Krawetz group publications  

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1) Krawetz, S.A. and Israelstam, G.F. (1978) Kinetics of pyridine nucleotide transhydrogenase from chlorella. Plant Science Letters 12:323-326.

2) Krawetz, S.A., Narayanan, A.S. and Anwar, R.A. (1983) In vitro translation of elastin mRNA and processing of the translated products and the signal sequence of elastin 'a'. Canadian Journal of Biochemistry and Cell Biology 61:274-286. [PubMed]

3) Krawetz, S.A. and Dixon G.H. (1984) Isolation and in vitro translation of a mammalian protamine mRNA. Bioscience Reports 4:593-603. [PubMed]

4) Krawetz, S.A. and Anwar, R.A. (1984) Optimization of the isolation of biologically active mRNA from chick embryo aorta. BioTechniques 2:342-347. [Biotechniques]

5) Raju, K., Rampersad, V., Pulleyblank, D.E., Krawetz, S.A. and Anwar, R.A. (1985) Bovine elastin cDNA clones: evidence for the occurrence of a new elastin related protein in fetal calf ligamentum nuchae. Bioscience Reports 5:633-641. [PubMed]

6) Aiken, J.M., Miller, F.D., Hagen, F., McKenzie, D.I., Krawetz, S.A., van de Sande, J.H., Rattner, J.B. and Dixon, G.H. (1985) Tandem repeats of a specific alternating purine-pyrimidine DNA sequence adjacent to protamine genes in the rainbow trout that can exist in the Z-conformation. Biochemistry 24:6268-6276. [PubMed]

7) Krawetz, S.A., States, J.C. and Dixon, G.H. (1986) Isolation and fractionation of total nucleic acids from tissues and cells. Journal of Biochemical and Biophysical Methods 12:29-36. [PubMed]

8) Krawetz, S.A., Connor, W., Cannon, P.D. and Dixon, G.H. (1986) Vector-primer-cloner-sequencer plasmid for the construction of cDNA libraries: evidence for a rat glyceraldehyde-3-phosphate dehydrogenase-like and a ferritin mRNA within testis. DNA 5:427-435. [PubMed]

9) Krawetz, S.A., Connor, W. and Dixon, G.H. (1986) Oligonucleotides as probes for mammalian protamine mRNA's. Bioscience Reports 6:585-590. [PubMed]

10) Kalisch, B.W., Krawetz, S.A., Schoenwaelder, K.H. and van de Sande, J.H. (1986) Covalently linked sequencing primer linkers (splinkers) for sequence analysis of restriction fragments. Gene 44:263-270. [PubMed]

11) Krawetz, S.A., Kalisch, B.W. and van de Sande, J.H. (1986) Covalently linked complementary oligodeoxynucleotides (splinkers) as tools for molecular biology. Nucleic Acids Research 14:7131. [PubMed]

12) Jankowski, J.M., Krawetz, S.A., Walczyk, E. and Dixon, G.H. (1986) In vitro expression of two proteins from overlapping reading frames in a eukaryotic DNA sequence. Journal of Molecular Evolution 24:61-71. [PubMed]

13) Krawetz, S.A., Connor, W. and Dixon, G.H. (1987) Cloning of a bovine protamine cDNA and the evolution of vertebrate protamines. DNA 6:47-57. [PubMed]

14) Krawetz, S.A. (1987) DNA sequencing with AMV (avian myoblastosis virus) reverse transcriptase and a modified T7 DNA polymerase (sequenase). BioTechniques 5:620-627. [Biotechniques]

15) Krawetz, S.A., Connor, W. and Dixon, G.H. (1988) Bovine protamine genes contain a single intron: the structures of the two alleles. The Journal of Biological Chemistry 263:321-326. [PubMed]

16) Krawetz, S.A. (1988) Recovery of in vitro translated proteins from polyacrylamide gels. American Biotechnology Journal 6:10-12.

17) Krawetz, S.A. and Dixon, G.H. (1988) Sequence similarities of the protamine genes: implications for regulation and evolution. The Journal of Molecular Evolution 27:291-297. [PubMed]

18) Krawetz, S.A., Bricker, R., Connor, W., Church, R.B. and Dixon, G.H. (1988) Restriction fragment length polymorphism (RFLP) analysis of bovine nuclear protein genes. Theoretical and Applied Genetics 5:402-409. 

19) Keenan, T.P. and Krawetz, S.A. (1988) Computer video acquisition and analysis system for biological data. Computer Applications in the Biological Sciences and Nucleic Acids Research Computer Review Issue, CABIOS 4:203-210. [PubMed]

20) Winkfein, R.J., Moir, R.D., Krawetz, S.A., Blanco, J., States, J.C. and Dixon, G.H. (1988) A new family of repetitive, retroposon-like sequences in the genome of rainbow trout. European Journal of Biochemistry 176:255-269. [PubMed]

21) Krawetz, S.A., Pon, R.T. and Dixon, G.H. (1989) Increased efficiency of the TAQ polymerase catalyzed polymerase chain reaction. Nucleic Acids Research 17:819. [PubMed]

22) Krawetz, S.A., Cannon, P.D., Joshi, R, and Dixon, G.H. (1989) Molecular probes for general testicular and specific spermatogenic function. Molecular and Cellular Probes 3:109-115. [PubMed]

23) Krawetz, S.A., Sellos, D., Wong, N.C.W. and Dixon, G.H. (1989) Phagemid VPCS vectors for priming, cloning and sequencing. Gene 82:317-320. [PubMed]

24) Krawetz, S.A. (1989) Sequence errors described in GenBank: a means to determine the accuracy of DNA sequence interpretation. Nucleic Acids Research 17:3951-3957. [PubMed]

25) Krawetz, S.A., Herfort, M.H., Hamerton, J.L., Pon, R.T. and Dixon, G.H. (1989) Chromosomal localization and structure of the human P1 protamine gene. Genomics 5:639-645. [PubMed]

26) Cassol, S.A., Pal, R., Naylor, M.J., Bowen, T.J., Culver-James, J., Poon, M-C., Russell, J.A., Krawetz, S.A., Pon, R.T. and Hoar, D.I. (1989) Primer mediated enzymatic amplification of cytomegalovirus (CMV) DNA: application to the early diagnosis of CMV infection in marrow transplant recipients. Journal of Clinical Investigation 83:1109-1115. [PubMed]

27) Twomey, T.A. and Krawetz, S.A. (1990) Parameters affecting hybridization of nucleic acids blotted onto nylon or nitrocellulose membranes. BioTechniques 8:1-3. [PubMed]

28) Krawetz, S.A., Herfort, M.H. and Dixon, G.H. (1990) In situ localization of a mammalian protamine gene: parameters affecting specificity of hybridization. Genome 33:459-463. [PubMed]

29) Sellos, D., Krawetz, S.A. and Dixon, G.H. (1990) Organization and complete nucleotide sequence of the core histone gene cluster of the annelid, platynereis dumerilii. European Journal of Biochemistry 190:21-29. [PubMed]

30) Svinarich, D.M., Shek, M. and Krawetz, S.A. (1991) Inexpensive isolation of poly (A+)-mRNA using chaotropic agents. Methods in Molecular and Cellular Biology 2:1-7.

31) Svensson, C., Welsh, N., Krawetz, S.A.and Welsh, M. (1991) Exhibition of specific alterations in activities and mRNA levels of rat islet glycolytic and mitochondrial enzymes in three different in vitro model systems for attenuated insulin release. Diabetes 40:771-776. [PubMed]

32) Threadgill, D.S., Kraus, J.P., Krawetz, S.A. and Womack, J.E. (1991) Evidence for the evolutionary origin of human chromosome 21 from comparative gene mapping in the cow and mouse. Proceedings of the National Academy of Science (U.S.A.) 88:154-158. [PubMed]

33) Nelson, J.E. and Krawetz, S.A. (1992) Purification of cloned and genomic DNA by guanidine thiocyanate/isobutyl alcohol fractionation. Analytical Biochemistry 207:197-201. [PubMed]

34) Svinarich, D.M., Twomey, T.A., Macauley, S.P., Krebs, C.J., Yang, T.P. and Krawetz, S.A. (1992) Characterization of the human lysyl oxidase gene locus. The Journal of Biological Chemistry 267:14382-14387. [PubMed]

35) Svinarich, D.M. and Krawetz, S.A. (1993) Gene assignment by quantitative hybridization analysis of somatic cell hybrids. BioTechniques 14:82-86. [PubMed]

36) Chang, Y.S., Svinarich, D.M., Yang, T.P. and Krawetz, S.A. (1993) The mouse lysyl oxidase gene resides on chromosome 18. Cytogenetics and Cell Genetics 63:47-49. [PubMed]

37) Nelson, J.E. and Krawetz, S.A. (1993) Linkage of human spermatid-specific basic nuclear protein genes: definition and evolution of the P1>P2>TP2 locus. The Journal of Biological Chemistry 268:2932-2936. [PubMed]

38) Krawetz, S.A., Sellos, D. and Dixon, G.H. (1993) Analysis of the core histone gene cluster of the annelid Platynereis dumerillii. DNA Sequence 4: 29-36. [PubMed]

39) Krebs, C.J. and Krawetz, S.A. (1993) Lysyl oxidase copper talon complex: a model. Biochemica et Biophysica Acta 1202: 7-12. [PubMed]

40) Krawetz, S.A. (1994) The origin of lysyl oxidase. Comparative Biochemistry and Physiology 108B:117-119. [PubMed]

41) McAlinden, T.P. and Krawetz, S.A. (1994) A practical method to screen libraries of cloned DNA. Analytical Biochemistry 218:237-238. [PubMed]

42) Gacheru, S., McGee, C., Uriu-Hare, J.Y., Kosonen, T., Packman, S., Tinker, D., Krawetz, S.A., Reiser, K., Keen, C.L. and Rucker, R.B. (1993) Expression and accumulation of lysyl oxidase, elastin and type I procollagen in human Menkes and mottled mouse fibroblasts. Archives of Biochemistry and Biophysics 301:325-329. [PubMed]

43) Singh, G.B. and Krawetz, S.A (1994) Computer based exon detection: an evaluation metric for comparison. International Journal of Genome Research 1:321-328.

44) De Jonckheere, J., Nelson, J.E., Ginsburg, K.A., Martin, L., Krawetz, S.A. (1994) GA repeat polymorphism at the PRM2 male fertility locus of chromosome 16. Human Molecular Genetics 3: 1915. [PubMed]

45) Nelson, J.E. and Krawetz, S.A. (1994) Easy read DNA sequencing gels. BioTechniques 17:416-418. [PubMed]

46) Nelson, J.E. and Krawetz, S.A. (1994) Characterization of a human locus in transition. The Journal of Biological Chemistry 269:31067-31073. [PubMed]

47) Singh, G.B., Nelson, J.E., McAlinden, T.P. and Krawetz, S.A. (1994) ISWAC: Proposed system for the integrated assembly of chromosomes. DNA Sequence 5:67-76. [PubMed]

48) Singh, G.B. and Krawetz, S.A. (1995) CLONEPLACER: A software tool for simulating contig formation for OSS Ordered Shotgun Sequencing. Genomics 25:555-558. [PubMed]

49) Wykes, S.M., Nelson, J.E., Visscher, D.W., Djakiew, D. and Krawetz, S.A. (1995) Coordinate expression of the PRM1, PRM2 and TNP2 multigene locus in human testis. DNA and Cell Biology 14:155-161. [PubMed]

50) Nelson, J.E. and Krawetz, S.A. (1995) Mapping the clonally unstable recombinogenic PRM1>PRM2>TNP2 region of human 16p13.2. DNA Sequence 5:163-168. [PubMed]

51) Choudhary, S. K, Wykes, S.M., Kramer, J.A., Mohamed, A.N., Koppitch, F., Nelson, J.E. and Krawetz, S.A. (1995) A Haploid expressed gene cluster exists as a single chromatin domain in human sperm. The Journal of Biological Chemistry 270:8755-8762. [PubMed] 

52) Singh, G.B. and Krawetz, S.A. (1995) DNAView: A quality assessment tool for the visualization of large sequenced regions. Computer Applications in the Biological Sciences 11:317-319. [PubMed]

53) Kramer, J.A. and Krawetz, S.A. (1995) Matrix associated regions in haploid expressed domains. Mammalian Genome 6:677-679. [PubMed]

54) McAlinden, T. P., Smith, D. I., Smith, S.E. and Krawetz, S.A. (1995) Isolation and characterization of a 1 Mb region of 5q23.3-q31.2 surrounding the human lysyl oxidase gene. The Journal of Molecular and Cellular Cardiology 27:2409-2413. [PubMed]

55) Khidhir, M.A., Stachecki, J.J., Krawetz, S.A. and Armant, D.R. (1995) Rapid inhibition of mRNA synthesis during preimplantation embryo development: vital permeabilization by lysolecithin potentiates the action of alpha-amanitin. Experimental Cell Research 219:619-625. [PubMed]

56) Nelson, J.E. and Krawetz, S.A. (1995) Computer assisted promoter analysis of a human sperm specific nucleoprotein gene cluster. DNA Sequence 5:329-337.[PubMed]

57) Kramer, J.A., Singh, G.B. and Krawetz, S.A. (1996) Computer assisted search for sites of nuclear matrix attachment. Genomics 33:305-308. [PubMed]

58) Kramer, J.A. and Krawetz, S.A. (1996) Analysis of transgenes by Polymerase Chain Reaction: establishing and maintaining the PRM1>PRM2>TNP2 line. Analytical Biochemistry 235:110-111. [PubMed]

59) Kramer, J.A. and Krawetz, S.A. (1996) Nuclear matrix interactions within the sperm genome. The Journal of Biological Chemistry 271:11619-11622. [PubMed]

60) Macauley, S.P., Schultz, G.S., Bruckner, B.A., Krawetz, S.A. and Yang, T.P. (1996) Effects of transforming growth factor a-1 on extracellular matrix gene expression by human fibroblasts from a laryngeal stenotic lesion. Wound Repair and Regeneration 4:269-277.

61) Wykes, S.M., Visscher, D.M. and Krawetz, S.A. (1997) Haploid expressed transcripts persist in mature human spermatozoa. Molecular Human Reproduction 3:15-19. [PubMed]

62) Singh, G.B., Kramer, J.A. and Krawetz, S.A. (1997) Mathematical model to predict regions of chromatin attachment to the nuclear matrix. Nucleic Acids Research 25:1419-1425. [PubMed]

63) Kramer, J.A. and Krawetz, S.A. (1997) A PCR-based assay to determine nuclear matrix association. BioTechniques 22:826-828. [PubMed]

64) Kramer, J.A. and Krawetz, S.A. (1997) Determining the potentiative state of a chromatin domain. BioTechniques 22:880-882. [PubMed]

65) Chung, I-B., Kramer, J.A., Johnson, M.P. Evans, M.I. and Krawetz, S.A. (1997) The use of cloned repetitive sequences as hybridization competitors to detect single copy sequences. Genetic Analysis: Biomolecular Engineering 14:13-15. [PubMed]

66) Sharma, R., Kramer, J.A. Krawetz, S.A. (1997) Lysyl oxidase, cellular senescence and tumor suppression. BioScience Reports 17:409-414. [PubMed]

67) Kramer, J.A., Zhang, S., Yaron, Y., Zhao, Y. and Krawetz, S.A. (1997) Genetic testing for male infertility: a postulated role for mutations in sperm nuclear matrix attachment regions. Genetic Testing 1:125-129. [PubMed]

68) Rout, U.K., Krawetz, S.A. and Armant, R.A. (1997) Ethanol-induced intracellular calcium mobilization rapidly alters gene expression in the mouse blastocyst. Cell Calcium 22:463-474. [PubMed]

69) Walter, W. R., Singh, G.B and Krawetz, S.A. (1998) MARs mission update. Biochemical Biophysical Research Communications. 242:419-422. [PubMed]

70) Singh, G.B., Stamper, D.E. and Krawetz, S.A. (1998) A Web tool for detecting matrix attachment regions. Trends in Genetics 14:83.

71) Yaron, Y., Kramer, J.A., Gyi, K., Ebrahim, S.A.D., Evans, M.I., Johnson, M.P. and Krawetz, S.A. (1998) Centromere sequences localize to the human sperm nuclear halo. International Journal of Andrology 21:13-18. [PubMed]

72) Kramer, J.A., Adams, M.D., Singh, G.B., Doggett, N.A. and Krawetz, S.A. (1998) Extended Analysis of the Region Encompassing the PRM1>PRM2>TNP2 Domain: Genomic Organization, Evolution and Gene identification. Journal of Experimental Zoology 282:245-253. [PubMed]

73) Kramer, J.A., Adams, M.D., Singh, G.B., Doggett, N.A. and Krawetz, S.A. (1998) A matrix associated region localizes the human SOCS-1 gene to chromosome 16p13.13. Somatic Cell and Molecular Genetics 24:131-133. [PubMed]

74) Kramer, J.A. and Krawetz, S.A. (1998) Genesis of a novel human sequence from the human protamine PRM1 gene. Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology 120:467-473. [PubMed]

75) Kramer, J.A., McCarrey, J. R., Djakiew, D. and Krawetz, S.A. (1998) Differentiation: the selective potentiation of chromatin domains. Development 125:4749-4755. [PubMed]

76) Stewart, K., Kramer, J.A., Evans, M.I. and Krawetz, S.A. (1999) Temporal expression of the transgenic human protamine gene cluster. Fertility and Sterility 71:739-745. [PubMed]

77) Leach, R., Ko, M. and Krawetz, S. (1999) Assignment of amyloid-precursor-like protein 2 gene (APLP2) to 11q25 by fluorescent in situ hybridization. Cytogenetics Cell Genetics. 87:215-216. [PubMed]

78) Yaron, Y., Diamond, M.P., Leach, R., Wykes, S., Barbour Smith, M. and Krawetz, S.A. (1999) Lysyl oxidase transcripts in peritoneal adhesions and incisional scars. The Journal of Reproductive Medicine 44:253-256. [PubMed]

79) Miller, D., Briggs, S., Snowden, H., Hamlington, J., Rollision, S., Lilford, R. and Krawetz, S.A. (1999) A complex population of RNAs in human ejaculate spermatozoa: implications for understanding molecular aspects of spermiogenesis. Gene 237:385-392. [PubMed]

80) Kramer, J.A., McCarrey, J.R., Djakiew, D. and Krawetz, S.A. (2000) Human spermatogenesis as a model to examine gene potentiation. Molecular Reproduction and Development 56:254-258. [PubMed]

81) Singh, G.B. and Krawetz, S.A. (2000) Data mining algorithm for discovering matrix association regions (MARs) Proceedings of Spie, Data Mining and Knowledge Discovery: Theory, Tools, and Technology II, 4057:330-341.

82) Wykes, S. M., Miller, D. and Krawetz, S.A. (2000) Mammalian spermatozoal mRNAs: tools for functional analysis of male gametes. Journal of Submicroscopic Cytology and Pathology 32:77-81. [PubMed]

83) Reid, R., Dix, D.J., Miller, D. and Krawetz, S.A. (2001) Recovering microarray data for pathways analysis using a multipoint alignment strategy. BioTechniques 30:762-767. [PubMed]

84) Draghici, S., Martins, R.P., Leach, R.E. and Krawetz, S.A. (2001) Expressed Sequenced Tag Data Mining: The Reality of Virtual Gene Expression. Atlantic Symposium on Computational Biology, and Genome Information Systems & Technology 39 - 41. 

85) Martins, R.P., Leach, R.E. and Krawetz, S.A. (2001) Whole body gene expression by data mining. Genomics 72:34-42. [PubMed]

86) Krawetz, S.A. and Womble, D. (2001) Design and Implementation of an Introductory Course for Computer Applications in Molecular Genetics: A Case Study. Atlantic Symposium on Computational Biology, and Genome Information Systems & Technology 230 -234.

87) Rockett, J.C., Luft, J.C., Garges, J.B., Krawetz, S.A., Hughes, M.R., Kim, K.W., Oudes, A.J. and Dix, D.J. (2001) Development of a 950-gene DNA array for examining gene expression patterns in mouse testis. Genome Biology 2:14.1-14.9. [PubMed]

88) Ye, C., Lu, W., Li, G., Bremer, S., Wang, Y., Moens, P., Hughes, M., Krawetz, S. A. and Heng H.H.Q. (2001) The combination of SKY and specific loci detection with FISH or immunostaining. Cytogenetics and Cell Genetics 93:195-202. [PubMed]

89) Martins, R. P., Ujfalusi, A.A., Csiszar, K. and Krawetz, S.A. (2001) Characterization of the region encompassing the human lysyl oxidase locus. DNA Sequence 12:215-227. 

90) Schmid, C., Heng, H.H.Q., Rubin, C., Ye, C.J. and Krawetz S.A. (2001) Sperm nuclear matrix association of the PRM1>PRM2>TNP2 domain is independent of Alu Methylation, Human Molecular Reproduction 7:903-911. [PubMed]

91) Leach, R., Duniec-Dmuchowski, Z., Tanaka, T., Ko, M. and Krawetz, S.A. (2001) Assignment of CGI-15 to 20 human chromosome band q13.1-13.2 by fluorescent in situ hybridization. Cytogenetics and Cell Genetics 94:252-253. [PubMed]

92) Khatri, P., Draghici, S., Ostermeier, G.C. and Krawetz, S.A. (2002) Profiling gene expression utilizing onto-express. Genomics 79:266-270. [PubMed]

93) Csiszar, K., Fong, S.F.T., Ujfalusi, A., Krawetz, S.A., Salvati, E.P., Mackenzie, J.W. and Boyd, C.D. (2002) Somatic mutations of the lysyl oxidase gene on chromosome 5q23.1 in colorectal tumors. International Journal of Cancer 97: 636-642. [PubMed]

94) Ostermeier,G.C., Dix, D. J. and Krawetz, S.A. (2002) A bioinformatic strategy to rapidly characterize cDNA libraries. Bioinformatics 18:949-952.  [PubMed]

95) Leach, R.E., Duniec-Dmuchowski, Z.M., Pesole, G., Tanaka, T.S., Ko, M.S.H., Armant, D.R. and Krawetz, S.A. Identification, Molecular Characterization, and Tissue Expression of OVCOV1 Mammalian Genome. 13:619-624.   [PubMed]

96) McCarrey, J.R., Watson, C., Atencio, J., Ostermeier, G.C., Marahrens, Y., Jaenisch, R., and Krawetz, S.A. (2002) X-chromosome inactivation during spermatogenesis is regulated by an Xist/Tsix-independent mechanism in the mouse. Genesis. 34:257-266.  [PubMed]

97) van Biljon, W., Wykes, M., Scherer, S., Krawetz, S.A. and Hapgood J. (2002) Type II gonadotropin-releasing hormone-receptor transcripts in human sperm. Biology of Reproduction. 67:1741-1749[PubMed]

98) Ostermeier, G.C., Dix, D.J., Miller, D., Khatri, P. and Krawetz, S.A. (2002) Spermatozoal RNA profiles of normal fertile men. The Lancet. 360:773-777.  [PubMed]

99) Draghici, S., Khatri, P., Martins, R.P., Ostermeier, G.C., and Krawetz, S.A. (2003) Global functional profiling of gene expression. Genomics. 81:98-104.  [PubMed]

100) Ostermeier, G.C., Liu, Z., Martins, R.P., Bharadwaj R.R., Ellis J., Draghici, S. and Krawetz, S.A. (2003) Nuclear matrix association of the human beta-globin locus utilizing a novel approach to quantitative real-time PCR. Nucleic Acids Research. 31:3257-3266.  [PubMed]

101) Draghici ,S., Khatri, P., Bhavsar, P., Shah, A., Krawetz, S.A. and Tainsky, M.A. (2003) Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. Nucleic Acids Research. 31:3775-3781. [PubMed]

102) Goodrich, R.J., Ostermeier, G.C. and Krawetz, S.A. (2003) Multitasking with molecular dynamics Typhoon: quantifying nucleic acids and autoradiographs. Biotechnol Lett. 25:1061-1065. [PubMed]

103) Wykes, S.M. and Krawetz, S.A. (2003) Separation of spermatogenic cells from adult transgenic mouse testes using unit-gravity sedimentation. Mol Biotechnol. 25:131-138. [PubMed]

104) Wykes, S.M. and Krawetz, S.A. (2003) Conservation of the PRM1 --> PRM2 --> TNP2 domain. DNA Seq. 14:359-367.  [PubMed]

105) Heng, H.H., Goetze, S., Ye, C.J., Liu, G., Stevens, J.B., Bremer, S.W., Wykes, S.M., Bode, J. and Krawetz, S.A. (2004) Chromatin loops are selectively anchored using scaffold/matrix-attachment regions. J Cell Sci. 117:999-1008. [PubMed]

106) Ostermeier, G.C., Miller, D., Huntriss, J.D., Diamond, M.P. and Krawetz SA. (2004) Reproductive biology: delivering spermatozoan RNA to the oocyte. Nature. 429:154.  [PubMed]

107) Martins, R.P. and Krawetz, S.A. (2004) Using multiplexed real-time polymerase chain reaction to rapidly identify single-copy transgenic animals. Anal Biochem. 329:337-339. [PubMed]

108) Martins, R.P., Ostermeier, G.C. and Krawetz, S.A. (2004) Nuclear matrix interactions at the human protamine domain: a working model of potentiation. J Biol Chem. 279:51862-51868 [PubMed]

109) Ostermeier, G.C., Goodrich, R.J., Moldenhauer, J.S., Diamond, M.P. and Krawetz, S.A. (2005) A Suite of Novel Human Spermatozoal RNAs. J Androl. 26:70-74 [PubMed]

110) Fayz B., Moldenhauer J.S., Wang D., Zhao C., Yao B., Liu D., Weinsheimer S., Gardner L., Johnson A., Womble D.D. and Krawetz, S.A. (2005) LARALink: a web application for cytogenetic linkage analysis. Clin Genet. 2005 Apr;67(4):314-21. [PubMed]

111) Krawetz, S.A. (2005) On the significance of RNA in human sperm. Zhonghua Nan Ke Xue. Mar;11(3):170-4. Chinese. [PubMed]

112) Miller D., Ostermeier G.C., and Krawetz, S.A. (2005) The controversy, potential and roles of spermatozoal RNA. Trends Mol Med. Apr;11(4):156-63. Review. [PubMed]

113) Martins R.P. and Krawetz, S.A. (2005) RNA in human sperm. Asian J Androl. Jun;7(2):115-20. Review. [PubMed]

114) Ostermeier G.C., Goodrich R.J., Diamond M.P., Dix D.J. and Krawetz, S.A. (2005) Toward using stable spermatozoal RNAs for prognostic assessment of male factor fertility. Fertil Steril. Jun;83(6):1687-94. [PubMed]

115) Krawetz S.A., Draghici S., Goodrich R., Liu Z., Ostermeier G.C.. (2005) In silico and wet-bench identification of nuclear matrix attachment regions. Methods Mol Med. 108:439-58. [PubMed]

116) Krawetz, S.A. (2005) Paternal contribution: new insights and future challenges. Nat Rev Genet. Aug;6(8):633-42. Review. [PubMed]

117) Platts A.E., Moldenhauer J.S., Fayz B., Wang D., Borgaonkar D.S., and Krawetz, S.A. (2005) LARaLink 2.0: a comprehensive aid to basic and clinical cytogenetic research. Genet Test. Winter;9(4):334-41. [PubMed]

118) Lu Y, Platts A.E., Ostermeier G.C. and Krawetz, S.A. (2006) K-SPMM: a database of murine spermatogenic promoters modules & motifs. BMC Bioinformatics. May 3;7:238.  [PubMed]

119) Platts A.E., Quayle A.K., and Krawetz, S.A. (2006) In-silico prediction and observations of nuclear matrix attachment. Cell Mol Biol Lett. 11(2):191-213. [PubMed]

120) Platts A.E., Dix D.J., Chemes H.E., Thompson K.E., Goodrich R., Rockett J.C., Rawe V.Y., Quintana S., Diamond M.P., Strader L.F. and Krawetz, S.A. (2007) Success and failure in human spermatogenesis as revealed by teratozoospermic RNAs. Hum Mol Genet. 1;16(7):763-73. [PubMed]

121) Martins R.P. and Krawetz, S.A. (2007) Decondensing the protamine domain for transcription. Proc Natl Acad Sci U S A. May 15;104(20):8340-5 [PubMed]

122) Martins R.P. and Krawetz, S.A. (2007) Nuclear organization of the protamine locus. Soc Reprod Fertil Suppl. 2007;64:1-12. Review. [PubMed]

123) Schwartz D.R., Moin K., Yao B., Matrisian L.M., Coussens L.M., Bugge T.H., Fingleton B., Acuff H.B., Sinnamon M., Nassar H., Platts A.E., Krawetz S.A., Linebaugh B.E. and Sloane B.F. (2007) Hu/Mu ProtIn oligonucleotide microarray: dual-species array for profiling protease and protease inhibitor gene expression in tumors and their microenvironment. Mol Cancer Res. 5(5):443-54. [PubMed]

124) Linnemann A.K., Platts A.E., Doggett N., Gluch A., Bode J. and Krawetz, S.A. (2007) Genomewide identification of nuclear matrix attachment regions: an analysis of methods. Biochem Soc Trans. 35(Pt 3):612-7. Review. [PubMed]

125) Martins R.P., Platts A.E. and Krawetz, S.A. (2007) Tracking chromatin states using controlled DNase I treatment and real-time PCR. Cell Mol Biol Lett. 2007;12(4):545-55. [PubMed]

126) Goodrich R., Johnson G. and Krawetz, S.A. (2007) The preparation of human spermatozoal RNA for clinical analysis. 53(3):161-7. [PubMed]

127) Stevens J.B., Liu G., Bremer S.W., Ye K.J., Xu W., Xu J., Sun Y., Wu G.S., Savasan S., Krawetz S.A., Ye C.J., and Heng H.H. (2007) Mitotic cell death by chromosome fragmentation. Cancer Res. 15;67(16):7686-94. [PubMed]

128) Lalancette C., Miller D., Li Y. and Krawetz, S.A. (2008) Paternal contributions: new functional insights for spermatozoal RNA. J Cell Biochem. 104(5):1570-9. Review. [PubMed]

129) Naismith L., Lalancette C., Platts A.E. and Krawetz, S.A. (2008) The KLAB Toolbox: a suite of in-house software applications for epigenetic analysis. Syst Biol Reprod Med. 54(2):97-108. [PubMed]

130) Li Y., Lalancette C., Miller D. and Krawetz, S.A. (2008) Characterization of nucleohistone and nucleoprotamine components in the mature human sperm nucleus. Asian J Androl. 10(4):535-41. [PubMed]

131) Krawetz, S.A. (2008) SBiRM: Systems Biology in Reproductive Medicine. Syst Biol Reprod Med. 54(1):1-2. No abstract available.  [PubMed]

132) Wirth J.J., Rossano M.G., Potter R., Puscheck E., Daly D.C., Paneth N., Krawetz S.A., Protas B.M. and Diamond M.P. (2008) A pilot study associating urinary concentrations of phthalate metabolites and semen quality. Syst Biol Reprod Med. 54(3):143-54. [PubMed]

133) Platts A.E., Johnson G.D., Linnemann A.K. and Krawetz, S.A. (2008) Real-time PCR quantification using a variable reaction efficiency model. Anal Biochem. 380(2):315-22. [PubMed]

134) Lalancette C., Platts A.E., Lu Y., Lu S. and Krawetz, S.A. (2008) Computational identification of transcription frameworks of early committed spermatogenic cells. Mol Genet Genomics. 280(3):263-74. [PubMed]

135) Ottaviani D., Lever E., Mitter R., Jones T., Forshew T., Christova R., Tomazou E.M., Rakyan V.K., Krawetz S.A., Platts A.E., Segarane B., Beck S. and Sheer D. (2008) Reconfiguration of genomic anchors upon transcriptional activation of the human major histocompatibility complex. Genome Res. 18(11):1778-86 [PubMed]

136) Linnemann A.K., Platts A.E. and Krawetz, S.A. (2009) Differential nuclear scaffold/matrix attachment marks expressed genes. Hum Mol Genet. 18(4):645-54 [PubMed]

137) Linnemann A.K. and Krawetz, S.A. (2009) Silencing by nuclear matrix attachment distinguishes cell-type specificity: association with increased proliferation capacity. Nucleic Acids Res. 37(9):2779-88 [PubMed]

138) Lalancette C., Platts A.E., Johnson G.D., Emery B.R., Carrell D.T. and Krawetz, S.A. (2009) Identification of human sperm transcripts as candidate markers of male fertility. J Mol Med. 87(7):735-48 [PubMed]

139) Arpanahi A., Brinkworth M., Iles D., Krawetz S.A., Paradowska A., Platts A.E., Saida M., Steger K., Tedder P., and Miller D. (2005) Endonuclease-sensitive regions of human spermatozoal chromatin are highly enriched in promoter and CTCF binding sequences. Genome Res. 19(8):1338-49 [PubMed]

140) Krawetz S.A., De Rooij D.G. and Hedger M.P.(2009) Molecular aspects of male fertility. International Workshop on Molecular Andrology. EMBO Rep. 10(10):1087-92 [PubMed]

141) Platts A.E., Lalancette C., Emery B.R., Carrell D.T. and Krawetz, S.A. (2010) Disease progression and solid tumor survival: A transcriptome decoherence model.Mol Cell Probes. 24(1):53-60 [PubMed]


go to:
invited reviews
books & chapters

van de Sande, J.H., Kalisch, B.W., Krawetz, S.A. and Schoenwaelder, K.H. Covalently linked complementary oligodeoxynucleotides as universal nucleic acid sequencing primer linkers. U.S. Patent Filing #801-900 (November 1985); Canada Patent Filing #523606-1 (November 1986); Japan Patent Filing #61-276870 (November 1986); Europe Patent Filing #86115701-4 (November 1986).

Ostermeier, G.C., Martins, R.P., Krawetz, S.A., Khatri, P. and Draghici, S. ONTO-EXPRESS. U.S. Patent Filing # 60/347,383 (January 9, 2002).


  invited reviews

go to:
most recent
books & chapters

1) Krawetz, S.A. (1988) Avian myoblastosis virus reverse transcriptase:a sequencing enzyme. Molecular Biology Reports 4:1-2. 

2) Krawetz, S.A. (1989) Polymerase chain reaction: opportunities for agriculture. AgBiotech News and Information 1:897-902. 

3) Krawetz, S.A. (1994) Meetings: Genome Sequencing and Analysis Conference V. AgBiotech News and Information 6:45N-46N.

4) Kramer, J.A. and Krawetz, S.A. (1997) RNA in sperm: implications for the alternative haploid genome. Molecular Human Reproduction 3:473-478. [PubMed]

5) Krawetz, S.A., Kramer, J.A. and McCarrey, J.R. (1999) Reprogramming the male gamete genome: a window to successful gene therapy. Gene 234:1-9. [PubMed]

6) Wykes, S. M. and Krawetz, S.A. (1999) Gene Potentiation: Forming long-range open chromatin structures. Gene Therapy and Molecular Biology 4:303-312.

7) Martins, R.P. and Krawetz, S.A. (2000) Characterizing a human lysyl oxidase chromosomal domain. Molecular Biotechnology 15:225-235. [PubMed]

8) Krawetz, S.A. and Womble, D.D. (2000) Design and implementation of an introductory course for computer applications in molecular genetics: A case study. Molecular Biotechnology 17:27-41. [PubMed]

9) Heng, H.H.Q., Krawetz, S.A., Lu, W., Bremer, S., Liu, G. and Yee, C.J. (2001) Re-defining the chromatin loop domain. Cytogenetics and Cell Genetics 93:155-161. [PubMed]

10) Bode, J., Goetze, S., Heng, H., Krawetz, S.A. and Benham, C. (2003) From DNA structure to gene expression: mediators of nuclear compartmentalization and dynamics. Chromosome Res. 11:435-445. [PubMed]

11) Moldenhauer, J.S., Ostermeier, G.C., Johnson, A., Diamond, M.P. and Krawetz, S.A. (2003) Diagnosing male factor infertility using microarrays. J Androl. 24:783-789. [PubMed]

Rockett, J.C., Burczynski, M.E., Fornace, A.J., Herrmann, P.C., Krawetz, S.A. and Dix, D.J. (2004) Surrogate tissue analysis: monitoring toxicant exposure and health status of inaccessible tissues through the analysis of accessible tissues and cells. Toxicol Appl Pharmacol. 194:189-199. [PubMed]

13) Liu, D.K., Yao, B., Fayz, B., Womble, D.D. andKrawetz, S.A.(2004) Comparative evaluation of microarray analysis software. Mol Biotechnol. 26:225-232. [PubMed]


  books and chapters

go to:
most recent
invited reviews

1) Nelson, J.E., Khidir, M. and Krawetz, S.A. (1994) Purification of DNA with Guanidine Thiocyanate by Isobutyl Alcohol Fractionation. CELL BIOLOGY: A LABORATORY HANDBOOK (ed. Celis, J.E) 1:674-679 Academic Press Inc.


3) Krawetz, S.A. (2000) Design and implementation of an introductory course for computer applications in molecular biology and genetics. in METHODS IN MOLECULAR BIOLOGY: BIOINFORMATICS METHODS AND PROTOCOLS (ed. Meisener, S. and Krawetz, S.A.) 449-460. Humana press.

4) Singh, G.B. and Krawetz S. (2001) Data Mining Matrix Associated Regions (MARs) for Gene Therapy. in Medical Data Mining and Knowledge Discovery, ed. Krzysztof J. Cios, Springer-Verlag Series: Studies in Fuzziness and Soft Computing. Volume 60:359-378.

5) Draghici, S. and Krawetz, S.A. (in press) Global Functional Profiling of Gene Expression Using Onto-Express. in Understanding And Using Microarray Analysis Techniques: A Practical Guide eds. Berrar, D.P., Dubitzky, W. and Granzow, M. Kluwer Academic Publishers, MA.

6) Introduction to Bioinformatics: A Theoretical and Practical Approach. Humana Press eds. Krawetz, S.A. and Womble, D. (in press)

7) Krawetz, S.A. (2009) Bioinformatics for Systems Biology. Human Press.

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