Faculty Directory › UConn Health

James C. Schaff, BS

Associate Professor, Department of Cell Biology
Center for Cell Analysis and Modeling


Academic Office Location: Cell Biology UConn Health 263 Farmington Avenue Farmington, CT 06030-6406
Phone:	860-679-2060
Fax:	860-679-1039
Email:	schaff@uchc.edu
Website(s):	Virtual Cell Project

Research
Publications

My research interests center on the development of abstractions, formalisms and numerical methods in biological modeling and simulatoin. I am the founding developer of the Virtual Cell project and currently lead our software development group.

We are also developing a suite of tools for the quantitative analysis of microscopy experiments which transparently leverage VCell technologies. The Virtual FRAP (VFRAP) tools is the first of these application, and facilitates the analysis of FRAP (Fluorescence Redistribution After Photobleaching) experiments.

I have been involved in the development of SBML from its inception and now serve as one of the SBML editors. Currently I am working toward the development of an SBML Level 3 extension for spatial modeling.

Journal Articles

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 Nucleic acids research 2022 May;
Compartmental and Spatial Rule-Based Modeling with Virtual Cell.
Blinov, Michael L; Schaff, James C; Vasilescu, Dan; Moraru, Ion I; Bloom, Judy E; Loew, Leslie M Biophysical journal 2017 Oct;113(7):1365-1372
Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology.
Schaff, James C; Gao, Fei; Li, Ye; Novak, Igor L; Slepchenko, Boris M PLoS computational biology 2016 Dec;12(12):e1005236
Rule-based modeling with Virtual Cell.
Schaff, James C; Vasilescu, Dan; Moraru, Ion I; Loew, Leslie M; Blinov, Michael L Bioinformatics (Oxford, England) 2016 Sep;32(18):2880-2
WormGUIDES: an interactive single cell developmental atlas and tool for collaborative multidimensional data exploration.
Santella, Anthony; Catena, Raúl; Kovacevic, Ismar; Shah, Pavak; Yu, Zidong; Marquina-Solis, Javier; Kumar, Abhishek; Wu, Yicong; Schaff, James; Colón-Ramos, Daniel; Shroff, Hari; Mohler, William A; Bao, Zhirong BMC bioinformatics 2015 Jan;16189
Pathway Commons at virtual cell: use of pathway data for mathematical modeling.
Blinov, Michael L; Schaff, James C; Ruebenacker, Oliver; Wei, Xintao; Vasilescu, Dan; Gao, Fei; Morgan, Frank; Ye, Li; Lakshminarayana, Anuradha; Moraru, Ion I; Loew, Leslie M Bioinformatics (Oxford, England) 2013 Nov;30(2):292-4
Spatial modeling of cell signaling networks.
Cowan, Ann E; Moraru, Ion I; Schaff, James C; Slepchenko, Boris M; Loew, Leslie M Methods in cell biology 2012 Jan;110195-221
Virtual Cell: computational tools for modeling in cell biology.
Resasco, Diana C; Gao, Fei; Morgan, Frank; Novak, Igor L; Schaff, James C; Slepchenko, Boris M Wiley interdisciplinary reviews. Systems biology and medicine 2012 Jan;4(2):129-40
Virtual NEURON: a strategy for merged biochemical and electrophysiological modeling.
Brown, Sherry-Ann; Moraru, Ion I; Schaff, James C; Loew, Leslie M Journal of computational neuroscience 2011 Oct;31(2):385-400
Modeling without borders: Creating and annotating Vcell models using the web.
Blinov M.L., Ruebenacker O., Schaff J.C., Moraru I.I. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2010 Jan;6053 LNBI3-17
Integrating BioPAX pathway knowledge with SBML models.
Ruebenacker, O; Moraru, I I; Schaff, J C; Blinov, M L IET systems biology 2009 Sep;3(5):317-28
Using the virtual cell simulation environment for extracting quantitative parameters from live cell fluorescence imaging data
Cowan A.E., Ye L., Morgan F.R., Koppel D.E., Slepchenko B.M., Loew L.M., Schaff J. Microscopy and Microanalysis 2009 Jan;15(SUPPL. 2):1522-1523
Virtual Cell modelling and simulation software environment.
Moraru, I I; Schaff, J C; Slepchenko, B M; Blinov, M L; Morgan, F; Lakshminarayana, A; Gao, F; Li, Y; Loew, L M IET systems biology 2008 Sep;2(5):352-62
Cell shape and negative links in regulatory motifs together control spatial information flow in signaling networks.
Neves, Susana R; Tsokas, Panayiotis; Sarkar, Anamika; Grace, Elizabeth A; Rangamani, Padmini; Taubenfeld, Stephen M; Alberini, Cristina M; Schaff, James C; Blitzer, Robert D; Moraru, Ion I; Iyengar, Ravi Cell 2008 May;133(4):666-80
Diffusion on a Curved Surface Coupled to Diffusion in the Volume: Application to Cell Biology.
Novak, Igor L; Gao, Fei; Choi, Yung-Sze; Resasco, Diana; Schaff, James C; Slepchenko, Boris M Journal of computational physics 2007 Oct;226(2):1271-1290
The Virtual Cell: a software environment for computational cell biology.
Loew, L M; Schaff, J C Trends in biotechnology 2001 Oct;19(10):401-6
An image-based model of calcium waves in differentiated neuroblastoma cells.
Fink, C C; Slepchenko, B; Moraru, I I; Watras, J; Schaff, J C; Loew, L M Biophysical journal 2000 Jul;79(1):163-83
Numerical Approach to Fast Reactions in Reaction-Diffusion Systems: Application to Buffered Calcium Waves in Bistable Models
Slepchenko B.M., Schaff J.C., Choi Y.S. Journal of Computational Physics 2000 Jan;162(1):186-218
Morphological control of inositol-1,4,5-trisphosphate-dependent signals.
Fink, C C; Slepchenko, B; Moraru, I I; Schaff, J; Watras, J; Loew, L M The Journal of cell biology 1999 Nov;147(5):929-36
Distributed architecture for a general cellular modeling and simulation framework
Schaff James C. Proceedings of the IEEE Symposium on Computer-Based Medical Systems 1999 Jan;303-306
Electrodiffusion of ions inside living cells
Choi Y.S., Resasco D., Schaff J., Slepchenko B. IMA Journal of Applied Mathematics (Institute of Mathematics and Its Applications) 1999 Jan;62(3):207-226
The virtual cell.
Schaff, J; Loew, L M Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1999 Jan;228-39
A general computational framework for modeling cellular structure and function.
Schaff, J; Fink, C C; Slepchenko, B; Carson, J H; Loew, L M Biophysical journal 1997 Sep;73(3):1135-46

Conference Papers

Kinetic Modeling using BioPAX ontology
Ruebenacker O., Moraru I.I., Schaff J.C., Blinov M.L. Proceedings - 2007 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2007 2007 Jan;339-346
Think simulation - Think experiment: The virtual cell paradigm
Moraru I.I., Schaff J.C., Loew L.M. Proceedings - Winter Simulation Conference 2006 Jan;1713-1719
The virtual cell: an integrated modeling environment for experimental and computational cell biology.
Moraru, Ion I; Schaff, James C; Slepchenko, Boris M; Loew, Leslie M Annals of the New York Academy of Sciences 2002 Oct;971595-6

Reviews

Quantitative cell biology with the Virtual Cell.
Slepchenko, Boris M; Schaff, James C; Macara, Ian; Loew, Leslie M Trends in cell biology 2003 Nov;13(11):570-6
Computational cell biology: spatiotemporal simulation of cellular events.
Slepchenko, Boris M; Schaff, James C; Carson, John H; Loew, Leslie M Annual review of biophysics and biomolecular structure 2002 Jan;31423-41
Analysis of nonlinear dynamics on arbitrary geometries with the Virtual Cell.
Schaff, James C.; Slepchenko, Boris M.; Choi, Yung-Sze; Wagner, John; Resasco, Diana; Loew, Leslie M. Chaos (Woodbury, N.Y.) 2001 Mar;11(1):115-131