Rui Chen, Ph.D.

I am currently Principal Scientist II (Senior Principal Scientist) at Roche Sequencing Solutions, leading the efforts of new sequencing technology evaluation and development in NGS Workflow Control and Reference Development (NGSWaR). Before joining Roche, I trained as Postdoctoral Scholar with Dr. Michael Snyder in the Department of Genetics at Stanford University focusing on data-driven wellness, and was later Research Scientist in the Snyder lab. I have extensive experience in disease-related research and disease-orientated technology development, and am spearheading personalized health monitoring and preventative medicine with next-generation, high-throughput technologies. I orchestrated the first personalized health monitoring and preventative medicine proof-of-principle study with integrative omics, which was published as the only research paper in the 2012 special issue of Cell. This paper was later selected as “Genome Advance of the Month” by the National Human Genome Research Institute (National Institutes of Health), and also into Cell—Best of 2012. Beyond integrative personal omics research, I have broad expertise in cancer immunology and chemoresistance, and disease-related research such as asthma, Myelodysplastic Syndromes, as well as rare Mendelian diseases. I received my Ph.D. degree from Yale University in 2008 with the John Spangler Nicholas Prize, a prestigious award for most outstanding Ph.D. candidates in Biology.

Google Scholar Profile (Click Here)

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)

Post-Doctoral Training:

2009 – 2014: Postdoctoral Scholar

Department: Genetics, Stanford University

2008 – 2009: Postdoctoral Associate

Department: Molecular, Cellular and Developmental Biology, Yale University

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 (03/2008).

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).

Accepted into Master of Science program at Fudan University with exemption from normally mandatory entrance examination due to academic excellence in 1999.

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).

Elected into the Advanced Science Class of Fudan University in 1997.

Publications:

(Please click on the links below to each of my publications)

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. Environ Health Perspect. 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, Beattie RM, Bernstein JA, Ennis S†, Snyder M†. 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.

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. doi: 10.1164/rccm.201408-1528OC. PMID: 26030479.

Chen R, Im H, Snyder M. Whole-Exome Enrichment with the Roche NimbleGen SeqCap EZ Exome Library SR Platform. Cold Spring Harbor Protocols. 2015. doi: 10.1101/pdb.prot084855.

Chen R, Im H, Snyder M. Whole-Exome Enrichment with the Agilent SureSelect Human All Exon Platform. Cold Spring Harbor Protocols. 2015. doi: 10.1101/pdb.prot084859.

Chen R, Im H, Snyder M. Whole-Exome Enrichment with the Illumina TruSeq Exome Enrichment Platform. Cold Spring Harbor Protocols. 2015. doi: 10.1101/pdb.prot084863.

The Integrative HMP (iHMP) Research Network Consortium. The Integrative Human Microbiome Project (iHMP): Dynamic Analysis of Microbiome­Host 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. Genet Med. 2014. doi: 10.1038/gim.2014.22. PMID: 24651605. (Author List Error, Corrigendum Click Here)

Kuleshov V*, Xie D*, Chen R*, Pushkarev D*, Ma Z, Blauwkamp T, Kertesz K, Snyder M. Whole-Genome Haplotyping Using Long Reads and Statistical Methods. Nat Biotechnol. 2014. doi: 10.1038/nbt.2833. PMID: 24561555.

Mias GI*, Chen R*, Zhang Y, Sridhar K, Sharon D, Xiao L, Im H, Snyder MP, Greenberg PL. Specific Plasma Autoantibody Reactivity in Myelodysplastic Syndromes. Sci Rep. 2013. Nov 22;3:3311. doi: 10.1038/srep03311. PMID: 24264604.

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. J Allergy Clin Immunol. 2013. pii: S0091-6749(13)00981-0. doi: 10.1016/j.jaci.2013.06.013. PMID: 23830146. (Second co-first author is collaborator PI)

Highlighted as Editors’ Choice. Identified TTC7A as the causal gene for the rare Mendelian disease CID-MIA.

Chen R, Snyder M. Promise of Personalized Omics to Precision Medicine. Wiley Interdiscip Rev Syst Biol Med. 2013;5(1):73-82. PMID: 23184638.

Article Featured by publisher on the Wiley Life Sciences Blog (WiSci) .

Chen R, Snyder M. Systems biology: personilized medicine for the future? Curr Opin Pharmacol. 2012;12(5):623-628. PMID: 22858243.

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):1293-307. PMID: 22424236. (Free Version in PMC Click Here)

Highlighted. In this study we performed the first integrative Personal Omics Profiling (iPOP) on a generally healthy individual for 14 months, by monitoring various blood components (Peripheral Blood Mononuclear Cells, serum and plasma). During the course we observed extensive, dynamic molecular changes through healthy states and 2 viral infections (Human Rhinovirus and Respiratory Syncytial Virus), as well as an unexpected onset of Type 2 Diabetes. Featured as the only research paper in the March 16th, 2012 special issue of Cell. F1000Prime RECOMMENDED.

Clark MJ*, Chen R*, Lam HY, Karczewski KJ, Euskirchen G, Butte AJ, et al. Performance comparison of exome DNA sequencing technologies. Nat Biotechnol. 2011;29(10):908-14.

Highlighted. In this study we compared 3 different human exome enrichment platforms from Roche Nimblegen, Agilent and Illumina. F1000Prime RECOMMENDED.

Chen R, Snyder M. Yeast proteomics and protein microarrays. J Proteomics. 2010;73(11):2147-57. PMCID: 2949546.

Sharon D*, Chen R*, Snyder M. Systems biology approaches to disease marker discovery. Dis Markers. 2010;28(4):209-24.

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):3545-53. PMCID: 2889129.

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):4712-23. PMCID: 3041589.

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):225-33. PMID: 18176604.

Chen R, Alvero AB, Silasi DA, Mor G. Inflammation, cancer and chemoresistance: taking advantage of the toll-like receptor signaling pathway. Am J Reprod Immunol. 2007;57(2):93-107. PMID: 17217363.

Clark MJ, Chen R, Snyder M. Exome Sequencing by Targeted Enrichment. Curr Protoc Mol Biol. 2013 April;Chapter7:Unit7.12. PMID: 23547016.

Lam HY, Clark MJ, Chen R, Natsoulis G, O'Huallachain M, Dewey FE, et al. Performance comparison of whole-genome sequencing platforms. Nat Biotechnol. 2012;30(1):78-82.

F1000Prime RECOMMENDED. First comparison of Illumina vs Complete Genomics platforms. Served as key experimentalist and coordinator.

Lam HY, Pan C, Clark MJ, Lacroute P, Chen R, Haraksingh R, et al. Detecting and annotating genetic variations using the HugeSeq pipeline. Nat Biotechnol. 2012;30(3):226-9.

Menon R, Im H, Zhang E, Wu S, Chen R, Snyder M, Hancock W, Omenn G. Distinct Splice Variants and Pathway Enrichment in the Cell Line Models of Aggressive Human Breast Cancer Subtypes. J Proteome Res. 2013. PMID: 24111759. (Epub Ahead of Print).

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. J Proteome Res. 2013;12(1):45-57. PMID: 23259914.

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. Nat Biotechnol. 2012;30(3):221-3.

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. (2012). Patient-specific induced pluripotent stem cells as a model for familial dilated cardiomyopathy. Sci Transl Med 4, 130ra147. PMID: 22517884.

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 Dev. 2011;25(7):767-78. PMCID: 3070938.

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 / BIG DATA (Accepted, Special Simultaneous Publication in Both Journals).

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):3204-16. PMCID: 2757274.

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):158-66. PMCID: 3041590.

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 Mol Biol. 2008;414:35-45. PMID: 18175810.

Silasi DA, Alvero AB, Illuzzi J, Kelly M, Chen R, Fu HH, et al. MyD88 predicts chemoresistance to paclitaxel in epithelial ovarian cancer. Yale J Biol Med. 2006;79(3-4):153-63. PMCID: 1994803. PMID: 17940625.

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. Am J Reprod Immunol. 2007;57(1):55-66. PMID: 17156192.

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 Res. 2006;66(7):3859-68. 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 Res. 2005;33(13):e121. PMCID: 1182331.

Jia H, Chen R, Cong B, Cao K, Sun C, Luo D. Characterization and transcriptional profiles of two rice MADS-box genes. Plant Sci. 2000;155(2):115-22. PMID: 10814814.

Gao ZZ, Chen R, et al. Detecting the Expression of a Flower Development MADS-box Gene in Rice. J. Fudan University (Nat. Sci.). 2002;41(1):52-56. [Article in Chinese, no PMID]

Chen R, Gao ZZ, Zhan SX, et al. Cloning and Structural Analysis of the Full-Length cDNA of Two Rice Flowering-Related MADS-box Genes. J. Fudan University (Nat. Sci.). 2003;42(4):570-575. [Article in Chinese, no PMID]