scientist
Resume:
Samuel Long Ph.D.
********@*****.***; ****@******.***.*******.***
***** **** ****** ****, **********, MD 20871
Research and Professional Experience
QIAGEN Frederick, MD June 2010 – December 2014
Senior Scientist, Research and Development
• Developed LncRNA functional genomics products (siRNA and gapmers)
• Developed real time PCR-based qBiomarker mutation PCR arrays/assays system
http://www.qiagen.com/us/products/catalog/assay-technologies/real-time-pcr-and-rt-pcr-reagents/qbiomarker-somatic-mutation-pcr-arrays/
http://www.qiagen.com/us/products/catalog/assay-technologies/real-time-pcr-and-rt-pcr-reagents/qbiomarker-somatic-mutation-pcr-assays/
• Developed real time PCR-based qBiomarker copy number PCR arrays/assays system
http://www.qiagen.com/us/products/catalog/assay-technologies/real-time-pcr-and-rt-pcr-reagents/qbiomarker-copy-number-pcr-arrays/
http://www.qiagen.com/us/products/catalog/assay-technologies/real-time-pcr-and-rt-pcr-reagents/qbiomarker-copy-number-pcr-assays/
• Engaged in direct marketing and market analysis activities for both products
• Developed an accessory product (preamp) for qBiomarker somatic mutation PCR assays/arrays
http://www.qiagen.com/us/products/catalog/sample-technologies/dna-sample-technologies/genomic-dna/qbiomarker-array-preamp-mix /
http://www.qiagen.com/us/products/catalog/assay-technologies/real-time-pcr-and-rt-pcr-reagents/qbiomarker-assay-preamp-mix/
• Prepared technical documents including white paper(s) for released products and
external/conference presentations
QIAGEN Frederick, MD (acquired SABiosciences 12/09) December 2009 – June 2010
Senior Scientist, Research and Development
Head, Microarray Service Core
• Developed CNV and cytogenetics assay and service on Illumina iScan
• Developed whole-genome methylation profiling service capacity on Illumina iScan
• Achieved Illumina CSPro (certified service provider) status for SABiosciences-QIAGEN
microarray service core on whole genome gene expression and Infinium genotyping-based
applications
• Directed service lab operation and execution of customer gene expression and genomic analysis
projects in the following areas: PCR array, individual RT-qPCR, GEArray, Agilent gene
expression DNA microarray, microRNA profiling arrays, DNA methylation profiling, ELISA,
Illumina whole genome gene expression, Illumina whole genome genotyping
SABiosciences Corporation Frederick, MD July 2008 – December 2009
Microarray Service Core:
Head (6/09-12/09)
Acting Manager (3/09- 6/09)
Senior Scientist R&D (7/08-12/09)
• Developed a qPCR-based CNV detection assay
• Developed array CGH (aCGH) service capability on the Agilent platform for regular and FFPE
samples
• Developed a qPCR-based kit for quantitating next generation sequencing input DNA
• Developed a deafness gene medical sequencing sample prep panel
• Performed analysis of the effect of RNA quality on PCR array performance
• Co-developed an S. Corporation version of 5’ nuclease hydrolysis probe-based gene expression
assays
• Co-developed a custom PCR array plate/panel for discriminating between human X and Y
chromosome homolog genes
• Conducted collaborative research on designing a stem cell differentiation biomarker panel
• Directed service lab (3 technicians, 1 manager) operation and execution of customer gene
expression and genomic analysis projects in the following areas: PCR array, individual RT-qPCR,
GEArray, Agilent gene expression DNA microarray, microRNA profiling arrays, DNA
methylation profiling, ELISA, Illumina whole genome gene expression
• Performed cost/benefit analysis and configured pricing structure for existing and new service
items
• Redesigned and rewrote SABiosciences Corporation service web content, launched new service
products including probe-based gene expression assays, DNA methylation profiling service, nano-
preamplification service for gene expression profiling, RNAi validation service and Agilent Array
CGH service; Illumina gene expression, genotyping, copy number variation, cytogenetics,
methylation profiling services
• Coauthored two industry contract service provider bidding proposals (both on >$0.2M scale)
• Conducted a comprehensive service customer survey to generate feedback on service quality and
new services to offer
• Authored and edited service product SOPs
• Initiated ABI 7900 HT real time PCR machine automation with Caliper Twister II
• Introduced and initiated gene expression and Infinium whole genome genotyping services based
on the Illumina iScan system and Illumina beadchips
• Introduced DASL service (FFPE sample expression profiling) on the Illumina platform
• Supervising and implementing GLP compliance for SABiosciences service core lab
• Supervising and implementing ISO 9001 certification for SABiosciences microarray service core;
hosting internal ISO 9001 auditing
Massachusetts General Hospital/Harvard Medical School Boston, MA June 2005 - June 2008
Instructor (Medicine)
Supervisor: Professor Joseph Avruch M.D.
• Conducted a Rheb systematic mutagenesis project to identify unique regions in Rheb critical for
signaling to downstream molecules
• Investigated the molecular mechanism through which amino acids signal to mTOR through the
type 3 PI-3K pathway and the intracellular degradation pathway
• Identified a stable modification on TOR that contributes to increased access of substrates to the
substrate-presenting component of the TORC1 complex, raptor
Massachusetts General Hospital/Harvard Medical School Boston, MA Feb. 2001 - June 2005
Research Fellow (Molecular Biology and Medicine)
Supervisor: Professor Joseph Avruch M.D.
• Identified Rheb as the GTPase that activates TOR kinase
• Discovered that a major mechanism through which amino acids regulate TOR is through
modulating the Rheb-TOR interaction
• Identified raptor as the substrate binding and presenting subunit of the TORC1 complex
• Characterized TOR deficiency phenotypes in C. elegans
Brandeis University Waltham, MA August 1994 – February 2001
PhD Student
Mentor: Professor Leslie Griffith M.D. Ph.D.
• Searched for Drosophila neuronal CaM Kinase II interacting proteins using a yeast two-hybrid
screen
• Isolated DmUba2 and DmUbc9 (putative SUMO-1 (small Ubiquitin-like modifier) modification
enzymes) as CaM Kinase II interacting proteins
• Studied Drosophila SUMO-1 conjugation in in vitro reconstitution and in vivo (in transgenic
flies); demonstrated that normal SUMO-1 conjugation activities are indispensable for normal
animal development and function
• Identified neuronal CaM Kinase II as a DmSUMO-1 modification substrate; mapped the SUMO-1
modification site on CaM Kinase
Technical Expertise
Molecular biology Gene and recombinant DNA cloning, genomic DNA extraction, quantitative real
time PCR, Mutation detection based on qPCR, TaqMan gene expression assay,
TaqMan SNP genotyping assay, CNV (copy number variation) detection based
on qPCR and Illumina SNP chip, Northern blot, Western blot,
immunofluorescence, RNAi (in mammalian cells and C. elegans), DNA
isolation from bacteria and human tissues, RNA extraction, PCR array, DNA
sequencing, site-directed mutagenesis, phage-library screening, yeast two-hybrid
screening and analysis, ELISA development and validation, Illumina Infinium
genotyping, Illumina gene expression, Illumina whole genome methylation
profiling, Illumina DASL (FFPE sample expression profiling), Illumina copy
number variation and cytogenetics analysis
Cell biology Mammalian cell culture, DNA transfection, live cell imaging, polytene
chromosome in situ hybridization, generation of polyclonal antibodies,
morphological analysis of organisms using differential interference or Nomarski
contrast optics
Biochemistry recombinant protein expression and purification, protein purification from
animal tissues, enzyme assays (in vitro kinase assay, thioester formation assay,
protein biotinylation)), biochemical methods for protein characterization (amino
acid sequencing, protein quantitation, proteolytic assays, sample preparation
strategies, immuno-detection), immunoprecipitation, gel-shift assay, in vitro
protein binding assay and multiple methods of protein-protein interactions
Genetics Drosophila and C. elegans genetics, germ-line transformation in Drosophila
Computer software Microsoft Word, Excel, PowerPoint, Adobe Photoshop, Paint, real-time PCR
data analysis software, Agilent Feature Extraction, GeneSpring and CGH
Analytics, Illumina GenomeStudio (whole genome genotyping analysis,
methylation analysis and gene expression analysis), Illumina KaryoStudio (for
cytogenetics analysis)
Training courses Maryland ISO Consortium Program, Modules 1 to 6 (University of Maryland)
Illumina certified:
Illumina Infinium whole genome genotyping on iScan
Illumina Infinium Chemistry
Illumina Infinium Lab Setup, Best Practices and Assay Procedures
Illumina Infinium Genotyping Data Analysis in GenomeStudio
Illumina whole genome gene expression on iScan
Illumina gene expression and genotyping CSPro
Managerial:
Effective Managerial Skills, Levels 1-6 (Professional Resources, Inc.)
Management foundations
Situational leadership
Delegation & employee motivation
Communication & conflict management
Coaching & feedback
Managing up & down-sustaining communication
Accounting:
Introduction to Financial Accounting (Business Learning Software, Inc.)
Education
2001 Ph.D. (Biochemistry) Brandeis University
1998 M.S. (Biochemistry) Brandeis University
1994 B.S.-equivalent University of Science & Technology of China
Postdoctoral Training
2001-2005 Mass. General Hospital / Harvard, Research Fellow (Molecular Bio. / Medicine)
Academic Appointments
2001-2005 Harvard Medical School, Research Fellow (Molecular Biology / Medicine)
2005-2008 Harvard Medical School, Instructor (Medicine)
Hospital or Affiliated Institution Appointments
2001-2008 Massachusetts General Hospital, Research Fellow (Molecular Biology)
2001-2005 Massachusetts General Hospital, Research Fellow (Medicine)
Professional Societies
1995- AAAS (member)
2003- Sigma Xi, the Scientific Research Society (full member)
2006- Sigma Xi, Harvard Chapter (nominating committee)
2006- American Society for Biochemistry and Molecular Biology (regular member)
2010-present AACR (full member)
Referee/Reviewer for Journals
2004 Current Biology
2006 Experimental Gerontology
The EMBO Journal
2007 Molecular and Cellular Biology
Cell Research
General and Comparative Endocrinology
The EMBO Journal
2008 American Journal of Physiology
Awards and Honors
2011 Sales support activity award (QIAGEN)
2011 Internal customer project support award (QIAGEN)
2007-2008 Concept grant award
(Department of Defense Tuberous Sclerosis Complex Research Program, Office
of the Congressionally Directed Medical Research Programs)
2004-2005 Postdoctoral Fellowship Award (MGH Fund for Medical Discovery)
2003 Sigma Xi (Harvard University)
2003 “Poster of Distinction” Award (The MGH XXVII Research Symposium)
1994-1998, 2000-2001 Tuition Scholarship (Brandeis University)
1998-2000 Graduate School of Arts and Sciences Scholarship (Brandeis University)
1995-1996 Fellowship (Afermow Fund)
1994-1995, 1996-1997 Fellowship (Brandeis University)
1994-1995 University Fellowship
(Northwestern University, Evanston, IL) (gratefully declined)
1994-1995 Presidential Fellowship
(SUNY-Buffalo Roswell Park Cancer Institute) (gratefully declined)
1990 Third Prize for Academic Excellence
(University of Science & Technology of China)
Bibliography
Articles
1. Samuel Long, Quan Peng, John Dicarlo, Yexun Wang and Eric Lader (2013) Multicopy reference
assay (MRef)-a superior normalizer of sample input in DNA copy number analysis. QIAGEN
white paper
2. Sally Yousif, Kara Pascarelli, Quan Peng, Ying Zhang, LesleyAnn Hawthorne, Dominique
Broccoli and Samuel Long Microarray data verification and rapid screening for copy number
alterations in cancer samples using qBiomarker Copy Number PCR Arrays, QIAGEN News 2012
3. Samuel Long, Min You, Liang Wang, and Yexun Wang (2012) Rapid and accurate cancer
somatic mutation profiling with qBiomarker somatic mutation PCR arrays, QIAGEN white paper
4. Samuel Long, Min You, Liang Wang, and Yexun Wang (2011) qBiomarker Somatic Mutation
PCR Arrays: A novel tool for pathway- and disease-focused cancer mutation profiling, QIAGEN
News 2011 e18
5. McNally B, Long X, Slepushkina N, Tian S (2010) Linking molecular mechanisms to biomarkers,
identifying pathways regulating cellular responses to a chemotherapy drug. Pathways, 11: 12-13
6. Avruch J, Long, X, Lin Y, Ortiz-Vega S, Rapley J, Oshiro N (2010) Regulation of TOR Complex
1 by amino acids through small GTPases. The Enzymes. Vol. XXVII (Elsevier Inc.) In press.
7. Avruch J, Long, X, Lin Y, Ortiz-Vega S, Rapley J, Papageorgiou A, Oshiro N, Kikkawa U.
(2009) Activation of mTORC1 in two steps: Rheb-GTP activation of catalytic function and
increased binding of substrates to raptor. Biochem Soc Trans. 37:223-6
8. Avruch J, Long, X, Ortiz-Vega S, Rapley J, Papageorgiou A, Dai N. (2009) Amino Acid
Regulation of TOR Complex 1. Am J Physiol Endocrinol Metab. 296:E592-602
9. Long, X., Lin, Y., Ortiz-Vega, S., Busch, S. and Avruch, J. (2007) The Rheb switch 2 segment is
critical for signaling to TOR Complex 1. J. Biol. Chem. 282, 18542-51
10. Long, X. (2007) TOR (Target of rapamycin). In Lipid Signaling Target Assessment M. Wymann,
A. Pemberton, ed. (Current Biodata Ltd)
11. Long, X., Ortiz-Vega, S., Lin, Y. and Avruch, J. (2005) Rheb binding to mammalian target of
rapamycin (mTOR) is regulated by amino acid sufficiency. J. Biol. Chem. 280, 234**-*****
12. Avruch, J., Hara, K., Lin, Y., Liu, M., Long, X., Ortiz-Vega, S. Yonezawa, K. (2006) Insulin and
amino acid regulation of mTOR signaling and kinase activity through the Rheb GTPase.
Oncogene 25, 6361-6372
13. Long, X., Lin, Y., Ortiz-Vegas, S., Yonezawa, K. and Avruch, J. (2005) Rheb binds and regulates
the mTOR kinase. Curr. Biol. 15, 702-713
14. Avruch, J., Lin, Y., Long, X., Murthy, S. and Ortiz-Vega, S. (2005) Recent advances in the
regulation of the TOR pathway by Insulin and Nutrients. Current Opinion in Clinical Nutrition
and Metabolic Care 8, 67-72
15. Long, X., Müller, F., and Avruch, J. (2004) TOR action in mammalian cells and in C. elegans. In
TOR: Target of Rapamycin (Curr Top Microbiol Immunol) M. Hall, D. Sabatini, G. Thomas, ed.
(Berlin-Heidelberg: Springer Verlag) 115-138
16. Long, X., Spycher, C., Han, Z.S., Rose, A.M., Müller, F. and Avruch, J. (2002) TOR Deficiency
in C. elegans Causes Developmental Arrest and Intestinal Atrophy by Inhibition of mRNA
Translation. Curr. Biol. 12, 1448-1461
17. Hara, K., Maruki, Y., Long, X., Yoshino, K., Oshiro, N., Hidayat, S., Tokunaga, C., Avruch, J.
and Yonezawa, K. (2002) Raptor, a Binding Partner of Target of Rapamycin (TOR), Mediates
TOR Action. Cell 110, 177-189
18. Long, X. and Griffith, L. (2000) Identification and Characterization of a SUMO-1 Conjugation
System That Modifies Neuronal CaMKII in Drosophila melanogaster. J. Biol. Chem. 275, 40765-
40776
Conference presentations
1. Evaluation of cancer-related mutations in tumorgraft models. Mariana Brait1, Luciane T.
Kagohara1, Evgeny Izumchenko1, Samuel Long2, Tin Khor3, Elizabeth Bruckheimer3, and David
Sidransky1. AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA
2. Sensitive somatic mutation detection in cell-free circulating DNA with qBiomarker somatic
mutation PCR array coupled with preamplification. (2014)Samuel Long and Eric Lader. 2014
ICCG annual conference, Bethesda, MD
3. Multicopy reference assay (MRef) a superior normalization tool for DNA copy
number analysis. Brian McNally, Samuel Long, Quan Peng, John DiCarlo, Yexun Wang, Eric
Lader. EACR summer conference: cancer genomics Jun 25-28, 2013, Churchill college,
Cambridge, UK
4. Long, S, Peng, Q, DiCarlo, J, Wang Y, Lader, E (2013) Multicopy reference assay(MRef)- a
superior normalizer of sample input in DNA copy number analysis . (Seattle Genomic Instability
and Cancer Symposium)
5. Samuel Long2, Kara Pascarelli, Ying Zhang2, Quan Peng2, Sally Yousif2, LesleyAnn Hawthorne3,
Margaret von Mehren4, Dina Lev 5 and Dominique Broccoli1 Real-Time PCR Arrays Used for
Cytogenomic Microarray Verification and Rapid Screening of Genomic Variations (2012)
International Standards for Cytogemomic Arrays (ISCA) conference, May, 2012
6. Samuel Long1, Sally Yousif1, Kara Pascarelli2, Ying Zhang1, Quan Peng1, Lesleyann
Hawthorn3, Dominique Broccoli2 and Eric Lader1. qBiomarker Copy Number PCR Arrays for
Copy Number Alteration Analysis in Cancer Samples 2012 CHI ADAPT conference, Washington
DC September 2012
7. Samuel Long1, Sally Yousif1, Lili Yang2, Daniel Groelz1, Karen Rodland1, Sunita Badola2 and
Eric Lader1 DNA quality measurement and somatic mutation profiling in PAXgene tissue
samples. 2012 CHI ADAPT conference, Washington DC September 2012
8. Bruce J, Long S, Sholl L, Multiplex PCR used for copy number alteration analysis in lung cancer
samples (2012), AMP annual conference 2012
9. Kara Pascarelli1, Samuel Long2, Ying Zhang2, Quan Peng2, Sally Yousif2, LesleyAnn Hawthorne3,
Margaret von Mehren4, Dina Lev 5 and Dominique Broccoli1 Real-Time PCR Arrays Used for
Cytogenomic Microarray Verification and Rapid Screening of Genomic Variations in liposarcoma
samples (2012) connective Tissue Society Meeting, November 2012
10. Long, S, You M, Wang J, Wang L, Wang Y, Rapid cancer somatic mutation profiling using
qBiomarker mutation PCR arrays. Epigenetics of Cancer and Stem Cells Symposium, Ontario
Cancer Institute (OCI). February 27-28, 2012 in Toronto, Canada
11. Long, S, You M, Wang J, Wang L, Wang Y, Rapid and accurate somatic mutation profiling using
qBiomarker somatic mutation PCR arrays. AACR 101 annual meeting, April 2011, Orlando,
Florida
12. Long, S, You M, Wang J, Wang L, Wang Y, Cancer somatic mutation profiling using qBiomarker
somatic mutation PCR arrays. CHI TriMed meeting, 2011, San Francisco, CA
13. Long, S, You M, Wang J, Wang L, Wang Y, Cancer somatic mutation profiling using qBiomarker
somatic mutation PCR arrays. Genentech Science Celebration Day, 2010, San Francisco, CA
14. Long, X., Lin, Y., Ortiz-Vega, S., Busch, S., Yin, Y. and Avruch, J. (2006) Regulation of mTOR
kinase by the small GTPase Rheb. (The MGH Research Career Development (ORCD) Poster Day,
Boston)
15. Long, X., Lin, Y., Liu, M., Ortiz-Vega, S., Yonezawa, K and Avruch, J. (2006) Insulin and Amino
Acid Regulation of mTOR Signaling and Kinase Activity through the Rheb GTPase. (The
Nutrient Sensing, Insulin Signaling, and Hamartoma Syndromes Meeting, NIH, NIDDK and NCI,
Bethesda, Maryland)
16. Long, X., Lin, Y., Ortiz-Vega, S., Liu, M. and Avruch, J. (2006) Rheb regulation of TOR
signaling. (The LAM Foundation Lymphangioleiomyomatosis International Research Conference,
Cincinnati, Ohio)
17. Long, X., Lin, Y., Oriz-Vega, S., Yonezawa, K., and Avruch, J. (2004) Insulin and nutrient
regulation of the TOR pathway. (Amino-Acid/Protein Metabolism in Health and Disease
International Congress, Milan, Italy)
18. Long, X., Han, Z.S., Spycher, C., Hara, K., Rose, A.M., Yonezawa, Y., Müller, F. and Avruch, J.
(2003) TOR- and raptor-deficiency in C. elegans causes larval arrest and severe intestinal atrophy.
(The MGH XXVII Research Symposium, Boston)
Professional References Available upon request
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