Nathan Siemers
Nathan Siemers
171 East Delaware Avenue
Pennington, NJ 08534
609 731 8472 (cell)
noscv @fiveprime.org
Nathan Siemers
Functional
Director of Research, Pharmaceutical Genomics. Manager of senior scientific staff,
Profile
internal division collaborations, external alliances, and interactions with regulatory
agencies. Architect of high performance computing hardware and software
infrastructure for modern pharmaceutical research.
Experience
17 years experience in Pharma and Biotech.
and Strengths Hands on experience in: Organic Chemistry; Molecular Biology; Biochemistry; Medical
Diagnostics; Genomics; Bioinformatics
26 years experience in the use, development, and administration of Informatics and High
Performance Computing tools.
Effective at attracting and retaining valuable Scientific staff.
Extensive background in the effective application of Genomic techniques and Scientific
Computing to all stages of Pharmaceutical R&D, from Exploratory Discovery to Phase IV
Development support of product labeling and new product indications.
Experience
2004 - Present
Bristol-Myers Squibb
Hopewell, New Jersey
Director R&D, Applied Genomics
§ Manage Bioinformatics and Protein Analytical Science (Proteomics) department s
responsible for support of Genomics ac tivities across the corporation.
§ Coordinate all aspects of Genomics support for Metabolic Disease and Cardiovascular
Disease areas.
§ Areas of direct development and support:
§ Profiling Technologies (RNA, Protein, Metabolite) for compound and drug target
validation.
§ Toxicogenomics
§ Proteomics
§ High Content Screening
§ RNAi
§ Human Genetics/Pharmacogenetics
§ Biomarker identification and validation
§ Therapeutic Area Biology Support
§ Sequence databases, analysis and mining
§ Systems Biology and Chemistry/Biology data integration
§ Model Systems Biology
§ Enterprise-wide Knowledge Management and Knowledge Bases
§ Identify, establish, and manage diverse Alliances in the areas of Target and Compound
Validation
§ Laboratory workflow support for all areas of Genomics
§ Control software and hardware budgets for Corporate-wide Genomics IT infrastructure,
vendor selection and negotiation.
§ Effective coordination of Bioinformatics activities with Corporate Informatics.
§ Communication of strategic needs and initiatives to R&D Leadership.
§ Training and education of Research and Development staff in the use of Genomic
tools.
2000 - 2004
Bristol-Myers Squibb
Hopewell, New Jersey
Associate Director, Applied Genomics
1998-2000
Bristol-Myers Squibb
Hopewell, New Jersey
Group Leader, Applied Genomics
1997-1998
Whitehead Institute
Cambridge, Mass.
Visiting Scientist, Functional Genomics (Eric Lander)
§ Early validation and analysis of Affymetrix transcriptional profiling device and software
technology
1996-1997
Bristol-Myers Squibb
Princeton, New Jersey
Research Investigator, Bioinformatics
§ Gene discovery: ion channels, G-protein coupled receptors, TNF receptor family
members.
§ Methods development for mining of genomic data.
§ System administration for Linux, SGI desktop, and SGI Origin supercomputers.
§ Staffing and management of BMS Core Sequencing Facility
1993-1996
Bristol-Myers Squibb
Seattle, Washington
Postdoctoral Fellow, Oncology Drug Discovery
§ Phage library construction and biochemical optimization of E. cloacae beta-lactamase
activity toward chemotherapeutic prodrugs for use in Antibody-Directed Enzyme-
Prodrug Therapy (ADEPT).
§ Design, construction, and expression (including process development) of L49-sfv-bL,
an antitumor antibody-bL fusion for use in chemotherapy. L49 antibody and sfv Fusion
protein now licensed to Genencor/Seattle Genetics.
1988-1993
Cornell University
Ithaca, New York
Research Assistant, Department of Chemistry
§ Organic Synthesis: Completed total syntheses of sesquiterpene pheromones
Periplanones C and D. Advisor: John McMurry
§ Computational Chemistry: Molecular Mechanics analyses of macrocycles and ring
closure stereochemistry in the low-valent titanium induced coupling of carbonyls.
1985-1988
Crystal Diagnostics
Woburn, Mass.
Research Scientist
§ Explored crystal nucleation as a detection method for chemical and enzymatic
diagnostic assays, including applications in Therapeutic Drug Monitoring, Cholesterol
testing, and Occupational Exposure.
1982-1983 Massachusetts Institute of Technology Cambridge, MA
Undergraduate Research
§ Elucidation of selective inhibitory activity of the bioflavinoid quercetin toward
isoenzymes of cytochromes P-450 (Michael Marletta, advisor)
Education
Cornell University, Ithaca, New York: PhD in Chemistry, 1993
Massachusetts Institute of Technology, Cambridge, Massachusetts:
B.S. in Chemistry 1985
Whitman College, Walla Walla, Washington.
Public Schools of Texas, Illinois, and Oregon
Awards
Campbell Scholar, Whitman College, 1982
Mattin Research Fellow, Cornell University, 1990, 1992
United States Department of Education Fellow, 1991
John James Blackmore Prize, Cornell University, 1992
President’s Award, Pravastatin Research, Bristol-Myers Squibb, 1998
Applied Biotechnology Collaboration Award, Bristol-Myers Squibb, 2003
Triumph Award, Target Validation and Due Diligence via In-depth Bioinformatics,
Bristol-Myers Squibb, 2003
Triumph Award, Metabonomics in Toxicology, 2005
Associations Member of the New York Academy of Sciences.
Manuscript review for the journals Bioconjugate Chemistry and Bioinformatics.
Grant reviewer for the Canadian Network Centres of Excellence Program.
Panel Member, National Science Foundation.
Grant reviewer, National Genome Research Network (NGFN), Germany
Interests
Music Performance (currently cellist in Westminster Conservatory Community
Orchestra, Princeton, NJ), Photography.
Publications
Duygu Ucar, Isaac Neuhaus, Petra Ross-MacDonald, Charles Tilford, Srinivasan
Parthasarathy, Nathan Siemers, Rui-Ru Ji: Construction of a reference gene
association network from multiple profiling data: application to data analysis.
Bioinformatics 23(20): 2716-2724 (2007)
Huttenhower, C., Flamholz, A., Landis, J., Sahi, S., Myers, C., Hibbs, M.,
Siemers, N., Troyanskaya, O. and Coller, H.A. (2007) Nearest Neighbor Networks:
Clustering expression data based on gene neighborhoods. BMC Bioinformatics. 2007
Jul 12; 8:250.
Constantine KL, Krystek SR, Healy MD, Doyle ML, Siemers NO, Thanassi J, Yan N,
Xie D, Goldfarb V, Yanchunas J, Tao L, Dougherty BA, Farmer BT 2nd. (2005)
Structural and functional characterization of CFE88: evidence that a conserved and
essential bacterial protein is a methyltransferase. Protein science: a publication of the
Protein Society 14 (6), 1472-84.
Vivekananda M. Vrudhula, David E. Kerr, Nathan O. Siemers, Gene M. Dubowchik
and Peter D. Senter (2003) Cephalosporin prodrugs of paclitaxel for immunologically
specific activation by L-49-sFv-beta-Lactamase fusion protein.
Bioorg Med Chem Lett, 13, 539.
David E. Kerr, Vivekananda M. Vrudhula, Hakan P. Svennson, Nathan O. Siemers,
and Peter D. Senter (1999) Comparison of recombinant and synthetically formed
monoclonal antibody-beta-lactamase conjugates for anticancer prodrug activation.
Bioconjugate Chemistry 10, 1084.
Trachette L. Jackson, Sharon R. Lubkin, Nathan O. Siemers, David E. Kerr, Peter D.
Senter, and James D. Murray (1999) Mathematical and Experimental Analysis of the
Localization Characteristics of Anti-Tumor Antibody-Enzyme Conjugates. British
Journal of Medicine. 80, 1747.
David E. Kerr, Nathan O. Siemers, Peter D. Senter, and Vivekananda M. Vrudhula
(1998) Development and Activities of a New Melphalan Prodrug Designed for Tumor-
Selective Activation. Bioconjugate Chemistry 9, 255.
Nathan O. Siemers and Peter D. Senter (1998) The Activation of Anticancer
Prodrugs by Monoclonal Antibody-Enzyme Conjugates. Antibodies in Diagnosis and
Therapy: Technologies, Mechanisms and Clinical Data. S. Matzku and R.A. Stahel,
Ed. Taylor & Francis.
Nathan O. Siemers, Susan Yarnold, Mark Stebbins, David E. Kerr, Vivekananda M.
Vrudhula, Ingegerd Hellström, Karl Erik Hellström, and Peter D. Senter (1997)
Construction, Expression, and Activities of L49-sFv-ß-Lactamase, a Single-Chain
Antibody Fusion Protein for Anticancer Prodrug Activation. Bioconjugate Chemistry 8,
510.
Nathan O. Siemers, Dale E. Yelton, Jürgen Bajorath, and Peter D. Senter (1996)
Modifying the Specificity and Activity of the Enterobacter cloacae P99 ß-Lactamase
by Mutagenesis Within an M13 Phage Vector. Biochemistry 35, 2104.
John E. McMurry and Nathan O. Siemers (1994) Periplanone Total Synthesis via
Intramolecular Pinacol Coupling. Tetrahedron Letters 35, 4505.
Nathan O. Siemers (1993) The Development of a Molecular Mechanics Based
Model to Predict Diol Stereochemistry in Low Valent Titanium Mediated Pinacol
Coupling Reactions. Successful Application of this Model Toward the Synthesis of
Periplanones C, D, and A. Dissertation, Cornell University.
John E. McMurry and Nathan O. Siemers (1993) The Stereochemistry of the
Titanium Induced Intramolecular Pinacol Coupling Reaction. Tetrahedron Letters 34,
7891.
Lee, Liana, M. ; Feder, John, N.; Siemers, Nathan, O.; Wu, Shujian; Chen, Jian
Published
(2004) Novel human cell surface protein with immunoglobulin folds, BGS-19
Patents
(US20040025195, WO2003083078).
Lee, Liana, M. ; Feder, John, N.; Siemers, Nathan, O.; Wu, Shujian (2003)
Polynucleotides encoding novel two splice variants of a human cell surface protein
with immunoglobulin folds, BGS5G and BGS5I (WO2003083076).
Feder, John, N. ; Lee, Liana, M.; Chen, Jian; Jackson, Donald; Ramanathan,
Chandra, S.; Siemers, Nathan, O.; Chang, Han (2003) Polynucleotide encoding a
novel human potassium channel beta- subunit, K+ Mbeta1 (US20030181711,
WO200248369).
Feder, John N. ; Lee, Liana; Chen, Jian; Jackson, Donald; Ramanathan, Chandra S.;
Siemers, Nathan O.; Chang, Han; Ryseck, Rolf-Peter; Watson, Andrew J.; Carroll,
Pamela (2003) Polynucleotide encoding a novel human potassium channel beta-
subunit, K+ betaM3 (US20030114371, WO2002068587).
Feder, John N. ; Lee, Liana; Chen, Jian; Jackson, Donald; Ramanathan, Chandra S.;
Siemers, Nathan O.; Chang, Han; Duclos, Franck; Krystek, Stanley R. (2003)
Polynucleotide encoding a novel potassium channel with homology to the ether-a-go-
go family, HEAG2 (US20030114354).
Feder, John N. ; Lee, Liana M.; Chen, Jian; Jackson, Donald; Ramanathan, Chandra;
Siemers, Nathan; Chang, Han (2003) Polynucleotide encoding a novel human
potassium channel alpha-subunit, K+ alphaM1, and variants thereof
(US20030059923, WO2002064732).
Feder, John N. ; Lee, Liana; Chen, Jian; Jackson, Donald; Ramanathan, Chandra S.;
Siemers, Nathan O.; Chang, Han; Carroll, Pamela (2003) Polynucleotide encoding
two novel human potassium channel beta-subunits, K+betaM4 and K+betaM5
(US20030054989, WO2002068604).
Feder, John N. ; Lee, Liana; Chen, Jian; Jackson, Donald; Ramanathan, Chandra S.;
Siemers, Nathan O.; Chang, Han (2003) Polynucleotide encoding a novel human
potassium channel beta-subunit, K+ betaM6, expressed highly in the small intestine
(US20030036115, WO2002070727).
Chang, Han ; Chen, Jian; Feder, John; Jackson, Donald; Lee, Liana; Ramanathan,
Chandra S.; Siemers, Nathan O.; Carroll, Pamela (2003) Polynucleotide encoding a
novel human potassium channel beta-subunit, K+ betaM2 (US20030032786,
WO2002066601).
Feder, John N. ; Lee, Liana; Chen, Jian; Jackson, Donald; Ramanathan, Chandra S.;
Siemers, Nathan O.; Chang, Han (2003) Polynucleotides encoding a novel glycine
receptor alpha subunit expressed in the gastrointestinal tract, HGRA4, and splice
variant thereof (US20030032608, WO2002066606).
Jackson, Donald, G. ; Feder, John; Nelson, Thomas; Mintier, Gabe; Ramanathan,
Chandra; Lee, Liana; Siemers, Nathan; Bol, David; Schieven, Gary; Finger, Joshua;
Todderud, C, Gordon.; Bassolino, Donna; Krystek, Stanley; Mcatee, Patrick;
Suchard, Susan; Bana (2002) POLYNUCLEOTIDES ENCODING NOVEL HUMAN
PHOSPHATASES (WO2002057460).
Siemers, Nathan O.; Yarnold, Susan; Senter, Peter D. (2000) Recombinant antibody-
enzyme fusion proteins (US6132722, EP0986576).
Bowen, Michael, A. ; Siemers, Nathan (2000) TUMOR NECROSIS FACTOR
RECEPTOR HOMOLOGUE-1 ("TRH1") (WO0034294).
Koocher, Martin ; Siemers, Nathan O. (1989) Method and Apparatus for Detecting
an Analyte of Interest Capable of Being converted Into a Carbonyl Containing
Composition (US4816414).
Public
Oracle Table Browser: advanced relational database browsing and mining tool.
Software
http://otb.sourceforge.net (John Hinsdale)
Releases
Xpress-Analyzer: analytical and statistical tools, including Analysis of Variance,
(myself and my Principal Components Analysis , General Linear Models.
group)
http://sourceforge.net/projects/xpress-analyzer (Isaac Neuhaus)
Flickr Hive Mind: data mining of the Flickr (http://flickr.com) database of
photography. An exercise in the use of modern Web APIs and Web Services.
http://www.fiveprime.org/flickr_hvmnd.cgi (Nathan Siemers)
Invited
Biopharmaceutical Statistics Workshop, Muncie, Indiana (2000). “Escape from
Presentations
Noise: Pre-Processing Transcriptional Profiling Data”.
1st Ontario Microarray Network Technology Symposium (2000). Invited Speaker:
“Know Thy Neighbor – An Exploration of KNN Techniques”.
