Manager, Bioinformatics Services
Contact Information
Norris Medical Library
2003 Zonal Avenue
Los Angeles, CA 90089-9130

(323) 442-3309
yibuchen@usc.edu

Yibu Chen

Liaison For

Bioinformatics

Library Responsibilities

Provides consulting services and training on the effective application of bioinformatics tools for specific research problems, such as visualizing, analyzing, manipulating and/or interpreting molecular data.

Develops and conducts a broad-based educational program related to the proper selection and use of bioinformatics resources and databases. Teaches workshops and coordinates additional educational workshops provided by vendors.

Engages in collaborative bioinformatics data analysis and provides grant application support for faculty members.

Oversees the licensing and user access of USC-licensed bioinformatics software.

Oversees the operation of NML bioinformatics computing resources.

Oversees the updating and maintenance of a bioinformatics web site to promote and support the use of available bioinformatics resources and keep researchers aware of new developments in bioinformatics and bio-computing.

Develops and analyzes USC user surveys as needed and prepares statistical reports for the Associate Dean of Health Sciences Libraries.

Maintains a current awareness of newly developed databases and resources and develops innovative approaches to disseminating this information.

Contact me regarding

Bioinformatics workshop content and schedules
Bioinformatics resources relevant to specific research needs
Application of bioinformatics tools in various stages of research
Analysis and interpretation of high-throughput genomics data

Educational Background

PhD, Biology, Biology Department, Rensselaer Polytechnic Institute, Troy, NY, 1998

MS, Biological Oceanography, Institute of Marine Sciences, University of Southern Mississippi, MS, 1994

BS, Marine Biology, Department of Biology, Ocean University of China, Qingdao, P.R. China, 1984

Selected Publications & Presentations

Zhao Y, Wu K, Nguyen C, Smbatyan G, Melendez E, Higuchi Y, Chen Y, Kahn M.  Small Molecule p300/Catenin Antagonists Enhance Hematopoietic Recovery After Radiation.  PLOS ONE 2017.  12(5): e0177245

Chen K, Kardys A, Chen Y, Flink S, Tabaoff B, Hong FU, Shih JC.  Altered Gene Expression in Early Postnatal Monoamine Oxidase A Knockout Mice.  Brain Research. 2017 1669:18-26

Ingles SA, Wu L, Liu BT, Chen Y, Wang CY, Templeman C, Bruggmann D.  Differential Gene Expression by 1,25(OH)2D3 in an Endometriosis Stromal Cell Line.  J Steroid Biochem Mol Biol. 2017 Jan 25. pii: S0960-0760(17)30011-0

Li Z, Hao P, Wu Q, Li F, Zhao J, Wu K, Qu C, Chen Y, Li M, Chen X, Stucky A, Zhong J, Li L, Zhong JF.  Genetic Mutations Associated with Metastatic Clear Cell Renal Cell Carcinoma.  Oncotarget. 2016 Mar 29;7(13):16172-9.

Boddupally K, Wang G, Chen Y and Kobielak A.  Lgr5 marks neural crest derived multipotent oral stem cells.  Stem Cells. 2016 34(3):720-31

Choi D, Ramu S, Park E, Jung E, Yang S, Jung W, Choi I, Lee S, Kim KE, Seong YJ, Hong M, Daghlian G, Kim D, Shin E, Seo JI, Khatchadourian V, Zou M, Li W, De Filippo R, Kokorowski P, Chang A, Kim S, Bertoni A, Furlanetto TW, Shin S, Li M, Chen Y, Wong A, Koh C, Geliebter J, Hong YK.  Aberrant Activation of Notch Signaling Inhibits PROX1 Activity to Enhance the Malignant Behavior of Thyroid Cancer Cells. Cancer Res. 2016 76(3):582-93

Lawrenson K, Li QY, Kar S., Seo JH, Tyrer J, Spindler TJ, Lee J, Chen YB and et al. Cis-eQTL analysis and functional validation of candidate susceptibility genes for high-grade serous ovarian cancer.  Nat Commun. 2015 6:8234

Yang R, Qu C, Zhou Y, Konkel JE, Shi S, Liu Y, Chen C, Liu S, Liu D, Chen Y, Zandi E, Chen W, Zhou Y, Shi S.  Hydrogen Sulfide Promotes Tet1- and Tet2-Mediated Foxp3 Demethylation to Drive Regulatory T Cell Differentiation and Maintain Immune Homeostasis.  Immunity. 2015 43(2):251-63

Leung Y, Kandyba E, Chen YB, Ruffins S, Chuong CM, and Kobielak K.  Bifunctional ectodermal organ stem cells around the nail:Dual fate homeostasis and adaptive wounding response toward nail regeneration.  Proc Natl Acad Sci U S A. 2014 Oct 21;111(42):15114-9

Zhang H, Boddupally K, Kandyba E, Kobielak K, Chen Y, Zu S, Krishnan R, Sinha U, Kobielak A.  Defining the localization and molecular characteristic of minor salivary gland label-retaining cells. Stem Cells 2014 32(8):2267-77

Leung Y, Kandyba E, Chen YB, Ruffins S, and Kobielak K.  Label-Retaining Cells (LRCs) with myoepithelial characteristic from the proximal acinar region define stem cells in the sweat gland.  PLOS ONE  2013 8(9):e74147

Meng L, Chen YB, and Clintworth WA.  Expanding roles in a library-based bioinformatics service program: a case study.  Journal of Medical Library Association. 2013 101(4):303-309.

Kandyba E, Leung Y, Chen YB, Widelitz R, Chuong CM, and Kobielak K.   Competitive balance of intrabulge BMP/Wnt signaling reveals a robust gene network ruling stem cell homeostasis and cyclic activation.  Proc Natl Acad Sci U S A.  2013 110(4):1351-1356

Ishii M, Arias AC, Liu L, Chen YB, Bronner ME, and Maxson RE.  A stable cranial neural crest cell line from mouse.  Stem Cells Dev. 2012 21(17):3069-80.

Cao C, Chen YB, Masood R, Sinha UK, and Kobielak A.  α-Catulin marks the invasion front of squamous cell carcinoma and is important for tumor cell metastasis.  Mol. Cancer Res. 2012 10(6):892-903

Dai Y, Guo L, Li M, and Chen YB.  Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results.  BMC Res. Notes 2012 5:282

Lacruz RS, Smith CE, Bringas P Jr, Chen YB, Smith SM, Snead ML, Kurtz I, Hacia JG, Hubbard MJ, and Paine ML.  Identification of novel candidate genes involved in mineralization of dental enamel by genome-wide transcript profiling.  J. of Cell Physiol. 2012 227(5):2264-75.

Chimge NO, Baniwal SK, Little GH, Chen YB, Kahn M, Tipathy D, Borok Z, and Frenkel B.  Regulation of breast cancer metastasis by Runx2 and estrogen signaling: the role of SNAI2.  Breast Cancer Res. 2011 13(6):R127

Lacruz RS, Smith CE, Chen YB, Snead ML, Hacia JG, Hubbard MJ, and Paine ML.  Gene-expression analysis of early- and late-maturation-stage rat enamel organ.  Eur J Oral Sci. 2014 Feb;122(1):21-6

Chen YB, Chattopadhyay A, Bergen P, Gadd C and Tannery N.  The online bioinformatics resources collection at the University of Pittsburgh Health Sciences Library System — A one-stop gateway to online bioinformatics databases and software tools.   Nucleic Acids Res. 2007 Jan;35(Database issue):D780-5

Giordano M, Chen YB, Koblizek M, and Falkowski PG.  Regulation of nitrate reductase in Chlamydomonas reinhardtii by the redox state of the plastoquinone pool.  Eur J Phycol. 2005 40: 345-352

Berman-Frank I, Chen YB, Gerchman Y, Dismukes GC, and Falkowski PG.  2005Inhibition of nitrogenase by oxygen in marine cyanobacteria controls the global nitrogen and oxygen cycles.  Biogeosciences Discussions 2005 2, 1–13.

Chen YB, Durnford DG, Koblizek M, and Falkowski PG.  Plastid regulation of Lhcb1 transcription in the chlorophyte alga Dunaliella tertiolecta.  Plant Physiol. 2004 Nov;136(3):3737-50

Berman-Frank I, Lundgren P, Chen YB, Küpper H, Kolber Z, Bergman B, and  Falkowski PG.  Segregation of nitrogen fixation and oxygenic photosynthesis in the marine cyanobacteria TrichodesmiumScience 2001 294:1534-1537

Dominic B, Zani S, Chen YB, Mellon MT, and Zehr JP.  Organization of nif genes of nonheterocystous cyanobacterium Trichodesmium sp. IMS101.  J Phycol.  2000 36:693-701.

Chen YB, Dominic B, Zani S, Mellon MT, and Zehr JP.  Expression of photosynthesis genes in relation to nitrogen fixation in the diazotrophic filamentous nonheterocystous cyanobacterium Trichodesmium sp. IMS 101.  Plant Mol Biol. 1999 41: 89-104

Chen YB, Dominic B, Mellon MT, and Zehr JP.  Circadian rhythm of nitrogenase gene expression in the filamentous nonheterocystous cyanobacterium Trichodesmium sp. IMS 101.  J Bacteriol. 1998 180:3598-3605

Dominic B, Chen YB, and Zehr JP.  Cloning and transcriptional analysis of the nifUHDK genes of Trichodesmium sp. IMS 101 reveals stable nifD, nifDK and nifK transcripts.  Microbiology (UK) 1998 144:3359-3368

Chen YB, Zehr JP, and Mellon MT.  1996.  Growth and nitrogen fixation of the diazotrophic filamentous nonheterocystous cyanobacterium Trichodesmium sp. IMS 101 in defined media: evidence for a circadian rhythm.  J Phycol. 1996  32:916-923.

Zehr JP, Braun S, Chen YB, and Mellon MT.  Nitrogen fixation in the marine environment: relating genetic potential to nitrogenase activity.  J. Exp Mar. Biol. Ecol. 1996 203:61-73.