Data Science Scientist

Manuel X. Duval, PhD CV. Mar **** */*

MANUEL X. DUVAL, PHD

Acton, MA 01720, USA

http://www.linkedin.com/in/manuelduval

https://manuelxduval.github.io/

860-***-**** Mar 2025 ******.*.*****@*****.***

SUMMARY

Binformatics specialist with expertise in managing and analyzing OMICs data sets. Proven ability to handle large-scale biological datasets including NGS data and develop efficient data curation pipelines for actionable insights. Adept at applying bio-informatics tools and computational methods to accelerate research in personalized medicine and therapeutic development. Passionate about solving complex biological challenges to drive innovation in healthcare. TECHNOLOGY COMPETENCIES

OMICS data exploration and visualization

Molecular Biology data management, analysis and reporting (with open source solutions like ggplot R or python plotly and COTs like Spotfire and GeneData Expressionist)

Data Curation: Skilled in creating workflows for ingestion, annotation, and harmonization of biological data (nf-core).

Data Analysis: Proficient in statistical modeling, hypothesis testing, and predictive analytics with R and python.

Large-Scale Data: Expertise in handling high-throughput sequencing datasets

(RNA-Seq, WES, GWAS).

Collaborative Research: Strong communicator and collaborator in interdisciplinary teams to drive project success.

Agile Data Science: Experienced in iterative, collaborative workflows for building and optimizing data science pipelines.

PROFESSIONAL EXPERIENCE

amplifiDx Inc May 2023 – Current

Bioinformatics Scientist, Waltham, MA

Designed, built, and deployed bioinformatics workflows to support the development of specific and sensitive Nucleic Acid Amplification Test (NAAT) assays.

Leveraged tools such as NextFlow and R to streamline assay design pipelines.

Ensured workflows met performance and scalability requirements for high- throughput and accurate target identification.

Collaborated with cross-functional teams, including molecular biologists and biochemists, to integrate computational methods into assay validation processes.

mindlance/Sanofi Pharmaceuticals Feb 2023 – May 2023 Business Analyst II (IT) contractor, Cambride, MA / Acton MA

Captured and documented user requirements from stakeholders, translating them into clear and actionable feature requests for developers.

Applied the Agile/Scrum methodology to manage development cycles, ensuring timely delivery of bioinformatics tools and workflows.

Facilitated sprint planning, retrospectives, and task prioritization to align development efforts with project goals.

Manuel X. Duval, PhD CV. Mar 2025 2/6

InfoJini/EMD Serono Feb 2022 – Dec 2022

Data Scientist contractor, Billerica, MA / Acton MA

Conducted pharmaco-genomics and RNA-Seq data analyses to support a clinical trial for an investigational small-molecule therapy targeting autoimmune indications.

Delivered germline candidate markers associated with inter-individual variability in drug exposure, contributing to patient stratification and personalized medicine strategies.

Applied advanced bioinformatics workflows and statistical approaches to analyze high-throughput sequencing datasets in compliance with clinical research protocols.

Collaborated with multidisciplinary teams to interpret findings and align insights with therapeutic development goals.

BonaDeaDiagnostics, April 2021 – Feb 2023

Scientist/Data Analyst consultant, Boston, MA/Acton MA

Designed Human genome specific reagents for the development of a non- invasive molecular test using Open Source bioinformatics application. Clear Gene Jun 2019 – July 2021

Senior Data Scientist Contractor, San Carlos, CA / Acton MA

Applied statistical machine learning methods to RNA-Seq-derived features to develop a predictive model of tumor residuals in solid biopsies.

Delivered comprehensive data analyses to support prospective studies and FDA submissions, ensuring regulatory compliance and robust scientific documentation.

Developed and maintained a custom R package to streamline the development and validation of a diagnostic test, enabling reproducible and scalable analyses.

Scipher Medicine Apr 2018 – Jun 2019

Senior Data Analyst contractor, Waltham, MA

Developed an RNA-Seq-based predictive test for precision medicine applications, focusing on patient response to existing therapies.

Conducted end-to-end data analysis, from processing raw FASTQ files to modeling results.

Generated data models from FPKM data matrices, applying robust statistical frameworks to ensure reproducibility and accuracy.

Delivered detailed analysis reports using RStudio IDE and R Markdown, enabling clear communication of results to stakeholders. AbbVie. Mar 2016 – Dec 2017

Senior Scientist III Bioinformatics Contractor, Worcester, MA

Delivered multi-omics data analyses for Translational Medicine projects, and RNA-Seq exosome technology deployment.

Inferred candidates subgroups of patients with a given autoimmune indication with peripheral blood metabonomics and proteomics data sets

Developed and deployed R shiny applications in the scope of enabling scientist to perform simple queries on large RNA-Seq data sets. COMMONWEALTH SCIENCES/Agios Aug 2015 – Mar 2016

Bioinformatician contractor, Cambridge, MA

Somatic variants detection and analyses from DNA re-sequencing data. Applied R packages (e.g. absolute) from DNA re-sequencing data with paired normal and tumor biopsies’ samples in order to infer clonality and normal Manuel X. Duval, PhD CV. Mar 2025 3/6

cell content from tumor biopsies.

BECKMAN COULTER GENOMICS May 2014 – May 2015

Staff Bioinformatician, Danvers, MA USA

Managed and analyzed Bioinformatics, NextGen DNA sequence data. Maintained whole DNA-Seq (WGS) and RNA-Seq workflows from Illumina HiSeq instruments to data packages delivery to customers. The workflows were developed with a combination of perl and linux bash scripts.

BOEHRINGER INGELHEIM PHARMACEUTICALS, INC Jul 2013 – May 2014 Senior Principal Bioinformatics contractor, Ridgefield, CT USA

Knowledge management bioinformatics, cardiovascular and metabolic disease drug discovery. Delivered RNA-Seq daat analyses in the scope of comparing the molecular effect of standard of care with candidate therapies. ENUMERAL BIOMEDICAL Feb 2012 – May 2013

Director of Bioinformatics, Cambridge, MA USA

Managed and analyzed therapeutics Antibodies Discovery and Preclinical data.

· Designed and implemented in-house antibody DNA sequence analyses workflow.

· Deployed solutions for cell cytometry data analyses for the development of novel antibody based biotherapeutics.

PFIZER PHARMACEUTICALS Jan 2001 – Aug 2011

Senior Principal Scientist, Groton, CT, USA

2008 – 2011

Managed Pharmacogenomics data in a clinical development lab. Provided and delivered statistical data analyses services for clinical and translational research programs. Conducted OMICs’ technologies evaluation in the scope of promoting the most relevant assays in terms of Drug Discovery and Development.

Principal Scientist, Groton, CT, USA

2004 – 2007

Deployed an enterprise information system for the storage and analysis of transcriptomics data associated with their cognate co-variates’ attributes. Supplied Computational Biology analyses and supported the preclinical models business needs with Bioinformatics services.

Bioinformatics Scientist, Fresnes, France

2001 – 2003

Bioinformatics lead in the Allergy and Respiratory Therapeutics Area functional genomics lab.

TEXAS A&M UNIVERSITY, DEPARTMENT OF BIOLOGY, College Station, TX Jan 1996 – Dec

-2000

Research Scientist

Conducted high-throughput DNA sequence data capture and data analyses.

· Set-up and applied a bioinformatics data pipeline that delivered an annotated database of more than 10,000 non-redundant Expressed Sequence Tags (EST) from raw Sanger-based DNA sequence data. Developed and deployed a DNA micro array platform.

· Contributed to the establishment of the Texas A&M Laboratory for Functional Genomics with the set-up of DNA micro array production (printed arrays). Manuel X. Duval, PhD CV. Mar 2025 4/6

TEACHING EXPERIENCE

Brandeis University Mar 2014 – Jun 2015

Graduate Professional Studies Instructor, Waltham, MA USA

Whole-genome Gene Expression Analysis class.

UNIVERSITY OF NEW HAVEN Sep 2011 – Jul 2015

Biology Adjunct, West Haven, CT, USA

Design and teach the Bioinformatics, Database systems for biological research and Bioinformatics courses. Introduction to NextGen DNA sequence analyses.

EDUCATION

· Post-baccalaureate non-degree, Computer Science, Texas A&M University, College Station, TX

C and Java programming; Data modeling and Relational Database

· PhD, Molecular and Microbiology, Université Grenoble Alpes, Grenoble, France Internship at the CNRS / Rhône-Poulenc joint laboratory (UMR41), CNRS, Lyon, France

· MS, Biochemistry, University of Aix-Marseille II, Faculté des Sciences, Marseille France

· BS, Math and Life Sciences, University of Aix-Marseille III, Faculté des Sciences et Techniques, Marseille, France

SPECIALIZED TRAINING

· Intensive Courses in Computational Molecular Biology, Washington University Institute for Biomedical Computing, St Louis, MO, July 2000

· Umetrics Academy, Multivariate Data Analysis, MKS Instruments, Andover, MA, July 2010

· Data and Models in Engineering, Science and Business [12.156s], MIT, Cambridge, MA, July 2012

PATENTS

· Patent Sequence conversion reaction. 2021. US20230220474A1Schoenbrunner, N., Duval, M., Schoenbrunner, E.R. C12Q1/6883 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material

· Patent: Monoclonal antibody based biomarker discovery and development platform. 2005. (PCT Int. Appl. WO 200-***-**** A2 20050825 CAN 143:210439 AN 2005:902753 CAPLUS), Takacs, L., Guttman, A., Hancock, W., Karger, B., Duval, M. and Berna, P., PGRD_Fresnes_Laboratories

· Patent: Systems and methods for sequence comparison. Nov 2003 (Application with the PCT, US Patent Application Ser. No. 10 / 723,522), Duval, M., Codani, J.J., Takacs, L. and Glemet, E., PGRD_Fresnes_Laboratories Manuel X. Duval, PhD CV. Mar 2025 5/6

· Patent: Seed specific biotinylated protein, SBP65, from leguminous plants. 1998. US 05837820. EP 0658625-A De Rose, R., Douce, R., Duval, M., Job, C. and Job, D. RHONE POULENC AGROCHIMIE (FR)

· Disclosure of Software: ClonePath1.0, The Texas A&M University System. September 2001, Grigoryan, A., Duval, M., Dougherty, E.D. and Thomas, T., Department of Biology, Texas A&M University, College Station, TX 77843 – 3258 and CAMDI Lab, Department of Electrical Engineering Texas A&M University, Texas A&M University, College Station, TX 77843 – 3128

· Disclosure of Invention TAMUS 1704 - 'Developing a Genomic Analysis Tool for Gene Expression in Response to Xenobiotic Compound and Development Cues'. May 2001, Thomas, T., Chuang, H.W., Hsieh, T.F. and Duval, M. PUBLICATIONS

· De Leeuw, M and Duval, M. The Presence of Periodontal Pathogens in Gastric Cancer. Exploratory Research and Hypothesis in Medicine 2020;5(3):87-96 doi: 10.14218/ERHM.2020.00024

· Srinivasan, S, Duval, M, Kaimal, V, Cuff, C, Clarke, S.H. Assessment of methods for serum extracellular vesicle small RNA sequencing to support biomarker development. Journal of extracellular vesicles, Nov. 2019. https://doi.org/10.1080/20013078.2019.1684425

· Duval, M. The Inadequacy of the Reductionist Approach in Discovering New Therapeutic Agents Against Complex Diseases Experimental Biology and Medicine 2018; 0: 1–10. DOI: 10.1177/1535370218794365

· Wong, V. and Duval, M. Inter-laboratory variability in array-based RNA quantification methods (2013). Genomics Insights 2013:6 13–24 doi: 10.4137/GEI.S11909.

· Tarone, S. and Duval, M. (2012). Engineering a single chain antibody-based biologic armed with an apoptotic executor. Technological Innovations In Life Sciences Vol. 5 Issue 1 DNA Press.

· Rajjou, L., Duval, M., Gallardo, K., Catusse, J., Bally, J., Job, C., and Job., D. (2011). Seed Germination and Vigor. Annual Review of Plant Biology 2011 May 4. [Epub ahead of print].

· Matteson, S., Paulauskis, J., Foisy, S., Hall S., and Duval, M., (2010), Opening the gate for genomics data into clinical research: a use case in managing patients’ DNA samples from the bench to drug development. Pharmacogenomics Vol. 11, No. 11, Pages 1603 – 1612, DOI 10.2217 / pages 10.151

· Pettit, S., des Etages, S.A., Mylecraine, L., Snyder, R., Fostel, J., Dunn, II, R.T., Haymes, K., Duval, M., Stevens, J., Afshari, C., and Vickers, A.,

(2009), Current and Future Applications of Toxicogenomics: Results Summary of a Survey from the HESI Genomics State of Science Subcommittee. Environmental Health Perspectives doi: 10.1289 / ehp.0901501

· Csanky, E., Olivova, P., Rajnavolgyi, E., Hempel, W., Tardieu, N., Toth, Katalin, E., Jullien, A., Malderes-Bloes, C., Kuras, M., Duval, M., Nagy, L., Manuel X. Duval, PhD CV. Mar 2025 6/6

Scholtz, B., Hancock, W., Karger, B., Guttman, A., and Takacs, L., (2007), Monoclonal antibody proteomics: Discovery and prevalidation of chronic obstructive pulmonary disease biomarkers in a single step. Electrophoresis 28(23), 4401 – 4406

· Duval, M. and Hsieh, T.F., (2006), Patenting applied to Genetic Sequence Information. In Biotechnology and Genetic Engineering Review (Publisher: Intercept Ltd., ISSN: 0264 – 8725). 23, 317 – 330

· Duval, M., (2004), Intellectual property and genetic sequences: moving toward an integrated information system. Journal of International Biotechnology Law, 01(04), 156 – 160

· Dufresne, G. and Duval, M., (2004), Genetic sequences: how are they patented. Nature Biotechnology, 22(2)

· Dufresne, G., Takacs, L., and Duval, M., (2004), Approximate string matching algorithm for DNA patenting evaluation in the pharmaceutical industry. In Chemical Genomics. (eds by F. Darvas and A. Guttman), Marcel Dekker, Inc., NY. ISBN: 0 – 8247 – 5490 – 5

· Anderle, P., Duval, M., Draghici, S., Kuklin, A., Littlejohn, T., Medrano, J.F., Vilanova, D., Roberts, M.A., (2003), Gene expression databases and data mining. Biotechniques. Mar; Suppl: 36 – 44

· Dufresne, G., Takacs, L., Heus, H.C., Codani, J.J. and Duval, M., (2002), Patent searches for genetic sequences: How to retrieve relevant records from patented sequence databases. Nature Biotechnology, 20(12): 1269 – 71

· Duval, M., (2002), DNA array information workflow and data management. In Microarray Image Analysis-Nuts and Bolts (eds S. Sha and G. Kamberova), DNA Press, LLC ISBN 0 – 9664027 – 5 – 8

· Chuang, H.W., Hsieh, T.F., Duval, M. and Thomas, T.L., (2002), Genomic analysis of Arabidopsis gene expression in response to a systemic fungicide. In Genomics of Plants and Fungi, (eds R.A. Prade and H.J. Bohnert), Marcel Dekker, Inc., NY. ISBN: 0 – 8247 – 4125 – 0

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