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Hire Dr. Stephanie D.

Belgium

USD 175 /hr

Genome assembly expert ‣ PhD in Bioengineering ‣ Scientific writer Eng/Nl/Fr ‣ Bioinformatician 15+ years of experience

Profile Summary

I currently work for Thinkubate, a life sciences consultancy specialised in: genomics, scientific writing, agriculture and aquaculture -->> www.thinkubate.io SERVICES: ‣ Genomics ‣ Research project management ‣ Scientific advice ‣ Scientific writing for life sciences and biotech: reports white papers academic publications funding applications ‣ ... Please take a look at the different skills I gathered from my previous work experience, they could be a match with your project! I have worked on plant diseases as a master student, on crustacean and bacterial genomics as a PhD and postdoc in bioinformatics, I have been a scientific collaborator at a blue biotech startup, a CEO at a medical testing company and now I work as the founder of a life sciences consultancy. During that journey, I have gathered skills in different domains: Analytical Skills · Project Management · Scientific writing · English · French · Dutch · Literature review · Life sciences · Linux · High performance computing (supercomputer) · Bioinformatics · Genome assembly · Genetics · PCR design · Genomics · Transcriptomics · Gene discovery · Experimental design · Problem Solving · Strategic Thinking · Presentations · Data Analysis · IP management · Novel food filing (EU) · Product Development · International project initiation and collaboration · Reporting · Agriculture · Aquaculture · Crustacean biology · Bacterial biology · Plant biology · PCR · Medical testing · Food supplements Below a more detailed description of my work experience previous to consultancy: CEO (2019 - 2020) Overarching leadership of three companies offering and developing solutions for chronic diseases: ‣ R.E.D. Laboratories NV: a specialized medical testing company ‣ Kalidashop BV: a web shop for science-based supplements offered to medical professionals and patients ‣ Protea Biopharma NV: an R&D company developing medical tests and supplements My responsibilities were: ‣ Development of policy and general strategy ‣ Effective management, general organization, including hiring personnel ‣ Upholding the scientific reputation of the company ‣ Collaboration with other (inter)national institutions ‣ Reporting to the Board of Directors ‣ Budgeting, valorisation of company results, use of resources ‣ Internal and external communication ‣ When appropriate, obtaining legal advice, taking legal action (incl. patent rights, suppliers,…) ‣ Final responsibility towards federal institutions, e.g., the Food Agency (FAVV) Postdoc in bioscience engineering at Ghent University (2016 - 2019) Several projects were part of this Postdoc: ‣ Assembly and annotation of the Artemia inbred genome ‣ International consortium and IP contract setup for the Artemia genome project ‣ Differential expression of genes related to Artemia extremophilic features ‣ Gene discovery in Artemia and in Litopenaeus Vannamei ‣ Genome assembly, annotation and characterization of a probiotic bacterium for aquaculture ‣ Setup of MinIon sequencing for beta testing Scientific collaborator at Ghent University (2014 - 2016) My responsibilities within this commercially oriented IOF project, aimed at creating a blue biotech spin-off, were: ‣ Assembly of novel genomes using bioinformatics tools ‣ Proving the concepts proposed within the project ‣ Communicating and Presenting the results to IOF, TechTransfer, stakeholders, companies and potential collaborators The outcome of this research remained in-house, considering the commercial aims of the project. PHD Student at VIB-Ghent University (2009 - 2014) Doctoral dissertation in crustacean genomics titled: "Artemia genomics: a new crustacean genome and discovery of sex-determining genes". The dissertation included: ‣ Performing bioinformatics on a large genome for genome assembly, SNP detection and differential gene expression analysis ‣ Wet lab work (AFLP, PCR, DNA and RNA extraction, flow cytometry for genome size determination, light microscopy, culture of Artemia, algae and bacteria) ‣ Tutoring tasks: tutoring a master student (Vibrio pathogenicity and virulence) and several bachelor students (AFLP mapping of a genome) ‣ Teaching tasks: teaching applied genomics (how to map, sequence and assemble a genome and find relevant markers for the industry), practical exercises in the wet lab (identifying different species and strains with simple and cheap RFLP markers) ‣ Presenting posters and giving presentations at congresses. Master student at Ghent University (2008) Master dissertation in plant pathology titled: "Characterization, pathogenicity and integrated control of Cuban Rhizoctonia solani isolates on bean". The dissertation included: ‣ Molecular work (RFLP) ‣ Fluorescence microscopy ‣ Statistical analysis ‣ Bean plant culture and plant treatments with riboflavin dilutions The dissertation included laboratory work at the Instituto Biotechnologico de Las Plantas in Cuba and was completed at the group of Crop protection at Ghent University. Obtained with distinction.

Subject Matter Expertise

• ★ Omics
• ★ Genome Sequencing
• ★ Technical & Scientific Writing
• ☆ Computational Biology
• ☆ Molecular Biology
• ☆ Biomarkers
• ☆ Genetics
• ☆ PCR
• ☆ Next Generation Sequencing (NGS)
• ☆ DNA Sequencing
• ☆ Gene Expression Analysis
• ☆ RNA Sequencing
• ☆ Marine Biology
• ☆ Biotechnology & Bioengineering
• ☆ Agricultural Engineering
• ☆ Aquaculture
• ☆ Computer Science
• ☆ Supercomputing
• ☆ Gene & Protein Expression Analysis
• ☆ Systems Biology
• ☆ Agricultural Biotechnology
• ☆ Hypothesis
• ☆ Peer Review
• ☆ Research Methodology
• ☆ Survey Design & Methodology
• ☆ Feasibility Studies
• ☆ Fact Checking
• ☆ Literature Search
• ☆ Gray Literature Search
• ☆ Experimental Protocols
• ☆ White Papers
• ☆ Textbook Content Writing
• ☆ Literature Review
• ☆ Traditional/Narrative Literature Review
• ☆ Scientific Proofreading & Editing
• ☆ Proofreading & Editing
• ☆ Language Translation
• ☆ Grant Writing

Services

• Writing
• Research
• Consulting
• Data & AI

Writing Technical Writing, General Proofreading & Editing, Translation

Research Feasibility Study, Fact Checking, Gray Literature Search, Scientific and Technical Research

Consulting Scientific and Technical Consulting

Data & AI Data Processing

Work Experience

Life sciences consultant, founder

Thinkubate bioinformatics

2021 - Present

CEO

R.E.D. Laboratories

September 2019 - April 2020

PostDoc in Bioscience engineering

Ghent University

2016 - 2019

Scientific collaborator BlueGene project

Ghent University

2014 - 2016

PhD in Bioscience Engineering

Ghent University

2009 - 2014

Education

PhD in Bioscience engineering

Ghent University & VIB-PSB

April 2009 - August 2014

PhD in Bioscience Engineering (Faculty of Bioscience Engineering)

Ghent University

2009 - 2014

Master in Bioscience Engineering

Ghent University (Belgium) & Instituto Biotechnologico de las plantas (Cuba)

September 2001 - June 2008

Master in Bioscience Engineering (Faculty of Bioscience Engineering)

Ghent University

2001 - 2008

Certifications

• Certification details not provided.

Publications

JOURNAL ARTICLE

Stephanie De Vos, Dung Nguyen Viet, Olivier Christiaens, Guy Smagghe, Peter Bossier (2022). The Sex-Specific Splicing of Doublesex in Brine Shrimp <i>Artemia franciscana</i> . Genes.

Stephanie De Vos, Stephane Rombauts, Louis Coussement, Wannes Dermauw, Marnik Vuylsteke, patrick sorgeloos, James S. Clegg, Ziro Nambu, Filip Van Nieuwerburgh, Parisa Norouzitallab, et al.(2021). The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments . BMC Genomics. 22. (1). Springer Science and Business Media {LLC}

Stephanie De Vos, Alireza Asem, Amin Eimanifar, Nasrullah Rastegar-Pouyani, Francisco Hontoria, Gilbert Van Stappen, Shi-Chun Sun(2020). An overview on the nomenclatural and phylogenetic problems of native Asian brine shrimps of the genus Artemia Leach, 1819 (Crustacea, Anostraca) . ZooKeys. 902. p. 1--15. Pensoft Publishers

Stephanie De Vos, Wisarut Junprung, Parisa Norouzitallab, Anchalee Tassanakajon, Dung Nguyen Viet, Gilbert Van Stappen, Peter Bossier(2019). Sequence and expression analysis of HSP70 family genes in Artemia franciscana . Scientific Reports. 9. (1). Springer Science and Business Media {LLC}

Stephanie De Vos, An-Qi Li, Zhan-Peng Sun, Xu Liu, Jin-Shu Yang, Feng Jin, Lin Zhu, Wen-Huan Jia, Gilbert Van Stappen, Peter Bossier, et al.(2019). The chloride channel cystic fibrosis transmembrane conductance regulator (CFTR) controls cellular quiescence by hyperpolarizing the cell membrane during diapause in the crustacean Artemia . Journal of Biological Chemistry. 294. (16). p. 6598--6611. Elsevier {BV}

Stephanie De Vos, G. Van Stappen, P. Sorgeloos, M. Vuylsteke, S. Rombauts, P. Bossier(2019). Identification of salt stress response genes using the Artemia transcriptome . Aquaculture. 500. p. 305--314. Elsevier {BV}

Stephanie De Vos, Nguyen Viet Dung, Olivier Christiaens, Duy Le Van Bao, Thomas H. MacRae, Guy Smagghe, Peter Bossier(2019). Identification of RNAi-related genes and transgenerational efficiency of RNAi in Artemia franciscana . Aquaculture. 501. p. 285--292. Elsevier {BV}

Stephanie De Vos, Alireza Asem, Weidong Li, Pei-Zheng Wang, Amin Eimanifar, Chun-Yang Shen, Gilbert Van Stappen(2019). The complete mitochondrial genome of <i>Artemia sinica</i> Cai, 1989 (Crustacea: Anostraca) using next-generation sequencing . Mitochondrial DNA Part B. 4. (1). p. 746--747. Informa {UK} Limited

Stephanie De Vos, Dong-Rui Li, Hui-Li Ye, Jin-Shu Yang, Fan Yang, Mo-Ran Wang, Marnik Vuylsteke, Patrick Sorgeloos, Gilbert Van Stappen, Peter Bossier, et al.(2017). Identification and characterization of a Masculinizer ( Masc ) gene involved in sex differentiation in Artemia . Gene. 614. p. 56--64. Elsevier {BV}

Stephanie De Vos, Hui-Li Ye, Dong-Rui Li, Jin-Shu Yang, Dian-Fu Chen, Marnik Vuylsteke, Patrick Sorgeloos, Gilbert Van Stappen, Peter Bossier, Hiromichi Nagasawa, et al.(2017). Molecular characterization and functional analyses of a diapause hormone receptor-like gene in parthenogenetic Artemia . Peptides. 90. p. 100--110. Elsevier {BV}

Stephanie De Vos, Peter Bossier, Gilbert Van Stappen, Ilse Vercauteren, Patrick Sorgeloos, Marnik Vuylsteke(2013). A first AFLP-Based Genetic Linkage Map for Brine Shrimp Artemia franciscana and Its Application in Mapping the Sex Locus . PLoS ONE. 8. (3). p. e57585. Public Library of Science ({PLoS})

Stephanie De Vos, Yaquelyn Nerey, Joke Pannecoucque, H&#233;ctor Pablo Hernandez, Manuel Diaz, Ray Espinosa, Sarah Van Beneden, Lidcay Herrera, Monica H&#246;fte(2010). Rhizoctonia spp. Causing Root and Hypocotyl Rot in Phaseolus vulgaris in Cuba . Journal of Phytopathology. 158. (4). p. 236--243. Wiley

DISSERTATION THESIS

Stephanie De Vos (2014). Genomic tools and sex determination in the extremophile brine shrimp Artemia franciscana .

Stephanie De Vos (2008). Characterization, pathogenicity and integrated control of Cuban Rhizoctonia solani‐isolates on bean.