Authors: Cheemalavagu, Neha, Shoger, Karsen E., Cao, Yuqi M., Michalides, Brandon A., Botta, Samuel A., Faeder, James R., Gottschalk, Rachel A.

Contributors: National Institute of General Medical Sciences, National Institute of Allergy and Infectious Diseases

Superior Title: Cell Systems ; volume 15, issue 1, page 37-48.e4 ; ISSN 2405-4712

Subject Terms: Cell Biology, Histology, Pathology and Forensic Medicine

Availability: https://doi.org/10.1016/j.cels.2023.12.006
https://api.elsevier.com/content/article/PII:S2405471223003605?httpAccept=text/xml
https://api.elsevier.com/content/article/PII:S2405471223003605?httpAccept=text/plain

Authors: Faeder, James R.^Aff1419, Bartol, Thomas M.^Aff1420, Dittrich, Markus^Aff1421, Migliore, Michele, Section editor^Aff1422, Linster, Christiane, Section editor^Aff1423, Cavarretta, Francesco, Section editor^Aff1424

Contributors: Jaeger, Dieter, editor^Aff1, Jung, Ranu, editor^Aff2

Superior Title: Encyclopedia of Computational Neuroscience. :1985-1988

Authors: Bogetti, Anthony T., Leung, Jeremy M. G., Russo, John D., Zhang, She, Thompson, Jeff P., Saglam, Ali S., Ray, Dhiman, Mostofian, Barmak, Pratt, A. J., Abraham, Rhea C., Harrison, Page O., Dudek, Max, Torrillo, Paul A., DeGrave, Alex J., Adhikari, Upendra, Faeder, James R., Andricioaei, Ioan, Adelman, Joshua L., Zwier, Matthew C., LeBard, David N., Zuckerman, Daniel M., Chong, Lillian T.

Superior Title: Living Journal of Computational Molecular Science; Vol. 5 No. 1 (2023); 1655 ; 2575-6524 ; 10.33011/livecoms.5.1

Subject Terms: enhanced sampling, molecular dynamics simulations

File Description: application/pdf

Relation: https://livecomsjournal.org/index.php/livecoms/article/view/v5i1e1655/1577; https://livecomsjournal.org/index.php/livecoms/article/view/v5i1e1655/1579; https://livecomsjournal.org/index.php/livecoms/article/view/v5i1e1655

Availability: https://doi.org/10.33011/livecoms.5.1.1655
https://doi.org/10.33011/livecoms.5.1
https://livecomsjournal.org/index.php/livecoms/article/view/v5i1e1655

Authors: Cheemalavagu, Neha, Shoger, Karsen E., Cao, Yuqi M., Michalides, Brandon A., Botta, Samuel A., Faeder, James R., Gottschalk, Rachel A.

Superior Title: bioRxiv

Subject Terms: Article

Relation: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10245690/; http://dx.doi.org/10.1101/2023.05.19.541151

Availability: https://doi.org/10.1101/2023.05.19.541151
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10245690/

Authors: Husar, Adam, Ordyan, Mariam, Garcia, Guadalupe C., Yancey, Joel G., Saglam, Ali S., Faeder, James R., Bartol, Thomas M., Kennedy, Mary B., Sejnowski, Terrence J.

Superior Title: PLoS Computational Biology; 4/24/2024, Vol. 20 Issue 4, p1-30, 30p

Subject Terms: PYTHON programming language, SIMULATION software, CHEMICAL models, CHEMICAL reactions, CELLULAR signal transduction, MODEL validation

Authors: 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.

Superior Title: Shaikh , B , Smith , L P , Vasilescu , D , Marupilla , G , Wilson , M , Agmon , E , Agnew , H , Andrews , S S , Anwar , A , Beber , M E , Bergmann , F T , Brooks , D , Brusch , L , Calzone , L , Choi , K , Cooper , J , Detloff , J , Drawert , B , Dumontier , M , Ermentrout , G B , Faeder , J R , Freiburger , A P , Fröhlich , F , ....

Subject Terms: /dk/atira/pure/sustainabledevelopmentgoals/good_health_and_well_being, name=SDG 3 - Good Health and Well-being

Relation: https://research.vu.nl/en/publications/5ad91f6b-16a1-4a95-a500-b320ccdadaa1

Availability: https://doi.org/10.1093/nar/gkac331
https://research.vu.nl/en/publications/5ad91f6b-16a1-4a95-a500-b320ccdadaa1
https://hdl.handle.net/1871.1/5ad91f6b-16a1-4a95-a500-b320ccdadaa1
http://www.scopus.com/inward/record.url?scp=85134730260&partnerID=8YFLogxK
http://www.scopus.com/inward/citedby.url?scp=85134730260&partnerID=8YFLogxK

Authors: Karr, Jonathan, Malik-Sheriff, Rahuman S., Osborne, James, Gonzalez-Parra, Gilberto, Forgoston, Eric, Bowness, Ruth, Liu, Yaling, Thompson, Robin, Garira, Winston, Barhak, Jacob, Rice, John, Torres, Marcella, Dobrovolny, Hana M., Tang, Tingting, Waites, William, Glazier, James A., Faeder, James R., Kulesza, Alexander

Subject Terms: Electronic computers. Computer science, Mathematics, Immunology, Biology

File Description: text

Relation: https://strathprints.strath.ac.uk/79975/1/Karr_etal_FSB_2022_Model_integration_in_computational_biology_the_role_of_reproducibility_credibility_utility.pdf; Karr, Jonathan and Malik-Sheriff, Rahuman S. and Osborne, James and Gonzalez-Parra, Gilberto and Forgoston, Eric and Bowness, Ruth and Liu, Yaling and Thompson, Robin and Garira, Winston and Barhak, Jacob and Rice, John and Torres, Marcella and Dobrovolny, Hana M. and Tang, Tingting and Waites, William and Glazier, James A. and Faeder, James R. and Kulesza, Alexander (2022 ) Model integration in computational biology : the role of reproducibility, credibility and utility. Frontiers in Systems Biology , 2. 822606. ISSN 2674-0702

Availability: https://doi.org/10.3389/fsysb.2022.822606
https://strathprints.strath.ac.uk/79975/
https://strathprints.strath.ac.uk/79975/1/Karr_etal_FSB_2022_Model_integration_in_computational_biology_the_role_of_reproducibility_credibility_utility.pdf

Authors: Taylor, D. Lansing^{Aff13, Aff14}, Gough, Albert^{Aff13, Aff14}, Schurdak, Mark E.^{Aff13, Aff14}, Vernetti, Lawrence^{Aff13, Aff14}, Chennubhotla, Chakra S.^{Aff13, Aff14}, Lefever, Daniel^Aff13, Pei, Fen^{Aff13, Aff14}, Faeder, James R.^{Aff13, Aff14}, Lezon, Timothy R.^{Aff13, Aff14}, Stern, Andrew M.^{Aff13, Aff14}, Bahar, Ivet^{Aff13, Aff14}

Contributors: Barrett, James E., Editor-in-Chief^{Aff1, Aff10}, Flockerzi, Veit, Editorial Board Member^Aff2, Frohman, Michael A., Editorial Board Member^Aff3, Geppetti, Pierangelo, Editorial Board Member^Aff4, Hofmann, Franz B., Editorial Board Member^Aff5, Michel, Martin C., Editorial Board Member^{Aff6, Aff12}, Page, Clive P., Editorial Board Member^{Aff7, Aff11}, Rosenthal, Walter, Editorial Board Member^Aff8, Wang, KeWei, Editorial Board Member^Aff9

Superior Title: Concepts and Principles of Pharmacology : 100 Years of the Handbook of Experimental Pharmacology. 260:327-367

Authors: Keating, Sarah M., Waltemath, Dagmar, König, Matthias, Zhang, Fengkai, Dräger, Andreas, Chaouiya, Claudine, Bergmann, Frank T., Finney, Andrew, Gillespie, Colin S., Helikar, Tomáš, Hoops, Stefan, Malikâ€Sheriff, Rahuman S., Moodie, Stuart L., Moraru, Ion I., Myers, Chris J., Naldi, Aurélien, Olivier, Brett G., Sahle, Sven, Schaff, James C., Smith, Lucian P., Swat, Maciej J., Thieffry, Denis, Watanabe, Leandro, Wilkinson, Darren J., Blinov, Michael L., Begley, Kimberly, Faeder, James R., Gómez, Harold F., Hamm, Thomas M., Inagaki, Yuichiro, Liebermeister, Wolfram, Lister, Allyson L., Lucio, Daniel, Mjolsness, Eric, Proctor, Carole J., Raman, Karthik, Rodriguez, Nicolas, Shaffer, Clifford A., Shapiro, Bruce E., Stelling, Joerg, Swainston, Neil, Tanimura, Naoki, Wagner, John, Meierâ€Schellersheim, Martin, Sauro, Herbert M., Palsson, Bernhard., Bolouri, Hamid, Kitano, Hiroaki, Funahashi, Akira, Hermjakob, Henning, Doyle, John C., Hucka, Michael, Adams, Richard R., Allen, Nicholas A., Angermann, Bastian R., Antoniotti, Marco, Bader, Gary D., ÄŒervený, Jan, Courtot, Mélanie, Cox, Chris D., Dalle Pezze, Piero, Demir, Emek, Denney, William S., Dharuri, Harish, Dorier, Julien, Drasdo, Dirk, Ebrahim, Ali, Eichner, Johannes, Elf, Johan, Endler, Lukas, Evelo, Chris T., Flamm, Christoph, Fleming, Ronan M. T., Fröhlich, Martina, Glont, Mihai, Gonçalves, Emanuel, Golebiewski, Martin, Grabski, Hovakim, Gutteridge, Alex, Hachmeister, Damon, Harris, Leonard A., Heavner, Benjamin D., Henkel, Ron, Hlavacek, William S., Hu, Bin, Hyduke, Daniel R., Jong, Hidde, Juty, Nick, Karp, Peter D, Karr, Jonathan R., Kell, Douglas B., Keller, Roland, Kiselev, Ilya, Klamt, Steffen, Klipp, Edda, Knüpfer, Christian, Kolpakov, Fedor, Krause, Falko, Kutmon, Martina, Laibe, Camille, Lawless, Conor, Li, Lu, Loew, Leslie M., Machne, Rainer, Matsuoka, Yukiko, Mendes, Pedro, Mi, Huaiyu, Mittag, Florian, Monteiro, Pedro T, Natarajan, Kedar Nath, Nielsen, Poul M. F., Nguyen, Tramy, Palmisano, Alida, Pettit, Jeanâ€Baptiste, Pfau, Thomas, Phair, Robert D., Radivoyevitch, Tomas, Rohwer, Johann M., Ruebenacker, Oliver A., Saezâ€Rodriguez, Julio, Scharm, Martin, Schmidt, Henning, Schreiber, Falk, Schubert, Michael, Schulte, Roman, Sealfon, Stuart C., Smallbone, Kieran, Soliman, Sylvain, Stefan, Melanie I., Sullivan, Devin P., Takahashi, Koichi, Teusink, Bas, Tolnay, David, Vazirabad, Ibrahim, Kamp, Axel, Wittig, Ulrike, Wrzodek, Clemens, Wrzodek, Finja, Xenarios, Ioannis, Zhukova, Anna, Zucker, Jeremy, SBML Level 3 Community members

Superior Title: Molecular Systems Biology, 16(8), Art. No. e9110, (2020-08)

Subject Terms: computational modeling, file format, interoperability, reproducibility, systems biology

Relation: https://doi.org/10.15252/msb.20199110; oai:authors.library.caltech.edu:2s3jq-t6239; eprintid:105126; resolverid:CaltechAUTHORS:20200827-073238775

Availability: https://doi.org/10.15252/msb.20199110

Authors: Gupta, Sanjana, Lee, Robin E. C., Faeder, James R.

Subject Terms: Research Article

Relation: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7082068/; http://www.ncbi.nlm.nih.gov/pubmed/32150537; http://dx.doi.org/10.1371/journal.pcbi.1007669

Availability: https://doi.org/10.1371/journal.pcbi.1007669
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7082068/
http://www.ncbi.nlm.nih.gov/pubmed/32150537

Authors: Keating, Sarah M, Waltemath, Dagmar, König, Matthias, Zhang, Fengkai, Dräger, Andreas, Chaouiya, Claudine, Bergmann, Frank T, Finney, Andrew, Gillespie, Colin S, Helikar, Tomáš, Hoops, Stefan, Malik‐Sheriff, Rahuman S, Moodie, Stuart L, Moraru, Ion I, Myers, Chris J, Naldi, Aurélien, Olivier, Brett G, Sahle, Sven, Schaff, James C, Smith, Lucian P, Swat, Maciej J, Thieffry, Denis, Watanabe, Leandro, Wilkinson, Darren J, Blinov, Michael L, Begley, Kimberly, Faeder, James R, Gómez, Harold F, Hamm, Thomas M, Inagaki, Yuichiro, Liebermeister, Wolfram, Lister, Allyson L, Lucio, Daniel, Mjolsness, Eric, Proctor, Carole J, Raman, Karthik, Rodriguez, Nicolas, Shaffer, Clifford A, Shapiro, Bruce E, Stelling, Joerg, Swainston, Neil, Tanimura, Naoki, Wagner, John, Meier‐Schellersheim, Martin, Sauro, Herbert M, Palsson, Bernhard, Bolouri, Hamid, Kitano, Hiroaki, Funahashi, Akira, Hermjakob, Henning, Doyle, John C, Hucka, Michael, Adams, Richard R, Allen, Nicholas A, Angermann, Bastian R, Antoniotti, Marco, Bader, Gary D, Červený, Jan, Courtot, Mélanie, Cox, Chris D, Pezze, Piero Dalle, Demir, Emek, Denney, William S, Dharuri, Harish, Dorier, Julien, Drasdo, Dirk, Ebrahim, Ali, Eichner, Johannes, Elf, Johan, Endler, Lukas, Evelo, Chris T, Flamm, Christoph, Fleming, Ronan MT, Fröhlich, Martina, Glont, Mihai, Gonçalves, Emanuel, Golebiewski, Martin, Grabski, Hovakim, Gutteridge, Alex, Hachmeister, Damon, Harris, Leonard A, Heavner, Benjamin D, Henkel, Ron, Hlavacek, William S, Hu, Bin, Hyduke, Daniel R, de Jong, Hidde, Juty, Nick, Karp, Peter D, Karr, Jonathan R, Kell, Douglas B, Keller, Roland, Kiselev, Ilya, Klamt, Steffen, Klipp, Edda, Knüpfer, Christian, Kolpakov, Fedor, Krause, Falko, Kutmon, Martina, Laibe, Camille

Superior Title: Molecular Systems Biology, vol 16, iss 8

Subject Terms: Bioengineering, Networking and Information Technology R&D (NITRD), Animals, Humans, Logistic Models, Models, Biological, Software, Systems Biology, computational modeling, file format, interoperability, reproducibility, SBML Level 3 Community members, Biochemistry and Cell Biology, Other Biological Sciences, Bioinformatics

File Description: application/pdf

Relation: qt5ch1p9qq; https://escholarship.org/uc/item/5ch1p9qq

Availability: https://escholarship.org/uc/item/5ch1p9qq

Authors: Wang, Qinsi^Aff16, Miskov-Zivanov, Natasa^Aff17, Liu, Bing^Aff18, Faeder, James R.^Aff18, Lotze, Michael^Aff19, Clarke, Edmund M.^Aff16

Contributors: Hutchison, David, Series editor^Aff1, Kanade, Takeo, Series editor^Aff2, Kittler, Josef, Series editor^Aff3, Kleinberg, Jon M., Series editor^Aff4, Mattern, Friedemann, Series editor^Aff5, Mitchell, John C., Series editor^Aff6, Naor, Moni, Series editor^Aff7, Pandu Rangan, C., Series editor^Aff8, Steffen, Bernhard, Series editor^Aff9, Terzopoulos, Demetri, Series editor^Aff10, Tygar, Doug, Series editor^Aff11, Weikum, Gerhard, Series editor^Aff12, Bartocci, Ezio, editor^Aff13, Lio, Pietro, editor^Aff14, Paoletti, Nicola, editor^Aff15

Superior Title: Computational Methods in Systems Biology : 14th International Conference, CMSB 2016, Cambridge, UK, September 21-23, 2016, Proceedings. 9859:289-305

Authors: Bartol, Thomas M.^Aff1410, Dittrich, Markus^Aff1411, Faeder, James R.^Aff149

Contributors: Jaeger, Dieter, editor^Aff1, Jung, Ranu, editor^Aff2

Superior Title: Encyclopedia of Computational Neuroscience. :1673-1676

Authors: Tapia, Jose-Juan, Saglam, Ali Sinan, Czech, Jacob, Kuczewski, Robert, Bartol, Thomas M., Sejnowski, Terrence J., Faeder, James R.

Subject Terms: Article

Relation: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6580425/; http://www.ncbi.nlm.nih.gov/pubmed/30945248; http://dx.doi.org/10.1007/978-1-4939-9102-0_9

Availability: https://doi.org/10.1007/978-1-4939-9102-0_9
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6580425/
http://www.ncbi.nlm.nih.gov/pubmed/30945248

Authors: Vodovotz, Yoram^Aff3, Azhar, Nabil^Aff4, Miskov-Zivanov, Natasa^Aff4, Buliga, Marius^Aff5, Zamora, Ruben^Aff6, Ermentrout, Bard^Aff7, Constantine, Gregory M.^Aff7, Faeder, James R.^Aff4, Pakpour, Nazzy^Aff8, Luckhart, Shirley^Aff9

Contributors: Vodovotz, Yoram, editor^Aff1, An, Gary, editor^Aff2

Superior Title: Complex Systems and Computational Biology Approaches to Acute Inflammation. :265-279

Degree: Ph.D.
B.S.
M.D.

Authors: Gupta, Sanjana, Hainsworth, Liam, Hogg, Justin S., Lee, Robin E. C., Faeder, James R.

Subject Terms: Article

Relation: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6116909/; http://dx.doi.org/10.1109/PDP2018.2018.00114

Availability: https://doi.org/10.1109/PDP2018.2018.00114
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6116909/

Authors: Tapia, Jose-Juan, Saglam, Ali Sinan, Czech, Jacob, Kuczewski, Robert, Bartol, Thomas M., Sejnowski, Terrence J., Faeder, James R.

Subject Terms: Quantitative Biology - Subcellular Processes

Relation: http://arxiv.org/abs/1810.12244

Availability: http://arxiv.org/abs/1810.12244

Authors: Gupta, Sanjana, Czech, Jacob, Kuczewski, Robert, Bartol, Thomas M., Sejnowski, Terrence J., Lee, Robin E. C., Faeder, James R.

Subject Terms: Quantitative Biology - Quantitative Methods

Relation: http://arxiv.org/abs/1810.00499

Availability: http://arxiv.org/abs/1810.00499

Authors: Singh, Manjulata, Warita, Katsuhiko, Warita, Tomoko, Faeder, James R., Lee, Robin E. C., Sant, Shilpa, Oltvai, Zoltán N.

Superior Title: Scientific Reports ; volume 8, issue 1 ; ISSN 2045-2322

Subject Terms: Multidisciplinary

Availability: https://doi.org/10.1038/s41598-018-27266-8
http://www.nature.com/articles/s41598-018-27266-8.pdf
http://www.nature.com/articles/s41598-018-27266-8

Authors: Gong, Haijun^Aff19, Zuliani, Paolo^Aff19, Komuravelli, Anvesh^Aff19, Faeder, James R.^Aff20, Clarke, Edmund M.^Aff19

Contributors: Hutchison, David, Series editor^Aff1, Kanade, Takeo, Series editor^Aff2, Kittler, Josef, Series editor^Aff3, Kleinberg, Jon M., Series editor^Aff4, Mattern, Friedemann, Series editor^Aff5, Mitchell, John C., Series editor^Aff6, Naor, Moni, Series editor^Aff7, Nierstrasz, Oscar, Series editor^Aff8, Pandu Rangan, C., Series editor^Aff9, Steffen, Bernhard, Series editor^Aff10, Sudan, Madhu, Series editor^Aff11, Terzopoulos, Demetri, Series editor^Aff12, Tygar, Doug, Series editor^Aff13, Vardi, Moshe Y., Series editor^Aff14, Weikum, Gerhard, Series editor^Aff15, Horimoto, Katsuhisa, editor^Aff16, Nakatsui, Masahiko, editor^Aff17, Popov, Nikolaj, editor^Aff18

Superior Title: Algebraic and Numeric Biology : 4th International Conference, ANB 2010, Hagenberg, Austria, July 31- August 2, 2010, Revised Selected Papers. 6479:117-135