Jacob Wesley Ulm, MD, PhD

Résumé and Annotated Summary of Publications

Professional summary: Harvard and MIT-trained (MD/PhD) physician-researcher with primary career focus in bioinformatics and advanced large dataset-driven drug discovery and global biomedical resource optimization; with additional experience in pharmaceutical research and repurposing, health and public policy, education and curriculum development, laboratory management, multilingual professional translation, technical writing and editing, and consulting

______________________________________________________HIGHLIGHTS_______________ _____ _____________________ _____ _

• MD/PhD dual-degree graduate of Harvard Medical School and MIT via the Harvard-MIT Division of Health Sciences and Technology (HST), funded by NIH Medical Scientist Training Program (MSTP) Fellowship, honored for significant contributions to the field of retroviral gene therapy
• Summa cum laude and Phi Beta Kappa gradúate of Duke University (top 1% of graduating class) with B.S. in Chemistry and Biochemistry
• Mission-critical biomedical database analytics, resource optimization, and subject matter expertise support for NIH’s globally utilized bioinformatics data resources for clinicians and researchers, with specialized assistance in efforts to manage the COVID-19 pandemic
• Authorship of multiple highly-cited peer-reviewed papers, reference chapters (books and encyclopedias), conference abstracts, and published theses in bioinformatics, gene therapy, molecular biology, human genetics, and hemoglobin kinetics and development of interdisciplinary data-mining tools to rapidly screen for new drug prospects, most recently for COVID-19 therapeutic agents (DOI: 10.1111/tbed.13710)
• Winner of multiple research prizes such as international second prize (2003) in National Neurofibromatosis (NF) Foundation competition for NF therapeutic development proposal (since incorporated into real-world treatment modalities); selection as Harvard Med representative to present research on siRNA-based therapies for chemotherapy-resistant cancers at International Cancer Gene Therapy Conference held in Singapore (2004); Finalist, David Rimoin Award for Research Excellence in Medical Genetics and Prizewinner, research presentation for Center for Duchenne Muscular Dystrophy (2014)
• Top-rated instructor for pre-health students and college and graduate school applicants
• Top champion of Jeopardy TV quiz program and Tournament of Champions competitor
• Valedictorian, T. C. Williams H.S. and National Merit Scholar
• Top scores (consistently 98-99^th percentile) on SAT, AP exams, MCAT, GRE and passing of USMLE medical licensing exam Steps I, II, and III all on first attempt

Language proficiencies (spoken)

Fluent (full professional proficiency, oral and written communication): Mandarin Chinese (experience as medical volunteer in China, hospital externship in Taiwan, presenter of popular online Mandarin lectures in genetics and molecular biology), Spanish, German

Advanced professional working proficiency (oral and written): Portuguese, French, Dutch, Italian

Basic conversational and written proficiency: Japanese, Russian, Ukrainian, Swedish, Danish, Farsi Persian

(programming and scripting)

High-level proficiency with extensive professional working experience: Python (incl. essential data science libraries such as pandas and numpy), SQL, R (certified); broad and specialized expertise for diverse applications across multiple platforms

Significant proficiency with some working experience: Perl, Pascal, Javascript, Matlab, HTML5

______________________________________________________EDUCATION________________ _____ _____________________ _____ __

HARVARD MEDICAL SCHOOL AND MIT Boston, MA

Joint MD/PhD Program 8/1996-5/2006

MD with PhD in Genetics and Gene Therapy

• PhD Dissertation Thesis: Discovery of retroviral capsid components critical for tissue-specific delivery in gene therapy protocols
• Published thesis results in Proc Natl Acad Sci (2004) and Virology (2007)
• Passage of USMLE clinical licensing exam Steps I, II, and III all on first attempt
• Overseas clinical fellowships in Taipei, Taiwan (National Taiwan University Hospital, 臺大醫院) and Munich, Germany (Ludwig-Maximilians-Universität München and the Dr. von Haunersches Kinderspital) in 2006

DUKE UNIVERSITY Durham, NC

Bachelor of Science in Chemistry and Biochemistry (summa cum laude) 8/1992-5/1996

• Phi Beta Kappa, American Chemical Society Certification, diploma awarded with highest honors (top 1% of graduating class, GPA: 3.9)
• Pre-college: National Merit Scholar and Valedictorian, T.C. Williams H.S.

______________________________________________ WORK AND RESEARCH EXPERIENCE______________________ _____ ___

National Institutes of Health (US Dept of Health and Human Services) Washington, D.C.

10/2020-present

• Bioinformatic scientific resource analyst and biomedical data specialist, with focus on optimization of globally utilized databases and clinical tools for clinicians and researchers
• Cross-domain bioinformatics skills sets and applications including:

o Application of multiple programming languages to critical tasks including Python, SQL, R, Perl, and Linux/Unix shell-scripting

o Data warehousing and ETL (Google BigQuery and Amazon Redshift)

o Software life cycle, development, and documentation

o Solutions architecting and project management

o GUI and Web deployment

o UX and KPI optimization, including user research and engagement

• Subject matter expert for global client inquiries and inter-agency clinical and research database optimization support, with extensive applications to mission-critical efforts including for the COVID-19 pandemic
• Longer-term specific aims to develop powerful new tools to assist with drug discovery, rapid sequencing interpretation, and examination of physiology and pathophysiology

UNIVERSITY OF PITTSBURGH MEDICAL CENTER (UPMC) Pittsburgh, PA

7/2019-9-2020

• Clinical Genetics Resident in UPMC Medical Genetics Fellowship Program
• Clinical and research experience in one of the nation’s top programs in this specialty, with publication of results from data-mining-based efforts to improve targeted treatment and drug repositioning for COVID-19
• Extensive experience working with special-needs children and adults with disabilities

CEDARS-SINAI MEDICAL CENTER/UCLA Los Angeles, CA

11/2013-11/2018

• Postdoctoral Fellow (Bioinformatics and Medical Genetics)
• Created improved data-mining modalities to facilitate and accelerate the development of more effective treatments for Duchenne Muscular Dystrophy and other genetic diseases through drug repositioning
• Expedited bench-to-bedside research and translational medicine through development of "intelligent" bioinformatic systems (through NLP and enhanced pattern-recognition tools) to predict the effectiveness of novel and established pharmaceuticals

MY TUTOR Los Angeles, CA

8/2009-11/2018

• Teacher and tutor for advanced topics (class-related) for H.S, college, and graduate and professional students
• Subjects spanning general biology, cell and molecular biology, genetics, physiology, nursing, history, languages (Spanish, French, German, Mandarin, Japanese), essay editing, sociology, psychology, education, geography, law, creative writing, technical writing, computer graphics and programming, philosophy, and literature

THE WASHINGTON POST COMPANY Multi-site

8/2009-11/2018

• Premed adviser and specialized instructor for students taking DAT, PCAT, MCAT, OAT professional school admissions exams, GRE, and other important standardized examinations

INDEPENDENT CONTRACTOR Multi-site

3/2010-11/2018

• Teacher, college adviser, local liaison, project manager, and translator for domestic and international students seeking American educational opportunities from middle school through graduate school, with specialization in high-level school and college placement for the Chinese community and concomitant corporate development and profitability for US-based companies in the field, in association with USA4YOU Corporation and independently

TRANSLATOR AND MULTILINGUAL PRESENTER Multi-site

5/2006-11/2018

• Translator of technical and other documents from several languages in which I have high proficiency including Mandarin Chinese, Spanish, German, Portuguese, French, Dutch, and presenter of live talks and recorded videos in key subjects e.g. genetics and cell biology

UCLA, CEDARS-SINAI, OLIVE VIEW HOSPITALS Greater LA Area, CA

6/2006-9/2009

· Resident physician successfully completed internship requirements and passed United States Medical Licensing Examination (USMLE) Step III on first attempt

o Case report on zoonotic bacterial infection in post-renal transplant pediatric patients, published in J Pediatr Inf Dis

o Roles as leader and teacher for various clinical teams

• Medical adviser and volunteer in Sichuan Province, China, in wake of 2008 earthquakes
• Due to severe respiratory condition and chronic complications secondary to life-threatening infection acquired on duty had to go on hiatus from clinical work, since recovered

HARVARD MEDICAL SCHOOL/MIT Boston, MA

DEPT. OF GENETICS, BOSTON CHILDREN'S HOSPITAL 1/1997-3/1999

10/2001-5/2004

• Gene therapy researcher in laboratory of Dr. Richard C. Mulligan, Mallinckrodt Professor of Genetics at Harvard Medical School, in Boston Children’s Hospital (Enders Building) and Harvard Gene Therapy Initiative, with focus on in situ gene therapy protocols (pre-CRISPR) and tissue targeting of retroviral vectors; MD/PhD thesis research funded by NIH Medical Scientist Training Program (MSTP) fellowship
• Made highly-cited discoveries published in multiple journals and dissertation, and generated dozens of plasmid DNA constructs with many used around the world for mission-critical gene therapy and virological research
• Honored as global expert and leader in field, invited author of two widely used chapters on the topic published in the standard reference Wiley Encyclopedia of Genetics (see Annotated Summary of Publications section below)
• Award-winning work on clinical applications of research, including international prize by the National Neurofibromatosis Foundation (NNFF) for protocol utilizing herpesvirus-based amplicons as treatment strategy for neurofibromatosis Type I
• Roles as supervisor, project leader and manager, teacher, and mentor for other team members and students while completing MD/PhD thesis work
• Technical expertise in recombinant DNA technology and site-directed mutagenesis, DNA amplification and purification, cell culture, genomics, flow cytometry and stem cell isolation, virology, RNA analysis, Southern and Western blotting

HARVARD MEDICAL SCHOOL/MIT Boston, MA

DANA-FARBER CANCER INSTITUTE 9/2000-5/2001

• Rotation research project in leukemic signal transduction (JAK-STAT pathways) with aim of unveiling new therapeutic targets and facilitating personalized medicine protocols based on specific oncogenic and tumor suppressor mutations, in laboratory of Dr. David Frank, Dana-Farber Cancer Institute

NATURAL STANDARD CORPORATION Somerville, MA

6/2001-2/2003

· Translator of scientific literature (peer-reviewed papers, abstracts, general documents) from German, Dutch, French, and Spanish to English

DUKE UNIVERSITY DEPT. OF CHEMISTRY Durham, NC

10/1995-5/1996

• Research associate in laboratory of Dr. Richard Palmer
• Focus on fast step-scan Fourier-transform infrared absorption-difference time-resolved spectroscopy (S² FT-IR DA TRS) as a tool to investigate and quantify kinetics of carbon monoxide binding to and dissociation from physiological oxygen carriers
• Submitted and accepted as undergraduate thesis project and published for American Chemical Society conference

DUKE UNIVERSITY MEDICAL CENTER Durham, NC

5/1995-8/1995

• Research associate in laboratory of Dr. Christian Raetz
• Studies examined enzyme-catalyzed palmitoylation of 2,3-diacylglucosamine-1-phosphate (Lipid X), an early precursor in bacterial Lipid A biosynthetic pathway, to form Lipid Y

DUKE UNIVERSITY DEPT. OF CHEMISTRY Durham, NC

9/1994-5/1995

• Research associate in laboratory of Dr. Bertram Fraser-Reid
• Studies focused on synthesis and kinetics of eight-carbon sugar 3-deoxy-D-manno-octulosonic acid (KDO), a potentially antibiotic-targetable component of Lipid A endotoxins in outer membranes of gram-negative bacterial cells
• Mentor to other undergraduate students in the lab

LOMBARDI CANCER CENTER, GEORGETOWN UNIVERSITY Washington, D.C.

6/1994-8/1994

• Research associate in laboratory of Dr. Matthew Ellis
• Studies focused on potentially differential influences of insulin-like growth factors (IGFs) I and II on expression of Wnt gene family, known to be involved in breast development of many organisms, and possible link to breast cancer

OFFICE OF DR. RAYMOND ELLIS Vienna, VA

6/1994-7/1994

• Official translator and interpreter of documents (from German to English) concerning training for the chemical industry in German-speaking countries, June 1994, for Dr. Raymond Ellis, in preparation for upcoming international conference in Geneva, Switzerland

LABORATORY OF TUMOR IMMUNOLOGY AND BIOLOGY Washington, D.C.

NATIONAL CANCER INSTITUTE, NIH 6/1993-8/1993

• Research associate in laboratory of Dr. Scott Abrams
• Focus on tumor immunology: immunogenicity of 9-mer and 13-mer peptide fragments of p21^ras protooncogene, presented on antigen-presenting cells, in stimulating MHC-based tumor-specific CTL immune response

Annotated Summary of Publications

Section 1: Refereed and published papers, book chapters for specialized readership in biomedical field (not including PhD thesis dissertation)

“COVID-19 drug repurposing: Summary statistics on current clinical trials and promising untested candidates.” Ulm JW, Nelson SF. Transboundary and Emerging Diseases. Manuscript accepted for publication and in press. DOI: 10.1111/tbed.13710

“Complex determinants within the Moloney murine leukemia virus capsid modulate susceptibility of the virus to Fv1 and Ref1-mediated restriction.” Ulm JW, Perron M, Sodroski J, Mulligan RC. Virology. 2007 Jul 5;363(2):245-55.

“TRIM5alpha mediates the postentry block to N-tropic murine leukemia viruses in human cells.” Perron MJ, Stremlau M, Song B, Ulm W, Mulligan RC, Sodroski J. Proc Natl Acad Sci U S A. 2004 Aug 10;101(32):11827-32.

Authorship of two chapters (text and figures) on gene therapy principles, relevant modern techniques, and disease targets for Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics, published September 2005 (John Wiley & Sons, Ltd.): Gene Therapy I: Principles and Clinical Applications and Gene Therapy II: Viral vectors and treatment modalities.

Co-authorship of Chapter 53, “Protein-based and gene therapies,” with contribution (text and figures) on gene therapy pharmaceuticals, vectors, disease targets, and novel modalities in textbook, Principles of Pharmacology: The Pathophysiologic Basis of Drug Therapy, edited by Dr. David Golan, Department of Pharmacology, Harvard Medical School; Lippincott Williams & Wilkins, April 2004

“Online Self-Report Data for Duchenne Muscular Dystrophy Confirms Natural History and Can Be Used to Assess for Therapeutic Benefits.” Wang RT, Silverstein Fadlon CA, Ulm JW, Jankovic I, Eskin A, Lu A, Rangel Miller V, Cantor RM, Li N, Elashoff R, Martin AS, Peay HL, Halnon N, Nelson SF. PLOS Currents Muscular Dystrophy. 2014 Oct 17. Edition 1. doi: 10.1371/currents.md.e1e8f2be7c949f9ffe81ec6fca1cce6a.

“Acinetobacter bacteremia following a hamster bite in a child with history of kidney transplant.” Azaran B, Puliyanda D, Ulm JW, Equils O. J Pediatr Infect Dis, 2010;5(3);158-163. doi: 10.3233/JPI-2010-0252

“Text mining-guided elucidation of high fidelity informatic proxy-based protocols to expedite drug repositioning and anticipate promising drug candidates for Duchenne muscular dystrophy: A pilot feasibility study” (report in progress)

Publication of detailed working Python computer language programming code on public Github site, as open-source software, for the BiomedScrape suite of text-mining and document comparison tools as well as the CorpusOptima project (developing large neutral pertinent semantic spaces for training advanced document comparison models) related to fellowship work; ongoing

Section 2: Conference papers for specialized audiences in biomedical field

“Development of the BiomedScrape Data-Mining Suite for Deep Semantic Structure-Based Drug Repurposing for DMD: A Pilot Feasibility Study”. Accepted abstract for 2018 American Society of Human Genetics annual meeting.

“Incorporation of Novel Categorical Data Parsing and Pattern-Recognition Tools in the Mining and Development of New Pharmacological Strategies for DMD Treatment and Management.” Abstract for 2016 UCLA Genetics Academic Retreat, American Society of Human Genetics, and Center for Duchenne Muscular Dystrophy annual meetings.

“Integrated Data-Aggregation and Mining Systems to Improve Detection of Meaningful Associations in DMD.” Abstract for 2015 UCLA Genetics Academic Retreat, American Society of Human Genetics, and Center for Duchenne Muscular Dystrophy annual meetings.

“Online DuchenneConnect self-report data indicates Exon 44 skippable DMD patients have prolonged wheelchair free survival.” Abstract for 2014 UCLA Genetics Academic Retreat, American Society of Human Genetics, and Center for Duchenne Muscular Dystrophy annual meetings.

“Herpesvirus Amplicon-based siRNA-expressing Vectors as a Therapeutic Strategy for Neurofibromatosis Type 1,” prize-winning (international 2^nd prize) research proposal for 2003 International NF Research Competition for Graduate Students and Postdoctoral Fellows, National Neurofibromatosis Foundation (NNFF), with subsequent invitation to NNFF International Consortium for the Molecular Biology of NF1 and NF2, May 2004 in Aspen, Colorado.

“AAV and HSV Amplicon-based si-RNA Expression Vectors as Therapeutic Modalities for Drug-Resistant Cancers.” Abstract for 2004 International Society for Cell and Gene Therapy of Cancer (ISCGT) conference in Singapore, Cancer Gene Therapy 11, 859 - 860 (01 Dec 2004).

“Application of fast step-scan Fourier-transform infrared absorption-difference time-resolved spectroscopy (S² FT-IR DA TRS) to examine association-dissociation kinetics of carbon monoxide and hemoglobin.” Abstract and oral presentation for American Chemical Society conference in North Carolina, spring 1996.

Section 3: Thesis dissertation and technical works for non-specialized audiences

PhD thesis dissertation: Elucidation of retroviral capsid residues involved in modulation of murine and human cell post-entry restriction. Approved November 2004, published in bound form (167 pages) April 2006, Graduate School of Arts and Sciences, Harvard Medical School.

Sole author of Fundamentals of Computer Science: A Study Guide, approx. 200-page problems workbook and guide for introductory computer science courses (algorithm design and Pascal programming), to accompany Great Ideas in Computer Science, textbook written by Dr. Alan Biermann of the Duke University Department of Computer Science; published at MIT Press, May 1996, and used at several universities nationwide.

Publication of research article on synthesis and kinetics of 3-deoxy-D-manno-octulosonic acid (KDO) and implications for novel gram-negative bacteria-specific antimicrobials in Vertices, Duke student science and technology magazine, Spring 1995 issue.