Authors: Glazier, James, Vanin, Joel, Mahony, Catherine, Knudsen, Thomas

Subject Terms: Toxicology incl. clinical toxicology

Availability: https://doi.org/10.23645/epacomptox.25678230
https://epa.figshare.com/articles/presentation/Developing_an_in_silico_Virtual_Cornea_for_Predictive_Toxicology/25678230

Authors: Glazier, James, Vanin, Joel, Mahony, Catherine, Knudsen, Thomas

Subject Terms: Toxicology incl. clinical toxicology

Relation: https://dx.doi.org/10.23645/epacomptox.25678230

Availability: https://doi.org/10.23645/epacomptox.25678230.v110.23645/epacomptox.25678230
https://epa.figshare.com/articles/presentation/Developing_an_in_silico_Virtual_Cornea_for_Predictive_Toxicology/25678230/1

Authors: Laubenbacher, Reinhard, Adler, Fred, An, Gary, Castiglione, Filippo, Eubank, Stephen, Fonseca, Luis L., Glazier, James, Helikar, Tomas, Jett-Tilton, Marti, Kirschner, Denise, Macklin, Paul, Mehrad, Borna, Moore, Beth, Pasour, Virginia, Shmulevich, Ilya, Smith, Amber, Voigt, Isabel, Yankeelov, Thomas E., Ziemssen, Tjalf

Subject Terms: Other Quantitative Biology q-bio.OT, FOS Biological sciences

Relation: https://dx.doi.org/10.1038/s41540-024-00345-5

Availability: https://doi.org/10.48550/arxiv.2310.1837410.1038/s41540-024-00345-5
https://arxiv.org/abs/2310.18374

Authors: Toledo-Marin, J. Quetzalcoatl, Glazier, James A., Fox, Geoffrey

Subject Terms: Computer Science - Machine Learning, Condensed Matter - Disordered Systems and Neural Networks

Relation: http://arxiv.org/abs/2302.03786

Availability: http://arxiv.org/abs/2302.03786

Authors: Laubenbacher, Reinhard, Adler, Fred, An, Gary, Castiglione, Filippo, Eubank, Stephen, Fonseca, Luis L, Glazier, James, Helikar, Tomas, Jett-Tilton, Marti, Kirschner, Denise, Macklin, Paul, Mehrad, Borna, Moore, Beth, Pasour, Virginia, Shmulevich, Ilya, Smith, Amber, Voigt, Isabel, Yankeelov, Thomas E, Ziemssen, Tjalf

Superior Title: Articles, Abstracts, and Reports

Subject Terms: washington, isb, machine learning, Artificial Intelligence and Robotics

Relation: https://digitalcommons.providence.org/publications/8627; https://pubmed.ncbi.nlm.nih.gov/38515550

Availability: https://digitalcommons.providence.org/publications/8627
https://pubmed.ncbi.nlm.nih.gov/38515550

Authors: Laubenbacher, Reinhard, Adler, Fred, An, Gary, Castiglione, Filippo, Eubank, Stephen, Fonseca, Luis L, Glazier, James, Helikar, Tomas, Jett-Tilton, Marti, Kirschner, Denise, Macklin, Paul, Mehrad, Borna, Moore, Beth, Pasour, Virginia, Shmulevich, Ilya, Smith, Amber, Voigt, Isabel, Yankeelov, Thomas E, Ziemssen, Tjalf

Superior Title: Articles, Abstracts, and Reports

Subject Terms: washington, isb, machine learning, Humans, Databases, Factual, Precision Medicine, Artificial Intelligence and Robotics, Databases and Information Systems, Medical Biotechnology

Relation: https://digitalcommons.providence.org/publications/8539; https://pubmed.ncbi.nlm.nih.gov/38365857

Availability: https://digitalcommons.providence.org/publications/8539
https://pubmed.ncbi.nlm.nih.gov/38365857

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

Superior Title: Frontiers in Systems Biology ; volume 2 ; ISSN 2674-0702

Availability: https://doi.org/10.3389/fsysb.2022.822606

Authors: Somogyi, Endre T., Coulter, Jeffery, Sun, Fanbo, Sauro, Herbert M., Glazier, James A.

Subject Terms: Quantitative Biology - Subcellular Processes

Relation: http://arxiv.org/abs/2105.02476

Availability: http://arxiv.org/abs/2105.02476

Authors: Toledo-Marín, J. Quetzalcóatl, Fox, Geoffrey, Sluka, James P., Glazier, James A.

Subject Terms: Condensed Matter - Soft Condensed Matter, Condensed Matter - Disordered Systems and Neural Networks, Computer Science - Machine Learning

Relation: http://arxiv.org/abs/2102.05527

Availability: http://arxiv.org/abs/2102.05527

Authors: Toledo-Marin, J. Quetzalcoatl, Glazier, James A.

Subject Terms: Computer Science - Machine Learning, Condensed Matter - Soft Condensed Matter

Relation: http://arxiv.org/abs/2102.05132

Availability: http://arxiv.org/abs/2102.05132

Authors: Toledo-Marín, J. Quetzalcóatl, Fox, Geoffrey, Sluka, James P., Glazier, James A.

Superior Title: Frontiers in Physiology ; volume 12 ; ISSN 1664-042X

Subject Terms: Physiology (medical), Physiology

Availability: https://doi.org/10.3389/fphys.2021.667828

Authors: de Almeida, Rita M. C., Giardini, Guilherme S. Y., Vainstein, Mendeli, Glazier, James A., Thomas, Gilberto L.

Subject Terms: Physics - Biological Physics

Relation: http://arxiv.org/abs/2002.00051

Availability: http://arxiv.org/abs/2002.00051

Authors: Piatkowska, Agnieszka M., Adhikari, Kaustubh, Moverley, Adam A., Turmaine, Mark, Glazier, James A., Plachta, Nicolas, Evans, Susan E., Stern, Claudio D.

File Description: application/pdf

Relation: https://oro.open.ac.uk/87075/1/87075VOR.pdf; Piatkowska, Agnieszka M.; Adhikari, Kaustubh ; Moverley, Adam A.; Turmaine, Mark; Glazier, James A.; Plachta, Nicolas; Evans, Susan E. and Stern, Claudio D. (2023). Sequential changes in cellular properties accompanying amniote somite formation. Journal of Anatomy (Early Access).

Availability: https://doi.org/10.1111/joa.13791
https://oro.open.ac.uk/87075/
https://oro.open.ac.uk/87075/1/87075VOR.pdf

Authors: Rockne, Russell C, Hawkins-Daarud, Andrea, Swanson, Kristin R, Sluka, James P, Glazier, James A, Macklin, Paul, Hormuth, David A, Jarrett, Angela M, Lima, Ernesto ABF, Oden, J Tinsley, Biros, George, Yankeelov, Thomas E, Curtius, Kit, Bakir, Ibrahim Al, Wodarz, Dominik, Komarova, Natalia, Aparicio, Luis, Bordyuh, Mykola, Rabadan, Raul, Finley, Stacey D, Enderling, Heiko, Caudell, Jimmy, Moros, Eduardo G, Anderson, Alexander RA, Gatenby, Robert A, Kaznatcheev, Artem, Jeavons, Peter, Krishnan, Nikhil, Pelesko, Julia, Wadhwa, Raoul R, Yoon, Nara, Nichol, Daniel, Marusyk, Andriy, Hinczewski, Michael, Scott, Jacob G

Superior Title: Physical Biology, vol 16, iss 4

Subject Terms: Cancer, Bioengineering, Computational Biology, Computer Simulation, Humans, Mathematics, Medical Oncology, Models, Biological, Theoretical, Neoplasms, Single-Cell Analysis, Systems Biology, mathematical oncology, mathematical modeling, modeling and simulation, computational oncology, Physical Sciences, Biological Sciences, Engineering, Biophysics

File Description: application/pdf

Relation: qt6rt6c6fh; https://escholarship.org/uc/item/6rt6c6fh

Availability: https://escholarship.org/uc/item/6rt6c6fh

Authors: Fox, Geoffrey, Glazier, James A., Kadupitiya, JCS, Jadhao, Vikram, Kim, Minje, Qiu, Judy, Sluka, James P., Somogyi, Endre, Marathe, Madhav, Adiga, Abhijin, Chen, Jiangzhuo, Beckstein, Oliver, Jha, Shantenu

Subject Terms: Computer Science - Distributed, Parallel, and Cluster Computing, Physics - Computational Physics

Relation: http://arxiv.org/abs/1902.10810

Availability: http://arxiv.org/abs/1902.10810

Authors: Rockne, Russell C, Hawkins-Daarud, Andrea, Swanson, Kristin R, Sluka, James P, Glazier, James A, Macklin, Paul, Hormuth, David A, Jarrett, Angela M, Lima, Ernesto A B F, Tinsley Oden, J, Biros, George, Yankeelov, Thomas E, Curtius, Kit, Al Bakir, Ibrahim, Wodarz, Dominik, Komarova, Natalia, Aparicio, Luis, Bordyuh, Mykola, Rabadan, Raul, Finley, Stacey D, Enderling, Heiko, Caudell, Jimmy, Moros, Eduardo G, Anderson, Alexander R A, Gatenby, Robert A, Kaznatcheev, Artem, Jeavons, Peter, Krishnan, Nikhil, Pelesko, Julia, Wadhwa, Raoul R, Yoon, Nara, Nichol, Daniel, Marusyk, Andriy, Hinczewski, Michael, Scott, Jacob G

Contributors: NIH NCI

Superior Title: Physical Biology ; volume 16, issue 4, page 041005 ; ISSN 1478-3967 1478-3975

Availability: https://doi.org/10.1088/1478-3975/ab1a09

Authors: Thomas, Gilberto L., Fortuna, Ismael, Perrone, Gabriel C., Glazier, James A., Belmonte, Julio M., de Almeida, Rita M. C.

Subject Terms: Physics - Biological Physics

Relation: http://arxiv.org/abs/1810.03597

Availability: http://arxiv.org/abs/1810.03597

Authors: Somogyi, Endre, Sluka, James P., Glazier, James A.

Contributors: National Institutes of Health, Falk Medical Research Trust Catalyst Program, Indiana University Cooperative Research

Superior Title: Proceedings of the ACM/IEEE 19th International Conference on Model Driven Engineering Languages and Systems

Availability: https://doi.org/10.1145/2976767.2976790

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

Subject Terms: Q Science (General), RA0421 Public health. Hygiene. Preventive Medicine

File Description: application/pdf

Relation: https://wrap.warwick.ac.uk/162582/7/WRAP-Model-integration-computational-biology-reproducibility-credibility-utility-2022.pdf; https://wrap.warwick.ac.uk/162582/1/WRAP-Model-integration-computational-biology-reproducibility-credibility-utility-2022.pdf; Karr, Jonathan, Sheriff, Rahuman S. Malik, Osborne, James, Gonzalez-Parra, Gilberton, Forgoston, Eric, Bowness, Ruth, Liu, Yaling, Thompson, Robin N., Garira, Winston , Barhak, Jacob, Rice, John, Torres, Marcella, Dobrovolny, Hana Maria, Tang, Tingting, Waites, William , Glazier, James A., Faeder, James and Kulesza, Alexander (2022) Model integration in computational biology : the role of reproducibility, credibility and utility. Frontiers in Systems Biology, 2 . 822606. doi:10.3389/fsysb.2022.822606 ISSN 2674-0702.

Availability: https://doi.org/10.3389/fsysb.2022.822606
https://wrap.warwick.ac.uk/162582/
https://wrap.warwick.ac.uk/162582/7/WRAP-Model-integration-computational-biology-reproducibility-credibility-utility-2022.pdf
https://wrap.warwick.ac.uk/162582/1/WRAP-Model-integration-computational-biology-reproducibility-credibility-utility-2022.pdf

Authors: Niarakis, Anna, Waltemath, Dagmar, Glazier, James, Schreiber, Falk, Keating, Sarah M., Nickerson, David, Chaouiya, Claudine, Siegel, Anne, Noël, Vincent, Hermjakob, Henning, Helikar, Tomáš, Soliman, Sylvain, Calzone, Laurence

Superior Title: Biochemistry -- Faculty Publications

Subject Terms: computational modelling, model annotations, reproducibility, systems biology, community standards, Biochemistry, Biophysics, and Structural Biology, Biotechnology, Life Sciences, Other Biochemistry

File Description: application/pdf

Relation: https://digitalcommons.unl.edu/biochemfacpub/549; https://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1550&context=biochemfacpub

Availability: https://digitalcommons.unl.edu/biochemfacpub/549
https://digitalcommons.unl.edu/cgi/viewcontent.cgi?article=1550&context=biochemfacpub