San Ming Wang

Summary

Affiliation: Northwestern University
Country: USA

Publications

  1. pmc Transcriptome study for early hematopoiesis--achievement, challenge and new opportunity
    San Ming Wang
    NorthShore University HealthSystem Research Institute, University of Chicago Pritzker School of Medicine, Evanston, Illinois, USA
    J Cell Physiol 223:549-52. 2010
  2. ncbi request reprint Long-short-long games in mRNA identification: the length matters
    San Ming Wang
    Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University, Evanston, IL 60201, USA
    Curr Pharm Biotechnol 9:362-7. 2008
  3. ncbi request reprint Understanding SAGE data
    San Ming Wang
    Center for Functional Genomics, ENH Research Institute, Robert H Lurie Comprehensive Cancer Center, Northwestern University, 1001 University Place, Evanston, IL 60201, USA
    Trends Genet 23:42-50. 2007
  4. ncbi request reprint Applying the SAGE technique to study the effects of electromagnetic field on biological systems
    San Ming Wang
    Center for Functional Genomics, ENH Research Institute, Department of Medicine, Northwestern University, Evanston, IL 60201, USA
    Proteomics 6:4765-8. 2006
  5. pmc Gene expression profiles in acute myeloid leukemia with common translocations using SAGE
    Sanggyu Lee
    Department of Medicine, University of Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 103:1030-5. 2006
  6. pmc Poly A- transcripts expressed in HeLa cells
    Qingfa Wu
    Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
    PLoS ONE 3:e2803. 2008
  7. pmc The transcriptome of human CD34+ hematopoietic stem-progenitor cells
    Yeong C Kim
    Department of Medicine, Division of Medical Genetics, Center for Functional Genomics, Evanston Northwestern Healthcare Research Institute, Northwestern University Feinberg School of Medicine, Evanston, IL 60201, USA
    Proc Natl Acad Sci U S A 106:8278-83. 2009
  8. pmc Pan-genome isolation of low abundance transcripts using SAGE tag
    Yeong Cheol Kim
    Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University, Evanston, IL 60201, USA
    FEBS Lett 580:6721-9. 2006
  9. pmc Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription
    Douglas Kyung Nam
    Department of Medicine, Center for Functional Genomics, University of Chicago, 5841 South Maryland Avenue, MC2115, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 99:6152-6. 2002
  10. pmc Scanning the human genome at kilobase resolution
    Jun Chen
    Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University, Evanston, Illinois 60201, USA
    Genome Res 18:751-62. 2008

Research Grants

  1. Identification of novel genes in human genome
    San Ming Wang; Fiscal Year: 2005

Collaborators

Detail Information

Publications33

  1. pmc Transcriptome study for early hematopoiesis--achievement, challenge and new opportunity
    San Ming Wang
    NorthShore University HealthSystem Research Institute, University of Chicago Pritzker School of Medicine, Evanston, Illinois, USA
    J Cell Physiol 223:549-52. 2010
    ..Using systems biology approach may reveal the insight of the genetic mechanisms controlling early hematopoiesis...
  2. ncbi request reprint Long-short-long games in mRNA identification: the length matters
    San Ming Wang
    Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University, Evanston, IL 60201, USA
    Curr Pharm Biotechnol 9:362-7. 2008
    ..Comparison of full-length cDNA, EST, 14-base SAGE, 21-LongSAGE, 26-SuperSAGE, and other variations shows that the sequenced length has been a key factor in determining the sensitivity and specificity for mRNA detection...
  3. ncbi request reprint Understanding SAGE data
    San Ming Wang
    Center for Functional Genomics, ENH Research Institute, Robert H Lurie Comprehensive Cancer Center, Northwestern University, 1001 University Place, Evanston, IL 60201, USA
    Trends Genet 23:42-50. 2007
    ..Understanding these basic features should aid the proper interpretation of SAGE data to address biological and medical questions...
  4. ncbi request reprint Applying the SAGE technique to study the effects of electromagnetic field on biological systems
    San Ming Wang
    Center for Functional Genomics, ENH Research Institute, Department of Medicine, Northwestern University, Evanston, IL 60201, USA
    Proteomics 6:4765-8. 2006
    ..This information should help investigators determine if the SAGE technique is an optimal method for evaluating the biological effects of EMF...
  5. pmc Gene expression profiles in acute myeloid leukemia with common translocations using SAGE
    Sanggyu Lee
    Department of Medicine, University of Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 103:1030-5. 2006
    ....
  6. pmc Poly A- transcripts expressed in HeLa cells
    Qingfa Wu
    Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
    PLoS ONE 3:e2803. 2008
    ..Most transcripts identified so far are poly A+ transcripts, whereas the poly A- transcripts remain largely unknown...
  7. pmc The transcriptome of human CD34+ hematopoietic stem-progenitor cells
    Yeong C Kim
    Department of Medicine, Division of Medical Genetics, Center for Functional Genomics, Evanston Northwestern Healthcare Research Institute, Northwestern University Feinberg School of Medicine, Evanston, IL 60201, USA
    Proc Natl Acad Sci U S A 106:8278-83. 2009
    ..The data generated from our study provide a comprehensive and uniform resource for studying hematopoiesis and stem cell biology...
  8. pmc Pan-genome isolation of low abundance transcripts using SAGE tag
    Yeong Cheol Kim
    Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University, Evanston, IL 60201, USA
    FEBS Lett 580:6721-9. 2006
    ..Our study shows the prevalence of novel low abundance transcripts that can be isolated efficiently through SAGE tags mis-priming...
  9. pmc Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription
    Douglas Kyung Nam
    Department of Medicine, Center for Functional Genomics, University of Chicago, 5841 South Maryland Avenue, MC2115, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 99:6152-6. 2002
    ....
  10. pmc Scanning the human genome at kilobase resolution
    Jun Chen
    Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University, Evanston, Illinois 60201, USA
    Genome Res 18:751-62. 2008
    ....
  11. pmc SAGE is far more sensitive than EST for detecting low-abundance transcripts
    Miao Sun
    Department of Medicine, University of Chicago, 5841 S, Maryland Avenue, MC2115, Chicago, Illinois 60637, USA
    BMC Genomics 5:1. 2004
    ..We compared the EST method and the SAGE method to determine which one is more sensitive and to what extent the sensitivity is great for the detection of low-abundance transcripts...
  12. pmc Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags
    Jianjun Chen
    Department of Medicine, University of Chicago, 5841 South Maryland, MC2115, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 99:12257-62. 2002
    ..Our study indicates that by using novel SAGE tags as probes, we should be able to identify efficiently many novel transcripts/novel genes in the human genome that are difficult to identify by conventional methods...
  13. ncbi request reprint A large quantity of novel human antisense transcripts detected by LongSAGE
    Xijin Ge
    Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, Northwestern University Feinberg School of Medicine 1001 University Place, Evanston, IL 60201 USA
    Bioinformatics 22:2475-9. 2006
    ....
  14. pmc SAGE detects microRNA precursors
    Xijin Ge
    Center for Functional Genomics, Division of Medical Genetics, Department of Medicine, ENH Research Institute, 1001 University Place, Evanston, IL 60201, USA
    BMC Genomics 7:285. 2006
    ..Yet experimental confirmation is difficult since miRNA expression is often specific to particular tissues and developmental stages...
  15. ncbi request reprint Identifying nonspecific SAGE tags by context of gene expression
    Xijin Ge
    Evanston Northwestern Healtcare Research Institute, Evanston, IL, USA
    Methods Mol Biol 387:199-204. 2008
    ..The database can be queried online at: http://www.basic.northwestern.edu/SAGE/. The accuracy of this database was confirmed by experimental data...
  16. pmc Detecting novel low-abundant transcripts in Drosophila
    Sanggyu Lee
    Department of Medicine, University of Chicago, IL 60637, USA
    RNA 11:939-46. 2005
    ..Our study reveals the presence of a significant number of novel low-abundant transcripts in Drosophila, and highlights the need to isolate these novel low-abundant transcripts for further biological studies...
  17. pmc Consistent deregulation of gene expression between human and murine MLL rearrangement leukemias
    Zejuan Li
    Department of Medicine, University of Chicago, Chicago, Illinois, USA
    Cancer Res 69:1109-16. 2009
    ..The identification and validation of consistent changes of gene expression in human and murine MLL rearrangement leukemias provide important insights into the genetic base for MLL-associated leukemogenesis...
  18. doi request reprint Simplified DGS procedure for large-scale genome structural study
    Yong Chul Jung
    Center for Functional Genomics, ENH Research Institute, Northwestern University, 1001 University Place, Evanston, IL 60201, USA
    Biotechniques 47:969-71. 2009
    ..This revised protocol further increases genome coverage and resolution and allows DGS to be used to analyze multiple genomes simultaneously...
  19. ncbi request reprint Correct identification of genes from serial analysis of gene expression tag sequences
    Sanggyu Lee
    Department of Medicine, University of Chicago, 5841 S Maryland, MC2115, Chicago, Illinois 60637, USA
    Genomics 79:598-602. 2002
    ....
  20. ncbi request reprint Annotating nonspecific SAGE tags with microarray data
    Xijin Ge
    Center for Functional Genomics, ENH Research Institute, Northwestern University, Chicago, IL 60611, USA
    Genomics 87:173-80. 2006
    ..The accuracy of gene annotation by this database was largely confirmed by experimental data. Our study shows that microarray data provide a useful source for annotating the nonspecific SAGE tags...
  21. ncbi request reprint 2.45 GHz radiofrequency fields alter gene expression in cultured human cells
    Sanggyu Lee
    Department of Medicine, University of Chicago, Chicago, IL 60637, USA
    FEBS Lett 579:4829-36. 2005
    ..We observed no significant increase in the expression of heat shock genes. These results indicate that the RF fields at 2.45 GHz can alter gene expression in cultured human cells through non-thermal mechanism...
  22. ncbi request reprint Interpreting expression profiles of cancers by genome-wide survey of breadth of expression in normal tissues
    Xijin Ge
    Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, 4 6 1 Komaba, Meguro ku, Tokyo 153 8904, Japan
    Genomics 86:127-41. 2005
    ....
  23. ncbi request reprint High-throughput GLGI procedure for converting a large number of serial analysis of gene expression tag sequences into 3' complementary DNAs
    Jianjun Chen
    Department of Medicine, University of Chicago, Chicago, IL 60637, USA
    Genes Chromosomes Cancer 33:252-61. 2002
    ..Applying this high-throughput procedure should accelerate the rate of gene identification significantly in the human and other eukaryotic genomes...
  24. ncbi request reprint Stable transcriptional status in the apoptotic erythroid genome
    Sanggyu Lee
    School of Life Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
    Biochem Biophys Res Commun 359:556-62. 2007
    ..Our study reveals that there is no genetic reprogramming for the transcriptional machinery in the apoptotic genome. Apoptosis, as defined by programmed cell death, is not a crisis but a peaceful physiological process...
  25. pmc Molecular portraits of B cell lineage commitment
    MARKUS MUSCHEN
    Institute for Genetics, University of Cologne, Weyertal 121, 50931 Cologne, Germany
    Proc Natl Acad Sci U S A 99:10014-9. 2002
    ....
  26. ncbi request reprint Computational Analysis of Gene Identification with SAGE
    Terry Clark
    Department of Computer Science, The University of Chicago, Chicago, IL 60637, USA
    J Comput Biol 9:513-26. 2002
    ..In the myeloid sample, we also found a correlation between multiple match severity and high copy number. We extrapolate these findings, providing insights into the use of UniGene Human as a reference for gene identification...
  27. pmc Generation of longer 3' cDNA fragments from massively parallel signature sequencing tags
    Ana Paula M Silva
    Laboratory of Molecular Biology and Genomics, Ludwig Institute for Cancer Research, São Paulo 01509 010, Brazil
    Nucleic Acids Res 32:e94. 2004
    ..A systematic large-scale analysis of the genome by MPSS, in combination with the use of GLGI-MPSS protocol, will certainly provide a complementary approach to generate the complete catalog of human transcripts...
  28. ncbi request reprint Stage-dependent gene expression profiles during natural killer cell development
    Hyung Sik Kang
    Hormone Research Center, School of Biological Sciences and Technology, Chonnam National University, Gwangju 500 757, Republic of Korea
    Genomics 86:551-65. 2005
    ..Identification of genome-wide profiles of gene expression in different stages of NK cell development affords us a fundamental basis for defining the molecular network during NK cell development...
  29. doi request reprint The birth and death of microRNA genes in Drosophila
    Jian Lu
    Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, Illinois 60637, USA
    Nat Genet 40:351-5. 2008
    ..The estimated net gain of long-lived miRNA genes, which is not strongly affected by either the depth or the breadth (number of tissues) of sequencing, is 0.3 genes per Myr in Drosophila...
  30. ncbi request reprint Generation of longer cDNA fragments from SAGE tags for gene identification
    Jian jun Chen
    Section of Hematology and Oncology, University of Chicago Medical Center, IL, USA
    Methods Mol Biol 221:207-22. 2003
  31. pmc Silencing of B cell receptor signals in human naive B cells
    Niklas Feldhahn
    Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, 50931 Koln, Germany
    J Exp Med 196:1291-305. 2002
    ..In memory B cells, facilitated responsiveness upon reencounter of the immunizing antigen may result from amplification of BCR signals at virtually all levels of signal transduction...
  32. pmc Serial analysis of gene expression study of a hybrid rice strain (LYP9) and its parental cultivars
    Jingyue Bao
    Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China
    Plant Physiol 138:1216-31. 2005
    ..Our study adds a new set of data crucial for the understanding of molecular mechanisms of heterosis and gene regulation networks of the cultivated rice...
  33. ncbi request reprint Screening poly [dA/dT(-)] cDNA for gene identification
    San Ming Wang
    Section of Hematology and Oncology, University of Chicago Medical Center, IL, USA
    Methods Mol Biol 221:197-205. 2003

Research Grants4

  1. Identification of novel genes in human genome
    San Ming Wang; Fiscal Year: 2005
    ..The information should also be useful for the improvement of genome annotation algorithms. Our approach should also be applicable for studies on other tissues of both human and non-human origins. ..