidelines for Reproducibly Building and Simulating Systems Biology Models
Medley, J. Kyle, Goldberg, Arthur P., Karr, Jonathan R.
Published in IEEE transactions on biomedical engineering (01.10.2016)
Published in IEEE transactions on biomedical engineering (01.10.2016)
Get full text
Journal Article
phraSED-ML: A paraphrased, human-readable adaptation of SED-ML
Choi, Kiri, Smith, Lucian P, Medley, J Kyle, Sauro, Herbert M
Published in Journal of bioinformatics and computational biology (01.12.2016)
Published in Journal of bioinformatics and computational biology (01.12.2016)
Get more information
Journal Article
BioSimulators: a central registry of simulation engines and services for recommending specific tools
Shaikh, Bilal, Smith, Lucian P, Vasilescu, Dan, Marupilla, Gnaneswara, Wilson, Michael, Agmon, Eran, Agnew, Henry, Andrews, Steven S, Anwar, Azraf, Beber, Moritz E, Bergmann, Frank T, Brooks, David, Brusch, Lutz, Calzone, Laurence, Choi, Kiri, Cooper, Joshua, Detloff, John, Drawert, Brian, Dumontier, Michel, Ermentrout, G Bard, Faeder, James R, Freiburger, Andrew P, Fröhlich, Fabian, Funahashi, Akira, Garny, Alan, Gennari, John H, Gleeson, Padraig, Goelzer, Anne, Haiman, Zachary, Hasenauer, Jan, Hellerstein, Joseph L, Hermjakob, Henning, Hoops, Stefan, Ison, Jon C, Jahn, Diego, Jakubowski, Henry V, Jordan, Ryann, Kalaš, Matúš, König, Matthias, Liebermeister, Wolfram, Sheriff, Rahuman S Malik, Mandal, Synchon, McDougal, Robert, Medley, J Kyle, Mendes, Pedro, Müller, Robert, Myers, Chris J, Naldi, Aurelien, Nguyen, Tung V N, Nickerson, David P, Olivier, Brett G, Patoliya, Drashti, Paulevé, Loïc, Petzold, Linda R, Priya, Ankita, Rampadarath, Anand K, Rohwer, Johann M, Saglam, Ali S, Singh, Dilawar, Sinha, Ankur, Snoep, Jacky, Sorby, Hugh, Spangler, Ryan, Starruß, Jörn, Thomas, Payton J, van Niekerk, David, Weindl, Daniel, Zhang, Fengkai, Zhukova, Anna, Goldberg, Arthur P, Schaff, James C, Blinov, Michael L, Sauro, Herbert M, Moraru, Ion I, Karr, Jonathan R
Published in Nucleic acids research (05.07.2022)
Published in Nucleic acids research (05.07.2022)
Get full text
Journal Article
Toward Community Standards and Software for Whole-Cell Modeling
Waltemath, Dagmar, Pir, Pinar, Alaybeyoglu, Begum, Aranganathan, Naveen K, Baghalian, Kambiz, Bittig, Arne T., Burke, Paulo E. Pinto, Cantarelli, Matteo, Chew, Yin Hoon, Costa, Rafael S., Cursons, Joseph, Karr, Jonathan R., Czauderna, Tobias, Goldberg, Arthur P., Gomez, Harold F., Hahn, Jens, Hameri, Tuure, Gardiol, Daniel F. Hernandez, Kazakiewicz, Denis, Kiselev, Ilya, Knight-Schrijver, Vincent, Knupfer, Christian, Bergmann, Frank T., Konig, Matthias, Lee, Daewon, Lloret-Villas, Audald, Mandrik, Nikita, Medley, J. Kyle, Moreau, Bertrand, Naderi-Meshkin, Hojjat, Palaniappan, Sucheendra K., Priego-Espinosa, Daniel, Scharm, Martin, Chelliah, Vijayalakshmi, Sharma, Mahesh, Smallbone, Kieran, Stanford, Natalie J., Song, Je-Hoon, Theile, Tom, Tokic, Milenko, Tomar, Namrata, Toure, Vasundra, Uhlendorf, Jannis, Varusai, Thawfeek M, Hucka, Michael, Watanabe, Leandro H., Wendland, Florian, Wolfien, Markus, Yurkovich, James T., Zhu, Yan, Zardilis, Argyris, Zhukova, Anna, Schreiber, Falk, Krantz, Marcus, Liebermeister, Wolfram, Mendes, Pedro, Myers, Chris J.
Published in IEEE transactions on biomedical engineering (01.10.2016)
Published in IEEE transactions on biomedical engineering (01.10.2016)
Get full text
Journal Article
BioSimulators: a central registry of simulation engines and services for recommending specific tools
Shaikh, Bilal, Smith, Lucian P, Vasilescu, Dan, Marupilla, Gnaneswara, Wilson, Michael, Agmon, Eran, Agnew, Henry, Andrews, Steven S, Anwar, Azraf, Beber, Moritz E, Bergmann, Frank T, Brooks, David, Brusch, Lutz, Calzone, Laurence, Choi, Kiri, Cooper, Joshua, Detloff, John, Drawert, Brian, Dumontier, Michel, Ermentrout, G. Bard, Faeder, James R, Freiburger, Andrew P, Fröhlich, Fabian, Funahashi, Akira, Garny, Alan, Gennari, John H, Gleeson, Padraig, Goelzer, Anne, Haiman, Zachary, Hellerstein, Joseph L, Hoops, Stefan, Ison, Jon C, Jahn, Diego, Jakubowski, Henry V, Jordan, Ryann, Kalaš, Matúš, König, Matthias, Liebermeister, Wolfram, Mandal, Synchon, McDougal, Robert, Medley, J. Kyle, Mendes, Pedro, Müller, Robert, Myers, Chris J, Naldi, Aurelien, Nguyen, Tung V. N, Nickerson, David P, Olivier, Brett G, Patoliya, Drashti, Paulevé, Loïc, Petzold, Linda R, Priya, Ankita, Rampadarath, Anand K, Rohwer, Johann M, Saglam, Ali S, Singh, Dilawar, Sinha, Ankur, Snoep, Jacky, Sorby, Hugh, Spangler, Ryan, Starruß, Jörn, Thomas, Payton J, van Niekerk, David, Weindl, Daniel, Zhang, Fengkai, Zhukova, Anna, Goldberg, Arthur P, Blinov, Michael L, Sauro, Herbert M, Moraru, Ion I, Karr, Jonathan R
Year of Publication 13.03.2022
Year of Publication 13.03.2022
Get full text
Journal Article
BioSimulators: a central registry of simulation engines and services for recommending specific tools
Shaikh, Bilal, Smith, Lucian P, Vasilescu, Dan, Marupilla, Gnaneswara, Wilson, Michael, Agmon, Eran, Agnew, Henry, Andrews, Steven S, Azraf Anwar, Beber, Moritz E, Bergmann, Frank T, Brooks, David, Brusch, Lutz, Calzone, Laurence, Choi, Kiri, Cooper, Joshua, Detloff, John, Drawert, Brian, Dumontier, Michel, G Bard Ermentrout, Faeder, James R, Freiburger, Andrew P, Fröhlich, Fabian, Funahashi, Akira, Garny, Alan, Gennari, John H, Gleeson, Padraig, Goelzer, Anne, Haiman, Zachary, Hellerstein, Joseph L, Hoops, Stefan, Ison, Jon C, Jahn, Diego, Jakubowski, Henry V, Jordan, Ryann, Kalaš, Matúš, König, Matthias, Liebermeister, Wolfram, Mandal, Synchon, McDougal, Robert, Medley, J Kyle, Mendes, Pedro, Müller, Robert, Myers, Chris J, Naldi, Aurelien, Nguyen, Tung V N, Nickerson, David P, Olivier, Brett G, Patoliya, Drashti, Paulevé, Loïc, Petzold, Linda R, Ankita Priya, Rampadarath, Anand K, Rohwer, Johann M, Saglam, Ali S, Singh, Dilawar, Sinha, Ankur, Snoep, Jacky, Sorby, Hugh, Spangler, Ryan, Starruß, Jörn, Thomas, Payton J, David van Niekerk, Weindl, Daniel, Zhang, Fengkai, Zhukova, Anna, Goldberg, Arthur P, Blinov, Michael L, Sauro, Herbert M, Moraru, Ion I, Karr, Jonathan R
Published in arXiv.org (13.03.2022)
Get full text
Published in arXiv.org (13.03.2022)
Paper