Dongquan Chen, PhD MSHI

Associate Professor
Division of Preventive Medicine

Contact Information:

Medical Towers 641
1717 11th Avenue South
Birmingham, Alabama 35205
Phone: (205) 975-7131
Fax: (205) 934-4262
This email address is being protected from spambots. You need JavaScript enabled to view it.

Research Interests

  • Informatics services for high throughput data including microarray and next generation sequencing (NGS)
  • Integration of Medical Informatics and Bioinformatics through data mining and information system development
  • Application of gene expression profiles for personalized medicine

Educational Background

  • UAB, MS Health Informatics, Birmingham, AL, USA, 2002
  • Mount Sinai -NYU Medical Center, PhD Biomedical Sciences, NY, USA, 1999
  • Bethune Medical University, MD, Changchun, China, 1986

Professional Activities

  • American Society of Gene Therapy (ASGT)
  • American Medical Informatics Association (AMIA)

Selected Recent Publications

  • Fulzele K, Riddle RC, DiGirolamo DJ, Cao X, Wan C, Chen D, Faugere M-C, Aja S, Hussain MA, Brüning JC, and Clemens TL.  Insulin receptor signaling in osteoblasts regulates postnatal bone acquisition and body composition. Cell. 142(2):309-319. 2010. PMID: 20655471. PMCID: PMC2925155.
  • Jian B, Yang S, Chen D, Zou L, Chatham JC, Chaudry I and Raju R. Aging influences cardiac mitochondrial gene expression and cardiovascular function following trauma-hemorrhage. Molecular Medicine. 17(5-6):542-9. 2011. PMID: 21193900. PMCID: PMC3105128.
  • Crasto C, Luo D, Yu F, Forero A and Chen D. GenDrux: A biomedical literature search system to identify gene expression-based drug sensitivity in breast cancer. BMC Medical Informatics and Decision Making. 11:28. 2011 (Corresponding author). PMID: 21545721. PMCID:PMC3116456
  • Katkoori VR, Shanmugam C, Jia X, Vitta SP, Sthanam M, Callens T, Messiaen L, Chen D, Zhang B, Bumpers HL, Samuel T, Manne U.  Prognostic Significance and Gene Expression Profiles of p53 Mutations in Microsatellite-Stable Stage III Colorectal Adenocarcinomas. PLoS ONE 7(1): e30020. 2012. PMID:22276141. PMCID: PMC3261849.
  • Luo D, Banerjee P, Harner J, Mobley J, Chen D. A cloud computing system to quickly implement new microarray data pre-processing methods.  The Open Bioinformatics Journal, 2012, 6, 37-42. (Corresponding author).
  • Tuomela J, Sandholm J, Karihtala P, Ilvesaro J, Vuopala KS, Kauppila JH, Kauppila S, Chen D, Pressey C, Härkönen P, Harris KW, Graves D, Auvinen PK, Soini Y, Jukkola-Vuorinen A, Selander KS. Low TLR9 expression defines an aggressive subtype of triple-negative breast cancer. Breast Cancer Res Treat. 2012 Jul 31.  PMID:22847512
  • Pei M, Zhang Y, Li J, Chen D. Antioxidation of decellularized stem cell matrix promotes human synovium-derived stem cell-based chondrogenesis. Stem Cells Dev 2013 Mar 15;22(6):889-900.   PMID: 23092115. PMCID: PMC3585742.
  • Fraser KB, Moehle MS, Daher JP, Webber PJ, Williams JY, Stewart CA, Yacoubian TA, Cowell RM, Dokland T, Ye T, Chen D, Siegal GP, Galemmo RA, Tsika E, Moore DJ, Standaert DG, Kojima K, Mobley JA, West AB. LRRK2 Secretion in Exosomes is Regulated by 14-3-3. Hum Mol Genet. 2013 Dec 15;22(24):4988-5000. PMID: 23886663 PMCID:PMC3836478
  • Duressa D, Anchieta A, Chen D, Klimes A, Garcia-Pedrajas MD, Dobinson KF and Klosterman SJ. RNA-seq analyses of gene expression in the microsclerotia of Verticillium dahlia BMC Genomics 2013 Sep 9;14(1):607. PMID: 24015849. PMCID:PMC3852263
  • Tuomela J, Sandholm J, Kaakinen M, Patel A, Kauppila JH, Ilvesaro J, Chen D, Harris KW, Graves D, Selander KS. DNA From Dead Cancer Cells Induces TLR9-Mediated Invasion and Inflammation In Living Cancer Cells.  Breast Cancer Research and Treatment. 2013 Dec;142(3):477-87 PMID: 24212717.

Awards

  • Individual Postdoctoral Fellowship in Applied Informatics from NLM/NIH. May 2001-April 2003
  • Charles Brooks Award for Creativity, UAB School of Health Professions. 2002
  • CUNY Fellowship for Ph.D. program in Biomedical Sciences. September 1993- September 1994
1.    Fulzele K, Riddle RC, DiGirolamo DJ, Cao X, Wan C, Chen D, Faugere M-C, Aja S, Hussain MA, Brüning JC, and Clemens TL.  Insulin receptor signaling in osteoblasts regulates postnatal bone acquisition and body composition. Cell. 142(2):309-319. 2010. PMID: 20655471. PMCID: PMC2925155.
2.    Jian B, Yang S, Chen D, Zou L, Chatham JC, Chaudry I and Raju R. Aging influences cardiac mitochondrial gene expression and cardiovascular function following trauma-hemorrhage. Molecular Medicine. 17(5-6):542-9. 2011. PMID: 21193900. PMCID: PMC3105128.
3.    Crasto C, Luo D, Yu F, Forero A and Chen D. GenDrux: A biomedical literature search system to identify gene expression-based drug sensitivity in breast cancer. BMC Medical Informatics and Decision Making. 11:28. 2011 (Corresponding author). PMID: 21545721. PMCID:PMC3116456
4.    Katkoori VR, Shanmugam C, Jia X, Vitta SP, Sthanam M, Callens T, Messiaen L, Chen D, Zhang B, Bumpers HL, Samuel T, Manne U.  Prognostic Significance and Gene Expression Profiles of p53 Mutations in Microsatellite-Stable Stage III Colorectal Adenocarcinomas. PLoS ONE 7(1): e30020. 2012. PMID:22276141. PMCID: PMC3261849.
5.    Luo D, Banerjee P, Harner J, Mobley J, Chen D. A cloud computing system to quickly implement new microarray data pre-processing methods.  The Open Bioinformatics Journal, 2012, 6, 37-42. (Corresponding author).
6.    Tuomela J, Sandholm J, Karihtala P, Ilvesaro J, Vuopala KS, Kauppila JH, Kauppila S, Chen D, Pressey C, Härkönen P, Harris KW, Graves D, Auvinen PK, Soini Y, Jukkola-Vuorinen A, Selander KS. Low TLR9 expression defines an aggressive subtype of triple-negative breast cancer. Breast Cancer Res Treat. 2012 Jul 31.  PMID:22847512
7.    Pei M, Zhang Y, Li J, Chen D. Antioxidation of decellularized stem cell matrix promotes human synovium-derived stem cell-based chondrogenesis. Stem Cells Dev 2013 Mar 15;22(6):889-900.   PMID: 23092115. PMCID: PMC3585742.
8.    Fraser KB, Moehle MS, Daher JP, Webber PJ, Williams JY, Stewart CA, Yacoubian TA, Cowell RM, Dokland T, Ye T, Chen D, Siegal GP, Galemmo RA, Tsika E, Moore DJ, Standaert DG, Kojima K, Mobley JA, West AB. LRRK2 Secretion in Exosomes is Regulated by 14-3-3. Hum Mol Genet. 2013 Dec 15;22(24):4988-5000. PMID: 23886663 PMCID:PMC3836478
9.    Duressa D, Anchieta A, Chen D, Klimes A, Garcia-Pedrajas MD, Dobinson KF and Klosterman SJ. RNA-seq analyses of gene expression in the microsclerotia of Verticillium dahlia BMC Genomics 2013 Sep 9;14(1):607. PMID: 24015849. PMCID:PMC3852263
10.    Tuomela J, Sandholm J, Kaakinen M, Patel A, Kauppila JH, Ilvesaro J, Chen D, Harris KW, Graves D, Selander KS. DNA From Dead Cancer Cells Induces TLR9-Mediated Invasion and Inflammation In Living Cancer Cells.  Breast Cancer Research and Treatment. 2013 Dec;142(3):477-87 PMID: 24212717.