jim-rathmans-group-modeling-complex-chemical-phenomena
Modeling Complex Chemical Phenomena
Chemical informatics, machine learning, and decision theory approaches to understanding chemical toxicity

About Us
Designing processes and products that have minimal negative impact on health and environment is essential in providing for the fast and economical development of pharmaceuticals, foods and food additives, consumer products, cosmetics, and specialty chemicals.
Our group devises computational methods to predict chemical toxicity and rapidly and cheaply screen massive amounts of compounds without the need for animal testing.
Professor Rathman is recognized for his exceptional teaching ability. Students emerge from his courses being challenged and taking away valuable skills and knowledge while gaining a good work ethic. He uses active learning techniques and assigns practical work to complement the theory behind chemical and biomolecular engineering, re-energizing students. Some students have stated that the problems he developed in his kinetics course were especially useful for their challenge and multifaceted learning goals.
Dr. Rathman's teaching has been recognized with the following awards:
- The Ohio State University Alumni Award for Distinguished Teaching (the highest teaching honor at Ohio State; 1996)
- Inducted into The Ohio State University Academy of Teaching (1996)
- The Ohio State University College of Engineering Charles E. MacQuigg Outstanding Teaching Award. This is student-nominated award which Dr. Rathman won in 1995, 2001, 2005 and 2011.

Professor Rathman is an award-winning teacher who uses computational methods to predict chemical toxicity.
Before coming to Ohio State in 1991, he spent seven years in industrial R&D with Conoco Inc. and The Clorox Company. His current research efforts focus on computational toxicology, quantitative structure-activity relationship (QSAR) modeling, statistical data analysis, and computational risk assessment of complex chemical systems.
KEY DISTINCTIONS
- Co-founder, Altamira, LLC
NATIONAL AND INTERNATIONAL
Japan Research Institute of Material Technology:
- Lectureship Award, 2002
- Member, ACS and ASEE
REGIONAL
The Ohio State University:
- President and Provost’s Award for Distinguished Faculty Service, The Ohio State University, 2016
- Alumni Award for Distinguished Teaching, 1996. (Ohio State's highest teaching honor.)
- College of Engineering Charles E. MacQuigg Outstanding Teaching Award, 1995, 2001, 2005, 2011
- College of Engineering Lumley Award for Excellence in Research, 1997
Research
The ability to predict chemical toxicity is important for many reasons. Designing processes and products that have minimal negative impact on health and environment is essential in the development of pharmaceuticals, foods and food additives, consumer products, cosmetics, and specialty chemicals. It is simply not possible to experimentally study every new or proposed chemical compound to determine its toxicity potential. Also, recent initiatives and regulations that limit the use of animal testing for certain types of products (e.g., cosmetics) have motivated the development of alternative ways to evaluate toxicity, especially in vitro experimental approaches (as replacements for in vivo assays) and in silico computational approaches.
We are developing computational modeling methods to meet this need. We are attempting to model extremely complex phenomena; for example, will a new drug candidate react with DNA to cause mutations? Will a proposed new cosmetics ingredient possibly be a skin sensitizer, eliciting an allergic response in some people? To answer such questions we combine cheminformatics methods with advanced computational modeling techniques, generally referred to as “machine learning”, to build predictive models. Our models are trained, tested and validated using the extensive and diverse databases available that summarize chemical property and biological endpoint data for many thousands of molecules for which experimental data from some of these endpoints are available.
In 2018 Rathman deployed the Dempster-Shafer theory for combining in silico evidence and estimating uncertainty in chemical
risk assessment.
Computational approaches for evaluating potential toxicity concerns in the safety and risk assessment of chemicals can be more cost-effective.


Publications
-
Chemical Research in Toxicology, 2021, 34, 189-216. https://doi.org/10.1021/acs.chemrestox.0c00264
A.M. Richard, R. Huang, S. Waidyanatha, P. Shinn, B. J. Collins, I. Thillainadarajah, C. J. Grulke, A.J. Williams, R.R. Lougee, R.S. Judson, K.A. Houck, M. Shobair, C. Yang, J.F. Rathman, A. Yasgar, S.C. Fitzpatrick, A. Simeonov, R.S. Thomas, K.M. Crofton, R.S. Paules, J.R. Bucher, C.P. Austin, R.J. Kavok, R.R. Tice.
“The Tox21 10K Compound Library: Collaborative Chemistry Advancing Toxicology” -
Chemical Research in Toxicology, 2021, 34, 601-615. https://doi.org/10.1021/acs.chemrestox.0c00423
J.F. Rathman, C. Yang, J. V. Ribeiro, A. Mostrag, S. Thakkar, W. Tong, B. Hobocienski, O. Sacher, T. Magdziarz, B. Bienfait
“Development of a Battery of In Silico Prediction Tools for Drug-Induced Liver Injury from the Vantage Point of Translational Safety Assessment” -
Chemical Research in Toxicology, 2021, 34, 616-633. https://doi.org/10.1021/acs.chemrestox.0c00429
C. Yang, J.F. Rathman, T. Magdziarz, A. Mostrag, S. Kulkarni, T.S. Barton-Maclaren
“Do Similar Structures Have Similar No Observed Adverse Effect Level (NOAEL) Values? Exploring Chemoinformatics Approaches for Estimating NOAEL Bounds and Uncertainties” -
Chemical Research in Toxicology, 2021, 34, 641-655. https://doi.org/10.1021/acs.chemrestox.0c00465
J.W. Firman, C. B. Pestana, J.F. Rathman, M. Vinken, C. Yang, M.T.D. Cronin
“A Robust, Mechanistically Based In Silico Structural Profiler for Hepatic Cholestasis” -
Food and Chemical Toxicology, 2020, 143, 111561. https://doi.org/10.1016/j.fct.2020.111561
C. Yang, M. Cheeseman, J.F. Rathman, A. Mostrag, N. Skoulis, V. Vitcheva, S. Goldberg
“A new paradigm in threshold of toxicological concern based on chemoinformatics analysis of a highly curated database enriched with antimicrobials” -
Regulatory Toxicology and Pharmacology, 2020, 114, 104658. https://doi.org/10.1016/j.yrtph.2020.104658
R. Benigni, R. Serafimova, J.M.P. Morte, C.L. Battistelli, C. Bossa, A. Giuliani, E. Fioravanzo, A. Bassan, M.F. Gatnik, J. Rathman, C. Yang, A. Mostrag-Szlichtyng, O. Sacher, O. Tscheremenskaia
“Evaluation of the applicability of existing (Q)SAR models for predicting the genotoxicity of pesticides and similarity analysis related with genotoxicity of pesticides for facilitating of grouping and read across: An EFSA funded project” -
Mutagenesis, 34(1), 2019, 3–16. https://doi.org/10.1093/mutage/gey031
M. Honma, A. Kitazawa, A. Cayley, R. Williams, C. Barber, T. Hanser, R. Saiakhov, S. Chakravarti, G. Myatt, K. Cross, E. Benfenati, G. Raitano, O. Mekenyan, P. Petkov, C. Bossa, R. Benigni, C. Battistelli, A. Giuliani, O. Tcheremenskaia, C. DeMeo, U. Norinder, H. Koga, C. Jose, N. Jeliazkova, N. Kochev, V. Paskaleva, C. Yang, P. Daga, R. Clark, J. Rathman
“Improvement of quantitative structure–activity relationship (QSAR) tools for predicting Ames mutagenicity: outcomes of the Ames/QSAR International Challenge Project“ -
European Food Safety Authority (EFSA) Supporting Publications, 16(3), 2019.
R. Benigni, C. Battistelli, C. Bossa, A. Giuliani, E. Fioravanzo, A. Bassan, M. Fuart Gatnik, J. Rathman, C. Yang, O. Tcheremenskaia
“Evaluation of the applicability of existing (Q)SAR models for predicting the genotoxicity of pesticides and similarity analysis related with genotoxicity of pesticides for facilitating of grouping and read across” -
Computational Toxicology 2018, 6, 16-31.
Rathman J.F., Yang C., Zhou H.
“Dempster-Shafer theory for combining in silico evidence and estimating uncertainty in chemical risk assessment.” -
Applied Chemoinformatics, 2018 T Engel and J Gasteiger, Ed. Wiley.
Rathman, J.F., Yang, C., Tarkhov, A., Sacher, O., Kleinoeder, T., Marusczyk, J., Mehta, D., Schwab, C., Bienfait, B.,
Chapter 8: “Role of chemoinformatics in regulatory science” -
Ann M. Richard, A.M., Judson, R.S., Houck, K.A., Grulke, C.M., Volarath, P., Thillainadarajah, I., Yang, C., Rathman, J.F., Martin, M.T., Wambaugh, J.F., Knudsen, T.B., Kancherla, J., Mansouri, K., Patlewicz, G., Williams, A.J., Little, S.B., Crofton, K.M., Thomas, R.S. “ToxCast Chemical Landscape: Paving the Road to 21st Century Toxicology,” Chemical Research in Toxicology, 29 (8), 1225-1251 (2016).
-
Yang, C, Tarkhov, A, Marusczyk, J, Bienfait, B., Gasteiger, J, Kleinoeder, T, Magdziarz, T, Sacher, O, Schwab, C, Schwoebel, J, Terfloth, L, Arvidon, K, Richard, A, Worth, A, Rathman, “New publicly available chemical query language, CSRML, to support chemotype representations for application to data mining and modeling,” J. J. Chem Inf Modeling 2015, 55(3), 510-528.
-
A. Cherkasov, E. N. Muratov, D. Fourches, A. Varnek, I. I. Baskin, M. Cronin, J. Dearden, P. Gramatica, Y. C. Martin, R. Todeschini, V. Consonni, V. E. Kuz’min, R. Cramer, R. Benigni, C. Yang, J. Rathman, L. Terfloth, J. Gasteiger, A. Richard, and A. Tropsha, “SAR Modeling: Where Have You Been? Where Are You Going To?” J. Medicinal Chemistry, 2013 ASAP.
-
Heath D.E., Hoy M., Rathman J.F., Rohdieck S., “Teaching Chemical Engineers about Teaching,” Chemical Engineering Education, 2013, 47(1), 38-47.
-
Leist M., Lidbury B.A., Yang C., Hayden P.J., Kelm J.M., Ringeissen S., Detroyer A., Meunier J.R., Rathman J.F., Jackson G.R., Stolper G., Hasiwa N., “Novel technologies and an overall strategy to allow hazard assessment and risk prediction of chemicals, cosmetics, and drugs with animal-free methods,” ALTEX, 2012, 29(4), 373-88.
-
Triplett, M.D., Rathman, J.F., “Optimization of b-carotene loaded solid lipid nanoparticles preparation using a high shear homogenization technique,” J. Nanoparticle Research, 2009, 11(3), 601-614.
-
Hu, W., Rathman, J.F., Chalmers, J.J., “An investigationof small-molecule surfactants to potentially replace Pluronic F-68 for reducing bubble-associated cell damage,” Biotechnology and Bioengineering, 2008, 101(1), 119-127.
-
Yang, C., Hasselgren, C.H., Boyer, S., Arvidson, K., Aveston, S., Dierkes, P., Benigni, R., Benz, R. D., Contrera, J.,Kruhlak, N. L., Matthews, E. J., Han, X., Jaworska, J., Kemper, R. A., Rathman, J. F., Richard, A. M., “Understanding Genetic Toxicity Through Data Mining: The Process of Building Knowledge by Integrating Multiple Genetic Toxicity Databases,” Toxicology Mechanisms and Methods, 2008, 18(2-3), 277-295.
-
Yang, L., Sostaric, J.Z., Rathman, J.F., and Weavers, L.K., “Effect of Ultrasound Frequency on Pulsed Sonolytic Degradation of Octylbenzene Sulfonic Acid,”J. Phys. Chem. B, 2008, 112(3) 852-858.
-
Goracci, L., Germani, R., Rathman, J.F., and Savelli, G., “Anomalous Behavior of Amine Oxide Surfactants at the Air/Water Interface,” Langmuir, 2007, 23(21), 10525-10532.
-
Yang, L.; Rathman, J.F.; Weavers, L.K., “Sonochemical degradataion of alkylbenzene sulfonate surfactants in aqueous mixtures,” Journal of Physical Chemistry B, 2006, 110(37), 18385-18391.
-
Yang, L.; Sostaric, J.Z.; Rathman, J.F.; Kuppusamy, P.; Weavers, L.K., ”Effects of pulsed ultrasound on the adsorption of n-alkyl anionic surfactants at the gas/solution interface of cavitation bubbles,” Journal of Physical Chemistry B, 2007, 111(6), 1361-1367.
-
Sun, P.; Jose, D.A.; Shukla, A.D.; Shukla, J.J.; Das, A.; Rathman, J.F., “A comparative Langmuir-Blodgett study on a set of covalently linked porphyrin-based amphiphiles: A detailed atomic force microscopy study,”Langmuir, 2005, 21(8), 3413-3423.
-
Rathman, J.F.; Sun, P., ”Biocomposite films synthesized at a fluid/fluid interface,” Faraday Discussions, 2005, 129, 193-203.
-
Yang, Limei; Rathman, James F.; Weavers, Linda K., ”Degradation of alkylbenzene sulfonate surfactants by pulsed ultrasound,” Journal of Physical Chemistry B, 2005, 109(33), 16203-16209.
-
Weavers, L.K.; Pee, G.Y.; Frim, J.A.; Yang, L.; Rathman, J.F., “Ultrasonic destruction of surfactants: Application to industrial wastewaters,” Water Environmental Research, 2005, 77(3), 259-265.
-
Yang, C.; Cross, K.; Myatt, G.J., Blower, P.E., Rathman, J.F., ”Building predictive models for protein tyrosine phosphatase 1B inhibitors based on discriminating structural features by reassembling medicinal chemistry building blocks,”Journal of Medicinal Chemistry, 2004, 47(24), 5984-5994.
-
Pee, Gim-Yang; Rathman, James F.; Weavers, Linda K., ”Effects of Surface Active Properties on the Cavitational Degradation of Surfactant Contaminants,” Industrial & Engineering Chemistry Research, 2004, 43(17), 5049-5056.
-
Lee, Y.S.; Rathman, J.F., ”Molecular Self-Assembly” (invited submission) accepted for publication in the Encyclopedia of Chemical Processing (July 2003).
-
Lee, Y.S.; Archer, J.R.; Rathman, J.F., ”Mesostructured silica films with crystalline domains and structural features on multiple length scales,” in “Studies in Surface Science and Catalysis,” 2003, Vol. 146 (Nanotechnology in Mesostructured Materials), 29-32.
-
Frim, J.A.; Rathman, J.F.; Weavers, L.K., ”Sonochemical destruction of free and metal-binding ethylenediaminetetraacetic acid,” Water Research, 2003, 37(13), 3155-63.
-
Sakai, H.; Yokoyama, W.; Rathman, J.F.; Abe, M., ”Nanoscale patterning of adsorbed amphiphile films with an atomic force microscope probe,” Langmuir, 2003, 19(7), 2845-2850.
-
Imura, T.; Otake, K.; Hashimoto, S.; Gotoh, T.; Yuasa, M.; Yokoyama, S.; Sakai, H.; Rathman, J.F.; Abe, M., “Preparation and physicochemical properties of various soybean lecithin liposomes using supercritical reverse phase evaporation method,” Colloids and Surfaces B: Biointerfaces, 2002, 27(2-3), 133-140.
-
Yang, C.; Bakshi, B.R., Rathman, J.F.; Blower, P.E., “Multiscale and Bayesian Approaches to Data Analysis in Genomics High Throughput Screening” (Invited submission), Current Opinion in Drug Discovery and Development, 2002, 5(3), 428-438.
-
Wang, Z.F.; Haung, Y.L.; Rathman, J.F., Yang, S.T., “Lecithin Enhanced Biotransformation of Cholesterol to Androsta-1,4-diene-3,17-dione and Androsta-4-ene-3,17-dione,” J. Chem. Technol. Biotechnol, 2002, 77(12), 1349-1357.
-
Lee, Y.S.; Rathman, J.F., "Synthesis of Mesoporous Films at Fluid/Fluid Interfaces" in "Reactions and Synthesis in Surfactant Solutions,” Texter, J., Ed.; Surfactant Science Series, Marcel Dekker, Inc., 2001, 779-96.
-
Battal, T.; Rathman, J.F., “Micellar Catalysis in Two-Phase Systems” in "Reactions and Synthesis in Surfactant Solutions", Texter, J., Ed.; Surfactant Science Series, Marcel Dekker, Inc., 2001, 359-72.
-
Lee,Y.S.; Surjadi, D., Rathman, J.F., "Compositional Effects and Hydrothermal Reorganization of Mesoporous Silicates Synthesized in Surfactant Solutions," Langmuir, 2000, 16(1), 195-201.
-
Bauer, T., Hancock, L., Rathman, J., Chalmers, J.J., "Cell-Microcarrier adhesion to Gas-Liquid Interfaces and Foam," Biotechnology Progress, 2000, 16, 125-132.
-
Clogston, J.; Rathman, J.F.; Tomasko, D.; Walker, H.; Caffrey, M., “Phase behavior of a monoacylglycerol (Myverol 19-99K)/water system,” Chemistry and Physics of Lipids 2000, 107, 191-220.
-
Lee, Y.S.; Surjadi, D.; Rathman, J.F., “Effects of Aluminate and Silicate Counterions on the Structure of Quaternary Ammonium Surfactant Aggregates” Langmuir 1997.
-
Siswanto, C.; Schuss, O.; Battal, T.; Rathman, J.F., “Alkylation of Phenol by Micellar Phase-Transfer Catalysis. 1. Single-Phase Systems,” Langmuir, 1997.
-
Siswanto, C.; Rathman, J.F., “Selective N-Alkylation of Aniline by Micellar Catalysis,” J. Colloid Interface Sci., 1997.
-
Battal, T.; Siswanto, C.; Rathman, J.F., “Alkylation of Phenol by Micellar Phase-Transfer Catalysis. 2. Two-Phase Emulsion Systems,” Langmuir, 1997.
-
Yang, C.; Rathman, J.F., “Relationship between Solution Structure and Adsorption Characteristics of Polyethyleneteraphthalate/Polyoxyethyleneteraphthalate (PET/POET) Polymeric Surfactants,” Polymer 1996, 37(20), 4621.
-
Rathman, J.F., “Micellar Catalysis,” Current Opinion in Colloid & Interface Science 1996, 1(4),514.
-
Kust, P.R.; Rathman, J.F., "Synthesis of Surfactants by Micellar Autocatalysis: N,N-Dimethyldocecylamine N-oxide," Langmuir 1995, 11, 3007.
-
Chattopadhyay, M.; Rathman, J.F.; Chalmers, J.J., “Thermodynamic Approach of Cell Adhesion to Air-Medium Interfaces,” Biotechnology and Bioengineering 1995, 48, 649.
-
Chattopadhyay, M.; Rathman, J.F.; Chalmers, J.J., “The Protective Effect of Specific Medium Additives with Respect to Bubble Rupture,” Biotechnology and Bioengineering, 1995, 45, 473.
-
Fan, L.-S.; Rathman, J.F.; Ghosh-Dastidar, A.; Weimer, A.W., Kimura, S., “Particle Technology: The Potential of Reaction Engineering,” Chemical Engineering Progress 1994, 90, 55.
-
Weers, J.G.; Rathman, J.F.; Axe, F.U.; Crichlow, C.A.; Foland, L.D.; Scheuing, D.R.; Zielske, A.G., "Effect of the Intramolecular Charge Separation Distance on the Solutions Properties of Betaines and Sulfobetaines," Langmuir 1991, 7, 854.
-
Weers, J.G.; Rathman J.F.; Scheuing, D.R., "Structure/Performance Relationships in Long Chain Dimethylamine Oxide/Sodium Dodecylsulfate Surfactant Mixtures," Colloid & Polymer Sci., 1990, 268, 832.
-
Rathman, J.F.; Christian, S.D., "Determination of Surfactant Activities in Micellar Solutions of Dimethyldodecylamine Oxide,"Langmuir 1990, 6, 391.
-
Rathman, J.F.; Scamehorn, J.F., "Determination of the Heat of Micelle Formation in Binary Surfactant Mixtures by Isoperibol Calorimetry," Langmuir 1988, 4, 474.
-
Rathman, J.F.; Scamehorn, J.F., "Counterion Binding on Mixed Micelles: Effect of Surfactant Structure," Langmuir 1987, 3, 372.
-
Nguyen, C.M.; Rathman, J.F.; Scamehorn, J.F., "Thermodynamics of Mixed Micelle Formation," J. Colloid Interface Sci. 1986, 112, 438.
-
Rathman, J.F.; Scamehorn, J.F., "Electrostatic Model to Describe Mixed Ionic/Nonionic Micellar Nonidealities," Langmuir 1986, 2, 354.
-
Rathman, J.F.; Scamehorn, J.F., "Counterion Binding on Mixed Micelles," J. Phys. Chem. 1984, 88, 5807.