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Keck Home Page >  Biotechnological Publications

Biotechnological Publications from the
W.M. Keck Foundation Biotechnology
Resource Laboratory at Yale University

  1. Williams, K.R., L'Italien, J.J., Guggenheimer, R.A., Sillerud, L., Spicer, E., Chase, J. and Konigsberg, W. (1982) Comparative peptide mapping by HPLC: identification of single amino acid substitutions in temperature sensitive mutants. In: Methods in Protein Sequence Analysis. (Elzinga, M., ed.) The Humana Press, Clifton, 499-507.
  2. Merrill, B.M., Williams, K.R., Chase, J.W. and Konigsberg, W.H. (1984) Photochemical cross-linking of the Eschericia coli single-stranded DNA-binding protein to oligodeoxynucleotides: identification of phenylalanine 60 as the site of cross-linking. J. Biol. Chem. 259, 10850-10856.
  3. Stone, K. and Williams, K.R. (1986) High-performance liquid chromatographic peptide mapping and amino acid analysis in the sub-nanomole range. J. Chrom. 359, 203-212.
  4. Stone, K.L., Williams, K.R., Rabin, B.A., Murphy, J.B., Chase, J.W. and Pfeifer, R. (1986) HPLC purification and identification of peptides using microbore columns. Waters Journal, 20-27.
  5. Williams, K.R., Stone, K.L., Fritz, M.K., Merrill, B.M., Konigsberg, W.H., Pandolfo, M., Valentini, O., Reddigari, S., Patel, G.L. and Chase, J.W. (1987) Use of HPLC comparative peptide mapping in structure/function studies. In: Proteins: Structure and Function. (L'Italien, J.J., ed.) Plenum Press, New York, 45-52.
  6. Coleman, J.E., Williams, K.R., King, G.C., Prigodich, R.V., Shamoo, Y. and Konigsberg, W.H. (1987) Mapping the functional domains in single-strand DNA-binding proteins gene 5 and gene 32. In: Protein Engineering. (Oxender, D. and Fox, C.F., eds.) Alan R. Liss, New York, 323-336.
  7. Williams, K.R., Stone, K.L., Fritz, M.K., Merrill, B.M., Konigsberg, W.H., Pandolfo, M., Valentini, O., Riva, S., Reddigari, S., Patel, G.L. and Chase, J.W. (1987) Use of HPLC comparative peptide mapping in structure/function studies. In: Proteins: Structure and Function. (L'Italien, J.J., ed.) Plenum Press, New York, 45-52.
  8. Stone, K.L. and Williams, K.R. (1988) Small bore HPLC purification of peptides in the subnanomole range. In: Macromolecular Sequencing and Synthesis. (Schlesinger, D.H., ed.) Alan R. Liss, Inc., New York, 7-24.
  9. Merrill, B.M., Stone, K.S., Cobianchi, F., Wilson, S.H., and Williams, K.R. (1988) Phenylalanines that are conserved among several RNA-binding proteins form part of a nucleic acid-binding pocket in the A1 heterogeneous ribonucleoprotein. J. Biol. Chem. 263, 3307-3313.
  10. Roberts, W.J., Elliott, J.I., McMurray, W.J., Williams, K.R. (1988) Synthesis of the p10 single-stranded nucleic acid binding protein from murine leukemia virus. Pept. Res. 1, 74-80.
  11. Shamoo, Y., Williams, K.R. and Konigsberg, W.H. (1988) Photochemical crosslinking of bacteriophage T4 single-stranded DNA-binding protein (gp32) to oligo-p(dT)8: Identification of phenylalanine-183 as the site of crosslinking. Proteins: Structure, Function, and Genetics 4, 1-6.
  12. Williams, K.R., Niece, R.L., Atherton, D., Fowler, A.V., Kutny, R. and Smith, A.J. (1988) The size, operation, and technical capabilities of protein and nucleic acid core facilities. FASEB J. 2, 3124-3130.
  13. Stone, K.L., LoPresti, M.L., Williams, N.D., Crawford, J.M., DeAngeles, R. and Williams, K.R. (1989) Enzymatic digestion of proteins and HPLC peptide isolation in the sub-nanomole range. Chap. 37. In: Techniques in Protein Chemistry. (Hugli, T.E., ed.) Academic Press, New York, 377-391.
  14. Stone, K.L., LoPresti, M.B., Crawford, J.M., DeAngelis, R. and Williams, K.R. (1989) Enzymatic digestion of proteins and HPLC peptide isolation. Chap. 2. In: A Practical Guide to Protein and Peptide Purification for Microsequencing. (Matsudaira, P., ed.) Academic Press, New York, 33-47.
  15. Niece, R.L., Williams, K.R., Wadsworth, C.L., Elliott, J., Stone, K.L., McMurray, W.J., Fowler, A., Atherton, D., Kutny, R. and Smith, A. (1989) A synthetic peptide for evaluating protein sequencer and amino acid analyzer performance in core facilities: Design and results. Chap. 10. In: Techniques in Protein Chemistry. (Hugli, T.E., ed.) Academic Press, New York, 89-101.
  16. Elliott, J., Stone, K., Roberts, W., LoPresti, M., Crawford, M., Kapouch, J., Jacobsen, E., Williams, K.R., McMurray, W., Meng, C., Mann, M. and Fenn, J. (1989) Structure of symposium test peptide-3. In: Techniques in Protein Chemistry. (Hugli, T.E., ed.) Academic Press, New York, 569-579.
  17. Roberts W.J., Pan, T., Elliott, J.I., Coleman, J.E., Williams, K.R. (1989) p10 single-stranded nucleic acid binding protein from murine leukemia virus binds metal ions via the peptide sequence Cys26-X2-Cys29-X4-His34-X4-Cys39. Biochemistry. 26, 10043-7.
  18. Stewart, A.F., Elliott, J.I., Burtis, W.J., Wu, T., Insogna, K.L. (1989) Synthetic parathyroid hormone-like protein-(1-74): Biochemical and physiological characterization. Endocrinology. 124, 642-8.
  19. Stone, K.L., Elliott, J.I., Peterson, G., McMurray, W. and Williams, K.R. (1990) Reversed-phase high-performance liquid chromatography for fractionation of enzymatic digests and chemical cleavage products of proteins. Chap. 21. In: Methods in Enzymology. Vol. 193. (McCloskey, J., ed.) Academic Press, New York, 389-412.
  20. Stone, K.L., LoPresti, M.B. and Williams, K.R. (1990) Enzymatic digestion of proteins and HPLC peptide isolation in the sub-nanomole range. In: Laboratory Methodology in Biochemistry: Amino Acid Analysis and Protein Sequencing. (Fini, C., Floridi, A., Finelli, V.N. and Wittman-Liebold, B., eds.) CRC Press, Boca Raton, 181-205.
  21. Speicher, D.W., Grant, G.A., Niece, R.L., Blacher, R.W., Fowler, A.V. and Williams, K.R. (1990) Design, characterization, and results of ABRF-89SEQ: A test sample for evaluating protein sequencer performance in protein microchemistry core facilities. In: Current Research in Protein Chemistry: Techniques, Structure, and Function. (Villafranca, J.J., ed.) Academic Press, New York, 159-166.
  22. Stone, K.L., LoPresti, M.B., Crawford J.M., DeAngelis, R. and Williams, K.R. (1991) Reverse-phase HPLC separation of sub-nanomole amounts of peptides obtained from enzymatic digests. In High Performance Liquid Chromatography of peptides and proteins: Separation, Analysis and Conformation. (Mant, C.T. and Hodges, R.S., eds.) CRC Press, Inc., Boca Raton, 669-677.
  23. Williams, K.R. and Konigsberg, W.H. (1991) Identification of amino-acid residues at the interface of protein:nucleic acid acid complexes by photochemical cross-linking. In Methods in Enzymology, Vol. 208 (Sauer, R., ed.) Academic Press, New York, 516-539.
  24. Niece, R.L., Ericsson, L.H., Fowler, A.V., Smith, A.J., Speicher, D.W., Crabb, J.W. and Williams, K.R. (1991) Amino acid analysis and sequencing - what is state-of-the-art? In Methods in Protein Sequence Analysis (Jornvall, H., Hoog, and Gustavsson, eds.) Birkhauser Verlag, Basel, 133-141.
  25. Yuksel, K.U., Grant, G.A., Mende-Mueller, L., Niece, R.L., Williams, K.R. and Speicher, D.W. (1991) Protein sequencing from polyvinylidenedifluoride membranes: design and characterization of a test sample (ABRF-90SEQ) and evaluation of results. In Techniques in Protein Chemistry II (Villafranca, J., ed.) Academic Press, New York, 151-162.
  26. Niece, R.L., Beach, C.M., Cook, R.F., Hathaway, G.M. and Williams, K.R. (1991) State-of-the-art biomolecular core facilities: a comprehensive survey. FASEB J. 5, 2756-2760.
  27. Nadler, S.G., Kapouch, J.L., Elliott, J.I. and Williams, K.R. (1992) Shuffling of amino acid sequence -an important control in synthetic peptide studies of nucleic acid binding domains: binding properties of fragments of a conserved eukaryotic RNA binding motif. J. Biol. Chem. 267, 3750-3757.
  28. Nadler, S.G., Kapouch, J.L., Elliott, J.I. and Williams, K.R. (1992) Randomization of amino acid sequence: an important control in synthetic peptide analogue studies of nucleic acid binding domains. In Techniques in Protein Chemistry III (Angeletti, R., ed.) Academic Press, New York, 163-170.
  29. Stone, K.L., McNulty, D.E., LoPresti, M.L., Crawford, J.M., DeAngelis, R. and Williams, K.R. (1992) Elution and internal amino acid sequencing of PVDF-blotted proteins. In Techniques in Protein Chemistry III (Angeletti, R., ed.) Academic Press, New York, 23-34.
  30. Smith, A.J., Young, J.D., Carr, S.A., Marshak, D.R., Williams, L.C. and Williams, K.R. (1992) State- of-the-art peptide synthesis: comparative characterization of a 16-mer synthesized in 31 different laboratories. In Techniques in Protein Chemistry III (Angeletti, R., ed.) Academic Press, New York, 219-229.
  31. Webster, K.R., Keill, S., Konigsberg, W.H., Williams, K.R. and Spicer, E.K. (1992) Identification of amino acid residues at the interface of the bacteriophage T4 regA protein-nucleic acid complex. J. Biol. Chem. 267, 26097-26103.
  32. Stone, K.L. and Williams, K.R. (1993) Enzymatic digestion of proteins and HPLC peptide isolation. In A Practical Guide to Protein and Peptide Purification for Microsequencing, 2nd ed. (Matsudaira, P.T., ed.) Academic Press, New York, 43-69.
  33. Williams, K.R., Kobayashi, R., Lane, W. and Tempst, P. (1993) Internal amino acid sequencing from four different laboratories. ABRF News 4, 7-12.
  34. Fields, G.B., Carr, S.A., Marshak, D.R., Smith, A.J., Stults, J.T., Williams, L.C., Williams, K.R. and Young, J.D. (1993) Evaluation of peptide synthesis as practiced in 53 different laboratories. In Techniques in Protein Chemistry IV(Angeletti, R.H., ed.) Academic Press, Orlando, 229-238.
  35. Elliott, J.I., Stone, K.L. and Williams, K.R. (1993) Synthesis and use of an internal amino acid sequencing standard peptide. Anal. Biochem.211, 94-101.
  36. Young, J.D., Angeletti, R.H., Carr, S.A., Marshak, D.R., Smith, A.J., Stults, J.T., Williams, L.C., Williams, K.R. and Fields, G.B. (1994) Multi-year, multi-center evaluation of solid-phase peptide synthesis. In Peptides: Chemistry, Structure and Biology (Hodges, R.S. and Smith, J.A., eds.) American Peptide Symposium, Excom, Leiden, The Netherlands, 1088-1090. (proceedings of the 13th American Peptide Symposium, June 20-25. 1993, Edmonton, Alberta, Canada).
  37. Williams, K.R. and Stone, K.L. (1994) Identifying sites of posttranslational modifications in proteins via HPLC peptide mapping. In Protein Stability and Folding (Shirley, B., ed.) Humana Press, Totowa, NJ, 157-175.
  38. Williams, K.R. and Stone, K.L. (1995) In gel digestion of SDS PAGE-separated Proteins: Observations from internal sequencing of 25 proteins. In Techniques in Protein Chemistry VI. (Crabb, J.W., ed.) Academic Press, Orlando, 143-152.
  39. Stone, K.L. and Williams, K.R. (1995) Digestion of proteins in gels for sequence analysis. In Current Protocols in Protein Science (Colligan, J., Smith, J., Ploegh, H., Speicher, D. and Wingfield, P., eds.) Greene Publishing Associates and John Wiley & Sons, New York, 11.3.1- 11.3.13.
  40. Williams, K.R. and Carr, S.A. (1995) Protein analysis: Integrated sample preparation, chemistry, and mass spectrometry. In Encyclopedia of Molecular Biology and Biotechnology (Meyers, R.A., ed.) VCH Publishers, New York, 731-737.
  41. Stone, K.L. and Williams, K.R. (1996) Enzymatic digestion of proteins in solution and in SDS polyacrylamide gels. In The Protein Protocols Handbook (Walker, J.M., ed.) Humana Press, Totowa, pp. 415-425.
  42. Stone, K.L. and Williams, K.R. (1996) Reverse phase HPLC separation of enzymatic digests of proteins. In The Protein Protocols Handbook (Walker, J.M., ed.) Humana Press, Totowa, pp. 427-434.
  43. Williams, K.R., Samandar, S.M., Stone, K.L., Saylor, M. and Rush, J. (1996) Matrix assisted-laser desorption ionization mass spectrometry as a complement to internal protein sequencing. In The Protein Protocols Handbook (Walker, J.M., ed.) Humana Press, Totowa, pp. 541-555.
  44. Pon, R.T., Buck, G.A., Hager, K.M., Naeve, C.W., Niece, R.L., Robertson, M. and Smith, A.J. (1996) Multi-facility survey of oligonucleotide synthesis and an examination of the performance of unpurified primers in automated DNA sequencing. BioTechniques 21, 680-685.
  45. DeJongh, K.S., Fernandez, J., Gambee, J.E., Grant, G.A., Merrill, B., Stone, K.L., and Rush, J. Design and Analysis of ABRF-95SEQ, a Recombinant Protein with Sequence Heterogeneity.in "Techniques in Protein Chemistry VII" (Marshak, D., ed.) Academic Press, pp. 347-358 (1996)
  46. Fernandez, J., Admon, A., DeJongh, K., Grant, G., Henzel, W., Lane, W.S., Stone, K.L. and Merrill, B. Evaluation of ABRF-96SEQ: a sequence assignment exercise in "Techniques in Protein Chemistry VIII" (Marshak, D.R., ed.) Academic Press, San Diego, pp 69-78 (1997).
  47. Williams, K.R., LoPresti, M. and Stone, K. Internal protein sequencing of SDS-PAGE-separated proteins: Optimization of an in gel digest protocol in "Techniques in Protein Chemistry VIII" (Marshak, D., ed.) Academic Press, pp. 79-90 (1997).
  48. Williams, K., Hellman, U., Kobayashi, R., Lane, W., Mische, S. and Speicher, D. Internal protein sequencing of SDS-PAGE separated proteins: A collaborative ABRF study in "Techniques in Protein Chemistry VIII" (Marshak, D., ed.) Academic Press, pp. 99-109 (1997).
  49. Williams, K.R. and Stone, K.L. Enzymatic cleavage and HPLC peptide mapping of proteins in "Molecular Biotechnology" (Walker, J., ed.) Humana Press, Totowa,, pp. 155-167 (1997).
  50. Kim, S., Merrill, B.M., Rajpurohit, R., Kumar, A., Stone, K.L., Szer, W., Wilson, S.H., Paik, W.K. and Williams, K.R. (1997) Identification of NG-methylarginine residues in human heterogeneous RNP protein A1: Phe/Gly-Gly-Gly-Arg-Gly-Gly-Gly/Phe is a preferred recognition motif. Biochemistry 36, 5185-5192.
  51. Stone, K.L., DeAngelis, R., LoPresti, M., Jones, J., Papov, V., and Williams, K. (1998) Use of liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) for routine identification of enzymatically digested proteins separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Electrophoresis 19, 1046-1052.
  52. Mische, S., Hellman, U., Speicher, D. and Williams, K. (1998) Internal Protein Sequencing in "Encyclopedia of Bioprocess Technology" (Flickinger, M.C. and Drew, S.W. eds.) in press.
  53. Kim, S. Park, G.H., Choo, W.A., Paik, W.K., Cook, R.J. and Williams, K.R. (1998) Identification of Protein-Arginine N-methyltransferase as 10-formyltetrahydrofolate dehydrogenase. J. Biol. Chem. 273, 27374-27382.
  54. Petra Ross-macdonald, Paulo S. R. Coelho, Terry Roemer, Seema Agarwal, Anuj Kumar, Ronald Jansen, Kei-hoi Cheung, Amy Sheehan, Dawn Symoniatis, Lara Umansky, Matthew Heidtman, F. Kenneth Nelson, Hiroshi Iwasaki, Karl Hager, Mark Gerstein, Perry Miller, G. Shirleen Roeder & Michael Snyder. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 402, 413-418 (1999).
  55. Karl M. Hager, Jay W. Fox, Martha Gunthorpe, Kathryn S. Lilley, and Anthony Yeung. (1999) Survey of Current Trends in DNA Synthesis Core Facilities. Journal of Biomolecular Techniques 10.
  56. Folta-Stogniew, E. and Williams, Kenneth R. (1999) Determination of molecular masses of proteins in solution: Implementation of an HPLC size exclusion Chromatography/Laser Light Scattering Service in a Core Laboratory. J. Biomolecular Techniques 10, 51-63.
  57. Mamula, M.J., R.J. Gee, J. Elliott, A. Sette, S. Southwood, P. James-Jones, and P. Blier (1999) Isoaspartyl post-translational modification triggers autoimmune responses to self proteins. J. Biol. Chem. 274:22321-22327.
  58. Stone, K. Fernandez, J., Admon, A. Henzel, W. Lane, W. Rohde, M. and Steinke, L. (1999) ABRF-97 SEQ: Sequencing Results of a Low-Level Sample. Journal of Biomolecular Techniques, Vol 10, Issue 1. pp. 26-32.
  59. Huszar, G. Stone, K. Dix, D. and Vigue, L. (2000) Putative creatine kinase M-isoform in human sperm is identified as the 70-kilodalton heat shock protein HspA2. Biol. Reprod. 63 (3), pp.925-932.
  60. Ma L-G, Li JM, Qu L-J, Hager J, Chen Z-L, Zhao H-L, Deng Z-W. (2001) Light control of Arabidopsis development entails co-ordinated regulation of genome expression and cellular pathways, Plant Cell, 13:2589-2607.
  61. Dillon DA, Stone K and Williams, K. "Potential Application for Proteomics in Oncology" in Progress in Oncology 2002, DeVita VT, Jr, Hellman S and Rosenberg SA, eds. Jones and Bartlett, Sudbury, MA, p 1-22, 2002.
  62. Cheung KH, White K, Hager J, Gerstein M, Reinke V, Nelson K, Masiar P, Srivastava R, Li Y, Li J, Li J.M, Allison D.B, Snyder M, Miller P, Williams K. (2002) YMD: A microarray database for large-scale gene expression analysis. Proceedings of the American Medical Informatics Association Annual Symposium 2002:140-4
  63. Cheung KH, Hager J, Nelson K, White K, Li Y, Snyder M, Williams K, Miller P. (2002) A dynamic approach to mapping coordinates between microplates and microarrays. J Biomed Inform. 35, 306-12.
  64. Yernool, Dinesh, Boudker, Olga, Folta-Stogniew,Ewa, and Gouaux, Eric. (2003) Trimeric Subunit Stoichiometry of the Glutamate Transporters from Bacillus
    caldotenax and Bacillus stearothermophilus. Biochemistry 2003, 42, 12981-12988
  65. D. P. Arnott, M. Gawinowicz, R. A. Grant, W. S. Lane, L. C. Packman, K.Speicher, and K. Stone (2002) Proteomics in Mixtures: Study Results of ABRF-PRG02. Journal of Biomolecular Techniques 13, 179-186.
  66. D.Arnott, M. Gawinowicz, R.A. Grant, T.A. Neubert, L.C. Packman, K.D. Speicher, K. Stone, and C.W. Turck. (2003) ABRF-PRG03: Phosphorylation Site Determination. Journal of Biomolecular Techniques 14, 205-215.
  67. Wu, B., Abbott, T., Fishman, D., McMurray, W., Mor, G., Stone, K., Ward, D., Williams, K., and Zhao, H. (2003) Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data. Bioinformatics 19, 1636-1643.
  68. Greenbaum, D.,Colangelo, C., Williams, K., and Gerstein, M. (2003) Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biology 4, 117.1-117.8.
  69. Cheung, K., Hager, J., Pan, D., Srivastava, R., Mane, S., Li, Y., Miller, P., and Williams, K.R. (2004) KARMA: A web server application for comparing and annotating heterogeneous microarray platforms. Nucleic Acids Research, Jul 1; 32(Web Server issue):W441-4.
  70. Folta-Stogniew, Ewa , O'Malley, Shawn, Gupta, Ravindra, Anderson, Karen S., and Radding, Charles M. (2004) Exchange of DNA Base Pairs that Coincides with Recognition of Homology Promoted by E. coli RecA Protein. Molecular Cell, Vol 15, 965-975, 24 September 2004.
  71. Hoek, K., Rimm, D.L., Williams, K.R., Zhao, H., Ariyan, S., Lin, A., Kluger, H.M., Berger, A.J., Cheng, E., Trombetta, E.S.,Wu, T., Niinobe, M., Yoshikawa, K., Hannigan, G.E., Halaban, R. (2004) Expression Profiling Reveals Novel Pathways in the Transformation of Melanocytes to Melanomas. Cancer Research 64, 5270-5282.
  72. Shi, Y., Xiang, R., Crawford, J. K., Colangelo, C. M., Horváth, C., and Wilkins, J. A. (2004). A Simple Solid Phase Mass Tagging Approach for Quantitative Proteomics. J Proteome Res, 2004,3,104-111
  73. Stone, K.L. and Williams, K.R. (2004) Enzymatic Digestion of Proteins in Gels for Mass Spectrometric Identification and Structural Analysis. In Current Protocols in Protein Science (J.E. Coligan, B.M. Dunn, H.L. Ploegh, D.W. Speicher, and P.T. Wingfield, eds.) pp. 11.3.1-11.3.XX. John Wiley & Sons, New York, in press.
  74. Williams, K., Wu, T., Colangelo, C., Nairn, A.C., (2004) Recent Advances in Neuroproteomics and potential application to studies of drug addiction. Neuropharmacology, in press.
  75. Meng, H., Hager, K., Rivkees, S.A. and Gruen, J.R. (2005) Detection of Turner syndrome using high-throughput quantitative genotyping.
    J Clin Endocrinol Metab. 90, 3419-22.
  76. Meng, H., Hager, K., Held, M., Page, G.P., Olson, R.K., Pennington, B.F., Defries, J.C., Smith, S.D., and Gruen, J.R. (2005) TDT-association analysis of EKN1 and dyslexia in a Colorado twin cohort. Hum Genet. 16, 1-4.
  77. Meng, H., Smith, S.D., Hager, K., Held, M., Liu, J., Olson, R.K., Pennington, B.F., Defries, J.C., Gelernter, J., O'reilly-Pol, T., Somlo, S., Skudlarski, P., Shaywitz, S.E., Shaywitz, B.A., Marchione, K., Wang, Y., Paramasivam, M., Loturco, J.J., Page, G.P., and Gruen, J.R. (2005) DCDC2 is associated with reading disability and modulates neuronal development in the brain. Proc Natl Acad Sci U S A. 102, 17053-8.
  78. Robert J. Klein, Caroline Zeiss, Emily Y. Chew, Jen-Yue Tsai, Richard S. Sackler, Chad Haynes, Alice K. Henning, John Paul SanGiovanni, Shrikant M. Mane, Susan T. Mayne, Michael B. Bracken, Frederick L. Ferris, Jurg Ott, Colin Barnstable, Josephine Hoh. (2005) Complement Factor H Polymorphism in Age-Related Macular Degeneration. (2005) Science. 308, 385-9.
  79. Hager J. (2006) Making and Using Spotted DNA Microarrays in an Academic Core Laboratory. In Methods in Enzymology (Alan Kimmel & Brian Oliver, eds.) Volume 410:135-68. DNA Microarrays Part A: Array Platforms & Wet-Bench Protocols. Elsevier, San Diego.
  80. Yasuo Yamakoshi, Jan C-C. Hu, Takanori Iwata, Kazuyuki Kobayashi, Makoto
    Fukae, and James P. Simmer. (2006) Dentin Sialophosphoprotein Is Processed by MMP-2 and MMP-20 in Vitro and in Vivo. J. Biol. Chem., Dec. 2006; 281:
    38235-38243.

  81. Patterson, T.A., Lobenhofer, E.K., Fulmer-Smentek, S.B., Collins, P., Chu, T-M., Bao, W., Fang, H., Kawasaki, E.S., Hager, J., Tikhonova, I.R., Walker, S.J., Zhang, L., Hurban, P., de Longueville, F., Fuscoe, J.C., Tong, W., Shi, L., and Wolfinger, R.D. (2006) Performance Comparison of One-Color and Two-Color Platforms Within the Microarray Quality Control (MAQC) Project. Nature Biotechnology.24(9), 1140-50.

  82. Shi, L. et al., MAQC Consortium. (2006) The MicroArray Quality Control (MAQC) project shows interplatform reproducibility of gene expression measurements. Nature Biotechnology, 24(9):1151-1161.

  83. Korbel, J. O.; Urban, A. E.; Affourtit, J. P.; Godwin, B.; Grubert, F.; Simons, J. F.; Kim, P. M.; Palejev, D.; Carriero, N. J.; Du, L.; Taillon, B. E.; Chen, Z.; Tanzer, A.; Saunders, A. C.; Chi, J.; Yang, F.; Carter, N. P.; Hurles, M. E.; Weissman, S. M.; Harkins, T. T.; Gerstein, M. B.; Egholm, M.; Snyder, M., Paired-end mapping reveals extensive structural variation in the human genome. Science 2007, 318, (5849), 420-6.

  84. Korbel, J. O.; Urban, A. E.; Grubert, F.; Du, J.; Royce, T. E.; Starr, P.; Zhong, G.; Emanuel, B. S.; Weissman, S. M.; Snyder, M.; Gerstein, M. B., Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome. Proceedings of the National Academy of Sciences of the United States of America 2007, 104, (24), 10110-5.

  85. Frost, A.; Perera, R.; Roux, A.; Spasov, K.; Destaing, O.; Egelman, E. H.; De Camilli, P.; Unger, V. M., Structural basis of membrane invagination by F-BAR domains.[see comment]. Cell 2008, 132, (5), 807-17.

  86. Weinberg, Z.; Regulski, E. E.; Hammond, M. C.; Barrick, J. E.; Yao, Z.; Ruzzo, W. L.; Breaker, R. R., The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches. Rna-A Publication of the Rna Society 2008, 14, (5), 822-8.

  87. Weinberg, Z.; Barrick, J. E.; Yao, Z.; Roth, A.; Kim, J. N.; Gore, J.; Wang, J. X.; Lee, E. R.; Block, K. F.; Sudarsan, N.; Neph, S.; Tompa, M.; Ruzzo, W. L.; Breaker, R. R., Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Research 2007, 35, (14), 4809-19.

  88. Ma, S.; Song, X.; Huang, J., Supervised group Lasso with applications to microarray data analysis. BMC Bioinformatics 2007, 8, 60.

  89. Leng, C.; Ma, S., Path consistent model selection in additive risk model via Lasso. Statistics in Medicine 2007, 26, (20), 3753-70.

  90. Rosengarten, R. D.; Sperling, E. A.; Moreno, M. A.; Leys, S. P.; Dellaporta, S. L., The mitochondrial genome of the hexactinellid sponge Aphrocallistes vastus: evidence for programmed translational frameshifting. BMC Genomics 2008, 9, 33.

  91. Zhou, X.; Tuck, D. P., MSVM-RFE: extensions of SVM-RFE for multiclass gene selection on DNA microarray data.[erratum appears in Bioinformatics. 2007 Aug;23(15):2029]. Bioinformatics 2007, 23, (9), 1106-14.

  92. Leng, C.; Ma, S., Accelerated failure time models with nonlinear covariates effects. Australian and New Zealand Journal of Statistics 2007, 49, (2), 155-172.

  93. Sudarsan N., L. E., Weinberg Z., Moy R., Kim J., Link K., Breaker, R., Riboswitches in Eubacteria Sense the Second Messenger Cyclic Di-GMP. Science 2008, 321, (5887), 411-413.

  94. Braithwaite, R. S.; Roberts, M. S.; Chang, C. C.; Goetz, M. B.; Gibert, C. L.; Rodriguez-Barradas, M. C.; Shechter, S.; Schaefer, A.; Nucifora, K.; Koppenhaver, R.; Justice, A. C., Influence of alternative thresholds for initiating HIV treatment on quality-adjusted life expectancy: a decision model. Annals of Internal Medicine 2008, 148, (3), 178-85.

  95. Carriero, N.; Osier, M. V.; Cheung, K.-H.; Miller, P. L.; Gerstein, M.; Zhao, H.; Wu, B.; Rifkin, S.; Chang, J.; Zhang, H.; White, K.; Williams, K.; Schultz, M., A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies. Journal of the American Medical Informatics Association 2005, 12, (1), 90-8.

  96. Bjornson, R. D.; Carriero, N. J.; Colangelo, C.; Shifman, M.; Cheung, K. H.; Miller, P. L.; Williams, K., X!!Tandem, an improved method for running X!tandem in parallel on collections of commodity computers. Journal of Proteome Research 2008, 7, (1), 293-9.
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