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Peer-reviewed Publications

    2011

  1. Loeser R.F., Olex A.L., McNulty M.A., Carlson C.S., Callahan M., Ferguson C., Chou J., Leng X. and Fetrow J.S. Microarray Analysis Reveals Age-related Differences in Gene Expression During the Development of Osteoarthritis in Mice. Arthritis & Rheumatism, accepted in Sept 2011.
  2. Olex A.L and Fetrow J.S. SC2ATmd: a tool for integration of the figure of merit with cluster analysis for gene expression data. Bioinformatics 2011, 27(9):1330-1331.
  3. Nelson K.J., Knutson S.T., Soito L., Klomsiri C., Poole L.B. and Fetrow J.S. Analysis of the peroxiredoxin family: Using active-site structure and sequence information for global classification and residue analysis. Proteins: Structure, Function, and Bioinformatics, 2011, 79:947964.


  4. 2010

  5. Soito L., Williamson C., Knutson S.T., Fetrow J.S., Poole L.B., and Nelson K.J. PREX: PeroxiRedoxin classification indEX, a database of subfamily assignments across the diverse peroxiredoxin family. Nucleic Acids Res. 2010, Oct 29, [Epub ahead of print], PMID: 21036863
  6. John D.J., Fetrow J.S., and Norris J.L. Continuous Cotemporal Probabilistic Modeling of Systems Biology Networks from Sparse Data. IEEE/ACM Trans Comput Biol Bioinform 2010, Sep 10. [Epub ahead of print], PMID: 20855920
  7. Olex A.L., Hiltbold E.M., Leng X., and Fetrow J.S. 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.
  8. Yuan Y., Knaggs M.H., Poole L.B., Fetrow J.S., and Salsbury F.R. Jr. Conformational and oligomeric effects on the cysteine pK(a) of tryparedoxin peroxidase. J Biomol Struct Dyn. 2010, 28(1):51-70


  9. 2008

  10. Salsbury, F.R. Jr., Knutson, S.T., Poole, L.B., Fetrow, J.S. Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid. Protein Sci 2008, 17(2):299-312.


  11. 2007

  12. Poole, L.B., Klomsiri, C., Knaggs, S.A., Furdui, C.M., Nelson, K.J., Thomas, M.J., Fetrow, J.S., Daniel, L.W., King, S.B. Fluorescent and affinity-based tools to detect cysteine sulfenic acid formation in proteins. Bioconjug Chem 2007, 18(6):2004-2017.
  13. Michalek, R.D., Nelson, K.J., Holbrook, B.C., Yi, J.S., Stridiron, D., Daniel, L.W., Fetrow, J.S., King, S.B., Poole, L.B., Grayson, J.M. The requirement of reversible cysteine sulfenic acid formation for T cell activation and function. J Immunol 2007, 179(10):6456-6467.
  14. Knaggs, M.H., Salsbury, F.R. Jr., Edgell, M.H., Fetrow, J.S. Insights into correlated motions and long-range interactions in CheY derived from molecular dynamics simulations. Biophys J 2007, 92(6):2062-2079.
  15. Olex, A.L., John, D.J., Hiltbold, E.M., Fetrow, J.S. Additional limitations of the clustering validation method figure of merit. In: 45th ACM Southeast Annual Conference: 2007; Winston-Salem, NC; 2007: 238-243.
  16. Budiman, M.E., Knaggs, M.H., Fetrow, J.S., Alexander, R.W. Using molecular dynamics to map interaction networks in an aminoacyl-tRNA synthetase. Proteins 2007, 68(3):670-689.


  17. 2006

  18. Baxter, S.M., Day, S.W., Fetrow, J.S., Reisinger, S.J. Scientific software development is not an oxymoron. PLoS Comput Biol 2006, 2(9):e87.
  19. 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.
  20. Knaggs, M.H., Salsbury, F.R., Edgell, M.H., Fetrow, J.S. Insights into CheY relaxation and relaxation derived from molecular dynamics simulations. Biophys. J. [Epub ahead of print 2006 Dec 15]
  21. Fetrow, J.S. and John, D.J. Bioinformatics and computing curriculum: A new model for interdisciplinary courses. Inroads--SIGSCE Bulletin. 2006. 38:185-190.
  22. 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]
  23. 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]


  24. 2005

  25. 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.
  26. 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.


  27. 2004

  28. 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.


  29. 2003

  30. 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.
  31. 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.
  32. 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.


  33. 2001

  34. 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 c. Biochemistry 2001 Dec 25;40(51):15846-15855.
  35. 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.
  36. 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.


  37. 1999

  38. 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.
  39. 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.
  40. 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.
  41. 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.
  42. Baxter, S.M. and Fetrow, J.S. Hydrogen exchange behavior of [ U- 15N]-labeled oxidized and reduced iso-1-cytochrome c. Biochemistry. 1999 Apr 6;38(14):4493-4503.
  43. 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.


  44. 1998

  45. 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.
  46. 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.
  47. 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.
  48. 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.
  49. 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 c. Biochemistry.1998;37(8):2477-2487.
  50. 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 c. Protein Sci . 1998 27(4):994-1005.
  51. Baxter, S.M., Boose, T.L., and Fetrow, J.S. 15N isotopic labeling and amide hydrogen exchange rates of oxidized iso-1-cytochrome c. J. Am. Chem. Soc. 1998 119(41):9899 -9900.
  52. 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.


  53. 1986-1997

  54. 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
  55. 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 c. Protein Sci. 1997 Jan;6(1):197-210.
  56. 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.
  57. 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 c. J. Biol. Chem. 1996 Apr 12;271(15):8633-8645.
  58. 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.
  59. 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.
  60. Hsieh, M., Helmsley, P., Brenowitz, M., and Fetrow, J.S. A molecular model of the inducer-binding domain of the galactose repressor of Escherichia coli. J. Biol. Chem. 1994 May 13;269(19):13825-13835.
  61. 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.
  62. 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. (1993) Proceedings: First International Conference on Intelligent Systems for Molecular Biology. p. 438-446. L. Hunter, D. Searls, J. Shavlik, eds.
  63. 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.
  64. Fetrow, J.S., Cardillo, T.S., and Sherman, F. Deletions and replacements of omega loops in yeast iso-1-cytochrome c. Proteins. 1989 6(4):372-381.
  65. 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.
    [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.]

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Invited Articles and Reviews

  1. 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.
  2. 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.
  3. 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.
  4. Fetrow, J., Giammona, D.A., Kolinski, A., Skolnick, J. The protein folding problem, a biophysical enigma. Curr Pharma Biotech. 2002;3(4):329-47.
  5. 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.
  6. 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.
  7. Skolnick, J., Fetrow, J.S., Kolinski, A. Structural genomics and its importance for gene function analysis. Nature Biotechnology. 2000 Mar;18(3):283-287.
  8. 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.
  9. 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.
  10. Fetrow, J.S. Omega Loops: Nonregular secondary structures significant in protein function and stability. FASEB J. 1995 Jun;9(9):708-717.
  11. 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.
  12. 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.
  13. Fetrow, J.S. and Bryant, S.H. New programs for protein tertiary structure prediction. Biotechnology. 1993 Apr;11(4):479-484.
  14. 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.
  15. Fetrow, J.S., Zehfus, M.H. and Rose, G.D. Protein folding—new twists. Bio/Technology. 1988;6:167-171.

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Patents and Patent Applications

  1. Sulfenic Acid-Reactive Compounds And Their Methods Of Synthesis And Use In Detection Or Isolation Of Sulfenic Acid-Containing Chemicals Or Proteins. US Patent Application Serial No. 60/620,263. Inventors: Poole, L.B., King, S.B., and Fetrow, J.S. Provisional application submitted October 2004; application submitted October 2005.
  2. Methods and Systems for Predicting Protein Function. US99/11913. Inventors: Skolnick, J. and Fetrow, J.S. US Patent #6,631,332, issued 10/7/03.
  3. Functional Site Profiles for Proteins and Methods of Making and Using Same. US027/23166. Inventors: Fetrow, J.S., Baxter, S.M., Hoffman, B.T., and Cammer, S.A. Patent application submitted.

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