Rebecca Panitch, Ph.D.
Bioinformatics, BUSM (2023)
Current Position: Bioinformatician, Watershed Informatics, Cambridge MA.
Devanshi Patel, Ph.D.
Bioinformatics – Computing & Data Sciences, Boston University (2020)
Current Position: Manager, Data Science & Analytics, AbbVie
Stephanie Correa, Ph.D.
Current Position: Postdoctoral Fellow, University of California, San Francisco
Kuang-Hung Chen, Ph.D.
CMB-Pathology, Boston University (2004)
Current Position: Assistant Professor, National Sun Yat-Sen University, Kaohsiung, Taiwan
Dhamaraj Chinnappan, Ph.D.
All India Institute of Med. Science, New Delhi, India (1994)
Current Position: Scientist, Broad Institute, Cambridge, MA
Porat M. Ehrlich, M.Sc., Ph.D.
Genetics program, Molecular Medicine, BUMC
Current Position: Research Associate at the Geisinger Center for Health Research.
Fangming Gao, Ph.D.
CMB-Pathology, Boston University (2008)
Current Position: Freelance Venture Capital Investor
Arthur W. Lambert, Ph.D.
Molecular and Translational Medicine, BUSM (2013)
Current Position: Post-Doctoral Fellow, Whitehead, MIT, Boston, MA
B.S. Animal Science/Pre-Veterinary Medicine , University of New Hampshire (2006)
TGFβ signaling and Smad proteins in breast and colon cancer
Elucidating the effect of perturbing the TGFβ signaling pathway during different stages of breast tumorigenesis using a cell line model system. Knockdown of Smad2 using shRNA is accomplished with a lentiviral expression system. Analysis includes, PCR, reverse-transcription PCR, real-time PCR,
methylation-specific PCR, Western Blotting and chromatin immunoprecipitation.
Examine the effect of cyclic nucleotide phosphodiesterase inhibitors on lymphoma cells obtained from an Eµ-Brd2 transgenic mouse model for non-Hodgkin’s lymphoma
Propagated lymphomas in recipient mice, isolated malignant lymphocytes and
treated cells with various PDE inhibitors (rolipram, IBMX, cilostamide,
dipyridamole, etc.). Analyzed apoptosis by flow cytometry. In a separate
project, followed tumor progression and aberrant blow flow in mice using
Analysis of the klotho promoter region
Created various truncated reporter constructs using site-directed mutagenesis to be used in a luciferase assay to determine the necessary regulatory elements in the promoter region. Additionally, used promoter trapping chromatography and western blotting to identify Sp1 as a transcription factor that binds specifically to the -300 bp region upstream of the transcription start site in vitro.
Investigation of feeding anticipatory activity in offshore Atlantic cod
Anticipatory activity was investigated in a novel manner using underwater cameras and analyzed using MotionApp software to detect relative pixel change in order to evaluate feeding and pre-feeding behavior.
– Gao, F., J. F. Ponte, P. Papageorgis, M. Levy, S. Ozturk, A. W. Lambert H. Pan, D. Chinnappan, B. Sullivan H. Abdolmaleky and S. Thiagalingam. 2009. hBub1 is a negative regulator of p53 mediated cell death upon activation of spindle assembly checkpoint. Manuscript submitted.
P. Papagerorgis, A.W. Lambert, S. Ozturk, H. Abdolmalcky and S. Thiagalingam. 2008. Smad signaling mediates epigenetic regulation of breast cancer progression. Evans Department of Medicine Research Days Abstract.
Papageorgis, P., A. W. Lambert, S. Ozturk, F. Gao, H. Abdolmaleky and S. Thiagalingam. 2008. Smad signaling mediates epigenetic regulation of EMT during breast cancer progression. Manuscript in preparation.
Ph.D. Candidate, Bioinformatics, BUSM
B.S. Genetics, B.S. Computer Science, University of Wisconsin – Madison
Daniel’s work focuses on analyzing endophenotypes relating to Alzheimer’s Disease. In particular, Daniel is interested in investigating neuroimaging phenotypes, as well as biomarkers that may be concordant in other neurodegenerative diseases
Gang Liu, Ph.D.
University of Kentucky, Lexington, KY (1999)
Current Position: Assistant Professor, Pulmonary Center, BUSM, Boston, MA
– Qianli received his masters degree in Bioinformatics in the Genetics program in 2005
Current Position: Biostatistician, University of Miami’s Health Services Research Center
Current Postion: Postdoctoral Research Scientist at Columbia University
Current Position: Computational Biologist at Health Tell, Inc.
Yan Meng, Ph.D.
Bioinformatics, Boston University
Current Position: Center Scientist, The Stanley Center for Psychiatric Research at the Broad Institute
Yan’s interest is the genetic analysis of complex diseases, using both quantitative and qualitative approaches. Yan’s focus is on the analysis of late onset Alzheimer’s disease.
Arasambattu K. Munirajan, Ph.D.
Madurai Kamaraj University, India
Current Position: Professor of Genetics, University of Madras, India
Sait Ozturk, Ph.D.
CMB-Molecular and Translational Medicine, Boston University (2013)
Current Position: Post-Doctoral Fellow, Tisch Cancer Institute at The Mount Sinai School of Medicine, NY
Hongjie Pan, Ph.D.
University of Georgia (2002)
Current Position: Research Associate, Duke University, NC
Panos Papageorgis Ph.D.
Genetics and Genomics/Cell and Molecular Biology, Boston University (2009)
Current Position: Senior Scientist, University of Cyprus and Assistant Professor, European University Cyprus
Molecular cloning and subcloning of genes, mammalian normoxic and hypoxic cell culture techniques, expression and isolation of recombinant fusion proteins using bacterial systems, retroviral and lentiviral-mediated stable gene transfer, lentiviral-mediated stable gene knock-down by shRNA, transient transfection assays, luciferase reporter assays, western blotting, nuclear and cytoplasmic cell fractionation, PCR, RT-PCR, real-time PCR, methylation specific PCR, quantitative-methylation specific PCR, bisulfite sequencing, methyl-DNA immunoprecipitation assay, chromatin immunoprecipitation assays, co-immunoprecipitation assays, cell proliferation assays, in vitro cell migration and invasion assays, zymogram assays, ELISA assays, immunofluorescent staining and cell imaging, gene expression microarray techniques and analysis using “ingenuity pathway” software, in vivo tumorigenesis assays by orthotopic and subcutaneous injections and in vivo metastasis assays by tail-vein injections in immunodeficient mice.
1. Papageorgis P., Lee R., Gao F. and Thiagalingam S. Smad4 inactivation promotes metastatic properties of colon cancer cells. In preparation.
2. Papageorgis P., Abdolmaleky H., Lambert AW. Ozturk S. and Thiagalingam S. Smad signaling mediates epigenetic regulation of breast cancer. Submitted.
3. Gao F., Ponte J., Levy, M, Papageorgis P., Ozturk S., Lambert AW., Thiagalingam A., Abdolmaleky H., Sullivan BA., and Thiagalingam S. hBub1 deficiency triggers a novel p53 mediated early apoptotic checkpoint pathway in mitotic spindle damaged cells. Cancer Biol Ther. 2009 Apr 1 8(7).
4. Gao F., Ponte J., Papageorgis P., Levy, M., Cook NM., Ozturk S., Lambert AW., Pan H., Chinnapan D., Cheng KH., Thiagalingam A., Abdolmaleky H. and Thiagalingam S. hBub1 negatively regulates p53 mediated early cell death upon mitotic checkpoint activation. Cancer Biol Ther. 2009 Apr 1 8(7).
5. Pan H, Gao F, Papageorgis P., Abdolmaleky HM, Faller DV, Thiagalingam S. Aberrant activation of γ-catenin promotes genomic instability and oncogenic effects during cancer progression. Cancer Biol Ther. 2007 Oct 6; (10):1638-43, 2007.
6. Abdolmaleky HM, Cheng KH, Faraone SV, Wilcox M, Glatt SJ. Gao F, Smith CL, Shafa R, Aeali B, Carnevale J, Pan H, Papageorgis P, Ponte JF, Sivaraman V, Tsuang MT, Thiagalingam S. Hypomethylation of MB-COMT promoter is a major risk factor for schizophrenia and bipolar disorder. Hum Mol Genet. 2006 Nov 1; 15(21):3132-45, 2006.
7. Thiagalingam S., Ponte J., Papageorgis P., Cheng K.H. Is epigenetic inactivation of Smad8 in cancer, a novel tumor marker for diagnosis and therapy? FASEB Journal. 2004 May 14; 18(8) Abstract B502.
8. Papageorgis P., Lambert A., Ozturk S. and Thiagalingam S. TGFβ and BMP signaling pathways in cancer. Systems Biology of Cancer, Cambridge University Press, 2009 in preparation.
9. Thiagalingam S. and Papageorgis P. DNA methylation profiles as prognostic markers for cancer. Cancer Epigenetics 335-348 Taylor & Francis, 2008.
Dorothy Pazin Ph.D.
Genetics and Genomics, Boston University (2009)
Current Position: Postdoctoral Fellow, Rosen Lab, Harvard School of Dental Medicine, Boston, MA
The mouse gonad provides a powerful tool for studying organogenesis. Similar to all organs, the development of the gonads utilizes growth factor and morphogen signaling. What is unique about the gonads, is that they develop from a bipotential progenitor that differentiates into either an ovary or testis. These facts suggest that gonad development employs sex-specific responses to, or expression of, certain growth factors and morphogens. Recent evidence suggests that molecules in the extracellular matrix (ECM) can influence how growth factors and morphogens diffuse and/or interact with their receptors, thereby modulating downstream signaling events. We hypothesize that some of these ECM-related molecules may modulate sex-specific responses to growth factors and/or morphogens.
My research interests involve studying the role of the ECM in embryonic gonad development. I have used RNA in situ hybridization, real-time RT-PCR and organ culture experiments to study the expression and regulation of several genes that encode ECM molecules. I also have analyzed mutant mice in order assess the roles that ECM-related genes play in gonad development.
1. Lee HJ, Pazin DE, Kahlon RS, Correa SM, Albrecht KH. Novel markers of early ovarian pre-granulosa cells are expressed in an Sry-like pattern. Developmental Dynamics. In press.
2. Liu P, Pazin DE, Merson RR, Albrecht KH, Vaziri C. The developmentally-regulated Smoc2 gene is repressed by aryl-hydrocarbon receptor (Ahr) signaling. Gene 2008.
Jose F. Ponte, Ph.D.
University of Vermont (1998)
Current Position: Senior Scientist, ImmunoGen, Inc., Waltham, MA
Bioinformatics, BU 2014
Current Position: Senior Bioinformatician at Expression Analysis, Inc.
Badri Vardarajan (Bioinformatics, BU 2013)
Current Position: Assistant Professor, Columbia University
Chen Khuan Wong, Ph.D.
Ph.D. in Genetics and Genomics, Boston University School of Medicine
B.S. Biotechnology, Indiana University Bloomington (2012)
- Dissecting the SMAD4 metastasis suppressor complex to identify novel prognostic biomarkers and therapeutic targets in colon cancer
- Identification of miRNA biomarkers for early diagnosis and therapy of triple-negative breast cancer
- Nanoparticles directed to IL13RA2 for targeted therapy of basal-like breast cancer
- Ozturk S, Wong CK, Papageorgis P, Lambert AW, Abdolmaleky HM, Thiagalingam A, Cohen HT, and Thiagalingam S (2016) SDPR functions as a metastasis suppressor in breast cancer by promoting apoptosis. Proceedings of the National Academy of Sciences. 113: 638-43.
- Lambert AW, Wong CK, Ozturk S, Papageorgis P, Raghunathan R, Alekseyev Y, Gower AC, Reinhard BM, Abdolmaleky HM, and Thiagalingam S (2016) Periostin regulates cytokine production to maintain breast cancer stem cells. Molecular Cancer Research. 14: 103-13.
- Papageorgis P, Ozturk S, Lambert AW, Neophytou CM, Tzatsos A, Wong CK, Thiagalingam S, and Constantinou AI (2015) Targeting IL13RA2 activates STAT6-TP63 pathway to suppress breast cancer lung metastasis. Breast Cancer Research.
- Li W, Kuzoff R, Wong CK, Tucker A, and Lynch M (2014) Characterization of newly gained introns in Daphniapopulations. Genome Biology and Evolution. 6: 2218-34
- Abdolmaleky HM, Nohesara S, Ghadirivasfi M, Lambert AW, Ozturk S, Wong CK, Shafa R, and Thiagalingam S (2013) DNA hypermethylation of serotonin transporter gene promoter in drug naïve patients with schizophrenia. Schizophrenia Research. 152: 373-80.
Jiayi Cox, Ph.D.
Ph.D in Genetics and Genomics, Boston University School of Medicine
B.S. Pharmacology, Sichuan University, West China School of Pharmacy
M.S. in Pharmacology and Experimental Therapeutics, Tufts University School of Biomedical Sciences
Use machine learning methods to understand the potential environmental factors that could contribute to drug cessation, furthermore, I’m working on combining the human genetic data with featured environmental factors to evaluate drug cessation outcome. In the end, mouse model and RNA-seq analysis will be used to find the converging evidence between mouse and human.
She is interested in using bioinformatics tools to understand addiction. Her project involves in interpreting and translating the genetic inherited information from mouse addictive traits and human population. Jiayi finished her TTPAS training program focusing on addiction research in December 2016.
- Stacey L. Kirkpatrick, Lisa R. Goldberg, Neema Yazdani, R. Keith Babbs,Jiayi Wu, Eric R. Reed, David F. Jenkins, Amanda Bolgioni, Kelsey I. Landaverde, Kimberly P. Luttik, Karen S. Mitchell, Vivek Kumar, W. Evan Johnson, Megan K. Mulligan, Pietro Cottone, Camron D. Bryant. Cytoplasmic FMR1-Interacting Protein 2 is a Major Genetic Factor Underlying Binge Eating. Biological Psychiatry, 2016; DOI: 10.1016/j.biopsych.2016.10.021
- Jiayi Wu, Devanshi Patel, Jaeyoon Chung, Samantha Lent, Virginia Fisher, Achilleas Pitsillides, Lindsay Farrer, Xiaoling Zhang.(Submitted) An Efficient Analytic Approach in Genome-wide Identification of Methylation Quantitative Trait Loci Response to Fenofibrate Treatment. GAW20.
Yi Yu, Ph.D.
Boston University (2009)
Current Position: Senior Scientist at Amgen, Inc.
1. Developed novel analytical tools to screen genetic markers associated with diseases in family-based data or sib-pair data by the modifications of random forest algorithm. New algorithm showed robustness to population admixture and enhanced statistical power especially when gene-gene interaction involved. (2005-present, Boston University)
2. Identified several genes associated with the substance dependence diseases. Genotypic and phenotypic information of subjects from four medical centers were imported into database and cleaned for errors and inconsistencies. Statistical analysis were performed by using FBAT, QTDT, or GEE for the family-based samples, or carried out by using chi-square test or logistic regression for population-based samples. (2005-present, Boston University)
3. Located several genetic regions linked with quantitative traits (QTL) of atherogenic dyslipidemia. Data from six international sites were integrated, cleaned and formatted. Statistical analysis were processed by SOLAR, GENEHUNTER, MERLIN. (2004-2005, Boston University)
1. Yu Y, Kranzler HR, Panhuysen C, Weiss R, Brady K, Poling J, Tsai Y, Farrer LA, Gelernter J: Substance Dependence Whole Genome Association Study In Two Distinct American Populations. Hum Genet (Accepted)
2. Yu Y, Panhuysen C, Kranzler HR, Hesselbrock V, Rounsaville B, Weiss R, Brady K, Farrer LA, Gelernter J: Intronic variants in the dopa decarboxylase (DDC) gene are associated with smoking behavior in European-Americans and African-Americans. Hum Mol Genet 2006, 15(14):2192-2199.
3. Gelernter J, Yu Y, Weiss R, Brady K, Panhuysen C, Yang BZ, Kranzler HR, Farrer L: Haplotype spanning TTC12 and ANKK1, flanked by the DRD2 and NCAM1 loci, is strongly associated to nicotine dependence in two distinct American populations. Hum Mol Genet 2006, 15(24):3498-3507.
4. Yu Y, Wyszynski DF, Waterworth DM, Wilton SD, Barter PJ, Kesaniemi YA, Mahley RW, McPherson R, Waeber G, Bersot TP et al: Multiple QTLs influencing triglyceride and HDL and total cholesterol levels identified in families with atherogenic dyslipidemia. J Lipid Res 2005, 46(10):2202-2213.
5. Yu Y, Meng Y, Ma Q, Farrell J, Farrer LA, Wilcox MA: Whole-genome variance components linkage analysis using single-nucleotide polymorphisms versus microsatellites on quantitative traits of derived phenotypes from factor analysis of electroencephalogram waves. BMC Genet 2005, 6 Suppl 1:S15.
6. Meng Y, Ma Q, Yu Y, Farrell J, Farrer LA, Wilcox MA: Multifactor-dimensionality reduction versus family-based association tests in detecting susceptibility loci in discordant sib-pair studies. BMC Genet 2005, 6 Suppl 1:S146.
7. Ma Q, Yu Y, Meng Y, Farrell J, Farrer LA, Wilcox MA: Genome-wide linkage analysis for alcohol dependence: a comparison between single-nucleotide polymorphism and microsatellite marker assays. BMC Genet 2005, 6 Suppl 1:S8.
8. Yu Y, Lundeberg T, Yu LC: Role of calcitonin gene-related peptide and its antagonist on the evoked discharge frequency of wide dynamic range neurons in the dorsal horn of the spinal cord in rats. Regul Pept 2002, 103(1):23-27.
CMB Genetics and Genomics (2014)
Current Position: Assistant Professor of Molecular Biology, Department of Health Sciences, European University, Cyprus