Sage Arbor

Computational Biochemist

**** ******* **.

Carmel, IN

864-***-****

adh3n2@r.postjobfree.com

PROFILE / SUMMARY v3.03

I have worked in most aspects of pharmaceutical and genomics development including: computational drug design, organic synthesis, pathway mapping, ADME analysis, 6σ improvement, management of analysts and globally distributed labs. Having worked in academia and multiple companies (e.g. Pfizer & Dupont), I have completed projects that increased the quality of deliverables despite competing demands, fixed time and costs. I am results-oriented, clarifying the assays & functionality needed for a project, while data-mining terabytes to increase the transparency of information and efficacy of solutions.

EDUCATION

Washington University, Ph.D Biochem/Computational Biology, 2001 - 2008, St. Louis, MO

Duke University, B.S. in Chemistry, B.S. in Biology, 1996 - 2000, Durham, NC SKILLS

Management Computational / Coding Lab Education

Six sigma (6σ) Python, C++,

Pandas, Jupyter

Spotfire,

Julia, Evince,

Protein

expression

Clinical &

biochem integration

Critical path analysis UNIX,

sed/awk

Protein

folding, docking

Peptide chemistry Interactive

content delivery

Scrum/waterfall

global management

DBs: SQL,

noSQL

Android,

ios, HTML

LCMS Curricular

design/mapping

Institution Tech transfer : liaising,

reports, presentations,

educator

Scientist : datamining, EMR,

coding, bench science

Management :

teams 10+

Dupont / Pioneer

Eurofins Scientific

Marian Univ. COM

Pfizer

Washington Univ. COM

National Academies

EXPERIENCE

Marian University - Assistant Professor of Biochemistry January 2013 - PRESENT Indianapolis, IN - 3200 Cold Spring Rd. Indianapolis, IN 46222

Research interests: health outcomes database development (normalization of all of PubMed for patient and physician retrieval and ranking), social fitness app development, triggers and datamining on Electronic Medical Records, probiotic and microbiome rxn and sequencing, Alzheimer's amyloid binding therapeutics, HIV drugs made by bread, engineered nanocomputers in a cell, public policy.

Course Director of Scientific Foundations, Reproduction, Pediatrics, Gerontology, and Psychiatry. Dupont & Pioneer - Manager & Senior Research Associate April 2010 - December 2012 Des Moines, IA - 7000 NW 62nd Avenue Johnston, IA 50131

Manager of computational biology group (10+) to develop databases, tools, web, and LIMS for the 8 largest scientific genotype labs worldwide (led 50+ globally in labs - Plan, Code, & manage team).

Manage “big” genomic data (terabytes) and application development to analyze SNP marker data. Use of various computational tools towards this end such as Spotfire, SQL, Uniflow, javascript.

Review project portfolio and re-evaluate project priorities

Examine production processes and workflows to identify deficiencies and bottlenecks

Training: Six Sigma (6σ), Project Management, Parallel Thinking Eurofins Scientific - Technical Manager & Scientist February 2009 - April 2010 Des Moines, IA - 2200 Rittenhouse St #175, Des Moines, IA 50321

Managed 10 chemists and microbiologists (analysts for vitamin testing of fat soluble, water soluble, and micro vitamins).

Roadmap development to improve speed, quality, financial bottom line, and deliver ISO certification.

Method development and validation of various tests for food, feed, and supplements. This includes work with microbiology, extraction, saponification, purification, HPLCs, UPLCs, MSMS, fluorometer, and robotics.

Pfizer - Computational Biologist III

June 2008 - December 2008 St. Louis, MO - 700 Chesterfield Pkwy W, St. Louis, MO 63198

Use of many computational tools such as Pathway Studio (Ariadne), Ingenuity, and Bibliosphere

(Genomatix) for pathway mapping, Evince for Principal Components Analysis, and Spotfire for analysis and presentation.

Developed a refined systems biology model of inflammation pathways in an effort to increase the success rate of compounds put into clinical trials.

Collaboration with every level of R&D process (i.e. technicians, scientists, group leaders, administrators) to refine current and define future R&D efforts.

Affymetrix and Agilent genome chip analysis for multiple projects. Analyzing all historical Pfizer mouse genome data across all time, comparing pathway analysis to explain confusing of ongoing clinical trial data.

In house file conversions/programming.

National Academies of Sciences - Science & Technology in Public Policy Fellow January 2008 - June 2008 Washington, D.C.- 2101 Constitution Ave NW, Washington, DC 20418

Researched and helped draft a report with guidelines for the publishing, sharing, and storage of digital research data.

Helped design and organize a National Academies symposium on international renewable energies. Wrote executive summary with symposium questions.

Researched and fact-checked Op-Ed reviewing US competitiveness in education and research funding for Norm Augustine (Chair for the Rising Above the Gathering Storm Committee and Report). Washington University - Biochemistry Graduate Student September 2001 - Mary 2008 St. Louis, MO

Design and synthesize rigidified cyclic peptides that mimic the Cα-Cβ vectors of β-turns found in the protein data bank (PDB). These compounds were classified generically to enable substitution of any 4 amino acid sequence for each β-turn type.

Computationally probe the energy landscape of cyclic tetrapeptides using conformational searches and density functional theory (Macromodel, Sybyl, and Gaussian software).

Synthesize cyclic peptides by Solid Phase Peptide Synthesis and purify by HPLC.

Validate stability of low energy conformation by NOESY NMR in CHCL3 and H2O.

Computationally screen low energy and NMR conformers for overlaps with Cα-Cβ vectors of β-turns found in the PDB to develop a library of β-turn mimics which mimicked over half of the reverse turns in the PDB.

Veritas Labs - Scientist

July 2000 - July 2001 Rockville, MD

R&D on SNP recognition and purification of biotinylated primers.

Various outsourcing projects: first NIH human genome sequencing, vector swapping, point mutation/deletion, preparation of bacteriophage libraries, primer synthesis. Stanford Biochemistry Lab - Lab Technician

June 1999 - August 1999 Palo Alto, CA

Purify proteins using affinity, gel, and substrate column chromatography.

Motility assays constructed around the Listeria M. bacterium movement in cytoplasm. Tested polymerization & force generated in movement of beads coated with protein ActA in extracts. National Institute of Standards and Technology (NIST) - Assistant Scientist Summers 1995 - 1998 Gaithersburg, MD

Enhanced atomic imaging using a Ultra High Vacuum Scanning Tunneling Microscope (UHV STM) by refining atomically sharp tips and streamlining imaging processes.

Used STM, FIM, and SEM hardware; Matlab & Mathematica software. Duke University - Assistant Chemist

1998 - 1999 Durham, NC

Designing improvements in signal to noise ratio of fluorescently labeled DNA. AWARDS

Association of Biochemistry Educators (ABE) - President Elect 2019

Association of Biochemistry Educators (ABE) Certificate of Appreciation - Leading national effort to build a med school secure testbank of questions (2017)

Sole Indiana Policy Ambassador for American Society for Biochemistry and Molecular Biology

(ASBMB), 2018 - present.

American Society for Biochemistry and Molecular Biology (ASBMB) Advocacy Training Program

(ATP) inaugural fellow, 2018.

Editor of Neural Regeneration Research

Faculty of 1000 Biology: for Arbor S et al Biopolymers 2008 90 (3) :384-93 http://www.f1000biology.com/article/id/1108327/evaluation

National Academies Science and Policy Fellowship (2008)

Young Scientist Program Mentor Award Recipient (2007)

NIH National Graduate Student Research Festival, funded participant

Computational Biology Training Grant (2003-2005)

Siteman Cancer Center Research Pathway Grant (2002-2004)

Microscopy Society of America Undergraduate Scholarship (1998) SELECT PRESENTATIONS

09/19/2019 - Becoming a Scientist. Invited speaker - Career Day, Pike HS Indianapolis, IN. Slidedeck at http://bit.ly/2lb3YKW.

05/15/2019 - Increasing Quality Adjusted Life Years (QALYs). Invited speaker - American Medical Student Association (AMSA). Slidedeck at http://bit.ly/2Dtxn8U .

05/09/2019 - Shared Medical School Lectures via Google Slides. ABE 2019 Conference. Slidedeck at http://bit.ly/2DFdThJ.

05/07/2019 - ABE Question Bank Review - a Workshop. ABE 2019 Conference.

11/30/2018 - Medical Marijuana CBD in Indiana. 37th Annual Winter Update Indiana Osteopathic Association. Invited speaker - Slidedeck.

6/6/2018 - “Medical student knowledge of religious bioethics & Trainability via a novel ethics grid”. Association of Fransciscan Colleges and Universities Symposium (AFCU) 2018 Slidedeck at http://bit.ly/2FV7Ch8.

6/4/2018 - “Federal vs State medical law – Funding, Incentives, & Enforcement”. American Medical Student Association (AMSA). Invited speaker. Slidedeck, Video.

5/11/2017 - “Mapping Curriculum across Disciplines and Time – Easy Generic ad hoc Databases”. Invited speaker at the 2017 biannual conference for the Association of Biochemistry Course Directors.

5/9/2017 - “Working to Create a Secure Biochemistry Question Bank: Student Objectives and Competencies in Biochemistry". Invited workshop speaker at the 2017 biannual conference for the Association of Biochemistry Course Directors.

5/8/2017 - "Using Competency-Based Assessments to Monitor and Coach Pre-Clerkship Medical Students". Invited panel member at the 2017 biannual conference for the Association of Biochemistry Course Directors.

4/5/2017 – “Medical Marijuana Use in Indiana - Navigating the Hazy Scientific, Legal, and Ethical Terrain”. Invited panel member to Airbanks Center For Medical Ethics Continuing Education Panel.

10/5/2016 – Personalized Medicine Roundtable. Invited speaker hosted by the American Cancer Society Cancer Action Network. Slidedeck at https://bit.ly/302CbgV.

5/11/2016 - Fostering Student Learning with Interactive Lectures and Polling. Invited speaker at Marian University Tech Summit 2016.

9/19/2015 – The Future of Epigenetics - Patient Power vs. BIG Pharma. Invited speaker for annual Pre-SOMA conference. Students of Osteopathic Medical Association.

6/2/2014 - American Chemical Society (ACS) - Invited speaker at a regional event held at Eli Lilly –

“Split inteins as invivo therapeutics”.

SELECT PUBLICATIONS

Sage Arbor*, Namita Biala, Scott Breeden. Bioethics versus World Religions Grid Resource and Online Quiz. MedEdPublish www.mededpublish.org 2019, submitted. SocArXiv. osf.io/preprints/socarxiv/8vh56.BiorXriv

Arbor, Sage*, Binstock J, Panini S, Rashid H, Ercikan Abali E. Development and Validation of a Shared Secure Biochemistry Test Bank for Medical, Dental, and Pharmacy Schools. MedSciEduc. 2020 Feb 3. doi:10.1007/s40670-020-00919-y.

Joe Bondi, Sage Arbor* (2019). The trend, frequency, and use of scientific sources in the United States Congress. Journal of Science Policy & Governance. Submitted. SocArXiv. August 6. doi:10.31235/osf.io/gb9w2.

Cumbay, M., LaFontaine, M., and Arbor, S. (2019). Mechanistic Insights into Neurodegenerative Diseases: The Potential for the Development of Novel Therapeutics. In Pathology, Prevention and Therapeutics of Neurodegenerative Disease, S. Singh, and N. Joshi, eds., pp. 225–240. doi:10.1007/978-***-**-****-1_20

Arbor, S. (2018). Where and How in the mTOR Pathway Inhibitors Fight Aging: Rapamycin, Resveratrol, and Metformin. Resveratrol - Adding Life to Years, Not Adding Years to Life. doi:10.5772/intechopen.79338

Brooks, S., Biala, N., and Arbor, S. (2018). A searchable database of medical education objectives - creating a comparable gold standard. BMC Med Educ 18, 31.Pdf.

Arbor, Sage. (2017)“Personalized Medicinal Complexity Beyond Single Clinical Trials: Gene Therapy, Pharmaceuticals Combinations, and Modular Biological Nanomachine Frameworks.” JBCS, 2018, 1: 24–27. doi:10.29199/JCAR-101015

Arbor, S. (2017). Targeting amyloid precursor protein shuttling and processing - long before amyloid beta formation. Neural Regen Res 2017 12, 207–209.

Arbor, S.C. *, LaFontaine, M., and Cumbay, M. (2016). Amyloid-beta Alzheimer targets — protein processing, lipid rafts, and amyloid-beta pores. Yale J Biol Med 89, 5–21.

Linda Berg-Cross, Sage Arbor. How the Internet is Changing the Business of Science: a Review of Science and the Internet: Communicating Knowledge in a Digital Age by Alan G. Gross and Jonathan Buehl. Psychcritiques August 15, 2016, Vol. 61, No. 33, Article 5

National Academy of Sciences (US), National Academy of Engineering (US) and Institute of Medicine (US) Committee on Ensuring the Utility and Integrity of Research Data in a Digital Age. Ensuring the Integrity, Accessibility, and Stewardship of Research Data in the Digital Age. Washington

(DC): National Academies Press (US); 2009. Available from: http://www.ncbi.nlm.nih.gov/books/NBK215264/

Arbor, S.C.*, Marshall G.R. A virtual library of constrained cyclic tetrapeptide that mimics all four side-chain orientations for over half the reverse turns in the protein data bank. Journal of Computer Aided Molecular Design,, 23: pp. 87-95, 2009.

Arbor, S.C.*, Kao, J., Wu, Y., Marshall G.R. c[D-pro-Pro-D-pro- N-Methyl-Ala] adopts a rigid conformation that serves as a scaffold to mimic reverse-turn. Biopolymers (Peptide Science), 90(3): pp. 384-393, 2007.

Silver, R.M., Singer, A.E., Carroll, C.L., Berg-Cross, S. C. and Potzick, "Optical Overlay Metrology at NIST" in Proceedings of the KLA MicroLithography Seminar, 1996. SELECT POSTERS

Sage Arbor*, Renee J. Chosed, Mike LaFontaine. Shared Medical School Lectures via Google Slides. ABE 2019 Conference.

Joe Bondi, Sage Arbor*. 3D printing phone case orbs to bend light as a geospatial fitness incentive. Marian University Research day 2018.

Alex Card, Jack Ravotto, Dr. Colleen Doci and Dr. Sage Arbor*. Bacterial Expression of NpuDnaE Split Inteins. Marian University School of Arts and Sciences, Intro to Biomedical Sciences Project Summary April 2017.

Scott Hines, Namita Biala, Daniel Hutchinson, Jacob Suazo, Sade Akinkuotu, Sage Arbor*. Doing research separated by distance and time with blinded duplication: Building an Epigenetic Database. Research Day – Marian University, October 2016.

Scott K. Breeden, Alex Card, Sage Arbor*. Split Intein Orthogonality Predicted Computationally. American Chemical Society National Meeting, 2016, Philadelphia. INTERESTS

Ethics: Plato, Aristotle, Stoics

Economics: Copenhagen Consensus, openAI

Climate Change: renewable energies, carbon tax, clean coal, conservation/efficiencies

Wrestling: Division I Duke wrestling, High School coach, Mixed Martial Arts (MMA) SKILLS (detailed list)

Computational =structure prediction, molecular and cellular biology, organic chemistry, data mining, database and web creation, manager (10 scientists), process management (6σ), and public policy. Computer experience = Coding: Python, Pandas, C++,C#, UNIX, shell, sed/awk, powershell, Perl, NativeScript, Angular2, Android, iOS, javascript, Ruby. Analysis: Julia, Spotfire, Matlab, Evince. Bioinformatics: Pathway Studio, Macromodel, Bibliosphere, Gaussian, SPL (Sybyl Programming Language), Empower, ACTA, MetaMorph, Nanoscope III, LIMS. Database/Misc: mySQL, MSSQL, Oracle, Database Administrator (DBA), Relational Database Management Systems (RDBMS), NoSQL

(Firebase, Hadoop, HBase), SCRUM, waterfall, six sigma (6σ), HTML, CSS, PHP, Node.js, Excel, Word, Powerpoint, Adobe Photoshop, Gimp2.

Instrumentation experience =Nanopore sequencing, Aquity UPLC, Waters 3100 LC/MS, Finnigan LCQ Classic LC/MS, Cary 50-Bio UV/VIS spectrophotometer, Varian Inova-600 NMR, GeneVac Mega 1200, circular dichroism spectroscopy, Ultra High Vacuum Scanning Tunneling Microscopy (STM), air STM, Scanning Electron Microscopy (SEM).

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