STEPHEN KRAWETZ

Summary

Affiliation: Wayne State University
Country: USA

Publications

  1. pmc Silencing by nuclear matrix attachment distinguishes cell-type specificity: association with increased proliferation capacity
    Amelia K Linnemann
    Department of Obstetrics and Gynecology, The Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
    Nucleic Acids Res 37:2779-88. 2009
  2. pmc Differential nuclear scaffold/matrix attachment marks expressed genes
    Amelia K Linnemann
    The Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, C S Mott Center, Detroit, MI48201, USA
    Hum Mol Genet 18:645-54. 2009
  3. pmc Stability, delivery and functions of human sperm RNAs at fertilization
    Edward Sendler
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
    Nucleic Acids Res 41:4104-17. 2013
  4. pmc A survey of small RNAs in human sperm
    Stephen A Krawetz
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
    Hum Reprod 26:3401-12. 2011
  5. pmc K-SPMM: a database of murine spermatogenic promoters modules & motifs
    Yi Lu
    Department of Computer Science, Wayne State University, Detroit, MI 48202, USA
    BMC Bioinformatics 7:238. 2006
  6. ncbi request reprint [On the significance of RNA in human sperm]
    Stephen A Krawetz
    Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Institute for Scientific Computing, Wayne State University School of Medicine, 275 E Hancock, Detroit, MI 48201, USA
    Zhonghua Nan Ke Xue 11:170-4. 2005
  7. ncbi request reprint Paternal contribution: new insights and future challenges
    Stephen A Krawetz
    Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Institute for Scientific Computing, Wayne State University School of Medicine, Detroit, Michigan 48201, USA
    Nat Rev Genet 6:633-42. 2005
  8. ncbi request reprint Reprogramming the male gamete genome: a window to successful gene therapy
    S A Krawetz
    Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201, USA
    Gene 234:1-9. 1999
  9. pmc Establishing a biologic specimens repository for reproductive clinical trials: technical aspects
    Stephen A Krawetz
    Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
    Syst Biol Reprod Med 57:222-7. 2011
  10. ncbi request reprint Design and implementation of an introductory course for computer applications in molecular genetics. A case study
    S A Krawetz
    Department of Obstetrics and Gynecology, Wayne State University School of Medicine, 253 C S Mott Center, 275 E Hancock, Detroit, MI 48201, USA
    Mol Biotechnol 17:27-41. 2001

Collaborators

Detail Information

Publications47

  1. pmc Silencing by nuclear matrix attachment distinguishes cell-type specificity: association with increased proliferation capacity
    Amelia K Linnemann
    Department of Obstetrics and Gynecology, The Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
    Nucleic Acids Res 37:2779-88. 2009
    ....
  2. pmc Differential nuclear scaffold/matrix attachment marks expressed genes
    Amelia K Linnemann
    The Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, C S Mott Center, Detroit, MI48201, USA
    Hum Mol Genet 18:645-54. 2009
    ..The varied functions of the S/MARs as revealed by the different extraction methods highlights their unique functional contribution...
  3. pmc Stability, delivery and functions of human sperm RNAs at fertilization
    Edward Sendler
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
    Nucleic Acids Res 41:4104-17. 2013
    ..The diverse and unique attributes of sperm transcripts that were revealed provides the first detailed analysis of the biology and anticipated clinical significance of spermatozoal RNAs...
  4. pmc A survey of small RNAs in human sperm
    Stephen A Krawetz
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
    Hum Reprod 26:3401-12. 2011
    ..While the cadre of spermatozoal mRNAs has been characterized, comparatively little is known about the distribution or function of the estimated 24,000 sncRNAs within each normal human spermatozoon...
  5. pmc K-SPMM: a database of murine spermatogenic promoters modules & motifs
    Yi Lu
    Department of Computer Science, Wayne State University, Detroit, MI 48202, USA
    BMC Bioinformatics 7:238. 2006
    ..Research has been hindered in part by an incomplete picture of the regulatory elements that are both characteristic of and distinctive to the broad population of spermatogenically expressed genes...
  6. ncbi request reprint [On the significance of RNA in human sperm]
    Stephen A Krawetz
    Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Institute for Scientific Computing, Wayne State University School of Medicine, 275 E Hancock, Detroit, MI 48201, USA
    Zhonghua Nan Ke Xue 11:170-4. 2005
    ..It is fully expected that a genetic fingerprint characteristic of the normal fertile spermatozoon can be identified and that deviations from this profile can be detected...
  7. ncbi request reprint Paternal contribution: new insights and future challenges
    Stephen A Krawetz
    Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Institute for Scientific Computing, Wayne State University School of Medicine, Detroit, Michigan 48201, USA
    Nat Rev Genet 6:633-42. 2005
    ..They are also beginning to appear in the forensic sciences and, within the next decade, might appear in the environmental sciences...
  8. ncbi request reprint Reprogramming the male gamete genome: a window to successful gene therapy
    S A Krawetz
    Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201, USA
    Gene 234:1-9. 1999
    ..It is likely that gene therapeutics capable of selectively potentiating individual genic domains in populations of differentiating and/or replicating cells that modify cellular phenotype will be developed in the next millennium...
  9. pmc Establishing a biologic specimens repository for reproductive clinical trials: technical aspects
    Stephen A Krawetz
    Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
    Syst Biol Reprod Med 57:222-7. 2011
    ..To facilitate such interoperability, the reagents and protocols that have been adopted by the RMN Biorepository for the collection and storage of serum, blood, saliva and sperm are described...
  10. ncbi request reprint Design and implementation of an introductory course for computer applications in molecular genetics. A case study
    S A Krawetz
    Department of Obstetrics and Gynecology, Wayne State University School of Medicine, 253 C S Mott Center, 275 E Hancock, Detroit, MI 48201, USA
    Mol Biotechnol 17:27-41. 2001
    ..In this review we present our experience with delivering a multidisciplinary campus-wide computational biology course to a new and widely diverse student body...
  11. ncbi request reprint Success and failure in human spermatogenesis as revealed by teratozoospermic RNAs
    Adrian E Platts
    Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
    Hum Mol Genet 16:763-73. 2007
    ..The origin of the perturbation could be traced as far back as the pachytene stage of spermatogenesis. It is anticipated that this diagnostic strategy will prove valuable for understanding male factor infertility...
  12. pmc Computational identification of transcription frameworks of early committed spermatogenic cells
    Claudia Lalancette
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 275 East Hancock, Detroit, MI 48201, USA
    Mol Genet Genomics 280:263-74. 2008
    ..These modules were biologically assessed in the context that they represent the key transcriptional mediators in the developmental transition from the spermatogonia to spermatocyte...
  13. pmc Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate
    Sorin Draghici
    Department of Computer Science, Wayne State University, 431 State Hall, Detroit, MI 48202, USA
    Nucleic Acids Res 31:3775-81. 2003
    ..All tools above are seamlessly integrated. The Onto-Tools are available online at http://vortex.cs.wayne.edu/Projects.html...
  14. ncbi request reprint Chromatin loops are selectively anchored using scaffold/matrix-attachment regions
    Henry H Q Heng
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48202, USA
    J Cell Sci 117:999-1008. 2004
    ..Consequently, S/MAR anchors were necessary but not sufficient for chromatin loops to form. These observations reconcile many seemingly contradictory attributes previously associated with S/MARs...
  15. ncbi request reprint Global functional profiling of gene expression
    Sorin Draghici
    Department of Computer Science, Wayne State University, 5143 Cass Avenue, Detroit, MI 48202, USA
    Genomics 81:98-104. 2003
    ..OE was able to identify correctly all biological processes postulated by the original authors, as well as discover novel relevant mechanisms...
  16. ncbi request reprint A bioinformatic strategy to rapidly characterize cDNA libraries
    G Charles Ostermeier
    Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, and Institute for Scientific Computing, Wayne State University, USA
    Bioinformatics 18:949-52. 2002
    ..Complementary DNA libraries can define the genetic constituents of specific cells and/or tissues. Their sequencing will illuminate the transcriptome but it is a monumental task requiring considerable resources...
  17. pmc Decondensing the protamine domain for transcription
    Rui Pires Martins
    Center for Molecular Medicine and Genetics, School of Medicine and Institute for Scientific Computing, Wayne State University, Detroit, MI 48201, USA
    Proc Natl Acad Sci U S A 104:8340-5. 2007
    ..This has provided a likely model of the events initiating potentiation, i.e., the opening of a chromatin domain...
  18. ncbi request reprint The structural organization of sperm chromatin
    Susan M Wykes
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan 48201, USA
    J Biol Chem 278:29471-7. 2003
    ..A discussion of these results and their functional significance is presented...
  19. ncbi request reprint In-silico prediction and observations of nuclear matrix attachment
    Adrian E Platts
    Department of Obstetrics and Gynecology, University School of Medicine, Detroit, MI 48201, USA
    Cell Mol Biol Lett 11:191-213. 2006
    ..Nuclear matrix binding may well be more complex than the widely accepted simple loop model...
  20. ncbi request reprint Nuclear matrix interactions at the human protamine domain: a working model of potentiation
    Rui Pires Martins
    Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan 4820, USA
    J Biol Chem 279:51862-8. 2004
    ..Thus, the MARs bounding the PRM1 --> PRM2 --> TNP2 protamine domain have many and varied functions...
  21. ncbi request reprint Reproductive biology: delivering spermatozoan RNA to the oocyte
    G Charles Ostermeier
    Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
    Nature 429:154. 2004
    ....
  22. ncbi request reprint Comparative evaluation of microarray analysis software
    Daniel K Liu
    WSU MCBI Bioinformatics Node, Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
    Mol Biotechnol 26:225-32. 2004
    ..We then conclude with a discussion of the subset of tools that are most commonly used and describe the features that would constitute the "ideal microarray analysis software suite."..
  23. ncbi request reprint Profiling gene expression using onto-express
    Purvesh Khatri
    Department of Computer Science, Wayne State University School of Medicine, Detroit, MI, 48201, USA
    Genomics 79:266-70. 2002
    ..The profiles created by Onto-Express fundamentally increase the value of gene expression analyses by facilitating the translation of quantitative value sets to records that contain biological implications...
  24. doi request reprint Paternal contributions: new functional insights for spermatozoal RNA
    Claudia Lalancette
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
    J Cell Biochem 104:1570-9. 2008
    ..This review presents and discusses the functional significance of spermatozoal RNA in relation to some recent advances in the field...
  25. ncbi request reprint The KLAB Toolbox: a suite of in-house software applications for epigenetic analysis
    Laura Naismith
    Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
    Syst Biol Reprod Med 54:97-108. 2008
    ..Using the protamine cluster as an example, we present a series of in-house applications that we have developed to integrate, contextualize and visualize datasets across multiple hierarchies...
  26. ncbi request reprint Tracking chromatin states using controlled DNase I treatment and real-time PCR
    Rui Pires Martins
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan, USA
    Cell Mol Biol Lett 12:545-55. 2007
    ..The utility of this assay and analytical paradigm as applied to nuclease-sensitivity mapping is presented...
  27. ncbi request reprint Spermatozoal RNA profiles of normal fertile men
    G Charles Ostermeier
    Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, and Institute for Scientific Computing, Wayne State University, Detroit, MI, USA
    Lancet 360:772-7. 2002
    ..Our aim was to determine whether we could use spermatozoal mRNAs to generate a genetic fingerprint of normal fertile men...
  28. ncbi request reprint Separation of spermatogenic cells from adult transgenic mouse testes using unit-gravity sedimentation
    Susan M Wykes
    Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, and Institute for Scientific Computing, Wayne State University, C S Mott Center, 275 E Hancock, Detroit, MI 48201, USA
    Mol Biotechnol 25:131-8. 2003
    ..A discussion of the CELSEP apparatus and the application of this methodology in our laboratory are presented...
  29. ncbi request reprint Identification of human sperm transcripts as candidate markers of male fertility
    Claudia Lalancette
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
    J Mol Med (Berl) 87:735-48. 2009
    ..The presence of pairs of stable transcripts suggests that among the heterogeneity observed in the sperm transcriptome, a distinct set is strictly regulated...
  30. pmc Disease progression and solid tumor survival: a transcriptome decoherence model
    Adrian E Platts
    The Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
    Mol Cell Probes 24:53-60. 2010
    ....
  31. ncbi request reprint The preparation of human spermatozoal RNA for clinical analysis
    Robert Goodrich
    Wayne State University School of Medicine, Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Institute for Scientific Computing, Detroit, MI 48201, USA
    Arch Androl 53:161-7. 2007
    ..The reliable and consistent isolation of high-quality RNA from mature spermatozoa will aid in the development of new tools for the clinical assessment of male-factor fertility...
  32. ncbi request reprint Identification, molecular characterization, and tissue expression of OVCOV1
    Richard E Leach
    Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
    Mamm Genome 13:619-24. 2002
    ..This gene is expressed in many tissues including those found in the reproductive tract. Its expression is regulated by oxygen tension and is unaffected by estradiol or progesterone treatment...
  33. ncbi request reprint Hu/Mu ProtIn oligonucleotide microarray: dual-species array for profiling protease and protease inhibitor gene expression in tumors and their microenvironment
    Donald R Schwartz
    Barbara Ann Karmanos Cancer Institute, Wayne State University, Detroit, Michigan, USA
    Mol Cancer Res 5:443-54. 2007
    ....
  34. pmc Characterization of nucleohistone and nucleoprotamine components in the mature human sperm nucleus
    Yan Li
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Wayne, MI 48201, USA
    Asian J Androl 10:535-41. 2008
    ..To simultaneously determine the localization of histones and protamines within human sperm nuclei...
  35. ncbi request reprint Toward using stable spermatozoal RNAs for prognostic assessment of male factor fertility
    G Charles Ostermeier
    Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan, USA
    Fertil Steril 83:1687-94. 2005
    ..To establish the stability of spermatozoal RNAs as a means to validate their use as a male fertility marker...
  36. pmc Nuclear matrix association of the human beta-globin locus utilizing a novel approach to quantitative real-time PCR
    G Charles Ostermeier
    Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
    Nucleic Acids Res 31:3257-66. 2003
    ..These results provide the first evidence that nuclear matrix association dynamically mediates the looping of the beta-globin locus to achieve transcriptional control...
  37. ncbi request reprint LARaLink 2.0: a comprehensive aid to basic and clinical cytogenetic research
    Adrian E Platts
    Bioinformatics, Applied Genomics Technology Center, Wayne State University, Detroit, MI 48201, USA
    Genet Test 9:334-41. 2005
    ..Unlimited access for researchers exploring disease-gene relationships and for clinicians extending practice in patient care is available at LARaLink.bioinformatics.wayne.edu:8080/ unigene...
  38. ncbi request reprint Diagnosing male factor infertility using microarrays
    Julie S Moldenhauer
    Department of Obstetrics and Gynecology, Center for Molecular Medicine, Institute for Scientific Computing, Wayne State University, Detroit, Michigan, USA
    J Androl 24:783-9. 2003
  39. ncbi request reprint A suite of novel human spermatozoal RNAs
    G Charles Ostermeier
    Charlotte B Failing Professor of Fetal Therapy and Diagnosis, 253 C S Mott Center, 275 East Hancock, Detroit, MI 48201, USA
    J Androl 26:70-4. 2005
    ..The results and implications of this study are described in this communication...
  40. ncbi request reprint RNA in human sperm
    Rui Pires Martins
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 275 E Hancock, Detroit, MI 48201, USA
    Asian J Androl 7:115-20. 2005
    ..It remains tempting to analogize them to maternally-derived transcripts active in early embryo patterning. Irrespective of their role in the embryo, their use as a means to assess male factor infertility is promising...
  41. ncbi request reprint Multitasking with molecular dynamics Typhoon: quantifying nucleic acids and autoradiographs
    Robert J Goodrich
    Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201, USA
    Biotechnol Lett 25:1061-5. 2003
    ..In addition, with a few simple modifications, autoradiographic film images can be scanned and quantified with the Typhoon series of scanners...
  42. ncbi request reprint In silico and wet-bench identification of nuclear matrix attachment regions
    Stephen A Krawetz
    Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
    Methods Mol Med 108:439-58. 2005
    ..In this chapter we review some of the in silico strategies that are currently available and a new in vivo method based on the real-time polymerase chain reaction, to assess regions of matrix association...
  43. ncbi request reprint Conservation of the PRM1 --> PRM2 --> TNP2 domain
    Susan M Wykes
    Department of Obstetrics and Gynecology, Center for Molecular Medicine and Genetics, Institute for Scientific Computing, Wayne State University, C S Mott Center, 275 E Hancock, Detroit, MI 48201, USA
    DNA Seq 14:359-67. 2003
    ..This further establishes the synteny of this region. Global structural similarities and the functional relevance of the associated candidate regulatory elements are discussed...
  44. pmc Real-time PCR quantification using a variable reaction efficiency model
    Adrian E Platts
    Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
    Anal Biochem 380:315-22. 2008
    ..Using a series of biological scenarios, we demonstrate that this approach can provide an accurate estimate of initial template concentration...
  45. ncbi request reprint The controversy, potential and roles of spermatozoal RNA
    David Miller
    Reproduction and Early Development Group, University of Leeds, Department of Obstetrics and Gynaecology, Level D, Clarendon Wing, Leeds General Infirmary, Belmont Grove, Leeds, LS2 9NS, UK
    Trends Mol Med 11:156-63. 2005
    ....
  46. ncbi request reprint X-chromosome inactivation during spermatogenesis is regulated by an Xist/Tsix-independent mechanism in the mouse
    John R McCarrey
    Department of Biology, University of Texas at San Antonio, San Antonio, Texas 78249, USA
    Genesis 34:257-66. 2002
    ....
  47. ncbi request reprint A pilot study associating urinary concentrations of phthalate metabolites and semen quality
    Julia J Wirth
    Department of Epidemiology, Michigan State University, East Lansing, Michigan, USA
    Syst Biol Reprod Med 54:143-54. 2008
    ..4, 95% CI: 0.9-13.8) were also found. A significant trend was observed for tertiles of MEP and low sperm concentration (p=0.05). Results suggest that ambient phthalate metabolite concentrations may adversely affect human semen quality...

Research Grants8

  1. GENETIC MECHANISMS THAT POTENTIATE HUMAN SPERMATOGENESIS
    STEPHEN KRAWETZ; Fiscal Year: 2000
    ..Successful completion will directly test the hypothesis that spermatogenesis is controlled by a non-repressive selective potentiative mechanism while providing the foundation to isolate these potentiative factors. ..
  2. GENETIC MECHANISMS THAT POTENTIATE HUMAN SPERMATOGENESIS
    STEPHEN KRAWETZ; Fiscal Year: 2001
    ..Successful completion will directly test the hypothesis that spermatogenesis is controlled by a non-repressive selective potentiative mechanism while providing the foundation to isolate these potentiative factors. ..
  3. GENETIC MECHANISMS THAT POTENTIATE HUMAN SPERMATOGENESIS
    STEPHEN KRAWETZ; Fiscal Year: 2002
    ..Successful completion will directly test the hypothesis that spermatogenesis is controlled by a non-repressive selective potentiative mechanism while providing the foundation to isolate these potentiative factors. ..
  4. GENETIC MECHANISMS THAT POTENTIATE HUMAN SPERMATOGENESIS
    STEPHEN KRAWETZ; Fiscal Year: 2005
    ..This milestone provides the foundation to isolate and functionally characterize the associated agents that open chromatin domains. ..
  5. GENETIC MECHANISMS THAT POTENTIATE HUMAN SPERMATOGENESIS
    STEPHEN KRAWETZ; Fiscal Year: 2007
    ..This milestone provides the foundation to isolate and functionally characterize the associated agents that open chromatin domains. ..
  6. GENETIC MECHANISMS THAT POTENTIATE HUMAN SPERMATOGENESIS
    STEPHEN KRAWETZ; Fiscal Year: 2009
    ..This milestone provides the foundation to isolate and functionally characterize the associated agents that open chromatin domains. ..
  7. GENETIC MECHANISMS THAT POTENTIATE HUMAN SPERMATOGENESIS
    STEPHEN KRAWETZ; Fiscal Year: 2006
    ..This milestone provides the foundation to isolate and functionally characterize the associated agents that open chromatin domains. ..