Name: Rui Chen
Email: rui.chen.rc2@roche.com (work); royalchan@me.com (personal)
Cell: (203) 479-2714
Personal Webpage: http://goo.gl/gZ7yC
Google Scholar Profile: http://goo.gl/zpMM9
LinkedIn Profile: https://www.linkedin.com/in/rui-chen-4a90609
HIGHLIGHTS
Extensive Experience in Bioinformatics and Experimental Workflow Using Cutting-Edge High-Throughput Technologies.
Spearheaded in Data-Driven Wellness, Personalized Precision Health Monitoring and Preventative Medicine.
Expertise in NGS Product Development from Business Development to Launch.
Insights into Human Disease-Oriented Research Utilizing High Throughput Technologies.
Doctoral Thesis on Molecular Mechanisms of Ovarian Cancer Chemoresistance.
Extensive Collaboration, Team Management and Project Leading Experience.
Forty-Three Peer-Reviewed Publications to Date, Including (Co-)First Author Papers in Cell, Nature Biotechnology, Nature Medicine, etc.
Six Publications F1000Prime RECOMMENDED.
EDUCATION
2002 – 2008 : Doctor of Philosophy (05/2008), Master of Science (05/2005)
Graduate School of Arts and Sciences, Yale University
Department: Molecular, Cellular and Developmental Biology
1999 – 2002 : Master of Science
School of Life Sciences, Fudan University, P. R. China
Program: Biochemistry and Molecular Biology (Entrance Exam Exempted)
1995 – 1999 : Bachelor of Science
School of Life Sciences, Fudan University, P. R. China
Program: Biology (09/1995-07/1997); Advanced Science Class (07/1997-07/1999)
POSTDOCTORAL TRAINING
2009 – 2014 : Postdoctoral Scholar
Department: Genetics, Stanford University School of Medicine
2008 – 2009 : Postdoctoral Associate
Department: Molecular, Cellular and Developmental Biology, Yale University
EMPLOYMENT
03/2018 – Present: Principal Scientist II (Senior Principal Scientist), Reagent and Assay Development (Previous Name: NGS Workflow Controls and References Development, NGSWaR). Roche Sequencing Solutions.
11/2015 – 02/2018: Principal Scientist, Early Development / NGSWaR. Roche Sequencing Solutions.
06/2014 – 11/2015: Basic Life Science Research Associate (Research Scientist) / Instructor. Stanford University School of Medicine.
RESEARCH & WORK EXPERIENCE
01/2019 – Present :Development Lead and Team Manager, RSS Reagent and Assay Development. I manage an interdisciplinary team focusing on development of the KAPA Target Enrichment products (KAPA HyperCap series) from business development activities to product launch and post-launch product care. My team also works closely with the software and bioinformatics teams to develop customer-facing data analysis pipeline support. The KAPA HyperExome and HyperChoice products, pioneers in this portfolio, were officially announced in AGBT 2020 and launched in March 2020, which already received positive feedbacks from our US and international customers.
11/2015 – 12/2018 :Team manager and bioinformatics lead in RSS Early Development / NGSWaR. My team’s responsibilities include next generation sequencing products development, business development-related technology evaluation and development, as well as business and product development associated bioinformatics support and algorithm development.
06/2014 – 11/2015 :Basic Life Science Research Associate (Research Scientist) / Instructor, focusing on a) personalized health monitoring and preventative medicine with integrative Personal Omics Profile (iPOP) analysis; b) Systems approach to understanding asthma with omics technologies.
08/2009 – 05/2014 :Postdoctoral Scholar, Advisor: Dr. Michael Snyder (Dept. of Genetics, Stanford University), focusing on a) personalized health monitoring and preventative medicine with integrative Personal Omics Profile (iPOP) analysis; b) Systems approach to understanding asthma; c) Unraveling Mendelian Diseases with high throughput sequencing; d) Autoantibody biomarker detection of Myelodysplastic Syndromes.
06/2008 – 07/2009 :Postdoctoral Associate, Advisor: Dr. Michael Snyder (Dept. of Molecular, Cellular and Developmental Biology, Yale University), studies on the identification of viral and autoantigen biomarkers of asthma using protein microarray technology as well as RNA-Sequencing.
08/2004 – 05/2008 :Ph.D. student, Advisor: Dr. Gil G. Mor (Dept. of OB/GYN, Yale University), studies on the molecular mechanisms linking inflammation with cancer development and chemoresistance, with a focus on the important role of the TLR4 pathway components, especially IKKβ and hsa-miR-199a in cancer progression and chemoresistance.
03/2003 – 08/2004 :Ph.D. student, Advisor: Dr. David C. Ward (Dept. of Genetics, Yale University), focusing on identification and characterization of genetic markers for susceptibility of malaria, diabetes, and Autism Spectrum Disorders, and development of optical thin film-based genotyping methods.
08/2002 – 02/2003 :Ph.D. student rotation research (Yale University): characterization of the function of TAK1 in Toll-like Receptor (TLR) signaling pathways; study on mechanism of immune induction of viral pathogens at the mucosal surfaces.
09/1998 – 07/2002 :Research Assistant and then M.S. student in the National Key Laboratory of Chinese Genome Research Project at Fudan University directed by Prof. Kaiming Cao, focusing on identification and characterization of flowering-related MADS-Box Genes in rice.
02/1998 – 07/1998 :Research Assistant in the Human Genome Lab at Fudan University directed by Prof. Long Yu, focusing on sequence-based prediction and identification of new genes.
09/1997 – 01/1998 :Practicum focusing on the mite pesticide efficiency.
AWARDS AND HONORS
DeLill Nasser Award for Professional Development in Genetics from the Genetics Society of America (05/2012).
John Spangler Nicholas Prize for Outstanding Doctoral Student in Experimental Zoology at the 2008 commencement of Yale University (05/2008).
SGI President’s Presenter Award and Wyeth Pharmaceuticals grant on the 2008 SGI (Society for Gynecologic Investigation) international meeting (03/2008).
Dudley Leland Wadsworth Fellowship Award (2004~2005 academic year).
Chinese Academy of Science Scholarship for Exceptional Graduate Student of Fudan University (2000~2001 academic year).
Exceptional Graduate Student Scholarship of Fudan University (1999~2000 academic year).
People’s Academic Scholarship of Fudan University (was awarded twice for both semesters) (1997-1998 academic year).
People’s Academic Scholarship of Fudan University (was awarded twice for both semesters) (1996-1997 academic year).
People’s Academic Scholarship of Fudan University (was awarded twice for both semesters) (1995-1996 academic year).
Ranked 1st /15 and 1st /27 in my B.S. and M.S. class at Fudan University.
Elected into the Advanced Science Class of Fudan University in 1997.
Accepted into Master of Science program at Fudan University with exemption from normally mandatory entrance examination due to academic excellence in 1999.
Acquired U.S. permanent residency as Alien with Extraordinary Ability (Category E16).
PATENTS
Improved Nucleic Acid Target Enrichment and Related Methods (P35336-WO). Rui Chen, Toumy Guettouche, Donald E. Sharon. (Pending)
Single Stranded Circular DNA Libraries for Circular Consensus Sequencing (EP3559269A1). Toumy Guettouche, Rui Chen, Aaron Richardson. (Published on 30OCT2019, Pending)
Asymmetric Templates and Asymmetric Method of Nucleic Acid Sequencing (US20190153515A1). Rui Chen, Toumy Guettouche, Loida Navarro, Aaron Richardson. (Published on 23MAY2019, Pending)
A system for identification of antigens recognized by t cell receptors expressed on tumor infiltrating lymphocytes (WO2019238939A1). Nelson R. Alexander, Aoune Barhoumi, Jan Berka, Rui Chen, Lisa L. Gallegos, Toumy Guettouche, Seoyoung Kim, Maeve E. O’Huallachain, Sedide Ozturk, Jigar Panel, Florian Rubelt, Stacey Stanislaw. (Published on 19DEC2019)
Generation of single-stranded circular dna templates for single molecule sequencing (WO2019166530A1). Aruna Arcot, Daleen Badenhorst, Rui Chen, Toumy Guettouche, Ashley Hayes, Jenny A. Johnson, Severine Margeridon, Martin Ranik, Persis Wadia, Alexandra Hui Wang. (Published on 06SEP2019)
PUBLICATIONS
(* Co-First Author)
Manuscripts Submitted:
Mias GI*, Im H*, Jiang L*, Mitsunaga E*, Chen R, et al. Network Inference, Integrative Dynamic Omics and Personalized Medicine.
Sharon D, Chen R, Mias G, Landegren N, Kämpe O, Bergquist J, et al. Consistently Mutating Genes Are Associated with Autoimmunity. Submitted to Nature.
Peer-Reviewed Publications (in reverse chronological order):
Chen R*, Xia L*, Tu K*, Duan M, Kukurba K, Li-Pook-Than J, et al. Longitudinal Personal DNA Methylome Dynamics Associate with a Chronic Condition. Nature Medicine. 2018;Nov 5. doi: 10.1038/s41591-018-0237-x. PMID: 30397358.
Cover story.
Im H*, Rao V*, Sridhar K*, Bentley J, Mishra T, Chen R, et al. Distinctive Transcriptomic and Exomic Abnormalities within Myelodysplastic Syndrome Marrow Cells. Leukemia & Lymphoma. 2018;Apr 4:1-11. doi: 10.1080/10428194.2018.1452210. PMID: 29616851.
Breton CV, Marsit CJ, Faustman E, Nadeau K, Goodrich JM, Dolinoy DC, Herbstman J, Holland N, LaSalle JM, Schmidt R, Youse P, Perera F, Joubert BR, Wiemels J, Taylor M, Yang IV, Chen R, et al. Small-Magnitude Effect Sizes in Epigenetic End Points Are Important in Children’s Environmental Health Studies: the Children’s Environmental Health and Disease Prevention Research Center’s Epigenetics Working Group. Environmental Health Perspectives. 2017;125(4):511-526. doi: 10.1289/EHP595. PMID: 28362264. PMCID: PMC5382002.
Takahashi S*, Andreoletti G*, Chen R, Munehira Y, Batra A, Afzal NA, et al. De novo and Rare Mutations in the HSPA1L Heat Shock Gene Associated with Inflammatory Bowel Disease. Genome Medicine. 2017;9(1):8. doi: 10.1186/s13073-016-0394-9. PMID: 28126021. PMCID: PMC5270254.
Rhodes CJ, Im H, Cao A, Hennigs JK, Wang L, Sa S, Chen PI, Nickel NP, Miyagawa K, Hopper RK, Tojais NF, Li CG, Gu M, Spiekerkoetter E, Xian Z, Chen R, et al. RNAseq Reveals a Novel Pathway of Endothelial Dysfunction in Pulmonary Arterial Hypertension. American Journal of Respiratory and Critical Care Medicine. 2015;192(3):356-366. doi: 10.1164/rccm.201408-1528OC. PMID: 26030479. PMCID: PMC4584250.
Chen R, Im H, Snyder M. Whole-Exome Enrichment with the Roche NimbleGen SeqCap EZ Exome Library SR Platform. Cold Spring Harbor Protocols. 2015;2015(7):634-641. doi: 10.1101/pdb.prot084855. PMID: 25762419. PMCID: PMC4490009.
Chen R, Im H, Snyder M. Whole-Exome Enrichment with the Agilent SureSelect Human All Exon Platform. Cold Spring Harbor Protocols. 2015;2015(7):626-633. doi: 10.1101/pdb.prot084859. PMID: 25762417. PMCID: PMC4490097.
Chen R, Im H, Snyder M. Whole-Exome Enrichment with the Illumina TruSeq Exome Enrichment Platform. Cold Spring Harbor Protocols. 2015;2015(7):642-648. doi: 10.1101/pdb.prot084863. PMID: 25762418. PMCID: PMC4490022.
The Integrative HMP (iHMP) Research Network Consortium. The Integrative Human Microbiome Project (iHMP): Dynamic Analysis of Microbiome-Host Omics Profiles During Periods of Human Health and Disease. Cell Host & Microbe. 2014;16(3):276-289. PMID: 25211071.
Enns GM, Shashi V, Bainbridge M, Gambello MJ, Zahir FR, Bast T, Crimian R, Schoch K, Platt J, Cox R, Bernstein JA, Scavina M, Walter RS, Bibb A, Jones M, Hegde M, Graham BH, Need AC, Oviedo A, Schaaf CP, Boyle S, Butte AJ, Chen R, et al. Mutations in NGLY1 Cause an Inherited Disorder of the Endoplasmic Reticulum-Associated Degradation Pathway. Genetics in Medicine. 2014;16(10):751-8. doi: 10.1038/gim.2014.22. PMID: 24651605. PMCID: PMC4243708.
(Corrigendum: http://www.nature.com/gim/journal/v16/n7/full/gim201461a.html)
F1000Prime RECOMMENDED.
Kuleshov V*, Xie D*, Chen R*, Pushkarev D*, Ma Z, Blauwkamp T, et al. Whole-Genome Haplotyping Using Long Reads and Statistical Methods. Nature Biotechnology. 2014;32(3):261-266. doi: 10.1038/nbt.2833. PMID: 24561555. PMCID: PMC4073643.
F1000Prime RECOMMENDED.
Kolker E, Özdemir V, Martens L, Hancock W, Dumbill E, Anderson N, Aynacioglu S, Baranova A, Campagna S, Chen R, et al. Towards more transparent and reproducible omics studies through a common metadata checklist and data publications. OMICS. 2014;18(1):10-14. doi: 10.1089/omi.2013.0149. PMID: 24456465. PMCID: PMC3903324. (Special Simultaneous Publication in Both Journals).
Kolker E, Özdemir V, Martens L, Hancock W, Dumbill E, Anderson N, Aynacioglu S, Baranova A, Campagna S, Chen R, et al. Towards more transparent and reproducible omics studies through a common metadata checklist and data publications. Big Data. 2013;1(4):196-201. doi: 10.1089/big.2013.0039. PMID: 27447251. (Special Simultaneous Publication in Both Journals).
Menon R, Im H, Zhang E, Wu S, Chen R, Snyder M, et al. Distinct splice variants and pathway enrichment in the cell line models of aggressive human breast cancer subtypes. Journal of Proteome Research. 2014;13(1):212-227. PMID: 24111759. PMCID: PMC3943430.
Mias GI*, Chen R*, Zhang Y, Sridhar K, Sharon D, Xiao L, et al. Specific plasma autoantibody reactivity in Myelodysplastic Syndromes. Scientific Reports. 2013;3:3311. doi: 10.1038/srep03311. PMID: 24264604. PMCID: PMC3837310. (www.nature.com/scientificreports).
Chen R*, Giliani S*, Lanzi G, Mias GI, Lonardi S, Dobbs K, et al. Whole-exome sequencing identifies Tetratricopeptide Repeat Domain 7A (TTC7A) mutations for Combined Immunodeficiency with Intestinal Atresias. Journal of Allergy and Clinical Immunology. 2013;132(3):656-664.e17. PMID: 23830146. PMCID: PMC3759618. (Second co-first author is collaborator PI)
Highlighted as Editors’ Choice.
Clark MJ, Chen R, Snyder M. Exome sequencing by targeted enrichment. Current Protocols in Molecular Biology. 2013 April;Chapter7:Unit7.12. PMID: 23547016.
Liu S, Im H, Bairoch A, Cristofanilli M, Chen R, Deutsch EW, et al. A Chromosome-Centric Human Proteome Project (C-HPP) to characterize the sets of proteins encoded in Chromosome 17. Journal of Proteome Research. 2013;12(1):45-57. PMID: 23259914.
Chen R, Snyder M. Promise of personalized omics to precision medicine. Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 2013;5(1):73-82. PMID: 23184638.
Article featured by publisher on the Wiley Life Sciences Blog (WiSci) [http://wisciblog.com/2013/08/14/molecular-snapshots-of-health-and-disease-omics-for-precision-medicine/].
Chen R, Snyder M. Systems biology: personalized medicine for the future? Current Opinion in Pharmacology. 2012;12(5):623-628. PMID: 22858243. PMCID: PMC4076046.
Sun N, Yazawa M, Liu J, Han L, Sanchez-Freire V, Abilez OJ, Navarrete EG, Hu S, Wang L, Lee A, Pavlovic A, Lin S, Chen R, et al. Patient-specific induced pluripotent stem cells as a model for Familial Dilated Cardiomyopathy. Science Translational Medicine. 2012;4(130):130ra147. PMID: 22517884. PMCID: PMC3657516.
Chen R*, Mias GI*, Li-Pook-Than J*, Jiang L*, Lam HY, Miriami E, et al. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell. 2012;148(6):1293-1307. PMID: 22424236. PMCID: PMC3341616.
Featured as the only research paper in the March 16th, 2012 special issue of Cell, and selected as the “Genome Advance of the Month” by the National Human Genome Research Institute. Selected into Cell -- Best of 2012. F1000Prime RECOMMENDED.
Lam HY, Pan C, Clark MJ, Lacroute P, Chen R, Haraksingh R, et al. Detecting and annotating genetic variations using the HugeSeq pipeline. Nature Biotechnology. 2012;30(3):226-229. PMID: 22398614.
Paik YK, Jeong SK, Omenn GS, Uhlen M, Hanash S, Cho SY, Lee HJ, Na K, Choi EY, Yan F, Zhang F, Zhang Y, Snyder M, Cheng Y, Chen R, et al. The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nature Biotechnology. 2012;30(3):221-223. PMID: 22398612.
Lam HY, Clark MJ, Chen R, Chen R, Natsoulis G, O'Huallachain M, et al. Performance comparison of whole-genome sequencing platforms. Nature Biotechnology. 2012;30(1):78-82. PMID: 22178993. PMCID: PMC4076012.
First comprehensive comparison of Illumina and Complete Genomics whole genome sequencing platforms. Served as leading experimentalist and coordinator. F1000Prime RECOMMENDED.
Clark MJ*, Chen R*, Lam HY, Karczewski KJ, Euskirchen G, Butte AJ, et al. Performance comparison of exome DNA sequencing technologies. Nature Biotechnology. 2011;29(10):908-914. PMID: 21947028. PMCID: PMC4127531.
First comprehensive comparison of three exome-sequencing platforms. F1000Prime RECOMMENDED.
Fasolo J, Sboner A, Sun MG, Yu H, Chen R, Sharon D, et al. Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes. Genes & Development. 2011;25(7):767-778. PMCID: 3070938. PMID: 21460040. PMCID: PMC3070938.
F1000Prime RECOMMENDED.
Chen R, Snyder M. Yeast proteomics and protein microarrays. Journal of Proteomics. 2010;73(11):2147-2157. PMID: 20728591. PMCID: PMC2949546.
Sharon D*, Chen R*, Snyder M. Systems biology approaches to disease marker discovery. Disease Markers. 2010;28(4):209-224. PMID: 20534906. PMCID: PMC3833409.
Yin G*, Chen R*, Alvero AB, Fu HH, Holmberg J, Glackin C, et al. TWISTing stemness, inflammation and proliferation of epithelial ovarian cancer cells through MIR199A2/214. Oncogene. 2010;29(24):3545-3553. PMID: 20400975. PMCID: PMC2889129.
Alvero AB, Montagna MK, Chen R, Kim KH, Kyungjin K, Visintin I, et al. NV-128, a novel isoflavone derivative, induces caspase-independent cell death through the Akt/mammalian target of rapamycin pathway. Cancer. 2009;115(14):3204-3216. PMID: 19472400. PMCID: PMC2757274.
Alvero AB, Chen R, Fu HH, Montagna M, Schwartz PE, Rutherford T, et al. Molecular phenotyping of human ovarian cancer stem cells unravels the mechanisms for repair and chemoresistance. Cell Cycle. 2009;8(1):158-166. PMID: 19158483. PMCID: PMC3041590.
Chen R, Alvero AB, Silasi DA, Kelly MG, Fest S, Visintin I, et al. Regulation of IKKbeta by miR-199a affects NF-kappaB activity in ovarian cancer cells. Oncogene. 2008;27(34):4712-4723. PMID: 18408758. PMCID: PMC3041589.
Chen R, Alvero AB, Silasi DA, Steffensen KD, Mor G. Cancers take their Toll--the function and regulation of Toll-like receptors in cancer cells. Oncogene. 2008;27(2):225-233. PMID: 18176604.
Silasi DA, Alvero AB, Mor J, Chen R, Fu HH, Montagna MK, et al. Detection of cancer-related proteins in fresh-frozen ovarian cancer samples using laser capture microdissection. Methods in Molecular Biology. 2008;414:35-45. PMID: 18175810.
Chen R, Alvero AB, Silasi DA, Mor G. Inflammation, cancer and chemoresistance: taking advantage of the toll-like receptor signaling pathway. American Journal of Reproductive Immunology. 2007;57(2):93-107. PMID: 17217363.
Fest S, Aldo PB, Abrahams VM, Visintin I, Alvero A, Chen R, et al. Trophoblast-macrophage interactions: a regulatory network for the protection of pregnancy. American Journal of Reproductive Immunology. 2007;57(1):55-66. PMID: 17156192.
Silasi DA, Alvero AB, Illuzzi J, Kelly M, Chen R, Fu HH, et al. MyD88 predicts chemoresistance to paclitaxel in epithelial ovarian cancer. Yale Journal of Biology and Medicine. 2006;79(3-4):153-163. PMID: 17940625. PMCID: PMC1994803.
Kelly MG, Alvero AB, Chen R, Silasi DA, Abrahams VM, Chan S, et al. TLR-4 signaling promotes tumor growth and paclitaxel chemoresistance in ovarian cancer. Cancer Research. 2006;66(7):3859-3868. PMID: 16585214.
Zhong XB, Leng L, Beitin A, Chen R, McDonald C, Hsiao B, et al. Simultaneous detection of microsatellite repeats and SNPs in the macrophage migration inhibitory factor (MIF) gene by thin-film biosensor chips and application to rural field studies. Nucleic Acids Research. 2005;33(13):e121. PMID: 16077028. PMCID: PMC1182331.
Jia H, Chen R, Cong B, Cao K, Sun C, Luo D. Characterization and transcriptional profiles of two rice MADS-box genes. Plant Science. 2000;155(2):115-122. PMID: 10814814.
Chen R, Gao ZZ, Zhan SX, Sun CR, Cao KM. Cloning and structural analysis of the full-length cDNA of two rice flowering-related MADS-box genes. Journal of Fudan University (Natural Science). 2003;42(4):570-576. [Article in Chinese, no PMID]
Gao ZZ, Chen R, Zhan SX, Sun CR, Cao KM. Detecting the expression of a flower development MADS-box gene in rice. Journal of Fudan University (Natural Science). 2002;41(1):52-56. [Article in Chinese, no PMID]
Manuscripts in Preparation:
Chen R*, Gu GJ*, Mias G, Sharon D, Patel J, Alexandridis R, Richmond T, Albert T, Snyder M. Dynamic Personalized Peripheral Blood Proteome and Antibodyome for Common Cold Viral Infections.
Chen R. Personalized Systems Biology in Precision Medicine. (Invited Book Chapter for Precision Medicine prepared by NCI/NIH)
Chen R, Bauer RN, Singh VV, Jenks JA, Lyu S, Runyon S, Li-Pook-Than J, Euskirchen G, Lacroute P, Mias GI†, Nadeau K†, Snyder M†. An Omics View of Asthma through Discordant Monozygotic Twins.
Li-Pook-Than J, Sharon D, Chen R, Mias GI, Holbert, B, Snyder M. Dynamic RNA Splicing and Edited Isoforms Identified in PBMCs.
Ph.D. Dissertation:
Molecular Mechanisms Linking Inflammation, Cancer and Chemoresistance (Yale University, 2008, ISBN 0549650202, 9780549650201).
Meeting Abstracts:
Chen R, Wu, B, Navarro L, Guettouche T. Towards One-Day Target Enrichment Sequencing Library Preparation Workflow with Short Hybridization Optimization (Advances in Genome Biology and Technology 2020 General Meeting, Marco Island, FL, 2020).
Chen R, Navarro L, Ramaswamy L, Lee J, et al. Optimization of Digital Droplet PCR Assays and Data Interpretation for Copy Number Determination (11th Diagnostics R&D Fair, Basel, Switzerland, 2018). [One of eight posters selected from ~2000 candidates at Roche Sequencing Solutions]
Chen R, Navarro L, Hoglund B, et al. An Amplicon Ladder-Based Quantitative Real-Time Polymerase Chain Reaction Method for Quantifiable DNA Quality Measurement (10th Diagnostics R&D Fair, San Francisco, CA, 2016).
Chen R, Runyon S, Li-Pook-Than J, et al. Asthma: An Omics View through Discordant Monozygotic Twins (ASHG 2012 Annual Meeting, San Francisco, CA, 2012).
Mias GI, Im H, Mitsunaga E, Chen R, et al. Network Inference, Integrative Dynamic Omics and Personalized Medicine (ASHG 2012 Annual Meeting, San Francisco, CA, 2012).
Dewey F, Cordero S, Wheeler M, Pavlovic A, Bommakanti K, Pan S, Caleshu C, Chen R, Snyder M, Ashley E. Whole Exome Sequencing and Hypertrophic Cardiomyopathy (ASHG 2012 Annual Meeting, San Francisco, CA, 2012).
Chen R*, Mias GI*, Li-Pook-Than J*, Jiang L*, et al. Integrative Personalized Omics Profiling Reveals Complex Molecular Phenotypes and Monitorable Medical Risks (US HUPO, San Francisco CA, 2012).
Chen R*, Mias GI*, Li-Pook-Than J*, Jiang L*, et al. Personalized Omics Profiling Unveils Complex Molecular Phenotypes and Monitorable Medical Risks (Keystone Symposia: Complex Traits: Genomics and Computational Approaches, Breckenridge, CO, 2012).
Mias G*, Chen R*, Li-Pook-Than J*, Jiang L*, et al. Personalized Medicine Through Integrative Dynamic Omics (The Biology of Genomes, Cold Spring Harbor, NY, 2012).
Mias G*, Chen R*, Li-Pook-Than J*, Jiang L*, et al. Personalized Medicine Through Integrative Dynamic Omics (HUPO 2012, Boston, MA, 2012).
Snyder M, Chen R, et al. Whole Omics Profiling Reveals Medical and Complex Molecular Phenotypes (American Society of Human Genetics/ICHG, Montreal, Canada, 2011).
Clark MJ, Chen R, et al. A Comprehensive Comparison of Whole Human Genome and Exome Sequencing Technologies (American Society of Human Genetics/ICHG, Montreal, Canada, 2011).
Pan S, Chen R, et al. Exome Sequencing and Linkage Filters Identify Novel Candidate Mutations in a Family with Left-Ventricular Non-Compaction (American Society of Human Genetics/ICHG, Montreal, Canada, 2011).
Li-Pook-Than J, Chen R, et al. Heteroallelic expression and RNA editing using high-throughput RNA sequencing (American Society of Human Genetics/ICHG, Montreal, Canada, 2011).
Dewey F, Cordero S, Wheeler MT, Pavlovic A, Bommakanti KK, Pan S, Caleshu C, Chen R, Snyder M and Ashley EA. Whole Exome Sequencing and Hypertrophic Cardiomyopathy (American Society of Human Genetics/ICHG, Montreal, Canada, 2011).
Mias GI*, Chen R*, et al. Proteomic Screening for Plasma Autoantibody Biomarkers in MDS Using Protein Microarrays (MDS 11th International Symposium, Edinburgh, UK, 2011). Leukemia Research 35:S23 (2011).
Chen R, Alvero AB, et al. Identification and characterization of miR-199a as regulator of IKKbeta expression and its function in ovarian cancer cells (55th Annual Meeting of the Society for Gynecologic Investigation, MAR 26-29, 2008 San Diego CA, Meeting Abstract 87). Reprod. Sci. 15(2):85A-85A (2008).
Chen R, Alvero AB, et al. Splitting the family: Characterization of two types of epithelial ovarian cancer cells (54th Annual Meeting of the Society for Gynecologic Investigation, MAR 14-17, 2007 Reno NV, Meeting Abstract 402). Reprod. Sci. 14(1):171A-171A (2007).
Silasi DA*, Chen R*, et al. Splitting the family: Molecular characteristics of chemoresistant versus chemosensitive epithelial ovarian cancer cells (Meeting Abstract 289). Gynecol. Oncol. 108(3):S127-S128 (2008).
Leiser A, Fu HH, Chen R, et al. Eriocalyxin B induces apoptosis of chemoresistant ovarian cancer cells through NF-kappaB inhibition (55th Annual Meeting of the Society-for-Gynecologic-Investigation, MAR 26-29, 2008 San Diego CA, Meeting Abstract 858). Reprod. Sci. 15(2):301A-302A (2008).
Silasi DA, Alvero AB, Kelly M, Chen R, et al. A novel approach to determine paclitaxel resistance in ovarian cancer (54th Annual Meeting of the Society for Gynecologic Investigation, MAR 14-17, 2007 Reno NV, Meeting Abstract 402). Reprod. Sci. 14(1):170A-171A (2007).
Zhong X, Wu C, Chen R, et al. Towards the development of a test for SARS virus detection at early infection stages (International Symposium on the Pathogenesis of SARS, July 12-13, 2003, Beijing, China, Meeting Abstract Accession Number: PREV200400241795). Applied Immunohistochem. & Mol. Morphol. 12(1):83-83 (2004).
PUBLIC PRESENTATIONS
03/2016: Invited Speaker (Opening Lecture). ERS Lung Science Conference 2016 (Estoril, Portugal). “Personal ‘Omics Profiling”.
10/2015: Invited Speaker. 2015 Keystone Symposia on Human Nutrition, Environment and Health (Beijing, China). “Longitudinal Omics in Humans”.
09/2015: Invited Speaker. UC Davis Genomics & Epigenetics Series (Davis, CA, USA). “Towards Precision Medicine with Integrative Personal Omics Profiles”.
10/2014: Invited Speaker. 2nd Thought Leaders Consortium in Personalized Lifestyle Medicine, the Personalized Lifestyle Medicine Institute (Seattle, WA, USA). “Towards Precision Medicine with Integrative Personal Omics Profiles”.
10/2014: Invited Guest Lecturer. Course: Intro to Genomics & Computational Biology, Princeton University (Princeton, NJ, USA). “Personal Omics for Personalized Medicine”.
10/2014: Invited Speaker. 1st Stanford Chinese Students and Scholars Symposium (Stanford, CA, USA). “Towards Precision Medicine with Integrative Personal Omics Profiles”.
09/2014: Invited Speaker. European Respiratory Society International Congress 2014 (Munich, Germany). “The 'omics revolution: the future of personalised medicine — Integrated 'omics predicts clinical outcomes”.
06/2014: Invited Speaker, Advisory Board Member and Session Chair. 2nd Annual Bioinformatics and Data Management Conference (San Diego, CA, USA). “Towards Precision Medicine with Integrative Personal Omics Profiles”.
04/2014: Invited Speaker. SELECTBIO’s Genomics Research: PCR & NGS conference (San Francisco, CA, USA). “Towards Precision Medicine with Integrative Personal Omics Profiles – To Genomics and Beyond”.
03/2014: Invited Speaker. Association of Biomolecular Resource Facilities (ABRF) 2014 Annual Conference (Albuquerque, NM, USA). “Dynamic Omics Methods for Personalized Medicine — High Throughput Profiling Methodologies”.
02/2014: Invited Speaker. Cambridge Healthtech Institute’s Tenth Annual Clinical and Translational Science, Strategies to Accelerate and De-Risk Clinical Development (The 21st Annual Molecular Medicine Tri-Conference) (San Francisco, CA, USA). “From Molecular Snapshots to Molecular Symptoms: Towards Precision Medicine with Integrative Personal Omics Profiles”.
09/2013: Invited Speaker. Stanford Immunology Annual Scientific Conference (Pacific Grove, CA, USA). “RNA Sequencing”.
05/2013: Invited Speaker. 3rd Annual World Pharmacogenomics (World PGx) Summit (San Francisco, CA, USA). “Measuring the True Impacts of Genomic Sequencing on Drug Development: A Personal Viewpoint”.
03/2013: Invited Speaker. AAAI (The Association for the Advancement of Artificial Intelligence) Spring Symposium Series – Data Driven Wellness: From Self Tracking to Behavior Change (Palo Alto, CA, USA). “Promise of Integrative Personalized Omics to Precision Medicine”.
02/2013: Invited Speaker. Molecular Medicine Tri-Conference (San Francisco, CA, USA). “Integrative Personal Omics Profiling for Personalized Medicine”.
12/2012: Invited Speaker. Genetics, Genomics, and Systems Biology, Earl Stadtman Symposium (Bethesda, MD, USA). “Towards Precision Medicine with Integrative Personal Omics Profiling”.
11/2012: Invited Speaker. The 11th International Society of Neuroimmunology (Boston, MA, USA). “Complex Molecular Phenotypes and Medical Risks Revealed by Integrative Personalized Omics Profile Analysis”.
09/2012: Invited Speaker. The 2012 European NGS Symposium (Basel, Switzerland). “Personalized Genomes and Beyond: Promise of Integrative Personal Omics Profiles (iPOP) to Precision Medicine”.
09/2012: Invited as Keynote Speaker. The Omics (R)evolution Workshop (Universiteit Antwerpen, Belgium). “Workshop on Integrative Personal Omics Profiling (iPOP)”.
07/2012: Invited Speaker. The 11th Surugadai-International Symposium (Tokyo, Japan). “Integrated Personal Omics Profile (iPOP) Reveals Dynamic Molecular and Medical Phenotypes”.
07/2012: Invited as Honorable Guest. The 2nd International Conference on Proteomics & Bioinformatics (Las Vegas, NV, USA). “Personal Health Monitoring and Preventative Medicine with integrative Personal Omics Profiling”.
07/2012: Invited Speaker. The 3rd International Conference on Biomarkers and Clinical Research (Las Vegas, NV, USA). “Personal Health Monitoring and Preventative Medicine with integrative Personal Omics Profiling”.
04/2012: Invited Speaker. Multiple Sclerosis and the Omics Spring Conference (Bilbao, Biscay, Spain). “Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes”.
03/2008: The 2008 SGI 55th Annual Scientific Meeting (San Diego, CA, USA). “Identification and Characterization of miR-199a as Regulator of IKKbeta Expression and Its Function in Ovarian Cancer Cells”.
03/2007: The 2007 SGI 54th Annual Scientific Meeting (Reno, NV, USA). “Serum Protein Markers for Early Detection of Ovarian Cancer”.
CONFERENCE ORGANIZATION
Advisory Board: 2nd Annual Bioinformatics and Data Management Conference (June 19-20, 2014, San Diego, California).
Organizing Committee: AAAI (The Association for the Advancement of Artificial Intelligence) 2014 Spring Symposium (March 24-26, 2014, Stanford, CA, USA).
Advisory Board: GTC’s Next Generation Sequencing Conference (October 7-11, 2013, Berlin, Germany).
MEMBERSHIPS
09/2013 ---- present : Data-Enabled Life Sciences Alliance
05/2012 ---- present : The American Society of Human Genetics
04/2012 ---- present : The Genetics Society of America
02/2012 ---- present : US HUPO (Human Proteome Organization)
11/2008 ---- present : American Association for Cancer Research
02/2007 ---- present : American Association for the Advancement of Science
09/2005 ---- present : New York Academy of Science
03/2007 ---- 09/2008: Society for Gynecologic Investigation
PEER REVIEW
Peer Review Referee for Astrobiology
Peer Review Referee for Future Medicine - Pharmacogenomics
Peer Review Referee for International Journal of Molecular Sciences
Peer Review Referee for Journal of Gastroenterology and Hepatology
Peer Review Referee for Journal of Proteome Research
Peer Review Referee for Molecular and Cellular Proteomics
Peer Review Referee for Clinical Epigenetics
TEACHING AND EXTRACURRICULAR ACTIVITIES
07-08/2005, 07-08/2006, 07-08/2007: Mentor: Discovery to Cure High School Program, Yale University
01/2006 ---- 05/2006 : Teaching Fellow Program Participant: Cell Biology, Yale University
09/2004 ---- 12/2004 : Teaching Fellow Program Participant: Genetics, Yale University
09/2000 ---- 01/2001 : Teaching Assistant: Advanced Techniques of Biochemistry B, Fudan University
09/1996 ---- 09/1997 : Class President
EXPERIMENTAL SKILLS
Omics Skills: Illumina Sequencing (whole genome, whole exome, whole transcriptome, whole methylome, whole hydroxymethylome), PacBio Sequencing, 10X Genomics Sequencing, Target Enrichment with Agilent, Nimblegen and Illumina Platforms, ATAC-Seq, ChIP-Seq, Ribosome Footprinting, Low Input Sequencing, NGS and SMRT Adapter Engineering, Mass Spectrometry (Tandom-Mass Tag Labeling), Protein and Peptide Microarrays, Optical Thin Film-Based Genotyping.
Molecular Skills: Droplet Digital PCR, PCR, qPCR, RT-PCR, Asymmetric PCR, Primer Design for PCR, Multiple Displacement Amplification, Rolling-Circle Amplification, 3’-RACE, 5’-RACE, Plasmid Construction, Telomere Length Measurement, Reporter Plasmid Construction and Detection, Point Mutation, Agarose Electrophoresis, SDS-PAGE, Southern Blot, Northern Blot, Western Blot, Genomic DNA/Plasmid Isolation, Total and Small RNA Isolation, Protein Isolation, in situ Hybridization, Immunocytochemistry, Immunohistochemistry, ELISA, LUMINEX-based Cytokine Detection.
Cellular Skills: E. coli, Insect and Mammalian Cell Culture, Transformation, Clone Selection and Storage, Primary Cancer Cell Isolation and Culture Establishment from Malignant Ascites or Solid Tumors, Conventional Cell Culture and Passage Skills, Lipid or Retro-virus-Mediated Mammalian Cell Transfection and Clone Selection, Protein Expression and Purification, Drug Treatment, Cell Viability Assay, Caspase Activity Assay.
Mouse Models and Other in vivo Skills: Subcutaneous (s.c.) and Intraperitoneal (i.p.) Ovarian Cancer Mouse Models Including Tumor Establishment and Treatments, s.c. Injection, i.p. Injection, Tail-Vein Injection, Retro-orbital Bleeding, Agrobacteria mediated Arabidopsis thaliana Transformation and relevant Transformants Screening.
COMPUTATIONAL SKILLS
Programming (Ordered by Proficiency Level): Perl, R (Including R Shiny Apps), Bash Shell, Java, Python, Sed, Awk, FORTRAN 77, BASIC.
Data Analyses: Machine Learning (Incl. Deep Learning), Time Series Analyses, Statistical Analyses, Algorithm Development, Feature Identification, Data Normalization and Transformation, Data Clustering and Classification (Supervised & Unsupervised), Data Visualization.
Applications: NGS Data Analysis Pipeline Infrastructure / Workflow Control Construction, AWS, BWA, BSMAP, GATK, Kallisto, Bowtie, Tophat, Cufflinks, Picard, SAMTools, VCFtools, BEDtools, ANNOVAR, Circos, Cytoscape, 10X GenomicsTM Software Suite, Complete GenomicsTM cgatools, MicrosoftTM Office.