Dr. Emily I. Chen, Ph.D.

An experienced scientific investigator committed to life sciences, cutting-edge proteomics technology, and business strategy.

California

Research Expertise

Multi-omics platform and data analysis
Proteomics technology and data analysis
Breast cancer research
Al and biological applications
Al and therapeutic applications

About

Dr. Emily I. Chen is a highly accomplished scientist with a strong background in molecular pathology and translational medicine. She earned her Ph.D. in Molecular Pathology from the University of California San Diego in 2002, and later received post-doctoral training at the Scripps Research Institute, where she specialized in studies of proteomics alterations in cancer and mechanisms of breast cancer metastasis. After completing her Ph.D., Dr. Chen joined as a principal investigator at Stony Brook University’s Department of Pharmacological Science, and later as the Director of the Proteomics Shared Resource at Columbia University Medical Center, where she led a team in the development and implementation of cutting-edge proteomic technologies for translational research. Her work at Columbia resulted in numerous publications and presentations at national and international conferences. In 2018, Dr. Chen joined Thermo Fisher Scientific as the Senior Director of the Precision Medicine Science Center. In this role, she oversaw a team of scientists who worked with academics and pharmaceutical businesses to create precision medicine technologies such as next-generation sequencing and companion diagnostic biomarker analysis. Throughout her career, Dr. Chen has been involved in numerous research initiatives and collaborations, resulting in over 60 publications in peer-reviewed journals. She is also a frequent conference speaker and has been recognized for her contributions to proteomics and translational research. Dr. Chen's expertise and leadership have made her a highly sought-after consultant and advisor for biotechnology and pharmaceutical companies. She continues to be a driving force in the advancement of precision medicine, with a focus on improving patient outcomes and revolutionizing healthcare.

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Publications

The perivascular niche regulates breast tumour dormancy
Nature Cell Biology
2013
Early-stage epigenetic modification during somatic cell reprogramming by Parp1 and Tet2
Nature
2012
Adaptation of Energy Metabolism in Breast Cancer Brain Metastases
Cancer Research
2007
Regulation of Pluripotency and Cellular Reprogramming by the Ubiquitin-Proteasome System
Cell Stem Cell
2012
Optimization of Mass Spectrometry-Compatible Surfactants for Shotgun Proteomics
Journal of Proteome Research
2007
Substrate Hydrolysis by Matrix Metalloproteinase-9*
Journal of Biological Chemistry
2001
Large Scale Protein Profiling by Combination of Protein Fractionation and Multidimensional Protein Identification Technology (MudPIT)
Molecular & Cellular Proteomics
2006
Identification of a stem-like cell population by exposing metastatic breast cancer cell lines to repetitive cycles of hypoxia and reoxygenation
Breast Cancer Research
2010
Macroautophagy deficiency mediates age-dependent neurodegeneration through a phospho-tau pathway
Molecular Neurodegeneration
2012
A Unique Substrate Recognition Profile for Matrix Metalloproteinase-2
Journal of Biological Chemistry
2002
Keratin 17 in premalignant and malignant squamous lesions of the cervix: proteomic discovery and immunohistochemical validation as a diagnostic and prognostic biomarker
Modern Pathology
2014
PatternLab for proteomics: a tool for differential shotgun proteomics
BMC Bioinformatics
2008
Proteomics-based discovery of a novel, structurally unique, and developmentally regulated plasminogen receptor, Plg-RKT, a major regulator of cell surface plasminogen activation
Blood
2010
FBXW7 modulates cellular stress response and metastatic potential through HSF1 post-translational modification
Nature Cell Biology
2015
MicroRNA-195 Regulates Metabolism in Failing Myocardium Via Alterations in Sirtuin 3 Expression and Mitochondrial Protein Acetylation
Circulation
2018
A Unique Substrate Binding Mode Discriminates Membrane Type-1 Matrix Metalloproteinase from Other Matrix Metalloproteinases
Journal of Biological Chemistry
2002
Raf-induced MMP9 disrupts tissue architecture of human breast cells in three-dimensional culture and is necessary for tumor growth in vivo
Genes & Development
2010
Cancer proteomics by quantitative shotgun proteomics
Molecular Oncology
2007
Neurotrophin-3 modulates breast cancer cells and the microenvironment to promote the growth of breast cancer brain metastasis
Oncogene
2012
Lambda Interferon Restructures the Nasal Microbiome and Increases Susceptibility to Staphylococcus aureus Superinfection
mBio
2016
Mitochondrial dysfunction and cancer metastasis
Journal of Bioenergetics and Biomembranes
2012
The hemopexin domain of MMP3 is responsible for mammary epithelial invasion and morphogenesis through extracellular interaction with HSP90β
Genes & Development
2013
Cancer stem cells, tumor dormancy, and metastasis
Frontiers in Endocrinology
2012
Comparisons of Mass Spectrometry Compatible Surfactants for Global Analysis of the Mammalian Brain Proteome
Analytical Chemistry
2008
Detecting the Immune System Response of a 500 Year-Old Inca Mummy
PLoS ONE
2012
SCCA1/SERPINB3 Promotes Oncogenesis and Epithelial–Mesenchymal Transition via the Unfolded Protein Response and IL6 Signaling
Cancer Research
2014
Serum exosomal protein profiling for the non-invasive detection of cardiac allograft rejection
The Journal of Heart and Lung Transplantation
2018
Precision Targeting with EZH2 and HDAC Inhibitors in Epigenetically Dysregulated Lymphomas
Clinical Cancer Research
2019
Maspin and tumor metastasis
IUBMB Life
2006
A Residue in the S2 Subsite Controls Substrate Selectivity of Matrix Metalloproteinase-2 and Matrix Metalloproteinase-9
Journal of Biological Chemistry
2003
Acquired resistance to innate immune clearance promotes Klebsiella pneumoniae ST258 pulmonary infection
JCI Insight
2016
Genetic reprogramming of tumor cells by zinc finger transcription factors
Proceedings of the National Academy of Sciences
2005
N-Cadherin Promotes Recruitment and Migration of Neural Progenitor Cells from the SVZ Neural Stem Cell Niche into Demyelinated Lesions
The Journal of Neuroscience
2014
Asparagine deprivation mediated by Salmonella asparaginase causes suppression of activation-induced T cell metabolic reprogramming
Journal of Leukocyte Biology
2015
Tuftsin Promotes an Anti-Inflammatory Switch and Attenuates Symptoms in Experimental Autoimmune Encephalomyelitis
PLoS ONE
2012
Tau and other proteins found in Alzheimer’s disease spinal fluid are linked to retromer-mediated endosomal traffic in mice and humans
Science Translational Medicine
2020
Maspin alters the carcinoma proteome
The FASEB Journal
2005
GO Explorer: A gene-ontology tool to aid in the interpretation of shotgun proteomics data
Proteome Science
2009
Cellular STAT3 Functions via PCBP2 To Restrain Epstein-Barr Virus Lytic Activation in B Lymphocytes
Journal of Virology
2015
Candidate protein markers for radiation biodosimetry in the hematopoietically humanized mouse model
Scientific Reports
2018
Members of the high mobility group B protein family are dynamically expressed in embryonic neural stem cells
Proteome Science
2013
Hnrpab regulates neural development and neuron cell survival after glutamate stimulation
RNA
2012
Identifying Predictors of Taxane-Induced Peripheral Neuropathy Using Mass Spectrometry-Based Proteomics Technology
PLOS ONE
2015
Identifying Urinary and Serum Exosome Biomarkers for Radiation Exposure Using a Data Dependent Acquisition and SWATH-MS Combined Workflow
International Journal of Radiation Oncology*Biology*Physics
2016
Rap1b Is an Effector of Axin2 Regulating Crosstalk of Signaling Pathways During Skeletal Development
Journal of Bone and Mineral Research
2017
Biochemical Characterization of Hpa2 and Hpa3, Two Small Closely Related Acetyltransferases from Saccharomyces cerevisiae
Journal of Biological Chemistry
2013
The Plasminogen Receptor, , and Macrophage Function
Journal of Biomedicine and Biotechnology
2012
Screening for Protease Substrate by Polyvalent Phage Display
Combinatorial Chemistry & High Throughput Screening
2005
Proline Hydroxylation Primes Protein Kinases for Autophosphorylation and Activation
Molecular Cell
2020
Mitogen-activated protein kinase signaling causes malignant melanoma cells to differentially alter extracellular matrix biosynthesis to promote cell survival
BMC Cancer
2016
New insight into the role of MMP14 in metabolic balance
PeerJ
2016
The Tumor Suppressor NKX3.1 Is Targeted for Degradation by DYRK1B Kinase
Molecular Cancer Research
2015
The actin modulator hMENA regulates GAS 6‐ AXL axis and pro‐tumor cancer/stromal cell cooperation
EMBO reports
2020
hMENA isoforms impact NSCLC patient outcome through fibronectin/β1 integrin axis
Oncogene
2018
Biological functions of membrane-type matrix metalloproteinases
Matrix Biology
2008
Integration of postmortem amygdala expression profiling, GWAS, and functional cell culture assays: neuroticism-associated synaptic vesicle glycoprotein 2A (SV2A) gene is regulated by miR-133a and miR-218
Translational Psychiatry
2020
A Substrate Phage Enzyme-Linked Immunosorbent Assay to Profile Panels of Proteases
Analytical Biochemistry
2001
Identification of the Novel Plasminogen Receptor, Plg-RKT
Proteomics - Human Diseases and Protein Functions
2012
Proteomics Analysis of Circulating Serum Exosomes
Methods in Molecular Biology
2017
Auto-thiophosphorylation activity of Src tyrosine kinase
BMC Biochemistry
2016
Quantitative Proteomics Using 15N SILAC Mouse
Journal of Proteomics And Genomics Research
2013
Proteome Scale-Protein Turnover Analysis Using High Resolution Mass Spectrometric Data from Stable-Isotope Labeled Plants
Unknown Venue
Non-motor Spindle Proteins as Cancer Chemotherapy Targets
Kinesins and Cancer
2015
Stage Specific and Progression Cervical Cancer Biomarkers: Discovery and Histologic Validation
Journal of the American Society of Cytopathology
2012
Abstract 16449: miR-195 Regulates Myocardial SIRT3 Expression and Mitochondrial Enzyme Acetylation
Circulation
2015
Receptor recognition specificity of plasminogen for the novel plasminogen receptor, Plg‐RKT
The FASEB Journal
2008
Abstract 16438: Serum Exosomal Protein Profiling for the Non-invasive Detection of Cardiac Allograft Rejection
Circulation
2015
Identifying predictors of taxane-induced peripheral neuropathy using shotgun proteomics technology.
Journal of Clinical Oncology
2015
Abstract PR13: Using a hypoxia-induced CSC tumor initiation model to improve predictive potential for patients with metastatic breast cancer
Molecular Cancer Research
2014
Discovery And Quantification In Mass Spectrometry-Based Proteomics
Journal of Proteomics And Genomics Research
2014
Abstract B54: Squamous cell carcinoma antigen 1 (SCCA1) promotes mammary tumorigenesis through the induction of misfolded protein stress
Cancer Research
2013
Abstract A1: NT-3 modulates HER2 signaling to promote the metastatic growth of HER2-positive breast cancer brain metastasis
Cancer Research
2011
Abstract SY02-02: Interaction of MMPs with oncogenic signaling: Disruption of dynamic reciprocity and tissue polarity
Cancer Research
2011
Adhesive Mechanisms in Breast Cancer Metastasis
Unknown Venue
2000
The role of co-operative education in ensuring students' success when transitioning from classroom to industry
2014 IEEE International Professional Communication Conference (IPCC)
2014

Education

University of California San Diego

Ph.D., Molecular Pathology / August, 2002

La Jolla, California, United States of America

Experience

Columbia University Medical Center

Director of Proteomics Shared Resource / September, 2013Present

Thermo Fisher

Sr. Director of Precision Medicine Science Center / January, 2018March, 2021

Develop application notes and marketing strategies for translational proteomics research.

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