Publications

Peer-reviewed Publications | Invited Articles and Reviews | Patents and Patent Applications

 

Peer-reviewed Publications

2017photo

  • Knutson ST, Westwood BM, Leuthaeuser JB, Turner B, Nguyendac D, Shea G, Kumar K, Hayden J, Harper A, Brown SD, Morris JH, Ferrin TE, Babbitt PC, Fetrow JS. An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences. Protein Sci. 2017 Apr;26(4):677-699. doi: 10.1002/pro.3112. Epub 2017 Mar 8. PMID: 28054422.
  • Harper AF, Leuthaeuser JB, Babbitt PC, Morris JH, Ferrin TE, Poole LP, Fetrow JS. An atlas of peroxiredoxins created using an active site profile-based approach to functionally relevant clustering of proteins. PLoS Comput Biol. 2017 Feb 10;13(2):e1005284. doi: 10.1371/journal.pcbi.1005284. eCollection 2017 Feb. PMID: 28187133.

2016

  • Leuthaeuser JB, Morris JH, Harper AF, Ferrin TE, Babbitt PC, Fetrow JS. DASP3: identification of protein sequences belonging to functionally relevant groups. BMC Bioinformatics. 2016 Nov 11;17(1):458. doi: 10.1186/s12859-016-1295-z. PMID: 27835946.
  • Olex AL, Turkett WH, Brzoza-Lewis KL, Fetrow JS, Hiltbold EM. Impact of the Type I Interferon Receptor on the Global Gene Expression Program During the Course of Dendritic Cell Maturation Induced by Polyinosinic Polycytidylic Acid. J Interferon Cytokine Res. 2016 Jun;36(6):382-400. doi: 10.1089/jir.2014.0150. Epub 2016 Apr 1. PMID: 27035059.
  • Gober JG, Rydeen A, Gibson-O’Grady E, Leuthaeuser J, Fetrow J, Brustad E. Mutating a Highly Conserved Residue in Diverse Cytochrome P450s Facilitates Diastereoselective Olefin Cyclopropanation. Chembiochem. 2016 Mar 2;17(5):394-7. doi: 10.1002/cbic.201500624. Epub 2016 Feb 4. PMID: 26690878.

2015

  • Leuthaeuser JB, Knutson ST, Kumar K, Babbitt PC, Fetrow JS. Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity. Protein Science. Sep 2015;24(9):1423-1439. doi: 10.1002/pro.2724. Epub 2015 Aug 18. PMID: 26073648.

2014

  • Olex AL, Turkett WH, Fetrow JS, Loeser RF. Integration of gene expression data with network-based analysis to identify signaling and metabolic pathways regulated during the development of osteoarthritis. Gene. 2014 May 25;542(1):38-45. doi: 10.1016/j.gene.2014.03.022. PMID 24630964.
  • Bansal N, Mims J, Kuremsky JG, Olex AL, Zhao W, Yin L, Wani R, Qian J, Center B, Marrs GS, Porosnicu M, Fetrow JS, Tsang AW, Furdui CM. Broad phenotypic changes associated with gain of radiation resistance in head and neck squamous cell cancer. Antioxid Redox Signal. 2014 Jul 10;21(2):221-36. doi: 10.1089/ars.2013.5690. PMID: 24597745.

2013

  • Lewis DR, Olex AL, Lundy SR, Turkett WH, Fetrow JS, Muday GK. A kinetic analysis of the auxin transcriptome reveals cell wall remodeling proteins that modulate lateral root development in Arabidopsis. Plant Cell. 2013 Sep;25(9):3329-46. doi: 10.1105/tpc.113.114868. PMID: 24045021.
  • Loeser RF, Olex AL, McNulty MA, Carlson CS, Callahan M, Ferguson C, Fetrow JS. Disease progression and phasic changes in gene expression in a mouse model of osteoarthritis. PLoS One. 2013;8(1):e54633. doi: 10.1371/journal.pone.0054633. PMID: 23382930.

2012

  • Salsbury Jr FR, Poole LB, Fetrow JS. Electrostatics of Cysteine Residues in Proteins: Parameterization and Validation of a Simple Model. Proteins. 2012 Nov;80(11):2583-91. doi: 10.1002/prot.24142. PMID: 22777874.
  • Salsbury Jr FR, Yuan Y, Knaggs MH, Poole LB, Fetrow JS. Structural and Electrostatic Asymmetry at the Active Site in Typical and Atypical Peroxiredoxin Dimers. J Phys Chem B. 2012 Jun 14;116(23):6832-43. doi: 10.1021/jp212606k. PMID: 22401569.
  • Loeser RF, Olex AL, McNulty MA, Carlson CS, Callahan MF, Ferguson CM, Chou J, Leng X, Fetrow JS. Microarray Analysis Reveals Age-related Differences in Gene Expression During the Development of Osteoarthritis in Mice. Arthritis Rheum. 2012 Mar;64(3):705-17. doi: 10.1002/art.33388. PMID: 21972019.

2011

  • Olex AL, Fetrow JS. SC2ATmd: a tool for integration of the figure of merit with cluster analysis for gene expression data. Bioinformatics 2011, 27(9):1330-1331. doi: 10.1093/bioinformatics/btr115. PMID: 21372084.
  • Soito L, Williamson C, Knutson ST, Fetrow JS, Poole LB, Nelson KJ. PREX: PeroxiRedoxin classification indEX, a database of subfamily assignments across the diverse peroxiredoxin family. Nucleic Acids Res. 2011 Jan;39(Database issue):D332-7. doi: 10.1093/nar/gkq1060. PMID: 21036863.
  • Nelson KJ, Knutson ST, Soito L, Klomsiri C, Poole LB, Fetrow JS. Analysis of the peroxiredoxin family: Using active-site structure and sequence information for global classification and residue analysis. Proteins: Structure, Function, and Bioinformatics, 2011, 79:947-964. doi: 10.1002/prot.22936. PMID: 21287625.
  • John DJ, Fetrow JS, Norris JL. Continuous Cotemporal Probabilistic Modeling of Systems Biology Networks from Sparse Data. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2011 Sep-Oct;8(5):1208-22. doi: 10.1109/TCBB.2010.95. PMID: 20855920.

2010

  • Olex AL, Hiltbold EM, Leng X, Fetrow JS. Dynamics of dendritic cell maturation are identified through a novel filtering strategy applied to biological time-course microarray replicates. BMC Immunology 2010, Aug 8, 11:41. doi: 10.1186/1471-2172-11-41. PMID: 20682054.
  • Marcott PF, Allen EE, Loeser RF, Fetrow JS. Computational Modeling of the Effects of Oxidative Stress on the IGF-1 Signaling Pathway in Human Articular Chondrocytes.  Proceedings of ACM BCB 2010 Conference (peer-reviewed full paper). P. 71-78. doi: 10.1145/1854776.1854791.
  • Black RA, John DJ, Fetrow JS, Norris JL. Examining Effects of Variability on Systems Biology Modeling Algorithms. Proceedings of ACM BCB 2010 Conference (short paper).  Pp. 374-377.  doi: 10.1145/1854776.1854883.
  • Allen EE, Norris JL, John DJ, Thomas SJ, Turkett WH Jr, Fetrow JS. Comparison of Co-Temporal Modeling Algorithms on Sparse Experimental Time Series Data Sets. 2010 IEEE International Conference on Bioinformatics and Bioengineering. (full conference paper) Philadelphia, Pennsylvania USA. May 31-June 03. doi: 10.1109/BIBE.2010.21.
  • Yuan Y, Knaggs MH, Poole LB, Fetrow JS, Salsbury FR Jr. Conformational and oligomeric effects on the cysteine pK(a) of tryparedoxin peroxidase. J Biomol Struct Dyn. 2010, 28(1):51-70. doi: 10.1080/07391102.2010.10507343. PMID: 20476795.

2008

  • Salsbury FR Jr, Knutson ST, Poole LB, Fetrow JS. Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid. Protein Sci 2008, 17(2):299-312. doi: 10.1110/ps.073096508. PMID: 18227433.

2007

  • Poole LB, Klomsiri C, Knaggs SA, Furdui CM, Nelson KJ, Thomas MJ, Fetrow JS, Daniel LW, King SB. Fluorescent and affinity-based tools to detect cysteine sulfenic acid formation in proteins. Bioconjug Chem 2007, 18(6):2004-2017. doi: 10.1021/bc700257a. PMID: 18030992.
  • Michalek RD, Nelson KJ, Holbrook BC, Yi JS, Stridiron D, Daniel LW, Fetrow JS, King SB, Poole LB, Grayson JM. The requirement of reversible cysteine sulfenic acid formation for T cell activation and function. J Immunol 2007, 179(10):6456-6467. doi: 10.4049/jimmunol.179.10.6456. PMID: 17982034.
  • John DJ, Fetrow JS, Norris JL. Metropolis-Hastings Algorithm and Continuous Regression for finding Next-State Models of Protein Modification using Information Scores. Proceedings of the 7th International Symposium of IEEE Bioinformatics and Bioengineering. 2007. Jack Y. Yang and Mary Qu Yang and Michelle M. Zhu and Yanqing Zhang and Hamid R. Arabnia and Youping Deng and Nikolaos Bourbakis, eds. p. 35-41. doi: 10.1109/BIBE.2007.4375542.
  • Budiman ME, Knaggs MH, Fetrow JS, Alexander RW. Using molecular dynamics to map interaction networks in an aminoacyl-tRNA synthetase. Proteins 2007, 68(3):670-689. doi: 10.1002/prot.21426. PMID: 17510965.
  • Allen EE, Diao L, Fetrow JS, John DJ, Loeser RF Jr, Poole LB. The shuffle index and evaluation of models of signal transduction pathways. Proceedings of the 45th ACM Southeast Regional Conference, Winston-Salem, NC. March 2007, p. 250-255. doi: 10.1145/1233341.1233386.
  • Olex AL, John DJ, Hiltbold EM, Fetrow JS. Additional limitations of the clustering validation method figure of merit. Proceedings of the 45th ACM Southeast Regional Conference, Winston-Salem, NC. March 2007, p. 238-243. doi: 10.1145/1233341.1233384.
  • Pryor EE Jr, Fetrow JS. PDB-SQL: A Storage Engine for Macromolecular Data. Proceedings of the 45th ACM Southeast Regional Conference, Winston-Salem, NC. March 2007, p. 260-265. doi: 10.1145/1233341.1233388.
  • Knaggs MH, Salsbury FR Jr, Edgell MH, Fetrow JS. Insights into correlated motions and long-range interactions in CheY derived from molecular dynamics simulations. Biophys J 2007, 92(6):2062-2079. doi:10.1529/biophysj.106.081950. PMID: 17172298.

graphic2006

  • Fetrow, J.S. and John, D.J. Bioinformatics and computing curriculum: A new model for interdisciplinary courses. Inroads–SIGSCE Bulletin. 2006. 38:185-190.
  • Fetrow, J.S., Knutson, S.T. and Edgell, M.H. Mutations in α-helical solvent exposed sites of eglin c have long-range effects: evidence from molecular dynamics simulations. Proteins: Struct Funct Bioinform. 2006 May 1;63(2):356-72. Epub 2005 Dec 9. PMID: 16342264.
  • Allen, E.E., Fetrow, J.S., John, D.J., Pecorella A. and Turkett, W. Re-constructing networks using co-temporal functions. Proceedings of the 44th ACM Southeast Conference, (Marius Silaghi, ed), Melbourne, Florida. March 2006, 417-422.
  • Allen, E.E., Fetrow, J.S., Daniel, L.W., Thomas, S.J., John, D.J. Algebraic dependency models of protein signal transduction networks from time-series data. J. Theor. Biol. 2006 Jan 21;238(2):317-30. Epub 2005 Jul 5. doi: 10.1016/j.jtbi.2005.05.010. PMID: 16002094.

2005

  • Huff, R. G., Bayram, E., Tan, H., Knutson, S.T., Knaggs, M.H., Richon, A.B., Santago II, P., and Fetrow, J.S. Chemical and Structural Diversity in Cyclooxygenase Protein Active Sites. Chemistry and Biodiversity. 2005. 2:1533-1552. doi: 10.1002/cbdv.200590125. PMID: 17191953.
  • Allen, E.E., Fetrow, J.S., John, D.J., Thomas, S.J. Heuristic dependency conjectures in proteomic signaling pathways. Proceedings of the 43 rd Annual Association for Computing Machinery Southeast Conference (Victor A. Clincy, ed.) Kennesaw, Georgia, March 2005.

2004

  • Baxter, S.M., Rosenblum, J.S., Knutson, S.T., Nelson, M.R., Montimurro, J.S., Di Gennaro, J.A., Speir, J.A., Burbaum, J.J. and Fetrow, J.S. Synergistic computational and experimental proteomics approaches for more accurate detection of active serine hydrolases in yeast. Mol Cell Proteomics. 2004 Mar;3(3):209-25. Epub 2003 Nov 25. doi: 10.1074/mcp.M300082-MCP200. PMID: PMID: 14645503.

2003

  • Cammer, S.A., Hoffman, B.T., Speir, J.A., Canady, M., Nelson, M.R., Knutson, S.T., Gallina, M., Baxter, S.M., and Fetrow, J.S. Structure-based active site profiles for genome analysis and sub-family classification. J. Mol. Biol. 2003 Nov 28;334(3):387-401.
  • Herrgard, S., Cammer, S.A., Speir, J.A., Hoffman, B.T., Knutson, S., Gallina, M., Fetrow, J.S., Baxter, S.M. Prediction of deleterious functional effects of amino acid mutations using a library of structure-based function descriptors. Proteins 2003, 53(4):806-816.
  • Zhou, H., Gallina, M., Mao, H., Betz, S.F., Fetrow, J.S., and Domaille, P.J. 1H, 13C, and 15N resonance assignments and secondary structure for the human protein tyrosine phosphatase, PRL-2. J. Biomol. NMR. 2003 27(4):397-398.

2001

  • DeWeerd, K., Grigoryants, V., Sun, Y., Fetrow, J.S., Scholes, C.P. EPR-detected folding kinetics of externally located cysteine-directed spin-labeled mutants of iso-1-cytochrome cBiochemistry 2001 Dec 25;40(51):15846-15855.
  • Di Gennaro, J.A., Siew, N., Hoffman, B.T., Zhang, L., Skolnick, J., Neilson, L.I., Fetrow, J.S. Enhanced functional annotation of protein sequences via the use of structural descriptors. J Struct Biol. 2001 May-Jun;134(2-3):232-245.
  • Fetrow, J.S., Siew, N., Di Gennaro, J.A., Martinez-Yamout, M., Dyson, H.J., Skolnick, J. Genomic-scale comparison of sequence- and structure-based methods of function prediction: does structure provide additional insight? Protein Sci. 2001 May;10(5):1005-1014.

1999

  • Fetrow, J.S., Siew, N., and Skolnick, J. Structure-based functional motif identifies a potential disulfide oxidoreductase active site in the serine-threonine protein phosphatase-1 subfamily. FASEB J. 1999 Oct;13(13):1866-1874.
  • Skolnick, J., Fetrow, J., Ortiz, A.R., and Kolinski, A. The role of computational biology in the genomics revolution Proceedings of the NRC Chemical Sciences Roundtable Workshop on the Impact of Advances in Computing and Communications Technologies on Chemical Sciences and Technology. 1999 44-61.
  • Zhang, B., Rychlewski, L., Pawlowski, K., Fetrow, J. S., Skolnick, J., Godzik, A. From fold predictions to function predictions: Automation of functional site conservation analysis for functional genome predictions. Protein Sci. 1999 May;8(5):1104-1115.
  • Fetrow, J.S. and Baxter, S.M. Assignment of 15N chemical shifts and 15N relaxation measurements for oxidized and reduced iso-1-cytochrome c. Biochemistry. 1999 Apr 6;38(14):4480-4492.
  • Baxter, S.M. and Fetrow, J.S. Hydrogen exchange behavior of [U15N]-labeled oxidized and reduced iso-1-cytochrome c. Biochemistry. 1999 Apr 6;38(14):4493-4503.
  • Mittermann, I., Fetrow, J.S. Schaak, D.L., Almo, S.C., Kraft, D., Heberle-Bors, E., Valenta, R. Oligomerization of profilins from birch, man and yeast. Profilin, a ligand for itself? Sexual Plant Reprod. 1998 11(4):183-191.
  • Fetrow, J.S. and Berg, G. Using information theory to discover side chain rotamer classes: Analysis of the effects of local backbone structure. Proceedings of the Pacific Symposium on Biocomputing ’98, World Sci. Publ. Pac Symp Biocomput. 1999 278-289.

1998

  • Zhang, L., Godzik, A., Skolnick, J., Fetrow, J. Functional analysis of Escherichia coli proteins for members of the a / b hydrolase family. Fold Des. 1998 3(6):535-548.
  • Fetrow, J., Godzik, A. and Skolnick, J. Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: Identification of proteins exhibiting the glutaredoxin/thioredoxin disulfide oxidoreductase activity. J. Mol. Biol. 1998 Oct 2;282(4):703-711.
  • Fetrow, J.S. and Skolnick, J. Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases. J. Mol. Biol. 1998 Sep 4;281(5):949-968.
  • Fetrow, J.S. and Godzik, A. Function driven protein evolution: A possible proto-protein for the RNA-binding proteins. Proceedings of Pacific Symposium on Biocomputing (Ed. R.B. Altman, A.K. Dunker, L. Hunter T. Klein). 1998 485-496.
  • Fetrow, J.S., Spitzer, J.S., Gilden, B.M., Mellender, S.J., Begley, T., Haas, B., and Boose, T.L. Structure, function, and temperature sensitivity analysis of directed, random mutants of proline 76 and glycine 77 in omega loop D of yeast iso-1-cytochrome cBiochemistry.1998;37(8):2477-2487.
  • Fetrow, J.S., Schaak, D.L., Dreher, U., Wiland, D.J., and Boose, T.L. Mutagenesis of histidine 26 demonstrates the importance of loop-loop and loop-protein attachments for the function of iso-1-cytochrome cProtein Sci . 1998 27(4):994-1005.
  • Baxter, S.M., Boose, T.L., and Fetrow, J.S. 15N isotopic labeling and amide hydrogen exchange rates of oxidized iso-1-cytochrome cJ. Am. Chem. Soc. 1998 119(41):9899 -9900.
  • Qu, K. Vaughn, J.L., Sienkiewicz, A. Scholes, C.P., and Fetrow, J.S. Kinetics and motional dynamics of spin labeled yeast iso-1-cytochrome c: 1. Stopped-flow EPR as a probe for protein folding/unfolding of the C-terminal helix spin labeled at cysteine 102. Biochemistry. 1998 36(10):2884-2897.

1986-1997

  • Fetrow, J.S., Palumbo, M.J., and Berg, G. Patterns, structures, and amino acid frequencies in structural building blocks, a protein secondary structure classification scheme. Proteins. 1997 Feb;27(2):249-71
  • Fetrow, J.S., Horner, S.R., Oehrl,W., Schaak, D.L., Boose, T.L., and Burton, R.E. Analysis of the structure and stability of omega loop A replacements in yeast iso-1-cytochrome cProtein Sci. 1997 Jan;6(1):197-210.
  • Shenkin, P.S., Farid, H., and Fetrow, J.S. Prediction and evaluation of side-chain conformations for protein backbone structures. Proteins. 1996 Nov;26(3):323-352.
  • Mulligan-Pullyblank, P. Spitzer, J.S., Gilden, B.M., and Fetrow, J.S. Loop replacement and random mutagenesis of omega loop D, residues 70-84, in iso-1-cytochrome cJ. Biol. Chem. 1996 Apr 12;271(15):8633-8645.
  • Castonguay, L.A., Bryant, S.H., Snow, P.M., and Fetrow, J.S. A proposed structural model for domain 1 of fasciclin III neural cell adhesion protein based on an inverse folding algorithm. Protein Sci. 1995 Mar;4(3):472-483. doi: 10.1002/pro.5560040314. PMID: 7795530.
  • Fumo, G. and Fetrow, J.S. A method of directed random mutagenesis of the yeast chromosome shows that iso-1-cytochrome c heme ligand His18 is essential. Gene. 1995 Oct 16;164(1):33-9.
  • Hsieh, M., Helmsley, P., Brenowitz, M., and Fetrow, J.S. A molecular model of the inducer-binding domain of the galactose repressor of Escherichia coliJ. Biol. Chem. 1994 May 13;269(19):13825-13835.
  • Murphy, M.E.P., Fetrow, J.S., Burton, R.E. and Brayer, G.D. The structure and function of omega loop A replacements in cytochrome c. Protein Sci. 1993 2(9):1429-1440.
  • Zhang, X., Fetrow, J.S., Rennie, W.A., Waltz, D.L., and Berg, G. Automatic derivation of substructures yields novel structural building blocks in globular proteins. Proc Int Conf Intell Syst Mol Biol. 1993;1:438-46. L. Hunter, D. Searls, J. Shavlik, eds. PMID: 7584368.
  • Fetrow, J.S., Sherman, F., and Rose, G.D. Deletion and replacement of omega loops in iso-1-cytochrome c from the yeast Saccharomyces cerevisiae. (October, 1989) Proceedings of the BioTech USA Conference. p. 327-336.
  • Fetrow, J.S., Cardillo, T.S., and Sherman, F. Deletions and replacements of omega loops in yeast iso-1-cytochrome cProteins. 1989 6(4):372-381.
  • Leszczynski (Fetrow), J.F. and Rose, G.D. Loops in globular proteins: Identification of a novel category of secondary structure. Science. 1986 Nov 14;234(4778):849-55. PMID: 3775366.
    [Reprinted in: Protein Folding: Deciphering the Second Half of the Genetic Code. (1990) King, J., and Gierasch, L., eds. American Association for the Advancement of Science.]

Invited Articles and Reviews

  1. Browne, Carole and Fetrow, Jacquelyn. Online and face-to-face education. In “Higher Ed Beta: MOOCS and Beyond”, Inside Higher Ed. March 17, 2014.
  2. Chan, Andrew and Fetrow, JS. Six tips for liberal arts colleges to produce employable grads. Op-Ed in The Washington Post. April 1, 2012.
  3. Fetrow J.S. Protein Function Annotation: The next frontier in molecular biology.  Protein Science. (Virtual Issue) Feb 2012.
  4. Baxter S.M., Day S.W., Fetrow J.S., Reisinger S.J. Scientific software development is not an oxymoron. PLoS Comput Biol. 2006 Sep 8;2(9):e87. PMID: 16965174.
  5. Fetrow, J.S. Active site profiling to identify protein functional sites in sequences and structures using the Deacon Active Site Profiler (DASP). Current Protocols in Bioinformatics 2006, Chapter 8:Unit 8 10.
  6. Creamer, T.P. and Fetrow, J.S. Rose is a Rose is a Rose. Especially if you’re a George. A Perspectives article in Proteins Struct. Funct. Bioinformatics. 2006 May 1;63(2):268-72. doi: 10.1002/prot.20945. PMID: 16493653.
  7. Baxter, S., Knutson, S. and Fetrow, J.S. The importance of structure-based function annotation to drug discovery. Protein Structure Determination, Analysis and Modeling for Drug Discovery. D. I. Chasman, Ed., Dekker Publishing. 2003. p. 369-387.
  8. Fetrow, J., Giammona, D.A., Kolinski, A., Skolnick, J. The protein folding problem, a biophysical enigma. Curr Pharma Biotech. 2002;3(4):329-47. PMID: 12463416.
  9. Betz, S., Baxter, S., Fetrow, J.S. Function first: a powerful approach to post-genomic drug discovery.
    Drug Discov Today. 2002;7(16):865-871. PMID: 12546953.
  10. Baxter, S.M., Fetrow, J.S. Sequence- and structure-based protein function prediction from genomic information. Curr Opin Drug Discov Devel. 2001 May;4(3):291-295. PMID: 11560060.
  11. Skolnick, J., Fetrow, J.S., Kolinski, A. Structural genomics and its importance for gene function analysis. Nature Biotechnology. 2000 Mar;18(3):283-287. PMID: 10700142.
  12. Skolnick, J. and Fetrow, J.S. From genes to structure: novel applications of computational approaches in the genomic era. Trends in Biotech. 2000 Jan;18(1):34-39. PMID: 10631780.
  13. Rudd, P.M., Wormald, M.R., Stanfield, R. Huang, M., Mattson, N., Speir, J.A., Di Gennaro, J.A., Fetrow, J.S., Dwek, R.A., and Wilson, I.A. Roles for glycosylation of cell surface receptors involved in cellular immune recognition. J. Mol. Biol. 1999 Oct 22;293(2):351-366. doi: 10.1006/jmbi.1999.3104. PMID: 10529350.
  14. Fetrow, J.S. Omega Loops: Nonregular secondary structures significant in protein function and stability. FASEB J. 1995 Jun;9(9):708-717. PMID: 7601335.
  15. Zhang, X., Fetrow, J.S., and Berg, G. Design of an Auto-associative Neural Network with Hidden Layer Activations that were used to Reclassify Local Protein Structures. (1994) Advances in Protein Chemistry V. J. Crabb, ed. p. 397-404.
  16. Fetrow, J. Molecular Modeling. In: Investigations in Modern Biology, 6th edition (A. Jacklet, ed.), Morton Publishing Co.; Englewood, Colorado. (Macromolecular modeling exercises for freshman biology laboratories) 1994:205-222.
  17. Fetrow, J.S. and Bryant, S.H. New programs for protein tertiary structure prediction. Biotechnology. 1993 Apr;11(4):479-484. PMID: 7763517.
  18. Fetrow, J.S. and Mulligan, P. Properties of cytochrome c hybrid proteins expressed in Bakers yeast. NIH Conference, Research Opportunities in Biomolecular Engineering: The Interface between Chemical Engineering and Biology. Washington DC, December 7-8, 1992. Invited participant and poster presenter.
  19. Fetrow, J.S., Zehfus, M.H. and Rose, G.D. Protein folding: new twists. Bio/Technology. 1988;6:167-171.

patentPatents and Patent Applications

  1. Method for detecting compounds containing sulfenic acid using a 1,3-cyclohexanedione-based probe. Patent #8,841,132. Issued September 23, 2014. Inventors: Poole, L.B., King, S.B., and Fetrow, J.S.
  2. Method of synthesizing 1,3-cyclohexadione derived reagents useful for detection or isolation of sulfenic acid-containing compounds. Patent #8,486,642. Issued July 16, 2013. Inventors: Poole, L.B., King, S.B., and Fetrow, J.S.
  3. Method for Detecting Target Compounds Containing Sulfenic Acids Using New Reagents. Patent #7,803,630, issued September 28, 2007. Inventors: Poole, L.B., King, S.B., and Fetrow, J.S.
  4. Sulfenic Acid-Reactive Compounds And Their Methods Of Synthesis. Patent #7,294,748, issued November 13, 2007. Inventors: Poole, L.B., King, S.B., and Fetrow, J.S.
  5. Methods and Systems for Predicting Protein Function. Patent #6,631,332, issued October 7, 2003. Inventors: Skolnick, J. and Fetrow, J.S.
  6. Functional Site Profiles for Proteins and Methods of Making and Using Same. Inventors: Fetrow, J.S., Baxter, S.M., Hoffman, B.T., and Cammer, S.A. Patent application #US027/23166 submitted.