Pierre J. - Postdoctoral Researcher

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Leipzig, Germany

Experience

Sep 2023 - Sep 2025

2 years 1 month

Dresden, Germany

Postdoctoral Researcher

Anna Poetsch’s Biomedical Genomics Group

Benchmarked multiple LLMs for genomic prediction tasks, ensuring rigorous evaluation across architectures and datasets.
Extended and streamlined in-lab LLM architecture, broadening its applicability and developing tools to enhance interpretability.
Identified sequence and epigenetic factors underlying human genome stability, enabling deeper insights into their distinct roles in genome biology.
Mentored and designed projects for several master’s students and interns, leading to highly graded reports and development of pipelines with lab-wide applications.

Jun 2022 - Jul 2022

2 months

South San Francisco, United States

Computational Biology Intern

Myriad Genetics

Constructed optimized data analysis pipeline that improved diagnostic accuracy of fetal aneuploidies in non-invasive prenatal testing.

Aug 2018 - May 2023

4 years 10 months

Berkeley, United States

Graduate Student

Ksenia Krasileva Lab, University of California, Berkeley

Developed and led projects in fungal plant pathogen evolution, bringing a new field of study to the lab.
Developed a novel sequencing and analysis pipeline for detecting circular DNAs, discovering a previously unknown aspect of fungal plant pathogen evolution.
Led international collaboration, generating sequences for 70 new fungal plant pathogen genomes.
Built scalable pipelines for genome assembly and data integration, NGS analysis, and scalable workflow development. Skilled in Python, R, HPC, and combining statistical and machine learning approaches to extract biological insights.
Identified epigenetic markers linked to genome evolution in fungal plant pathogens, paving the way for improved disease resistant crop selection.
Mentored and designed project for an undergraduate researcher resulting in a co-first author publication.

Jun 2017 - Jun 2018

1 year 1 month

Seattle, United States

Research Scientist

Sharon Doty Lab, University of Washington

Oct 2015 - Jun 2017

1 year 9 months

Seattle, United States

Undergraduate Researcher

Sharon Doty Lab, University of Washington

Discovered and characterized plant-associated microbes later licensed for agricultural applications.
Led training and supervision of undergraduate researchers in molecular biology, experimental design and writing, resulting in increased lab productivity and fellowship success rates.
Performed supply management and budgeting, reducing waste and material costs.

Summary

Computational biologist with expertise in multi-omics data integration, NGS analysis, and scalable workflow development.

Skilled in Python, R, HPC, and combining statistical and machine learning approaches to extract biological insights.

Passionate about translating data-driven discoveries into advances in drug development and human health.

Skills

Reproducible data analysis with Python, R, bash, git.
Expertise in NGS data analysis and multi-omics.
Experience with workflow managers (WDL, Snakemake), HPC and cloud environments.

Languages

English

Native

German

Elementary

Education

Aug 2018 - May 2023

University of California, Berkeley

PhD in Microbiology with Designated Emphasis in Computational and Genomic Biology · Microbiology with Designated Emphasis in Computational and Genomic Biology · Berkeley, United States

Sep 2013 - Jun 2017

University of Washington

B.S. Biology (Molecular, Cellular, and Developmental) · Biology (Molecular, Cellular, and Developmental) · Seattle, United States

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Mathew D.

Experience

Postdoctoral Researcher

Anna Poetsch’s Biomedical Genomics Group

Computational Biology Intern

Myriad Genetics

Graduate Student

Ksenia Krasileva Lab, University of California, Berkeley

Research Scientist

Sharon Doty Lab, University of Washington

Undergraduate Researcher

Sharon Doty Lab, University of Washington

Summary

Skills

Languages

Education

University of California, Berkeley

PhD in Microbiology with Designated Emphasis in Computational and Genomic Biology · Microbiology with Designated Emphasis in Computational and Genomic Biology · Berkeley, United States

University of Washington

B.S. Biology (Molecular, Cellular, and Developmental) · Biology (Molecular, Cellular, and Developmental) · Seattle, United States

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