Roger Perkins

 

I am The Virtual Fossil Museum's primary webmaster. Vocationally, I am currently a computational biologist; here I list and store my publications so as not to lose them on my hard drive. My avocational interests include evolutionary biology (especially Precambrian and Cambrian), paleontology, and science education advocacy. I also contribute to the Palaeos and Western Trilobite Association websites.

 

Publications as a bioinformaticist / computational biologist:

  • Minjun Chen, Leming Shi, Reagan Kelly, Roger Perkins, Hong Fang, Weida Tong, Selecting a single model or combining multiple models for microarray-based classifier development? – A comparative analysis based on large and diverse datasets generated from the MAQC-II project, BMC Bioinformatics, 12(Suppl 10):S2 2011. [Pubmed, HTML, PDF]
  • Huixiao Hong, Svetoslav Slavov, Weigong Ge, Feng Qian, Zhenqiang Su, Hong Fang, Yiyu Cheng, Roger Perkins, Leming Shi, Weida Tong, Mold2 molecular descriptors for QSAR, Book: Statistical Analysis of Molecular Descriptors, Wiley & Sons, 2011.
  • Zhenqiang Su, Baitang Ning, Hong Fang, Huixiao Hong, Roger Perkins, Weida Tong and Leming Shi, Next-generation sequencing and its applications in molecular diagnostics, Expert Review of Molecular Diagnostics, Volume 11, Number 3, 2011. [HTML]
  • Zhenqiang Su, Zhiguang Li, Tao Chen, Quan-zhen Li, Hong Fan, Don Ding, Weigong Ge, Baitang Ning, Huixiao Hong, Roger Perkins, Weida Tong and Leming Shi, Comparing Next-Generation Sequencing and Microarray Technologies in a Toxicological Study of the Effects of Aristolochic Acid on Rat Kidneys, Chem. Res. Toxicol., 24 (9), pp 1486–1493 2011. [Pubmed, HTML, PDF]
  • Zhenqiang Su, Hong Fang, Weida Tong, Huixiao Hong, Roger Perkins, and Leming Shi, Approaches and Practical Considerations for the Analysis of Toxicogenomics Data, Book: Application of Toxicogenomics in Safety Evaluation and Risk Assessment, John Wiley & Sons, Inc., 2011. [HTML]
  • Zhenqiang Su, Hong Fang, Huixiao Hong, Roger Perkins, Baitang Ning, Weida Tong and Leming Shi, Next-generation sequencing: A Revolutionary Tool for Toxicogenomics, Book: Handbook of Systems Toxicology, to be published by John Wiley and Sons. 2010. [HTML, PDF]
  • Don Ding, Lei Xu, Hong Fang, Huixiao Hong, Roger Perkins, Steve Harris, Leming Shi, and Weida Tong, The EDKB, an Established Knowledge Base for Endocrine Disrupting Chemicals, BMC Bioinformatics, 11(Suppl 6):S5, 2010. [HTML, PDF]
  • Huixiao Hong, Leming Shi, Zhenqiang Su, Weigong Ge, Wendell D Jones, Wendy Czika, Kelci Miclaus, Christophe G Lambert, Silvia C Vega, John Zhang, Baitang Ning, Jie Liu, Bridgett Green, Lei Xu, Hong Fang, Roger Perkins, Simon M Lin, Nadereh Jafari, Kyunghee Park, Taejin Ahn, Marco Chierici, Cesare Furlanello, Li Zhang, Russell D Wolfinger, Federico Goodsaid, Weida Tong, Assessing sources of inconsistencies in genotypes and their effects on genome-wide association studies with HapMap samples, Pharmacogenomics J, 10, 364–374, 2010. [Pubmed, HTML, PDF]
  • The MicroArray Quality Control (MAQC) Consortium, The MAQC-II Project: A comprehensive study of common practices for the development and validation of microarray-based predictive models, Nat Biotechnol, 28:827–838, 2010. [Pubmed, HTML, PDF]
  • Dhivya Arasappan, Hong Fang, Roger Perkins, Weida Tong, Chapter 2.34: Interpretation of Toxicogenomics Data, Book: Comprehensive Toxicology, 2nd edition on Cellular and Molecular Toxicology; Editor: Kenneth Ramos, Elsevier, 663-683, 2010.
    10. Xiaohui Fan, Leming Shi, Hong Fang, Yiyu Cheng, Roger Perkins, Weida Tong, DNA Microarrays Are Predictive of Cancer Prognosis: A Re-evaluation, Clinical Cancer Research, 16(2):629-636, 2010 [Pubmed, HTML, PDF]
  • Huixiao Hong, Zhenqiang Su, Weigong Ge, Leming Shi, Roger Perkins, Hong Fang, Donna Mendrick, Weida Tong, Evaluating Variations of Genotype Calling: A Potential Source of Spurious Associations in Genome-Wide Association Studies, J. Genetics 89(1): 55-64, 2010. [Pubmed, HTML, PDF]
  • Huixiao Hong, Qilong Hong, Roger Perkins, Leming Shi, Hong Fang, Zhenqiang Su, Yvonne Dragan, James C. Fuscoe, Weida Tong. The Accurate Prediction of Protein Family from Amino Acid Sequence by Measuring Features of Sequence Fragments. Journal of Computational Biology, 2009, 16(12): 1671-1688. [Pubmed, HTML, PDF]
  • Hong Fang, Stephen C. Harris, Zhenjiang Su, Minjun Chen, Feng Qian, Leming Shi, Roger Perkins, Weida Tong, ArrayTrack – An FDA and Public Genomic Tool, Book: Protein Networks and Pathway Analysis; Editor: Yuri Nikolsky and Julie Bryant; Humana Press (London), 2009
  • Hong Fang, Roger Perkins, Leming Shi, Daniel M. Sheehan and Weida Tong, The FDA’s Endocrine Disruptor Knowledge Base (EDKB) – Lessons Learned in QSAR Modeling and Applications, Book: QSAR models designed for endocrine disruption, CRC Press, 2009. [Pubmed, HTML, PDF]
  • Xiaohui Fan, Leming Shi, Hong Fang, Stephen Harris, Roger Perkins and Weida Tong, Investigation of reproducibility of differentially expressed genes in DNA microarrays through statistical simulation, BMC Proceedings, 2009, 3(Suppl 2):S4. [Pubmed, HTML, PDF]
  • Stephen C. Harris, Hong Fang, Zhenjiang Su, Minjun Chen, Feng Qian, Leming Shi, Dhivya Arasappan, Weigong Ge, Xiaohui Fan, Huixiao Hong, Joshua, Xu, Steven Tuner, Michelle Bishop, Martin Jackson, Roger Perkins, Weida Tong, FDA Bioinformatics Tool for Public Use – ArrayTrack, Regulatory Research Perspectives, 8(1), 2009. [Pubmed, HTML, PDF, Wikipedia]
  • Xiaohui Fan, Hong Fang, Huixiao Hong, Roger Perkins, Leming Shi, Weida Tong, Correlation Analysis of External RNA controls Reveals Its Utility for Assessment of Microarray Assay, Analytical Biochemistry, 385:203-207, 2009. [Pubmed, HTML, PDF]
  • Huixiao Hong, Zhenqiang Su, Weigong Ge, Leming Shi, Roger Perkins, Hong Fang, Joshua Xu, James J. Chen, Tao Han, Jim Kaput, James C. Fuscoe, Weida Tong, Assessing Batch Effects of Genotype Calling Algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500K Array Set Using 270 HapMap Samples, BMC Bioinformatics, 9(Suppl 9):S17 (2008). [Pubmed, HTML, PDF]
  • Hong, Huixiao, Qian Xie, Weigong Ge, Feng Qian, Hong Fang, Leming Shi, Zhenqiang Su, Roger Perkins, Weida Tong, Mold2, Molecular Descriptors from 2D Structures for Chemoinformatics and Toxicoinformatics, J. Chem. Inf. Model, 48:1337-1344 (2008) [Pubmed, HTML, PDF]
  • Zhenqiang Su, Huixiao Hong, Hong Fang, Leming Shi, Roger Perkins, Weida Tong, Very Important Pool (VIP) Genes - An Application for Microarray-Based Molecular Signatures, BMC Bioinformatics, 9(Suppl 9):S17 (2008). [Pubmed, HTML, PDF]
  • Leming Shi, Wendell D. Jones, Roderick V. Jensen, Stephen C. Harris, Roger G. Perkins, Federico M. Goodsaid, Lei Guo, Lisa J. Croner, Cecilie Boysen, Hong Fang, Shashi Amur, Wenjun Bao, Catalin C. Barbacioru, Vincent Bertholet, Xiaoxi Megan Cao, Tzu-Ming Chu, Patrick J. Collins, Xiao-hui Fan, Felix W. Frueh, James C. Fuscoe, Xu Guo, Jing Han, Damir Herman, Huixiao Hong, Ernest S. Kawasaki, Quan-Zhen Li, Yuling Luo, Yunqing Ma, Nan Mei, Ron L Peterson, Raj K. Puri, Feng Qian, Richard Shippy, Zhenqiang Su, Yongming Andrew Sun, Hongmei Sun, Brett Thorn, Yaron Turpaz, Charles Wang, Sue Jane Wang, Janet A. Warrington, James C. Willey, Jie Wu, Qian Xie, Liang Zhang, Lu Zhang, Sheng Zhong, Russell D. Wolfinger, and Weida Tong, The Balance of Reproducibility, Sensitivity, and Specificity of Lists of Differentially Expressed Genes in Microarray Studies, BMC Bioinformatics, 9(Suppl 9):S10 (2008). [Pubmed, HTML, PDF]
  • Leming Shi, Roger G. Perkins, Hong Fang, and Weida Tong, Reproducible and reliable microarray results through quality control: good laboratory proficiency and appropriate data analysis practices, Current Opinion in Biotechnology 19:10-18, 2008. [Pubmed, HTML, PDF]
  • Leming Shi, Roger G. Perkins, and Weida Tong, The Current Status of DNA Microarrays, Book chapter on Microarrays: New Development Towards Recognition of Nucleic Acid and Protein Signatures, K. Dill, R. Liu, and P. Grodzinski (ed.), Springer (2007). [Pubmed, HTML, PDF]
  • Weida Tong, Stephen C. Harris, Hong Fang, Leming Shi, Roger Perkins, Federico Goodsaid and Felix W. Frueh, An Integrated Bioinformatics Infrastructure Essential for Advancing Pharmacogenomics And Personalized Medicine in the Context of the FDA’s Critical Path Initiative, Drug Discovery Today, 4(1):3-8, 2007. [Pubmed, HTML, PDF]
  • Hong Fang, Roger Perkins and Weida Tong, Omics Data Integration – A Systems Approach View, American Drug Discovery, 2(4):49-52 (2007). [Pubmed, HTML, PDF]
  • Hong Fang, Xiao-Hui Fan, Lei Guo, Leming Shi, Roger Perkins, Weigong Ge, Yvonne P. Dragan and Weida Tong, Evaluation of Self-Self Hybridization as an Alternative Experiment Design to Dye Swap for Two Channel Microarrays, OMICS: A Journal of Integrative Biology, 11(1):14-24, (2007). [Pubmed, HTML, PDF]
  • Zhenqiang Su, Huixiao Hong, Weida Tong, Roger Perkins, Xueguang Shao, Wensheng Cai. Identification of differentially expressed genes using disjoint principal component analysis coupled with genetic algorithm. Chemical Journal of Chinese Universities. 28 (9):1640-1644 (2007). [Pubmed, HTML, PDF]
  • Zhenqiang Su, Huixiao Hong, Roger Perkins, Xueguang Shao, Wensheng Cai, Weida Tong, Consensus Analysis of Multiple Classifiers Using Non-Repetitive Variables: Diagnostic Application to Microarray Gene Expression Data, Computational Biology and Chemistry, 31(1):48-56, (2007). [Pubmed, HTML, PDF]
  • Shi, L., Reid, et. al. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements, Nat. Biotechnol., 24,1151-1161. (2006). [Pubmed, HTML, PDF]
  • Shi, L., Reid, et. al. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements, Nat. Biotechnol., 24,1151-1161. (2006) [Pubmed Abstract Journal PDF]
  • Sun H, Fang H, Chen T, Perkins R, Tong W, GOFFA: Gene Ontology for Functional Analysis – A FDA Gene Ontology Tool for Analysis of Genomic and Proteomic Data. (2006) BMC Bioinformatics 7(Suppl 2):S23 [Pubmed Journal PDF]
  • Fang H, Xie Q, Boneva R, Fostel J, Perkins R, Tong W. Gene Expression Profile Exploration of a Large Dataset on Chronic Fatigue Syndrome, Pharmacogenomics 7(3), 429-440, (2006) [Pubmed Journal PDF]
  • Weida Tong, Hong Fang, Qian Xie, Huixiao Hong, Leming Shi, Roger Perkins, Uwe Scherf, Federico Goodsaid, Felix Frueh, Gaining confidence on molecular classification through consensus modeling and validation, Toxicology Mechanisms and Methods, 16(2-3):59-68, 2006 [Draft Pubmed Abstract Journal PDF]
  • Shi L, Tong W, Su Z, Han T, Han J, Puri R, Fang H, Frueh F, Goodsaid F, Guo L, Branham W, Chen J, Xu Z, Harris S, Hong H, Xie Q, Perkins R, Fuscoe J. Microarray scanner calibration curves: characteristics and implications, BMC Bioinformatics, 6(Suppl 2):S11 (2005) [Pubmed Journal PDF]
  • Perkins R, Gaining Wider Acceptance of QSARs in Regulation, Invited, 3rd International Symposium: Computational Methods in Toxicology and Pharmacology, Shanghai, China, Oct 29- Nov 1, 2005.
  • Shi L, Tong W, Fang H, Scherf U, Han J, Puri R, Frueh F, Goodsaid F, Guo L, Su Z, Han T, Fuscoe J, Xu Z, Patterson T, Hong H, Xie Q, Perkins R, Chen J, Casciano D. Cross-platform Comparability of Microarray Technology: Intra-platform Consistency and Appropriate Data Analysis Procedures Are Essential, BMC Bioinformatics 6(Suppl 2):S12 (2005). [Draft Pubmed Abstract Journal PDF New Hot papers Review]
  • Hong H, Dragan Y, Epstein J, Teitel C, Chen B, Xie Q, Fang H, Shi L, Perkins R, Tong W. Quality Control and Quality Assessment of Data from Surface-enhanced Laser Desorption/Ionization (SELDI) Time-of Flight (TOF) Mass Spectrometry (MS), BMC Bioinformatics 6(Suppl 2):S5 (2005). [Pubmed Journal PDF]
  • Xie Q, Ratnasinghe L, Hong H, Perkins R, Tang Z, Hu N, Taylor P, Tong W. Decision Forest Analysis of 61 Single Nucleotide Polymorphisms in a Case-Control Study of Esophageal Cancer; a novel method, BMC Bioinformatics. 6(Suppl 2):S4 (2005) [Pubmed Journal PDF]
  • Fang H, Tong W, Perkins R, Shi L, Hong H, Cao X, Xie Q, Yim SH, Ward JM, Pitot HC, Dragan YP. Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling, BMC Bioinformatics, 6(Suppl 2):S6 (2005). [Pubmed Journal PDF]
  • Netzeva T, Worth A, Aldenberg T, Benigni R, Cronin M, Bramatics P, Jaworska J, Kahn S, Klopman G, Marchant C, Myatt G, Nikolova-Jaliazkova N, Patlewicz G, Perkins R, Roberts D, Schultz T, Stanton D, Sandt J, Tong W, Veith G, Yang C. Current Status of Methods for Defining the Applicability Domain of (Quantitative) Structure-Activity Relationships, Alta,33(1-19) (2005) [Pubmed PDF]
  • Hong H, Tong W, Xie Q, Fang H, Perkins R. An In Silico Ensembel Method for Lead Discovery: Decision Forest, SAR and QSAR in Enviromental Research, 0:1-9 (2005).
  • Tong W, Hong H, Xie Q, Shi L, Fang H, Perkins R. Assessing QSAR Limitations - A Regulatory Perspective, Current Computer-Aided Drug Design, 1:65-72 (2005) .
  • Tong W, Hong H, Fang H, Xie Q, Perkins R, Sheehan D: From Decision Tree to Decision Forest - A Novel chemometrics approach for Structure Activity Relationship Modeling. In: Chemometrics and Cheminformatics. Edited by Lavine BK. Washington DC, USA: ACS; 2005: 173-185.
  • Hong H, Tong W, Perkins R, Fang H, Xie Q, Shi L: Multi-Class Decision Forest - A Novel Pattern Recognition Method for Multi-Class Classification in Microarray Data Analysis. DNA Cell Biol. 2004 Oct;23(10):685-94. [Draft Pubmed Abstract Journal PDF]
  • Tong W, Xie Q, Hong H, Fang H, Shi L, Perkins R, Petricoin E. Using Decision Forest to classify prostate samples based on SELDI-TOF MS data – Assessing prediction confidence and chance correlation, EHP Toxicogenomics, 112(12): 1249-1254, 2004
  • Tong W, Harris S, Cao X, Fang H, Shi L, Sun H, Fuscoe J, Harris A, Hong H, Xie Q, Perkins R, Casciano D: Development of public toxicogenomics software for microarray data management and analysis. Mutat Res 2004, 549(1-2):241-253. [Pubmed Abstract Journal PDF]
  • Tong W, Xie Q, Hong H, Shi L, Fang H, Perkins R: Assessment of prediction confidence and domain extrapolation of two structure-activity relationship models for predicting estrogen receptor binding activity. Environ Health Perspect 2004, 112(12):1249-1254. [Pubmed Abstract Journal PDF]
  • Tong W, Fang H, Hong H, Xie Q, Perkins R, Sheehan D: Receptor-Mediated Toxicity: QSARs for Oestrogen Receptor Binding and Priority Setting of Potential Oestrogenic Endocrine Disruptors. In: Predicting Chemical Toxicity and Fate. Edited by Livingstone MTDCaDJ. New York, London, Boca Raton: CRC press; 2004.
  • Walker JD, Fang H, Perkins R, Tong W: QSAR's for Endocrine Disruption Priority Setting Database 2: The Integrated 4-Phase Model. QSAR Comb Sci 2003, 22(1):89-105.
  • Tong W, Fang H, Hong H, Xie Q, Perkins R, Anson JF, Sheehan D: Regulatory application of SAR/QSAR for priority setting of endocrine disruptors - A perspective. Pure and Applied Chemistry 2003, 75(11-12):2375-2388. Pubmed Journal
  • Tong W, Hong H, Fang H, Xie Q, Perkins R: Decision forest: combining the predictions of multiple independent decision tree models. J Chem Inf Comput Sci 2003, 43(2):525-531. Pubmed Journal
  • Perkins R, Fang H, Tong W, Welsh WJ: Invited Review: Quantitative structure-activity relationship methods: perspectives on drug discovery and toxicology. Environ Toxicol Chem 2003, 22(8):1666-1679. [Pubmed Abstract Journal PDF]
  • Tong W, Welsh WJ, Shi L, Fang H, Perkins R: Invited Review: Structure-activity relationship approaches and applications. Environ Toxicol Chem 2003, 22(8):1680-1695. [Pubmed Abstract Journal PDF]
    30. Tong W, Cao X, Harris S, Sun H, Fang H, Fuscoe J, Harris A, Hong H, Xie Q, Perkins R: ArrayTrack--supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research. Environ Health Perspect 2003, 111(15):1819-1826. Pubmed Journal
    31. Hong H, Fang H, Xie Q, Perkins R, Sheehan DM, Tong W: Comparative molecular field analysis (CoMFA) model using a large diverse set of natural, synthetic and environmental chemicals for binding to the androgen receptor. SAR QSAR Environ Res 2003, 14(5-6):373-388. Pubmed
    32. Fang H, Tong W, Branham WS, Moland CL, Dial SL, Hong H, Xie Q, Perkins R, Owens W, Sheehan DM: Study of 202 natural, synthetic, and environmental chemicals for binding to the androgen receptor. Chem Res Toxicol 2003, 16(10):1338-1358. Pubmed Journal
    33. Tong W, Perkins R, Fang H, Hong H, Xie Q, Branham SW, Sheehan DM, Anson JF: Development of Quantitative Structure-Activity Relationships (QSARs) and their use for priority setting in the testing strategy of endocrine disruptors. Regulatory Research perspectives 2002, 1(3):1-16. Pubmed Journal
  • Shi L, Tong W, Fang H, Xie Q, Hong H, Perkins R, Wu J, Tu M, Blair RM, Branham WS et al: An integrated "4-phase" approach for setting endocrine disruption screening priorities--phase I and II predictions of estrogen receptor binding affinity. SAR QSAR Environ Res 2002, 13(1):69-88. Pubmed Journal
  • Hong H, Tong W, Fang H, Shi L, Xie Q, Wu J, Perkins R, Walker JD, Branham W, Sheehan DM: Prediction of estrogen receptor binding for 58,000 chemicals using an integrated system of a tree-based model with structural alerts. Environ Health Perspect 2002, 110(1):29-36. Pubmed Journal
  • Branham WS, Dial SL, Moland CL, Hass BS, Blair RM, Fang H, Shi L, Tong W, Perkins RG, Sheehan DM: Phytoestrogens and mycoestrogens bind to the rat uterine estrogen receptor. J Nutr 2002, 132(4):658-664. Pubmed Journal
  • Shi LM, Fang H, Tong W, Wu J, Perkins R, Blair RM, Branham WS, Dial SL, Moland CL, Sheehan DM: QSAR models using a large diverse set of estrogens. J Chem Inf Comput Sci 2001, 41(1):186-195. Pubmed Journal
  • Fang H, Tong W, Shi LM, Blair R, Perkins R, Branham W, Hass BS, Xie Q, Dial SL, Moland CL et al: Structure-activity relationships for a large diverse set of natural, synthetic, and environmental estrogens. Chem Res Toxicol 2001, 14(3):280-294. [Pubmed Journal PDF]
  • Tu M, Tong W, Perkins R, Valentine C. Predicted changes in pre-mrna secondary structure vary in their association with exon skipping for mutations in exons 2,4, and 8 of the hprt gene and exon 51 of the fibrillin gene. Mutat Res Genomics 432:15-32, 2000.
  • Perkins RG, Anson JF, Blair RM, Branham WS, Chen Y, Dial SL, Fang H, Hass BS, Jackson MA, Lu M, Meehan JF, Moland CL, Nossaman RK, Shi LM, Tong W, Tu M, Welsh WJ, and Sheehan DM. Book Chapter: The Estrogen Knowledge Base: A Prototype Toxicological Knowledge Base and Predictive Models for Endocrine Disrupting Compounds, 2000, Walker JD, SETAC, Pensacola, FL
  • Blair R, Fang H, Branham WS, Hass B, Dial SL, Moland CL, Tong W, Shi L, Perkins R, Sheehan DM. Estrogen Receptor Relative Binding Affinities of 188 Natural and Xenochemicals: Structural Diversity of Ligands. Toxicol Sci 54:138-153; 2000.
  • Tong W, Perkins R, Wu J, Shi L, Tu M, Fang H, Blair R, Branham W, Sheehan DM. An intergrated computational approach for prioritizing potential estrogens. Proceeding of the International Symposium on Environmental Endocrine Disruptors, Dec, Kobe, Japan, 1999.
  • Xing L, Welsh WJ, Tong W, Perkins R, Sheehan DM. Comparison of estrogen receptor alpha and beta subtypes based on comparative molecular field analysis (CoMFA). SAR/QSAR Environ Res 10:215-237; 1999.
  • Perkins R, Branham W, Blair R, Hass B, Fang H, Shi L, Tong W, Chen Y, Meehan J, Nossaman R, Welsh W, Sheehan D. A Toxicological Knowledge Base for Endocrine Disrupting Compounds. In: Society of Toxicology Annual Meeting, New Orleans, LA, March 18-21, 1999.
  • Perkins R, Anson J, Tong W, Branham W, Blair R, Hass B, Fang H, Shi L, Chen Y, Meehan J, Nossaman R, Welsh W, Sheehan D. A Knowledge Base for Mining of Endocrine Disruptor Data. In: 217th American Chemical Society National Meeting, Anaheim, CA, March 21-25, 1999.
  • Tong W, Perkins R, Fang H, Shi L, Chen Y, Sheehan D. Computational Approaches to Determining Estrogenic Effects (Invited Talk). In: Keystone Symposia on Endocrine Disruptors, Granlibakken, California, February 1-5, 1999.
  • Perkins R, Anson J, Branham W, Fang H, Tong W, Welsh W, Chen Y, Meehan J, Jackson M, Nossaman R, Shi L, Sheehan D. The Estrogen Knowledge Base (EKB), A Prototype Toxicological Knowledge Base for Endocrine Disrupting Compounds. In: 8th International Workshop on Quantitative Structure-Activity Relationships (QSARs) in the Environmental Sciences, QSARs to predict the endocrine disruption and environmental/health effects, Baltimore, Maryland, May 16-20, 1998.
  • Perkins R, Tong W, Sheehan D. A Prototype Toxicological Knowledge Base. In: 1998 Toxicology Forum Satellite Meeting on Toxicological Databases, Washington, D.C., February 2-3, 1998.
  • Shi LM, Tong WD, Perkins R, Chen Y, Fang H, Poirier L, Sheehan D. Classification Methods for Toxicity Prediction and Anticancer Drug Discovery. In: 1998 Joint Annual Meeting of the Classification Society of North America and the Psychometric Society, Urbana, Illinois, June 17-21, 1998.
  • Tong W, Perkins R, Shi L, Chen Y, Fang H, Sheehan D. Evaluation of Various QSAR Methods for the Large Scale Prediction of Estrogen Compounds. In: 8th International Workshop on Quantitative Structure-Activity Relationships (QSARs) in the Environmental Sciences (SETAC meeting), QSARs to predict the endocrine disruption and environmental/health effects, Baltimore, Maryland, May 16-20, 1998.
  • Tong W, Perkins R, Sheehan DM. Perspectives on Three-Dimensional Quantitative Structure-Activity Relationship (3D-QSAR)/Comparative Molecular Field Analysis (CoMFA) in Determining Estrogenic Effects. Invited Review. Japan Chemistry Today 2:50-57; 1999.
  • Tong W, Perkins R, Wu J, Shi L, Tu M, Fang H, Blair R, Branham W, Sheehan DM. An integrated computational approach for prioritizing potential estrogens. Yokohama Workshop on Environmental Endocrine Disruptors '99: Possible Effect on Human and Wildlife, p.247-254, Yokohama, Japan, 1999.
  • Sheehan DM, Branham WS, Tong W, Perkins R. Phytoestrogens and Synthetic chemicals as Developmental Endocrine Disruptors. Newsletter Japan 2:3; 1998.
  • Tong W, Lowis DR, Perkins R, Chen Y, Welsh WJ, Goddette DW, Heritage TW, Sheehan DM. Evaluation of quantitative structure-activity relationship methods for large-scale prediction of chemicals binding to the estrogen receptor. J. Chem. Inf. Comput. Sci. 38:669-77; 1998. [Pubmed Abstract Journal PDF]
  • Tong W, Perkins R, Strelitz R, Collantes ER, Keenan S, Welsh WJ, Branham WS, Sheehan DM. Quantitative structure-activity relationships (QSARs) for estrogen binding to the estrogen receptor: predictions across species. Environ Health Perspect 105:1116-24; 1997.
    56. Tong W, Perkins R, Xing L, Welsh WJ, Sheehan DM. QSAR models for binding of estrogenic compounds to estrogen receptor alpha and beta subtypes. Endocrin 138:4022-5; 1997.
  • Perkins R, Anson J, Blair R, Branham W, Chen Y, Dial S, Fang H, Hass B, Jackson M, Lu M, Meehan J, Moland C, Nossaman R, Shi L, Tong W, Welsh WJ, Sheehan DM. The Endocrine Disruptor Knowledge Base: A Prototype Toxicological Knowledge Base and Predictive Models for Endocrine Disrupting Compounds. In: QSARs for Endocrine Disruption, Pollution Prevention, Toxicity Screening and Persistence Prediction, vol. in press: Society of Environmental Toxicology and Chemistry, 1999.
  • Perkins R, Sheehan D, Tong W, Branham WS. A Tiered Testing Scheme and Knowledge Base for Estrogenic Endocrine (Invited talk). In: IBC’s Second Annual International Congress on Endocrine Disrupting Compounds, Washington, D.C., May 5-6, 1997.
  • Tong W, Perkins R, Sheehan W. QSAR Studies of Estrogen Receptor Binding Affinity. In: 213th American Chemical Society National Meeting, San Francisco, CA, April 13-17, 1997.
  • Tong W., Perkins R., Sheehan D. Computational Models for Screening, Prediction and Classification of Estrogenic Compounds. In: IBC’s Second Annual International Environmental Congress on Endocrine Disruptors, Washington, D.C., May 5-6, 1997.
  • Tong W, Lowis D, Perkins R, Welsh WJ, Sheehan D. Application of the Holographic QSAR (HQSAR) Method to Predict the Biological Activity of Environmental Estrogens. In: 214th American Chemical Society National Meeting, Las Vegas, Nevada, September 7-11, 1997;COMP 81.
  • Perkins R, Branham W, Blair R, Hass B, Fang H, Shi L, Tong W, Chen Y, Meehan J, Nossaman R, Welsh W, Sheehan D. A Knowledge Base and QSAR and Chemometric Predictive Models for Endocrine Disrupting Compounds. In: Keystone Symposium on Endocrine Disruptors, Granlibakken, California, February 1-5, 1999.
  • Shi L, Tong W, Perkins R, Chen Y, Tu M, Meehan J, Nossaman R, Welsh WJ, Fang H, Branham W, Blair B, Hass B, Sheehan D. QSAR Models for multiple estrogenic endpoints. In: Keystone Symposium on Endocrine Disruptors, Granlibakken, California, February 1-5, 1999.
    Welsh WJ, Yu SJ, Tong W, Perkins R, Chen Y, Sheehan D. Quantitative Structure-Activity Relationship (QSAR) Models for Predicting the Estrogenic Activity of Xenoestrogens. In: Keystone Symposium on Endocrine Disruptors, Granlibakken, California, Feb 1-5, 1999.
  • Welsh WJ, Yu S-J, Chen Y, Tong W, Perkins R, Sheehan D. Quantitative Structure-Activity Relationship (QSAR) Models Useful for Risk Assessment in Predicting Suspected Endocrine Disrupting Compounds (EDCs). In: National Meeting of the American Chemical Society, Anaheim, CA, April 1999.
  • Yu S-J, Welsh WJ, Chen Y, Tong W, Perkins R, Sheehan D. Quantitative Structure-Activity Relationship (QSAR) Models for Predicting the Estrogenic Activity of Xenoestrogens. In: National Meeting of the American Chemical Society, Anaheim, CA, April 1999.
  • Chen Y, Xing L, Welsh WJ, Tong W, Perkins R, Sheehan DM. A QSAR Study of the Binding of Suspected Endocrine Disrupting Compounds (EDCs) to the Estrogen Receptor. In: Workshop on Computational Methods in Toxicology, Dayton, OH, April 1998.
  • Chen Y, Xing L, Welsh WJ, Tong W, Perkins R, Sheehan DM. A QSAR study of the binding of suspected endocrine disrupting compounds (EDCs) to the estrogen receptor. In: Endocrine disruptor Investigators Meeting, NIEHS and EPA, Research Triangle Park, NC, Oct. 7-9, 1998.
  • Fang H, Tong W, Perkins R, Soto A, Sheehan D. Quantitative comparison of in vitro assays. In: Gordon Research Conference on Environmental Endocrine Disruptors, Plymouth, New Hampshire, July 12-17, 1998.
  • Fang H, Tong W, Perkins R, Soto A, Sheehan DM. Quantitative Comparisons of in vitro Assays for Estrogenicity. In: 1998 FDA Science Forum, Natcher Conference Center, NIH, Bethesda, Maryland, December 8-9, 1998.
  • Perkins R, Anson J, Branham W, Hass B, Fang H, Shi L, Tong W, Chen Y, Meehan J, Jackson M, Nossaman R, Welsh W, Sheehan D. The Estrogen Knowledge Base (EKB), A Toxicological Knowledge Base for Endocrine Disrupting Compounds. In: Gordon Research Conference on Environmental Endocrine Disruptors, Plymouth, New Hampshire, July 12-17, 1998.
  • Perkins R, Chen Y, Dawson S, Meehan J, Shi L, Tong W, Tu M, Unruh L, Wu J, Anson J. NCTR’s Center for Computational Toxicology: A Resource to Foster Toxicological and Regulatory Research. In: FDA Science Forum, Natcher Conference Center, NIH, Bethesda, Maryland, December 1998.
  • Tong W, Welsh W, Chen Y, Shi L, Perkins R, Sheehan DM. Structure-Based Predictive Models for Endocrine Disruption. In: Gordon Research Conference on Environmental Endocrine Disruptors, Plymouth, New Hampshire, July 12-17, 1998.
  • Tu M, Tong W, Perkins R, Valentine C. Characteristics of single-base substitutions in the Hypoxanthine-guanine phosphoribosyltransferase (hprt) gene. In: 2nd Annual Conference on Computational Genomics, Reston VA, October 31-November 3, 1998.
  • Xing L, Welsh WJ, Tong W, Perkins R, Sheehan DM. 3D-QSAR/CoMFA Models for the Binding of Estrogenic Compounds to the Estrogen Receptor a and b Subtypes. In: 8th International Workshop on Quantitative Structure-Activity Relationships (QSARs) in the Environmental Sciences: QSARs to Predict the Endocrine Disruption and Environmental/Health Effects, Baltimore, MA, May 1998.
  • Chen Y, Xing L, Welsh WJ, Tong W, Perkins R, Sheehan DM. A QSAR Study of the Binding of Potential Endocrine Disrupting Compounds to the Estrogen Receptor. In: 32nd Midwest ACS Meeting, Tan-Tar-A Resort, Lake of the Ozarks, Osage Beach, Missouri, October 1997.
  • Meehan J, Jackson M, Nossaman R, Tong W, Chen Y, Fang H, Perkins R, Sheehan DM. The Estrogen Knowledge Base Software and Website. In: 1997 FDA Science Forum, Natcher Conference Center, NIH, Bethesda, Maryland, December 1997.
  • Perkins R, Sheehan DM, Branham WS, Hass B, Fang H, Welsh W, Xing L, Tong W, Chen Y, Meehan J, Jackson M, Nossaman R, Strelitz R, Anson J. The Estrogen Knowledge Base (EKB): A Prototype Research/Review Model. In: 1997 FDA Science Forum, Natcher Conference Center, NIH, Bethesda, Maryland, December 1997.
  • Sheehan DM, Tong W, Branham WS, Perkins R. The Estrogen Knowledge Base: Predicting Toxicity and Risk. In: 1997 FDA Science Forum, Natcher Conference Center, NIH, Bethesda, Maryland, December 1997.
  • Tong W, Perkins R, Lowis D, Welsh WJ, Sheehan D. HQSAR: A Rapid Highly Predictive QSAR Method Based on Molecular Fragments. In: 1997 QSAR Gordon Research Conference, Tilton, New Hampshire, August 3-8, 1997.
  • Tong W, Perkins R, Welsh WJ, Sheehan D. QSAR Models for Estrogen Binding to Estrogen Receptors Alpha and Beta Nevada. In: ENVR 102, 214th American Chemical Society National Meeting, Las Vegas, Nevada, September 7-11, 1997.
  • Tong W, Perkins R, Welsh WJ, Strelitz R, Sheehan D. Quantitative Structure-Activity Relationships (QSARs) for Estrogen Binding to the Estrogen Receptor: Predictions Across Species. In: ENVR 101, 214th American Chemical Society National Meeting, Las Vegas, Nevada, September 7-11, 1997.
  • Tong W, Welsh W, Chen Y, Shi L, Perkins R, Sheehan DM. Structure-Based Predictive Models for the Estrogen Knowledge Base. In: 1997 FDA Science Forum, Natcher Conference Center, NIH, Bethesda, Maryland, December 1997.
  • Xing L, Welsh WJ, Tong W, Perkins R, Sheehan DM. 3D-QSAR/CoMFA Models for the Binding of Estrogenic Compounds to the Estrogen Receptor a and b Subtypes. In: 32nd Midwest ACS Meeting, Tan-Tar-A Resort, Lake of the Ozarks, Osage Beach, Missouri, October 1997.
  • Perkins R, Tong W, Sheehan DM, Branham WS. A Knowledge Base for Prediction of Estrogenicity—A Method Towards a Regulatory Paradigm. In: 1996 FDA Science Forum, Washington D.C., October 1996.

Supercomputer Center Management Years:

  • Supporting an Environment with Unpredictable Demand, Research Consortium, Inc., Invited talk at Conference on Top Management Strategies for High Performance Computing, Boston, MA., October 9-12, 1990.

Nuclear Reactor Physics Years:

  • Neutronics Calculations for the McClellan AFB Stationary Neutron Radiography System (SNRS), GA Technologies Triga Reactor Report NR 29, April 20, 1987.
  • Radiation Transport Phenomena in SP 100 Shielding Designs, Proceedings of the 3rd Symposium on Space Nuclear Power Systems, Albuquerque, NM, January 13 16, 1986.
  • United States Patent 4530812 Composite coils for toroidal field coils and method of using same 07/23/1985
  • Compact Tokamak Hybrid Reactor Systems, Proceedings of the Tenth International Conference on Plasma Physics and Controlled Nuclear Fusion Research, International Atomic Energy Agency, London, United Kingdom, September 12 19, 1984.
  • Neutronics Calculations for Normal Conducting Copper RIGGATRON Tokamaks, Journal of Fusion Energy, January 1984.
  • RIGGATRON Fusion Power Core Driven Hybrid Electric Plant Based on LMFBR Technology, Transactions of the American Nuclear Society, 45, 186, San Francisco, California, October 30 November 3, 1983.
  • A Systematic Approach to Activation Analysis for the RIGGATRON Fusion Demonstration Experiment, Transactions of the American Nuclear Society, 43, 631, Washington, D.C., November 14 18, 1982.
  • Fuel Cycles and Advanced Core Designs for the Gas Cooled Fast Reactor, Department of Energy (GA A15603), General Atomic Company, July 1982.
  • Requirements for the Gas Cooled Fast Reactor Plenum Streaming Experiment, Department of Energy (GA A16062), General Atomic Company, September 1980.
  • Impact on Spectral Dependent Irradiation Effects Data on Gas Cooled Fast Reactor Demonstration Plant Shield Design, Advances in Reactor Physics and Shielding, American Nuclear Society Topical Meeting, Sun Valley, Idaho, September 14 17, 1980.
  • Gas Cooled Fast Reactor Shielding Design and Supporting Experimental Programs, Proceedings of the Second Annual GCFR Program Technical Review, Helium Breeder Associates, Rancho Bernardo, California, June 4 6, 1980.
  • Design of the Gas Cooled Fast Reactor Demonstration Plant Reactor Shielding System, Transactions of the American Nuclear Society, 33, 704, San Francisco, California, November 11 15, 1979.
  • Physics Design of the 300 MW(e) Gas Cooled Fast Reactor, Transactions of the American Nuclear Society, Canada, June 14 16, 1976.
  • Radiation Streaming in a 300 MW(e) Gas Cooled Fast Reactor, Transactions of the American Nuclear Society, Toronto, Canada, June 14 16, 1976.
  • Gamma Ray Heating in a 300 MW(e) Gas Cooled Fast Reactor, General Atomic Company, Department of Energy (GA A13790), January 1976.
  • AUXTRAN A FORTRAN V Program for Simulating the Dynamic Performance of the Gas Cooled Fast Reactor Core Auxiliary Cooling System General Atomic Company, Department of Energy (GA D13292), January 1975.
  • Thesis: Disposing of Waste Heat from Advanced Power Sources by Infrared Radiative Transfer to Space University of Florida, June 1974.