Tony Frudakis

Data Scientist, Computational Biologist, Former Biotech Founder and Thought Leader- EXPERIENCE OVERVIEW  Data Scientist specializing in Computational Biology (biotech, pharma) and Financial Modeling / Time Series projection. o Highly accomplished Molecular/Cell and Computational Biologist with expertise in all areas of life sciences research and development. o Expertise with wide variety of data science packages (Python) incorporating AI/Machine Learning and original algorithm development for understanding single cell genomics and clinomics data from the perspective of high throughput drug screening, target characterization and patient chemosensitivity. o Particularly accomplished with use of AI and ML for the identification of drug or cellular subtype activated signal transduction and gene expression pathways, mechanisms of tissue-specific compound activity profiles, cellular subtype developmental ontologies, in-silico drug screening, defined media detailing for ex-vivo cultures, chemosensitivity, identification and curation of drug targets with both deeper Computational Biology or routine Bioinformatics; for example has extensive hands-on experience with relatively mundane tasks such as drug target informatics and characterization, having written a large number of original software programs for curating drug targets by scraping key information from publicly available databases (Pyuniprot, Ensembl, Pubmed, GO networks, etc.), but has also developed original algorithms for the identification of intersecting activated gene expression regulatory networks from single cell and bulk genomics data which have resulted in the discovery of previously unknown connections between cellular states and developmental processes. For more detail on life sciences computational biology please see my cover letter. o Built successful deep learning prediction models for use in algorithmic trading of forex pair– one of the few ensemble systems that actually generates consistent profit (even in the literature, this is rare. For more detail on my adventures in finance and market prediction please enquire.  Built and staffed the world’s first company to develop consumer products from raw human genome data in 1999 DNAPrint genomics. Founded in 1999, staffed with a dozen scientists, and managed for 10 years, during which time the company literally made history: o Developed, published and commercialized the world’s very first consumer genomics databases and products, which trailblazed today’s $1B/year Modern Genetic Ancestry Testing market (e.g. Ancestry.com, 23andMe, GEDmatch etc.). Were it not for our pioneering work in the early 2000s, many of these companies and databases wouldn’t exist today. o Developed, published and commercialized the world’s first human phenotyping products applied in Forensic Casework, which today represents the basic foundation for the phenotyping kits sold by Human Identity market leaders today (Verogen, Applied Biosystems et al.) o Received substantial media attention around the world including from the New York Times, US News and World Report, ABC Prime Time Live, CBS Evening News, Popular Science and two separate Forensic Files programs were devoted to cases we helped solve with our new technology (episodes “Tight Fitting Genes” and “Good as Gold”). o Forged new thought and opinion, as a thought leader, in the emerging field of genomics-based phenotyping and identification. I was voted “Most Influential in SNPs and Genotyping Category” by readers of Genome Technology Magazine.  Authored seminal books and manuscripts in fields of molecular biology, human genomics, pharmacogenet/genomics introducing this new science including a graduate-level textbook published by Academic Press/Elsiever, which today represents the primary reference introducing the fields of Deep (Biogeographical) Genomic Geneology and Forensic Phenotyping. o Contributor to numerous highly publicized and private (classified) forensic genetic/genomic investigations including serial killers both modern and historical (e.g. Jack the Ripper).  Fourteen years of experience as a Chief Executive Officer (CEO) for both private and publicly traded firms and five years experience as CSO. Each of these companies got their start with the development of innovative algorithms. o Raised over $40M from grants, and angel / venture capitalists.  Former Professor of Biological Sciences.  Extensive History as Technology Scout and Angel Investor, to date having investing over $2M in personal funds to date, and generating over $35M in profits for investors in my projects. o Technology Licensing Expertise, with Talent for IP Carve Out and Value Augmentation.  Won and managed accreditation for numerous ISO17025 laboratories. o Over 12 years of experience in GLP laboratory environments as founder, architect, Principal Investigator, manager and analyst. EDUCATION/TRAINING: - Ph.D. B.S. Magna Cum Laude Molecular and Cell Biology Biological Sciences University of California, Berkeley University of California, Irvine PROFESSIONAL EXPERIENCE: Data science and Bioinformatics Consulting October 2022 to Present http://www.glgpharma.com/about-us Leverage expertise with wide variety of data science packages (Python) incorporating AI/Machine Learning and original algorithm development for understanding time series and other structured datasets in life sciences R&D and equity markets research. Projects have contributed to ex vivo tissue growth, high throughput drug screening, drug target characterization, patient chemosensitivity and personalized medicine, forex market time series projections, machine-learning enabled stock picking and AgBio time series projections. One notable project used of AI and ML driven identification of ontological signal transduction and gene expression pathways for the creation of defined media enabling ex vivo tissue growth from pluripotent stem cells. Another identified the pathways involved in off-label effects of an approved compound, and another enabled accurate stock price performance and foreign exchange currency pair predictions resulting in profitable investments. CEO June 2021 to October 2022 Senior Scientist April 2018 – June 2021 http://www.glgpharma.com/about-us Executive VP / Director of Genomic Medicine Senior Scientist. Intellectual author for a novel ex-vivo chemosensitivity/drug development and precision oncology platform to personalize oncology therapy assessments on living patient cancer cells. Original contributions to complex 3D tumor-microenvironment technology and sole intellectual author original single cell genomics platforms and data science packages (Python) incorporating AI/Machine Learning for understanding single cell genomics data from the perspective of high throughput drug screening and patient chemosensitivity testing. I forged new supplier relationships for ovarian and breast tumor samples and obtained Investigational Review Board approval for the underlying work. Authored two grants, conceived partner study designs, laboratory execution with state-of-art single cell genomics, bulk genomics and standard molecular and cell biology, original LIMS and AI/ML bioinformatics software development, big/wide data analysis, manuscript preparation and conference presentations. Executive VP / Director of Genomic Medicine. GLG is a private, clinical-stage biotechnology company delivering next-generation precision oncology therapies for STAT3 driven hyperproliferative and viral diseases. I have developed several of our programs from basic ideas to licenses and presented them at various conferences and investor audiences, including cell therapy for Host vs. Graft (HVG) disease treatments. Wrote numerous AI/ML software for mining STAT3 relevant information from bulk and single cell genomics resources. Intellectually authored the concept of the Consortial Platform, involving multiple partners, where the product for the patient becomes greater than the sum of its individual parts, and helped forge not only a new type of Pharma business model but an innovative approach within the emerging field of Precision Oncology. C e d w a t i S w d B p i o t d e s April 2017 to April 2018 http://go.spcollege.edu Adjunct Professor of Biological Sciences (BSC 1005C). Achieved highest instructor ratings for the college in many years and was offered a more advanced position within the college. Curriculum taught covers the range from Cell Biology, Molecular Biology, Biochemistry, Genetics, Ecology, Evolution, Biotechnology, Zoology, Anatomy/Physiology, Botany and Microbiology. Laboratory course focused on microscopy, measurement and application of the scientific method to varied local ecological problems. My student evaluations were excellent – well above average for general instructor, science instructor and biology instructor at SPC. Adjunct Professor of Biological Sciences CEO. Founded Okeanos Technologies in 2009 to develop an innovative cleanenergy microdevice with potential to drop the cost of seawater desalination by more than an order of magnitude and simultaneously address a number of profound environmental, energy, economic and human health related problems. In taking the desalination problem from todays macroscale, where the physics and dynamics are inefficient, to the nanoscale where the physics is far more efficient, the WaterChip TM represented a potential paradigm shift in desalination and water treatment. As the firms founder, I scouted the predecessor to the technology, authored and won an EPA SBIR grant to develop the technology from basic science to commercial product, engaged sponsored academic research at a major US university towards that end, licensed the resulting technology from this university, won $100K Ocean Exchange Gulfstream Navigator Award and Fast Company top 50 Hot Companies awards, and raised seed capital ($2.5M). CEO, Founder CEO, Founder Founded DNAPrint genomics in 1999 and served as the leader of this firm until 2008. I started with nothing more than an idea, secured angel investment, built a laboratory, and ran the firm as CEO for several years. Performed human genome research and product development, hired a laboratory staff, converted the lab to GLP, and intellectually authored an innovative human genome-based product portfolio which soon after made history in the field of forensic genetics, receiving considerable international media attention (New York Times, ABC News, various television shows such as Forensic Files, etc.). I authored a textbook on the underlying technology (“Molecular Photofitting – Predicting Ancestry and Phenotype from DNA” Elsiever Academic Press). Our flagship product – DNAWITNESS – was used by forensic investigators to construct a physical profile of an individual that left DNA at a crime scene and was instrumental in the resolution of over a dozen serial homicide cases. We also pioneered today’s consumer genomics market with the introduction of the first Genomic Ancestry product – AncestrybyDNA, Numerous copy-cat firms came on the scene after this introduction . We eventually evolved to become a small personalized (e.g. pharmacogenomics enabled) drug development company, prosecuting a clinical trial of a dimerized, genetically engineered form of Erythropoietin lincensed from Beth Israel Deaconess Medical Center. I brought DNAPrint public, managed the firm as CEO of the resulting publicly reporting, SEC compliant firm for 8 years and in 2003 I brought in outside management to help take the company to the next level, taking the role of Chief Scientific Officer. The firm was sold to one of its shareholders in 2008. Honors- Winner of Ocean Exchange Navigator Award and $100,000 prize. Company I founded (Okeanos) wins of Fast Company’s “One of the worlds most innovative companies” Selected by Sarasota Magazine as one of 10 up and coming Entrepreneurs in South Florida. Voted “Most Influential in SNPs and Genotyping Category” by readers of Genome Technology Magazine. Woods Hole Oceanographic Institute (WHOI) Fellowship Inducted into Phi Beta Kappa Honor Society Magna Cum Laude, University of California, Irvine. (Graduated 2nd of 1,100 students). Golden Key National Honor Society Appointed (Congressional) to United States Naval Academy – accepted appointment Appointed (Vice Presidential) to United States Air Force Academy – declined appointment SELECT PUBLICATIONS Books 1. Frudakis, T.N. Molecular Photofitting: Predicting Ancestry and Phenotype from DNA. 2007. Academic Press Publishers (Elsiever). 695 pages; Graduate level textbook. 2. Frudakis, T.N. A Guide to Forensic DNA Profiling. Phenotype (Chapter 27). Peer-Reviewed Papers Published in Scientific Journals (chronological order starting with most recent) 1. Robert K. Valenzuela, M.S., Miquia S. Henderson, B.S., Monica H. Walsh, B.S., Nanibaa’A. Garrison, Ph.D., Jessica T. Kelch, B.S., Orit Cohen-Barak, Ph.D., Drew T. Erickson, Ph.D., F. John Meaney, Ph.D., J. Bruce Walsh, Ph.D., Keith C. Cheng, M.D., Ph.D.,Shosuke Ito, Ph.D., Kazumasa Wakamatsu, Ph.D., Tony Frudakis, Ph.D., Matthew Thomas, Ph.D., and Murray H. Brilliant, Ph.D. Predicting Phenotype from Genotype: Normal Pigmentation. J Forensic Sci. 2010 Mar 1; 55(2):-. Wilson RT, Roff A, Dai PJ, Fortugno T, Douds J, Chen G, Grove G, Ongeri S, Barnholtz-Sloan J, Frudakis T, Chinchilli V, Hartman T, Demers L, Shriver M, Canfield V and Cheng K. Genetic ancestry, skin reflectance and pigmentation genotypes in association with serum vitamin D metabolite balance. Horm Mol Biol Clin Invest 2011;7(1):279-293. 3. Shekar SN, Duffy DL, Frudakis T, Sturm RA, Zhao ZZ, Montgomery GW, Martin NG. Linkage and association analysis of spectrophotometrically quantified hair color in Australian adolescents: the effect of OCA2 and HERC2. 2008. J Invest Dermatol, 12:2807-14. 4. Shekar S, Duffy D, Frudakis T, Montgomery G, James M, Sturn R and N Martin. 2008. Spectrophotometric methods for quantifying pigmentation in human hair – influence of MC1R genotype and environment. Photochemistry and Photobiology, 2008, 84: 719-726. 5. Frudakis, T. DNAPrint Genomics, Inc.: better drugs for segmented markets. Pharmacogenomics. 2008 Feb;9(2):247-51 6. Halder I, Shriver M, Thomas M, Fernandez J, Frudakis T. 2007. A panel of ancestry informative markers for estimating individual biogeographical ancestry and admixture from four continents: utility and applications. 2008 May;29 Human Mutation (5):648-58. doi: 10.1002/humu.20695. 7. Frudakis, T. Thomas, M., Ginjupalli, S., Handelin, R. Gabriel, HJ Gomez. 2007. CYP2D6*4 polymorphism is associated with statin-induced muscle effects. Pharmacogenet Genomics. 2007 Sep;17(9):695-707. 8. Frudakis T, Terravainen T, Thomas M. Multilocus OCA2 genotypes specify human iris colors. Hum Genet. 2007 Nov;122(3-4):311-26 9. Kishi S, Cheng C, French D, Pei D, Das S, Cook E, Hiiva N, Rizzari C, Rosner G, Frudakis T, Pui C, Evans W, Relling M. 2007. Ancestry and pharmacogenetics of antileukemic drug toxicity. Blood. May 15; 109(10):4151-7. 10. Shriver M., Frudakis T, Budowle B. 2005. Getting the science and the ethics right in forensic genetics. Nature Genetics May; 37(5):-. Sturm, R. and T. Frudakis. Eye colour: portals into pigmentation genes. 2004. Trends in Genetics 20(8):-. Mirhashemi R, Arena JF, Frudakis T, Lambrou N, Arboleda J, Hunt M, Medranda M, Averette H, Penalver M.. Candidate gene in predicting in vivo ovarian cancer response to combination therapy with paraplatin and Paclitaxel. ScientificWorldJournal. 2002 Jan 2;2(1 Suppl 2):19-20. 13. Frudakis T, Thomas M, Gaskin Z, Venkateswarlu K, Chandra S, Ginjupalli S, Gunturi S, Natrajan S, Ponnuswamy V, and Ponnuswamy K. 2004. Sequences associated with human iris pigmentation. Genetics, 165:-. Frudakis, Tony, Venkateswarlu Kondragunta, Matthew Thomas, Zach Gaskin, Siva Ginjupalli, Sitarama Gunturi, Viswanathan Ponnuswamy, Sivamiani Natarajan, and Ponnuswamy Kolathupalayam Nachimuthu A Classifier for SNP- Based Inference of Ancestry. Journal of Forensics Sciences, July 2003, Vol. 48(4):-. Houghton RL, Dillon DC, Molesh DA, Zehentner BK, Xu J, Jiang J, Schmidt C, Frudakis (Anthony), Repasky E, Filho AM, Nolasco M, Badaro R, Zhang X, Roche PC, Persing DH, and Reed SG. Transcriptional complementarity in breast cancer: Application to detection of circulating tumor cells. Mol. Diagn.6/79-91. 16. Frudakis, T. and F. Wilt. 1994. Two different cis elements collaborate to spatially repress transcription from a sea urchin promoter. Developmental Biology. 172:-. Akasaka, K., Frudakis, T., Killian, C.E., George, N.C., Khaner, O., Yamasu, K., and F. Wilt. 1994. The organization of the spicule matrix gene, SM30, in the sea urchin Strongylocentrotus purpuratus. Journal of Biological Chemistry. 269:-. Patents Issued 1. Frudakis; Tony Nick (Sarasota, FL), Kondragunta; Venkateswarlu (Sarasota, FL), Natarajan; Sivamani (Sarasota, FL) Methods and apparatus for complex genetics classification based on correspondence analysis and linear/quadratic analysis. Patent No. 7,640,113, Dec. 29, 2009. 2. Frudakis; Tony Nick (Sarasota, FL). Methods and apparatus for use in genetics classification including classification tree analysis. Patent No. 7,593,816, September 22, 2009. 3. Frudakis; Tony Nick (Sarasota, FL). Efficient methods and apparatus for high-throughput processing of gene sequence data. Patent No.7,110,885, September 19, 2006. 4. Frudakis; Tony N. (Seattle, WA), Smith; John M. (Everett, WA), Reed; Steven G. (Bellevue, WA). Compositions and methods for the treatment and diagnosis of breast cancer. Patent No. 6,225,054, May 1, 2001. 5. Frudakis; Tony N. (Seattle, WA), Smith; John M. (Everett, WA), Reed; Steven G. (Bellevue, WA). Compositions and methods for the treatment and diagnosis of breast cancer. Patent No. 6,344,550. February 5, 2002. 6. Frudakis; Tony N. (Sarasota, FL), Reed; Steven G. (Bellevue, WA), Smith; John M. (Everett, WA), Misher; Lynda (Seattle, WA) Compositions and methods for the treatment and diagnosis of breast cancer Patent No. 6,586,570, July 1, 2003 7. Frudakis; Tony N. (Sarasota, FL), Reed; Steven G. (Bellevue, WA), Smith; John M. (Columbia Heights, MN), Misher; Lynda E. (Seattle, WA), Dillon; Davin C. (Issaquah, WA), Retter; Marc W. (Carnation, WA), Wang; Aijun (Issaquah, WA), Skeiky; Yasir A. W. (Bellevue, WA), Harlocker; Susan L. (Seattle, WA). Compositions and methods for the therapy and diagnosis of breast cancer. Patent No. 6,828,431. December 7, 2004. 8. Frudakis; Tony Nick (Bradenton, FL). Methods for the identification of genetic features for complex genetics classifiers. Patent No. 7,107,155. September 12, 2006. ORAL PRESENTATIONS: 1. Frudakis, T. “Data mining and corporate development issues”. BioPartnering Conference. London, UK. October 12, 2000. 2. Frudakis, T. “Complex Pharmacogenomics at DNAPrint Genomics”. Cambridge Healthtech Institute’s Fourth Annual Genomic Partnering: Emerging and Early-Stage Companies.. Genome 2001 Tri-Conference. March 3, 2001. 3. Frudakis, T. “A classifier for the inference of eye color from DNA”. TIGR’s Genome Sequence and Analysis Conference. San Diego, CA. October 15, 2001. 4. Frudakis, T. “Innovations for Pharmacogenomics algorithms”. BIOIT world Expo. Boston, MA. March 15, 2002. 5. Frudakis, T. “Inference of Iris Color and Biogeographical Ancestry from DNA”. CHIs 5 th Annual DNA Forensics Meeting, Washington, D.C. June 2002. 6. Frudakis, T. “Pharmacogenomics as a paradigm shift”. 7 th Annual Disease Management Congress, Chicago, IL. 2002. 7. Frudakis, T. “ Molecular Photofitting”. Biometrics Roundtable: Transnational Threats Initiative Center for Strategic and International Studies,j Washington DC. November 2003. 8. Frudakis, T. “Population Structure as a tool for identifying loci that underlie variable drug response”. Moffit Cancer Center Grand Rounds, November 2003. 9. Frudakis, T. “Molecular Photofitting” 2003. Dutch Forensic Institute (NFI in Rijswijk, the Netherlands) 10. Frudakis, T. “Admixture Mapping “ 2004. Lorne Genome Conference, Lorne Victoria, Australia 11. Frudakis, T. “East Asian admixture in Native Americans”, part of the Zehg He Voyages Series. 2005. United States Library of Congress, Washington DC. 12. Frudakis T. “Correcting for the confounding influence of population structure on association screens”. American Society of Clinical Therapeutics and Pharmacology Annual Meeting. March, 2005. MAJOR RECENT ACCOMPLISHMENTS.  As covered by the New York Times, US News and World Report, Popular Science, USA Today, CBS Evening News, ABC News, Discovery Magazine and a variety of other media outlets - Developed a DNA based technology that was instrumental in solving a serial killer case (Multiagency Homocide Task Force Serial Homocide Investigation, http://www.dnaprint.com/welcome/press/press_recent/2003/june_5/), and subsequently used to solve a number of other homicide investigations (Mammoth Lakes Murder, Napa Double Murder, Precious Doe case, Concord Trailside Killer Investigation, , Sarasota FL Walker murder, Operation Minstead – New Scotland Yard, UK, and most recently an LAPD serial homicide investigation). The technology has bee used to provide direction to a a number of other, as yet to be solved cases (e.g. Susanna Chase murder – Boulder CO,). This technology is the first genomics technology to ever be applied for forensic casework.  Was PI and inventor of technology that represents the first ever for the prediction of a multifactorial human phenotype (human iris color) from DNA (publication 15 above).  Functioned with a team of management I selected to build a drug development pipeline at DNAPrint, including compounds for anemia, depression, addiction, ophthalmic diseases, and a diagnostic for diabetes.  Discovered the major cause of the potentially dangerous statin side-effect myalgia. MEDIA INTERVIEWS 1. Forensics Files. Episode: “Tight Fitting Genes” Originally aired September 14, 2005. Featured application of my DNAWITNESS assay as it helped redirect and shape the investigation by the that lead to the arrest and conviction of the Louisiana Serial Killer. I appear in multiple interviews for this episode.. 2. Forensics Files. Episode: “Good as Gold”. Originally aired 1/28/2008. Featured application of my DNAWITNESS assay as it helped redirect and shape the investigation that lead to the arrest and conviction of a double murder in Napa, California. 3. ABCTV PrimeTime Thursday with Dianne Sawyer and Patricia Cornwell, regarding DNAPrint’s use of new genomics technology to assist with the successful resolution of the Louisiana Serial Killer Case (Louisiana Multiagency Homocide Task Force). 4. CBS News with Dan Rather. “Personalized Genetics”. Interviewed by Wyatt Andrews . March 2, 2003. Program also aired on CBS Sunday Morning show. 5. New York Times. “For Sale, a DNA Test to Measure Racial Mix” by author Nicholas Wade. October 1, 2002. 6. US News and World Report. “Getting DNA to bear witness: Genetic tests can reveal ancestry, giving police a new source of clues” June 23, 2003 by Dana Hawkins Simons. 7. Popular Science. “DNA and a New Kind of Racial Profiling”. By Jessica Snyder Sachs. December 2003. 8. Popular Science. “Putting the Gene Back in Genealogy”. Rebecca Skloot. January, 2004. 9. Germany’s ZDTV news program. Fall 2003. 10. Australias ABC news program. Fall 2003. 11. Wired Magazine. “Genetics Testing and Native Americans”. Brendan I. Koerner. May 2005. 12. CBS Radio News, interviewed by Robert Adler, May 2005. 13. VGBH-NOVA. Topic: DNA Dragnets. Barbara Moran. March 2005. 14. Biotechnology Healthcare Magazine. Topic: Personalized Medicine. Author: Bob Carlson. March 2005. 15. KTLA-Fargo ND. Topic: Consumer Genetics. By: Jane Alexander. 16. WBCC-Atlanta, GA. Topic: Forensic Genetics. Benji Shepard. April, 2004. 17. New York Times. Topic: Ancestry Testing Debunks Misconceptions about “Race”. Author: Amy Harmon. Article to appear in July 2005. 18. Business Week. Interviewed by Cathy Yang. 19. Readers Digest. “Nabbed!” These Forensic Breakthroughs are Helping Police Crack Their Toughest Cases.” By Tony Dawe. October 2004. 20. Readers Digest. “Nabbed!” These Forensic Breakthroughs are Helping Police Crack Their Toughest Cases.” By Ann Chandler. February 2005. 21. Public Library of Science Biology Journal. Topic: Genetics of Eye Color. By: Helen Dell. March 2004. 22. Good Housekeeping. January 29, 2004 23. ScienCentral News. Topic: Ancestry Testing By: Joyce Gramza. July 2003 24. NPR’s All Things Considered. “Researchers Discover Skin Color Gene” by Nell Boyce Health & Science editor. December 2005 (storyID-) TEACHING EXPERIENCE 1. Adjunct Professor Biological Sciences BSC1003. Saint Petersburg College, Saint Petersburg, Florida. Spring 2017 to Spring 2018. 2. Assistant Graduate Instructor MCB130 Developmental Biology at University of California Berkeley Fall 1994. Student reviews of my performance were excellent. 3. Assistant Graduate Instructor MCB130L Developmental Biology Laboratory at University of California Berkeley Spring 1994. Student reviews of my performance were excellent.