Publications


60. Joughin B.A., Liu, C., Lauffenburger, D.A., Hogue, C.W.V, and Yaffe, M.B. Protein kinases display minimal interpositional dependence on substrate sequence: potential implications for the evolution of singalling networks. 2012  Philos Trans R Soc Lond B Biol Sci. 367 :2574-83.

59. Liu, C., Yao, M., and Hogue, C.W.V., Near-membrane ensemble elongation in the proline-rich LRP6 intracellular domain may explain the mysterious initiation of the Wnt signaling pathway. BMC Bioinformatics. 2011 BMC Bioinformatics 12:S13. PMC3278829

58. Zhang B, and Hogue C.W.V.  Dependencies reveal the evolutionary steps that formed the ribosome. In M. Kreimeyer, J. Maier, G. Fadel and U. Lindemann, editor, Proceedings of the 11th International DSM Conference, Greenville, SC, 12 - 13 October 2009 , page 369-381. Publisher: Hanser, Munich  ISBN: 978-3-446-42194-3.

57.Hogue C.W.V. The other side of staying out of a BIND. Nature Biotechnology 2007 25:971

56.  Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stumpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H. Broadening the Horizon - Level 2.5 of the HUPO-PSI Format for Molecular Interactions.  BMC Biology 2007 5:44

55. Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stümpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, De Las Rivas J, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H. The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol. 2007 8:894-8

54. Betel D, Breitkreuz KE, Isserlin R, Dewar-Darch D, Tyers M, and Hogue CWV. Structure-templated predictions of novel protein interactions from sequence information. PLOS Computational Biology 2007 3:1783-9.

53. Willis R. and Hogue CWV. Searching, Viewing, and Visualizing Data in the Biomolecular Interaction Network Database (BIND).  Current Protocols in Bioinformatics.  2006 Unit 8.9.

52.  Snyder, K.A. Feldman, H.J., Dumontier, M., Salama J.J., and Hogue CWV. Domain-based Small Molecule Binding Site Annotation.  BMC Bioinformatics.  2006  7:152.

51.  Feldman, H.J., Snyder, K.A, Ticoll, A., Pintilie, G., and Hogue CWV.  A Complete Small Molecule Dataset from the Protein Data Bank.  FEBS Lett. 2006 580:1649-53.

50.  Feldman, H.J,, Dumontier, M., Ling, S., Haider, N., Hogue, CWV.  CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules. FEBS Lett. 2005. 579:4685-91.

49.  Pintilie, G.D., Tuekam, B., and Hogue CWV.  Generation of Glyphs for Conveying Complex Information, with Application to Protein Representations.  Lecture Notes in Computer Science (LNCS) 2005. 3638:90-102.

48.  Dumontier, M., Yao, R., Feldman, HJ, Hogue, CWV. Armadillo: Domain Boundary Prediction by Amino Acid Composition. 2005. Journal of Molecular Biology. 350: 1061-1073..

47.  Alex, Anish T., Dumontier, Michel, Rose, Jonathan S., Hogue, Christopher W.V. Hardware-Accelerated Protein Identification for Mass Spectrometry. 2005. Rapid Communications in Mass Spectrometry. 19(6): 833-837.

46.  Portet, S., Tuszynski, J.A., Hogue, C.W.V., Dixon, J.M. Elastic vibrations in seamless microtubules.  The European Biophysics Journal. 2005. In Press. PMID:15886985

45.  Alfarano C, Andrade CE, Anthony K, Bahroos N, Bajec M, Bantoft K, Betel D, Bobechko B, Boutilier K, Burgess E, Buzadzija K, Cavero R, D'Abreo C, Donaldson I, Dorairajoo D, Dumontier MJ, Dumontier MR, Earles V, Farrall R, Feldman H, Garderman E, Gong Y, Gonzaga R, Grytsan V, Gryz E, Gu V, Haldorsen E, Halupa A, Haw R, Hrvojic A, Hurrell L, Isserlin R, Jack F, Juma F, Khan A, Kon T, Konopinsky S, Le V, Lee E, Ling S, Magidin M, Moniakis J, Montojo J, Moore S, Muskat B, Ng I, Paraiso JP, Parker B, Pintilie G, Pirone R, Salama JJ, Sgro S, Shan T, Shu Y, Siew J, Skinner D, Snyder K, Stasiuk R, Strumpf D, Tuekam B, Tao S, Wang Z, White M, Willis R, Wolting C, Wong S, Wrong A, Xin C, Yao R, Yates B, Zhang S, Zheng K, Pawson T, Ouellette BF, Hogue CW. 2005. The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Research. 33(Database Issue):D418-D424.

44.  Portet, S., Vassy, J., Hogue, C.W.V., Arino, J. Arino, O. 2004. Intermediate filament networks in vitro and in vivo assembly kinetic models. Comptes Rendus: Biologies. 327(11): 970-976.

43.  *Lewis, K.N., Robinson, M. D., Hughes, T. R. Hogue, C.W.V.  2004. MyMED: A database system for biomedical research on MEDLINE data. IBM Systems Journal 43 (4) 756

42.  Betel, D, Isserlin, R, Hogue C.W.V. 2004.  Analysis of domain correlations in yeast protein complexes. Bioinformatics. 20(1): i55-i62

41.  Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R. 2004 The HUPO PSI’s molecular interaction format – a community standard for the representation of protein interaction data.  Nature Biotechnology. 22(2): 177-83

40.  Acchione M., Guillemette JG., Twine SM., Hogue CW, Rajendran B, and Szabo AG. 2003.  Fluorescence-based structural analysis of tryptophan analogue-AMP formation in single tryptophan mutants of Bacillus stearothermophilus tryptophanyl-tRNA synthetase.  Biochemistry. 42:14994-5002.

39.  Donaldson, I., Martin, J., De Bruijn, B., Wolting, C., Lay, V., Tuekam, B., Zhang, S., Baskin, B., Bader, G.D., Michalickova, K., Pawson, T., Hogue C.W.V. 2003.  PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine. BMC Bioinformatics. 4(1): 11

38.  Bader, G.D., Hogue, C.W. 2003.  An automated method for finding molecular complexes in large protein interaction networks.  BMC Bioinformatics. 4(1): 2

37.  Bader, G.D., Betel, D., Hogue, C.W. 2003. BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res. 31(1): 248-50

36.  Dumontier M., Michalickova, K., and Hogue, C.W. 2002 Species-Specific Protein Sequence and Fold Optimizations. BMC Bioinformatics 3: 39

35. Hogue, C. 2002. The bioinformatics of molecular interactions: What do Saccharomyces cerevisiae interaction networks tell us about human cells?  Ann N Y Acad Sci. 971: 588

34. Michalickova, K., Bader, G.D., Dumontier, M., Lieu, H.C., Betel, D., Isserlin, R., Hogue, C.W. SeqHound: biological sequence and structure database as a platform for bioinformatics research. BMC Bioinformatics 2002 3: 32

33. Bader GD, Hogue CW. Analyzing yeast protein-protein interaction data obtained from different sources. Nature Biotechnol 2002 Oct, 20:991-7

32. Betel D, Hogue CW Kangaroo - A pattern-matching program for biological sequences. BMC Bioinformatics 2002 3:20

31. Flora, K.K., Keeling-Tucker, T., Hogue C.W., and Brennan, J.D.  Screening of antagonists based on induced dissociation of a calmodulin-melittin interaction entrapped in a sol-gel derived matrix.  Analytica Chimica Acata 2002

30.  Dumontier M, Hogue CW NBLAST: a cluster variant of BLAST for NxN comparisons. BMC Bioinformatics 2002 3:13

29. Salama JJ, Donaldson I, Hogue CW Automatic annotation of BIND molecular interactions from three-dimensional structures. Biopolymers 2001-2002, 61:111-20

28. Park J, Betel D, Gryfe R, Michalickova K, Di Nicola N, Gallinger S, Hogue CW, Redston M Mutation profiling of mismatch repair-deficient colorectal cancers using an in silico genome scan to identify coding microsatellites.  Cancer Res 2002  62:1284-8

27.  Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sørensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M  Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.  Nature 2002  415:180-3

26. Tong AH, Drees B, Nardelli G, Bader GD, Brannetti B, Castagnoli L, Evangelista M, Ferracuti S, Nelson B, Paoluzi S, Quondam M, Zucconi A, Hogue CW, Fields S, Boone C, Cesareni G A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules.  Science 2002  295:321-4

25. Feldman HJ, Hogue CW Probabilistic sampling of protein conformations: new hope for brute force?  Proteins 2002  46:8-23

24. Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Pagé N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H, Andrews B, Tyers M, Boone C Systematic genetic analysis with ordered arrays of yeast deletion mutants.  Science 2001  294:2364-8

23. Salama J.J., Feldman H.J., Hogue C.W. VISTRAJ: exploring protein conformational space. Bioinformatics 2001 17:851-2

22. Bader, G.D., Donaldson, I, Wolting, C., Ouellette, B.F.F., Pawson T., and Hogue, C.W.V.  BIND – The Biomolecular Interaction Network Database.  Nucleic Acids Research Jan 2001 29:242-245.

21.  *Michalickova, K., Dharsee, M., and Hogue, C.W.V.  Sequence Analysis on a 216-Processor Beowulf Cluster. (2000)  Atlanta Linux Showcase.  USENIX Conference Proceedings. 111-119.

20.  *Dharsee, M., and Hogue, C.W.V.   MoBiDiCK: A Tool for Distributed Computing on the Internet  (2000) Heterogeneous Computing Workshop Proceedings, Cancun Mexico. IEEE Computer Science Society. 323-335.

19. Bader, G.D., and Hogue, C.W.V. (2000) BIND – A data specification for storing and describing biomolecular interactions, molecular complexes and pathways.  Bioinformatics, 16: 465-477.

18. Feldman, H.J., and Hogue, C.W.V. (2000) A fast method to sample real protein conformational space.  Proteins 39:112-131.

17. Steven, R., Kubiseski, T., Zheng, H., Kulkarni, S., Mancillas, J., Ruiz, A., Hogue, C.W.V., Pawson, T., and Culotti, J. (1998).  UNC-73 activates the Rac GTPase required for cell and growth cone migrations in C. elegans.  Cell  92: 785-795.

16. Zheng, L., Hogue, C.W.V., and Brennan, J.D. (1998)  Effects of metal binding affinity and metal loading on the chemical and thermal stability of site-directed mutants of rat oncomodulin. Biophys. Chem. 20: 157-172.

15. Ross, J.BA., Szabo, A.G and Hogue, C.W.V. (1997)  Enhancement of protein spectra with tryptophan analogs:  Exposing the molecular details of protein-protein and protein-nucleic acid interactions. Methods in Enzymology, Editors: L. Brand and M. L. Johnson. 278:151-190.

14. Hogue, C.W.V. (1997) Cn3D: a new generation of three-dimensional molecular structure viewer.  Trends in Biochemical Sciences 22:314-316.

13. Brennan,J.D., Hogue, C.W.V., Rajendran, B., Willis, K.J., and A.G. Szabo. (1997)  Preparation of enantiomerically pure L-7-Azatryptophan by an enzymatic method and its application to the development of a fluorimetric activity assay for tryptophanyl-tRNA synthetase. Analytical Biochemistry 252:2660-270.

12.  Hogue, C.W.V., Ohkawa, H., and Bryant, S.H. (1996) A dynamic look at structures: WWW-Entrez and the Molecular Modeling Database.  Trends in Biochemical Sciences 21: 226-229.

11.  Hogue, C.W.V., Doublié, S., Carter, C.W. Jr., Xue, H., Wong, J.T. and Szabo, A.G. (1996).  A concerted tryptophanyl-adenylate dependent conformational change in B. subtilis tryptophanyl-tRNA synthetase revealed by the fluorescence of Trp-92.  J. Mol. Biol. 260:446-466.

10.  Brennan, J.D., Clark, I.D., Hogue, C.W.V., Ito, A., Juliano, L., Pavia, A., Rajendran, B., and Szabo, A.G. (1995) Interaction of enantiomers of lysyl-7-azatryptophyl-lysine with acidic phopholipid vesicles: A Fluorescence Study.  Applied Spectroscopy. 49:51-59.

9.  Clark, I.D., Bruckman, A.J., Hogue, C.W.V., MacManus, J.P., and Szabo, A.G. (1994) Effects of metal ion binding on an oncomodulin mutant containing a novel calcium-binding loop. J. Fluorescence. 4:235-242.

8.  Hill, I., Hogue, C.W.V., Clark, I.D., MacManus, J.P., and Szabo, A.G. (1993) Detection of calcium-binding proteins  on polyacrylamide gels using time-resolved lanthanide luminescence photography.  Anal. Biochem. 216, 439-443.

7.  Hogue, C.W.V. and Szabo, A.G. (1993) Characterization of aminoacyl-adenylates in B. subtilis tryptophanyl-tRNA synthetase, by the fluorescence of tryptophan analogs 5-hydroxytryptophan and 7-azatryptophan. Biophys. Chem. 48, 159-169.

6.  Hogue, C.W.V., Rasquinha, I., Szabo, A.G., and MacManus, J.P. (1992) A new intrinsic probe for proteins - biosynthetic incorporation of 5-hydroxytryptophan into oncomodulin FEBS Letters 310, 269-272.

5.  Hogue, C.W.V., MacManus, J.P., Banville, D., and Szabo, A.G. (1992) Comparison of terbium(III) luminescence enhancement in mutants of EF-hand calcium-binding proteins. J. Biol. Chem. 267, 13340-13348.

4.  MacManus, J.P., Hogue, C.W., Marsden, B.J., Sikorska, M., Szabo, A.G.  (1990) Terbium luminescence in synthetic peptide loops from calcium-binding proteins with different energy donors. J. Biol. Chem. 265.18, 10358-10366.

3.  Habowsky J.E.J., Sands, T.W., Hogue, C.W.V., and Stager, R.A. (1990) The database as a learning tool. Journal of College Science Teaching May, 363-367.

2.  Habowsky J.E.J., Sands, T.W., Hogue, C.W.V., Stager, R.A. and Postlethwait, S.N. (1990) An audio-directed multimedia lab.  Journal of College Science Teaching February, 232-234.

1. Hogue, C.W.V. and Fackrell, H.B. (1987) The menu workbench: An automatic menu generator for biomedical programs.  International Journal of Bio-Medical Computing 21, 253-264.


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