PNNL

Dr. Wiley is a systems biologist in the Functional and Systems Biology group in the Environmental Molecular Sciences Division and the Environmental Molecular Sciences Laboratory (EMSL) user program. He combines molecular and cellular biology with both biochemical and optical assays to generate quantitative data to build computational models of cellular processes. Wiley is the author or co-author of more than 200 scientific publications, including more than 130 articles in peer-reviewed scientific journals, and 30 review articles and book chapters. He also has written several commercial graphics and data analysis software packages. Dr. Wiley has served as a reviewer for more than 30 scientific journals, is an associate editor of Frontiers in Genetics and is on the editorial board of The Scientist and BMC Biology. 

Dr. Wiley's research interests are focused on understanding the systems-level design principles that underlie regulatory networks in both prokaryotic and eukaryotic cells. This work also focuses on how these regulatory networks become dysfunctional in diseases, such as cancer, and how they can be modified for both therapeutic and biological engineering applications. More recently, his work has focused on using new CRISPR-based technologies in combination with proteomics, gene expression and biochemical assays to build improved mechanistic models of signaling and metabolic networks. This work requires the creation of a scalable computational infrastructure for integrating multidimensional data sets as well as development of the underlying analytical technologies. 

• BA in Biology, University of Tennessee, Knoxville, 1974 

• PhD in Biochemistry/Cell Biology, University of Tennessee, 1979 

• American Association for the Advancement of Science 

• American Society of Cell Biology 

• American Society of Biochemistry and Molecular Biology 

• Biophysical Society 

• Award for Distinguished Technical Communication (2011) 

• Faculty of 1000 Member for Cell Biology (2011) 

• Elected AAAS Fellow (2005) 

• R&D 100 Award for designing single-chain antibody library in a yeast-display system (2004) 

• Laboratory Fellow, Pacific Northwest National Laboratory (2000) 

• National Institutes of Health Research Career Development Award (1988 – 1993) 

• Phi Kappa Phi Honor Society, University of Tennessee (1979)

2020 

• Habowski A.N., J.L. Flesher, J.M. Bates, C. Tsai, K.D. Martin, R. Zhao, and A.K. Ganesan, et al. 2020. "Transcriptomic and Proteomic Signatures of Stemness and Differentiation in the Colon Crypt." Communications Biology 3. PNNL-SA-153928. doi:10.1038/s42003-020-01181-z 

• Habowski, A. N., J. L. Flesher, J. M. Bates, C. F. Tsai, K. Martin, R. Zhao, A. K. Ganesan, R. A. Edwards, T. Shi, H. S. Wiley, Y. Shi, K. J. Hertel, and M. L. Waterman. 2020. “Transcriptomic and Proteomic Signatures of Stemness and Differentiation in the Colon Crypt.” Communications Biology 3 (1). https://doi.org/10.1038/s42003-020-01181-z. 

• Gerosa L., C. Chidley, F. Froehlich, G. Sanchez, S.K. Lim, J. Muhlich, and J. Chen, et al. 2020. " Receptor-driven ERK pulses reconfigure MAPK signaling and enable persistence of drug-adapted BRAF-mutant melanoma cells." Cell Systems. PNNL-SA-147461. doi: 10.1016/j.cels.2020.10.002   

2019 

• Zhang P., M.J. Gaffrey, Y. Zhu, W.B. Chrisler, T.L. Fillmore, L. Yi, and C.D. Nicora, et al. 2019. "Carrier-assisted single-tube processing approach for targeted proteomics analysis of low numbers of mammalian cells." Analytical Chemistry 91, no. 2:1441-1451. PNNL-SA-138130. doi:10.1021/acs.analchem.8b04258 

2018 

• Lee J., G.M. Fujimoto, R.E. Wilson, H. Wiley, and S.H. Payne. 2018. "Blazing Signature Filter: a library for fast pairwise similarity comparisons." BMC Bioinformatics 19. PNNL-SA-126956. doi:10.1186/s12859-018-2210-6 

• Shi T., M.J. Gaffrey, T.L. Fillmore, C.D. Nicora, L. Yi, P. Zhang, and A.K. Shukla, et al. 2018. "Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells." Communications Biology 1, no. 1:Article No. 103. PNNL-SA-130600. doi:10.1038/s42003-018-0107-6 

• Wells A., and H. Wiley. 2018. "A Systems Perspective of Heterocellular Signaling." Essays in Biochemistry 62, no. 4:607-617. PNNL-SA-135065. doi:10.1042/EBC20180015 

• Wiley H. 2018. "Receptors: How low can you go?." eLife 7. PNNL-SA-131431. doi:10.7554/eLife.33604 

• Yi L., T. Shi, M.A. Gritsenko, C. Chan, T.L. Fillmore, B.M. Hess, and A.C. Swensen, et al. 2018. "Targeted Quantification of Phosphorylation Dynamics in the Context of EGFR-MAPK Pathway." Analytical Chemistry 90, no. 8:5256-5263. PNNL-SA-31519.  doi:10.1021/acs.analchem.8b00071 

2017 

• Bethel E.W., M. Greenwald, K. Kleese van Dam, M. Parashar, S. Wild, and H. Wiley. 2017. "Management, Analysis, and Visualization of Experimental and Observational Data - The Convergence of Data and Computing." In IEEE 12th International Conference on eScience (e-Science 2016), October 23-27, 2017, Baltimore, MD, 213-222. Piscataway, New Jersey: IEEE. PNNL-SA-123213. doi:10.1109/eScience.2016.7870902 

• Lindemann S.R., J.M. Mobberley, J.K. Cole, L. Markillie, R.C. Taylor, E.L. Huang, and W.B. Chrisler, et al. 2017. "Predicting Species-Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an Integrated 'Omics Approach." Frontiers in Microbiology 8. PNNL-SA-129376. doi:10.3389/fmicb.2017.01020 

• Wiley H. 2017. "Decoding Signal Processing at the Single Cell Level." Cell Systems 5, no. 6:542-543. PNNL-SA-131446. doi:10.1016/j.cels.2017.12.003 

2016 

• Shi T., M. Niepel, J.E. McDermott, Y. Gao, C.D. Nicora, W.B. Chrisler, and L.M. Markillie, et al. 2016. "Conservation of Protein Abundance Patterns Reveals the Regulatory Architecture of the of the EGFR-MAPK Pathway." Science Signaling 9, no. 436:rs6. PNNL-SA-115056. doi:10.1126/scisignal.aaf0891 

2014 

• Beliaev A.S., M.F. Romine, M. Serres, H.C. Bernstein, B.E. Linggi, L.M. Markillie, and N.G. Isern, et al. 2014. "Inference of Interactions in Cyanobacterial-Heterotrophic Co-Cultures via Transcriptome Sequencing." The ISME Journal 8, no. 11:2243-2255. PNNL-SA-98626. doi:10.1038/ismej.2014.69 

• Shi T., Y. Gao, M.J. Gaffrey, C.D. Nicora, T.L. Fillmore, W.B. Chrisler, and M.A. Gritsenko, et al. 2014. "Sensitive Targeted Quantification of ERK Phosphorylation Dynamics and Stoichiometry in Human Cells without Affinity Enrichment." Analytical Chemistry 87, no. 2:1103-1110. PNNL-SA-103421. doi:10.1021/ac503797x 

• Wiley H.S. 2014. "Open questions: The disrupted circuitry of the cancer cell." BMC Biology 12. PNNL-SA-106172. doi:10.1186/s12915-014-0088-y 

• Zhou Z.N., V.P. Sharma, B.T. Beaty, M. Roh-Johnson, E.A. Peterson, N. Van Rooijen, and P.A. Kenny, et al. 2014. "Autocrine HBEGF expression promotes breast cancer intravasation, metastasis and macrophage-independent invasion in vivo." Oncogene 33, no. 29:3784-3793. PNNL-SA-105934. doi:10.1038/onc.2013.363 

2013 

• Hess B.M., J. Xue, L.M. Markillie, R.C. Taylor, H.S. Wiley, B.K. Ahring, and B.E. Linggi. 2013. "Coregulation of terpenoid pathway genes and prediction of isoprene production in Bacillus subtilis using transcriptomics." PLoS One 8, no. 6:e66104. PNNL-SA-93488. doi:10.1371/journal.pone.0066104 

• Taylor R.C., B.M. Webb-Robertson, L.M. Markillie, M.H. Serres, B.E. Linggi, J.T. Aldrich, and E.A. Hill, et al. 2013. "Changes in Translational Efficiency is a Dominant Regulatory Mechanism in the Environmental Response of Bacteria." Integrative Biology 5, no. 11:1393-1406. PNNL-SA-95628. doi:10.1039/C3IB40120K 

2012 

• Shankaran H., Y. Zhang, W.B. Chrisler, J.A. Ewald, H.S. Wiley, and H. Resat. 2012. "Integrated Experimental and Model-based Analysis Reveals the Spatial Aspects of EGFR Activation Dynamics." Molecular Biosystems 8, no. 11:2868-2882. PNNL-SA-80743. doi:10.1039/C2MB25190F 

• Waters K.M., T. Liu, R.D. Quesenberry, A.R. Willse, S. Bandyopadhyay, L.E. Kathmann, and T.J. Weber, et al. 2012. "Network Analysis of Epidermal Growth Factor Signaling using Integrated Genomic, Proteomic and Phosphorylation Data." PLoS One 7, no. 3:Article No. e34515. PNNL-SA-85737. doi:10.1371/journal.pone.0034515 

• Wiley H.S. 2012. "Cooking Up Creative Solutions." The Scientist 26, no. 5:26-27. PNNL-SA-88063. 

2011 

• Ahring B.K., N.S. Baliga, J.R. Frederickson, S. Kaplan, H.B. Pakrasi, J.G. Pounds, and I. Shah, et al. 2011. Biological Interactions and Dynamics Science Theme Advisory Panel (BID-STAP). PNNL-20717. Richland, WA: Pacific Northwest National Laboratory. Biological Interactions and Dynamics Science Theme Advisory Panel (BID-STAP) 

• Brown G.E., A. Chaka, D.K. Shuh, E.E. Roden, C.J. Werth, N.J. Hess, and A.R. Felmy, et al. 2011. EMSL Geochemistry, Biogeochemistry and Subsurface Science-Science Theme Advisory Panel Meeting. PNNL-20601. Richland, WA: Pacific Northwest National Laboratory. EMSL Geochemistry, Biogeochemistry and Subsurface Science-Science Theme Advisory Panel Meeting 

• Labaj P.P., G.G. Leparc, B.E. Linggi, L.M. Markillie, H.S. Wiley, and D.P. Kreil. 2011. "Characterization and Improvement of RNA-Seq Precision in Quantitative Transcript Expression Profiling." Bioinformatics 27, no. 13:I383-I391. PNNL-SA-77408. doi:10.1093/bioinformatics/btr247 

• Wiley H.S. 2011. "At the Tipping Point." The Scientist 25, no. 2:28. PNNL-SA-77373. 

• Wiley H.S. 2011. "Integrating Multiple Types of Data for Signaling Research: Challenges and Opportunities." Science Signaling 4, no. 160:pe9. PNNL-SA-77372. doi:10.1126/scisignal.2001826 

2010 

• Joslin E.J., H. Shankaran, L.K. Opresko, N. Bollinger, D.A. Lauffenburger, and H.S. Wiley. 2010. "Structure of the EGF receptor transactivation circuit integrates multiple signals with cell context." Molecular Systems Biology 6, no. 7:1293-1306. PNNL-SA-66134. doi:10.1039/c003921g 

• Prince R.N., E.R. Schreiter, P. Zou, H.S. Wiley, A.Y. Ting, R.T. Lee, and D.A. Lauffenburger. 2010. "The heparin-binding domain of HB-EGF mediates localization to sites of cell-cell contact and prevents HB-EGF proteolytic release." Journal of Cell Science 123, no. 13:2308-2318. PNNL-SA-73406. doi:10.1242/jcs.058321 

• Shankaran H., and H.S. Wiley. 2010. "Oscillatory Dynamics of the Extracellular Signal-regulated Kinase Pathway." Current Opinion in Genetics & Development 20, no. 6:650-655. PNNL-SA-74761. doi:10.1016/j.gde.2010.08.002 

• Weber T.J., H. Shankaran, H.S. Wiley, L.K. Opresko, W.B. Chrisler, and R.D. Quesenberry. 2010. "Basic Fibroblast Growth Factor Regulates Persistent ERK Osciliations in Premaligant but not Malignant JB6 Cells." Journal of Investigative Dermatology 130, no. 5:144-156. PNNL-SA-59833. 

• Wiley H.S. 2010. "Down with Reviews." The Scientist 24, no. 4:31. PNNL-SA-72081. 

• Wiley H.S. 2010. "Keep it Simple." The Scientist 24, no. 5:37. PNNL-SA-72919. 

• Wiley H.S. 2010. "Mind Your Manners." The Scientist 24, no. 1:23. PNNL-SA-70034. 

• Wiley H.S. 2010. "One of the Good Guys." The Scientist 24, no. 10:36. PNNL-SA-75424. 

• Wiley H.S. 2010. "Scientists vs. Engineers." The Scientist 24, no. 7:29. PNNL-SA-74758. 

• Wiley H.S. 2010. "Think Outside the Bio-Box." The Scientist 24, no. 6:31. PNNL-SA-72920. 

• Wiley H.S. 2010. "To Join or Not to Join." The Scientist 24, no. 3:33. PNNL-SA-72083. 

• Wiley H.S. 2010. "Why I Love Vendors." The Scientist 24, no. 2:23. PNNL-SA-72084. 

2009 

• Heibeck T.H., S. Ding, L.K. Opresko, R. Zhao, A.A. Schepmoes, F. Yang, and A.V. Tolmachev, et al. 2009. "An Extensive Survey of Tyrosine Phosphorylation Revealing New Sites in Human Mammary Epithelial Cells." Journal of Proteome Research 8, no. 8:3852-3861. PNNL-SA-63993. 

• Shankaran H., D.L. Ippolito, W.B. Chrisler, H. Resat, N. Bollinger, L.K. Opresko, and H.S. Wiley. 2009. "Rapid and Sustained Nuclear-Cytoplasmic ERK Oscillations Induced by Epidermal Growth Factor." Molecular Systems Biology 5. PNNL-SA-54421. doi:10.1038/msb.2009.90 

• Taylor R.C., M. Singhal, D.S. Daly, J.M. Gilmore, W.R. Cannon, K.O. Domico, and A.M. White, et al. 2009. "An analysis pipeline for the inference of protein-protein interaction networks." International Journal of Data Mining and Bioinformatics 3, no. 4) (Sp. Iss. SI:409-430. PNNL-SA-59756. doi:10.1504/IJDMB.2009.029204 

• Wiley H.S. 2009. "Bring Back Reprint Requests." The Scientist 23, no. 9:29-29. PNNL-SA-68429. 

• Wiley H.S. 2009. "Collaborations: Challenging, but Key." The Scientist 23, no. 10:29. PNNL-SA-69042. 

• Wiley H.S. 2009. "Facts First." The Scientist 23, no. 2:29. PNNL-SA-64882. 

• Wiley H.S. 2009. "Give Young Scientists a Break." The Scientist 23, no. 11:27. PNNL-SA-69043. 

• Wiley H.S. 2009. "Heroes and Villains." The Scientist 23, no. 5:27-27. PNNL-SA-66133. 

• Wiley H.S. 2009. "Quitters sometimes win." The Scientist 23, no. 7:27-27. PNNL-SA-67239. 

• Wiley H.S. 2009. "Speak Your Mind." The Scientist 23, no. 12:25. PNNL-SA-70023. 

• Wiley H.S. 2009. "Stimulus Application? Not Me." The Scientist 23, no. 6:25. PNNL-SA-66769. 

• Wiley H.S. 2009. "The Problem of Perception." The Scientist 23, no. 3:31. PNNL-SA-64883. 

• Wiley H.S. 2009. "Timing is Everything." The Scientist 23, no. 8:25-25. PNNL-SA-67375. 

• Wiley H.S. 2009. "Why don't we share data?" The Scientist 23, no. 4:33-33. PNNL-SA-65489. 

• Wiley H.S. 2009. Implementation Plans for a Systems Microbiology and Extremophile Research Facility. PNNL-19073. Richland, WA: Pacific Northwest National Laboratory. Implementation Plans for a Systems Microbiology and Extremophile Research Facility 

• Zhang Y., L.K. Opresko, H. Shankaran, W.B. Chrisler, H.S. Wiley, and H. Resat. 2009. "HER/ErbB Receptor Interactions and Signaling Patterns in Human Mammary Epithelial Cells." BMC Cell Biology 10. PNNL-SA-64538. doi:10.1186/1471-2121-10-78 

2008 

• Jacobs J.M., K.M. Waters, L.E. Kathmann, D.G. Camp, H.S. Wiley, R.D. Smith, and B.D. Thrall. 2008. "The Mammary Epithelial Cell Secretome and its Regulation by Signal Transduction Pathways." Journal of Proteome Research 7, no. 2:558-569. PNNL-SA-56310. doi:10.1021/pr0704377 

• Pelletier D.A., G.B. Hurst, L.J. Foote, P.K. Lankford, C.K. McKeown, T.S. Lu, and D.D. Schmoyer, et al. 2008. "A general system for studying protein-protein interactions in gram-negative bacteria." Journal of Proteome Research 7, no. 8:3319-3328. PNNL-SA-58778. doi:10.1021/pr8001832 

• Rodland K.D., N. Bollinger, D.L. Ippolito, L. Opresko, R.J. Coffey, R.C. Zangar, and H.S. Wiley. 2008. "Multiple Mechanisms are Responsible for Transactivation of the Epidermal Growth Factor Receptor in Mammary Epithelial Cells." Journal of Biological Chemistry 283, no. 46:31477-31487. PNNL-SA-59460. doi:10.1074/jbc.M800456200 

• Rogers S., M. Girolami, M. Girolami, W. Kolch, K.M. Waters, T. Liu, and B.D. Thrall, et al. 2008. "Investigating the Correspondence Between Transcriptomic and Proteomic Expression Profiles Using Coupled Cluster Models." Bioinformatics 24, no. 24:2894-2900. PNNL-SA-61286. doi:10.1093/bioinformatics/btn553 

• Wiley H.S. 2008. "Big biology is here to stay." The Scientist 22, no. 8:27. PNNL-SA-62007. 

• Wiley H.S. 2008. "Hypothesis-free? No such thing." The Scientist 22, no. 5:31. PNNL-SA-60389. 

• Wiley H.S. 2008. "Hypothesis-free? No such thing." The Scientist 22, no. 5:31. PNNL-SA-61703. 

• Wiley H.S. 2008. "It's not just about innovation." The Scientist 22, no. 3:33. PNNL-SA-59510. 

• Wiley H.S. 2008. "My favorite fraud." The Scientist 22, no. 9:29. PNNL-SA-62006. 

• Wiley H.S. 2008. "No to negative data." The Scientist 22, no. 4:39. PNNL-SA-59968. 

• Wiley H.S. 2008. "Peer review isn't perfect but it's also not a conspiracy." The Scientist 22, no. 11:31. PNNL-SA-63211. 

• Wiley H.S. 2008. "Research locally, think globally." The Scientist 22, no. 7:29. PNNL-SA-61209. 

• Wiley H.S. 2008. "Telling science's stories." The Scientist 22, no. 1:27. PNNL-SA-58288. 

• Wiley H.S. 2008. "Think Like a Cockroach: How I Survived an Extinction Event in Biological Research." The Scientist 22, no. 2:29. PNNL-SA-58583. 

• Wiley H.S. 2008. "Waiting for Einstein." The Scientist 22, no. 10:31. PNNL-SA-63212. 

• Wiley H.S. 2008. "Why national labs?" The Scientist 22, no. 6:31. PNNL-SA-60752. 

• Wiley H.S., and H. Shankaran. 2008. "Smad Signaling Dynamics: Insights from a Parsimonious Model." Science Signaling 1, no. 36:pe41. PNNL-SA-61962. 

2007 

• Joslin E.J., L. Opresko, A. Wells, H.S. Wiley, and D.A. Lauffenburger. 2007. "EGF-Receptor-Mediated Mammary Epithelial Cell Migration is Driven by Sustained ERK Signaling from Autocrine Stimulation." Journal of Cell Science 120, no. 20:3688-3699. PNNL-SA-54757. doi:10.1242/jcs.010488 

• Perrine K.A., B.L. Lamarche, D.F. Hopkins, S.E. Budge, L. Opresko, H.S. Wiley, and M.B. Sowa. 2007. "High Speed Method for in Situ Multispectral Image Registration." Microscopy Research and Technique 70, no. 4:382-389. PNNL-SA-52092. doi:10.1002/jemt.20423 

• Shah A.R., M. Singhal, K.R. Klicker, E.G. Stephan, H.S. Wiley, and K.M. Waters. 2007. "Enabling high-throughput data management systems biology: The Bioinformatics Resource Manager." Bioinformatics 23, no. 7:906-909. PNNL-SA-49327. doi:10.1093/bioinformatics/btm031 

• Shankaran H., H. Resat, and H.S. Wiley. 2007. "Cell surface receptors for signal transduction and ligand transport - a design principles study." PLoS Computational Biology 3, no. 6:e101. PNNL-SA-51724. doi:10.1371/journal.pcbi.0030101 

• Shankaran H., H.S. Wiley, and H. Resat. 2007. "Receptor downregulation and desensitization enhance the information processing ability of signaling receptors." BMC Systems Biology 1. PNNL-SA-53292. doi:10.1186/1752-0509-1-48 

• Sharp J.L., K.K. Anderson, G.B. Hurst, D.S. Daly, D.A. Pelletier, W.R. Cannon, and D.L. Auberry, et al. 2007. "Statistically Inferring Protein-Protein Associations with Affinity Isolation LC-MS/MS Assays." Journal of Proteome Research 6, no. 9:3788-3795. PNNL-SA-57329. doi:10.1021/pr0701106 

2006 

• Shankaran H., H.S. Wiley, and H. Resat. 2006. "Modeling the effects of HER/ErbB1-3 co-expression on receptor dimerization and biological response." Biophysical Journal 90, no. 11:3993-4009. PNNL-SA-47882. 

• Shankaran H., H.S. Wiley, and H. Resat. 2006. "Modeling the Effects of HER/ErbB1-3 Coexpression on Receptor Dimerization and Biological Response." Biophysical Journal 90, no. 11:3993-4009. PNNL-SA-45412. doi:10.1529/biophysj.105.080580 

• Wiley H.S. 2006. "Systems Biology." The Scientist Vol. 20 No. 6, no. June 2006:52-57. PNNL-SA-49943. 

2005 

• Dong J., L. Opresko, W.B. Chrisler, G. Orr, R.D. Quesenberry, D.A. Lauffenburger, and H.S. Wiley. 2005. "The Membrane-anchoring Domain of Epidermal Growth Factor Receptor Ligands Dictates Their Ability to Operate in Juxtacrine Mode." Molecular Biology of the Cell 16, no. 6:2984-2998. PNWD-SA-7019. 

• Hendriks B.S., G. Orr, A.H. Wells, H.S. Wiley, and D.A. Lauffenburger. 2005. "Parsing ERK Activation Reveals Quantitatively Equivalent Contributions From Epidermal Growth Factor Receptor and HER2 In Human Mammary Epithelial Cells." Journal of Biological Chemistry 280, no. 7:6157-6169. PNNL-SA-43533. 

• Markillie L.M., C.T. Lin, J.N. Adkins, D.L. Auberry, E.A. Hill, B.S. Hooker, and P.A. Moore, et al. 2005. "Simple Protein Complex Purification and Identification Method Suitable for High- throughput Mapping of Protein Interaction Networks." Journal of Proteome Research 4, no. 2:268-274. PNNL-SA-42494. doi:10.1021/pr049847a 

• Miller J.H., F. Zheng, S. Jin, L. Opresko, H.S. Wiley, and H. Resat. 2005. "A Model of cytokine shedding induced by low doses of gamma radiation." Radiation Research 163, no. 3:337-342. PNNL-SA-40412. 

• Monine M.I., A.M. Berezhkovskii, E.J. Joslin, H.S. Wiley, D.A. Lauffenburger, and S. Shvartsman. 2005. "Ligand Accumulation in Autocrine Cell Cultures." Biophysical Journal 88, no. 4:2384-2390. PNNL-SA-44686. 

• Orr G., D. Hu, S. Ozcelik, L. Opresko, H.S. Wiley, and S.D. Colson. 2005. "Cholesterol Dictates the Freedom of EGF Receptors and HER2 in the Plane of the Membrane." Biophysical Journal 89, no. 2:1362-1373. PNNL-SA-44634. doi:10.1529/biophysj.104.056192 

2004 

• Chen W.U., R.L. Woodbury, L.E. Kathmann, L. Opresko, R.C. Zangar, H.S. Wiley, and B.D. Thrall. 2004. "Induced autocrine signaling through the epidermal growth factor receptor contributes to the response of mammary epithelial cells to tumor necrosis factor alpha." Journal of Biological Chemistry 279, no. 18:18488-18496. PNNL-SA-40802. 

• Maly I.V., H.S. Wiley, and D.A. Lauffenburger. 2004. "Self-Organization of Polarized Cell Signaling via Autocrine Circuits: Computational Model Analysis." Biophysical Journal 86, no. 1:10-22. PNNL-SA-40760. 

• Resat M.S., J.C. Solinsky, H.S. Wiley, K.A. Perrine, T.A. Seim, and S.E. Budge. 2004. "3-D Multispectral Monitoring of Living-Cell Signaling Using Confocal-Imaging and FPGA Processing." In International Symposium on Biomedical Imaging, 2004 Proceedings, IEEE, 1, 680-683. Piscataway, New Jersey:IEEE. PNNL-SA-41577. 

• Shvartsman S., H.S. Wiley, and D.A. Lauffenburger. 2004. "Epidermal growth factor receptor signaling in tissue." IEEE Control Systems Magazine 24, no. 4:53-61. PNNL-SA-42510. doi:10.1109/MCS.2004.1316653 

• Varnum S.M., D.N. Streblow, M.E. Monroe, P. Smith, K.J. Auberry, L. Pasa-Tolic, and D. Wang, et al. 2004. "Identification of Proteins in Human Cytomegalovirus (HCMV) Particles: the HCMV Proteome." Journal of Virology 78, no. 20:10960-10966. PNNL-SA-43398. 

• Wiley H.S., and G.S. Michaels. 2004. "Should software hold data hostage?" Nature Biotechnology 22, no. 8:1037-1038. PNNL-SA-42214. 

2003 

• Feldhaus M., R.W. Siegel, L. Opresko, J.R. Coleman, J.M. Feldhaus, Y.A. Yeung, and J.R. Cochran, et al. 2003. "Flow-Cytometric Isolation of Human Antibodies from a Nonimmune Saccharomyces cerevisiae Surface Display Library." Nature Biotechnology 21, no. 2:163-170. PNNL-SA-36938. 

• Hendriks B.S., L. Opresko, H.S. Wiley, and D.A. Lauffenburger. 2003. "Coregulation of Epidermal Growth Factor Receptor/Human Epidermal Growth Factor Receptor 2 (HER2) Levels and Locations: Quantitative Analysis of HER2 Overexpression Effects." Cancer Research 63, no. 5:1130-7. PNNL-SA-41392. 

• Hendriks B.S., L. Opresko, H.S. Wiley, and D.A. Lauffenburger. 2003. "Quantitative Analysis of HER2-mediated Effects on HER2 and Epidermal Growth Factor Receptor Endocytosis: DISTRIBUTION OF HOMO- AND HETERODIMERS DEPENDS ON RELATIVE HER2 LEVELS." Journal of Biological Chemistry 278, no. 26:23343-23351. PNWD-SA-5918. 

• Resat H., J.A. Ewald, D.A. Dixon, and H.S. Wiley. 2003. "An Integrated Model of Epidermal Growth Factor Receptor Trafficking and Signal Transduction." Biophysical Journal 85, no. 2:730-743. PNNL-SA-38098. 

• Wiley H.S. 2003. "Trafficking of ErbB receptors and its influence on signaling." Experimental Cell Research 284, no. 1:78-88. PNNL-SA-41391. doi:10.1016/S0014-4827(03)00002-8 

• Wiley H.S. 2003. "Trafficking of the ErbB Receptors and its Influence on Signaling." Experimental Cell Research 284, no. 1:78-88. PNWD-SA-5888. 

• Wiley H.S., S. Shvartsman, and D.A. Lauffenburger. 2003. "Computational modeling of the EGF-receptor system: a paradigm for systems biology." Trends in Cell Biology 13, no. 1:43-50. PNNL-SA-38177. 

2002 

• Buchanan M.V., F. Larimer, H.S. Wiley, S.J. Kennel, T.C. Squier, J.M. Ramsey, and K.D. Rodland, et al. 2002. "Genomes to Life "Center for Molecular and Cellular Systems": A research program for identification and characterization of protein complexes." OMICS. A Journal of Integrative Biology 6, no. 4:287-303. PNWD-SA-6390. 

• Dewitt A., T. Iida, H. Lam, V. Hill, H.S. Wiley, and D.A. Lauffenburger. 2002. "Affinity Regulates Spatial Range of EGF Receptor Autocrine Ligand Binding." Developmental Biology 250, no. 2:305-316. PNNL-SA-41390. 

2001 

• Burke P., K. Schooler, and H.S. Wiley. 2001. "Regulation of Epidermal Growth Factor Receptor Signaling by Endocytosis and Intracellular Trafficking." Molecular Biology of the Cell 12, no. 6:1897-1910. PNWD-SA-5383. 

• Dewitt A.E., J.Y. Dong, H.S. Wiley, and D.A. Lauffenburger. 2001. "Quantitative Analysis of the EGF Receptor Autocrine System Reveals Cryptic Regulation of Cell Response by Ligand Capture." Journal of Cell Science 114, no. 12:2301-2313. PNWD-SA-5371. 

• Holtom G.R., B.D. Thrall, B. Chin, H.S. Wiley, and S.D. Colson. 2001. "Achieving molecular selectivity in imaging using multiphoton Raman spectroscopy techniques." Traffic 2, no. 11:781-788. PNNL-SA-35318. 

• Maheshwari G., H.S. Wiley, and D.A. Lauffenburger. 2001. "Autocrine epidermal growth factor signaling stimulates directionally persistent mammary epithelial cell migration." Journal of Cell Biology 155, no. 7:1123-1128. PNNL-SA-36069. 

• Resat H., H.S. Wiley, and D.A. Dixon. 2001. "Probability-Weighted Dynamic Monte Carlo Method for Reaction Kinetics Simulations." Journal of Physical Chemistry B 105, no. 44:11026-11034. PNNL-SA-34648. 

• Resat H., H.S. Wiley, and D.A. Dixon. 2001. "Probability-Weighted Dynamic Monte Carlo Method for Reaction Kinetics Simulations." Journal of Physical Chemistry B 105, no. 44:11026-11034. PNNL-SA-38067. 

• Shvartsman S., M.P. Hagan, A. Yacoub, P. Dent, H.S. Wiley, and D.A. Lauffenburger. 2001. "Autocrine loops with positive feedback enable context-dependent cell signaling." American Journal of Physiology. Cell Physiology 282, no. 3:C545-C559. PNNL-SA-36711. 

• Wiley H.S., and P.M. Burke. 2001. "Regulation of Receptor Tyrosine Kinase Signaling by Endocytic Trafficking." Traffic 2, no. 1:12-18. PNWD-SA-5372.