Research Topics
Genomes and Genes
| San Ming WangSummaryAffiliation: Northwestern University Country: USA Publications
Research Grants
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Detail Information
Publications
Transcriptome study for early hematopoiesis--achievement, challenge and new opportunitySan 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...
Long-short-long games in mRNA identification: the length mattersSan 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...- Understanding SAGE dataSan 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... - Applying the SAGE technique to study the effects of electromagnetic field on biological systemsSan 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... - The transcriptome of human CD34+ hematopoietic stem-progenitor cellsYeong 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... - Gene expression profiles in acute myeloid leukemia with common translocations using SAGESanggyu Lee
Department of Medicine, University of Chicago, IL 60637, USA
Proc Natl Acad Sci U S A 103:1030-5. 2006.... - Poly A- transcripts expressed in HeLa cellsQingfa 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... - Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcriptionDouglas 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.... - Pan-genome isolation of low abundance transcripts using SAGE tagYeong 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... - Scanning the human genome at kilobase resolutionJun 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.... - SAGE is far more sensitive than EST for detecting low-abundance transcriptsMiao 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... - Identifying novel transcripts and novel genes in the human genome by using novel SAGE tagsJianjun 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... - A large quantity of novel human antisense transcripts detected by LongSAGEXijin 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..CONCLUSIONS: Our study highlights the benefits of exploring SAGE data for comprehensive identification of human antisense transcripts and demonstrates the prevalence of antisense transcripts in the human genome... - SAGE detects microRNA precursorsXijin 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... - Identifying nonspecific SAGE tags by context of gene expressionXijin 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... - Consistent deregulation of gene expression between human and murine MLL rearrangement leukemiasZejuan 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... 
Simplified DGS procedure for large-scale genome structural studyYong 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...- Detecting novel low-abundant transcripts in DrosophilaSanggyu 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... - Correct identification of genes from serial analysis of gene expression tag sequencesSanggyu Lee
Department of Medicine, University of Chicago, 5841 S. Maryland, MC2115, Chicago, Illinois 60637, USA
Genomics 79:598-602. 2002.... - Annotating nonspecific SAGE tags with microarray dataXijin 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... - 2.45 GHz radiofrequency fields alter gene expression in cultured human cellsSanggyu 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... - Interpreting expression profiles of cancers by genome-wide survey of breadth of expression in normal tissuesXijin 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.... - High-throughput GLGI procedure for converting a large number of serial analysis of gene expression tag sequences into 3' complementary DNAsJianjun 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... - Stable transcriptional status in the apoptotic erythroid genomeSanggyu 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... - Molecular portraits of B cell lineage commitmentMARKUS MUSCHEN
Institute for Genetics, University of Cologne, Weyertal 121, 50931 Cologne, Germany
Proc Natl Acad Sci U S A 99:10014-9. 2002.... - Computational Analysis of Gene Identification with SAGETerry 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... - Generation of longer 3' cDNA fragments from massively parallel signature sequencing tagsAna 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... - Stage-dependent gene expression profiles during natural killer cell developmentHyung-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... - The birth and death of microRNA genes in DrosophilaJian 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... - Generation of longer cDNA fragments from SAGE tags for gene identificationJian-Jun Chen
Section of Hematology and Oncology, University of Chicago Medical Center, IL, USA
Methods Mol Biol 221:207-22. 2003 - Silencing of B cell receptor signals in human naive B cellsNiklas Feldhahn
Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, , 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... - Serial analysis of gene expression study of a hybrid rice strain (LYP9) and its parental cultivarsJingyue 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... - Screening poly [dA/dT(-)] cDNA for gene identificationSan Ming Wang
Section of Hematology and Oncology, University of Chicago Medical Center, IL, USA
Methods Mol Biol 221:197-205. 2003
Research Grants
- Identification of novel genes in human genomeSan 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. ..