Anthony Fullam - Bioinformatics Software Engineer

Anthony Fullam
Bioinformatics Software Engineer @ EMBL • Heidelberg, Germany

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0 Citations

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Featured Work

Tools and research making an impact in bioinformatics

GUNC: Detecting the invisible contamination in prokaryotic genomes

Discovered that 15-30% of "high-quality" metagenome-assembled genomes were actually chimeras - contamination that existing quality control tools completely missed. GUNC detects chimerism by analyzing the lineage homogeneity of individual contigs, revealing hidden genome assembly artifacts.

Impact

Revealed 15-30% of 'high-quality' MAGs were undetected chimeras
250+ citations since 2021 publication in Genome Biology
Improved quality standards for prokaryotic genome databases worldwide

Python Bioinformatics algorithms Taxonomic classification HPC/parallel processing

GitHub Paper Docs

proGenomes: 2 million consistently annotated prokaryotic genomes

Led development of proGenomes3 and proGenomes4, the world's largest consistently processed and annotated database of high-quality prokaryotic genomes. Provides researchers with a reliable foundation for comparative genomics, phylogenetics, and functional studies across bacterial and archaeal diversity.

Impact

Scaled from 87K genomes (proGenomes2) to 2 million (proGenomes4)
Consistent annotation pipeline ensures comparability across all genomes
Used by thousands of researchers for comparative genomics
Integrated with major bioinformatics tools and workflows

Python Nextflow pipelines Database management Large-scale data processing Web interfaces

Website GitHub Paper

SPIRE: Integrating metagenome-derived data at planetary scale

Co-led development of SPIRE, a comprehensive resource integrating consistently processed metagenome-derived microbial data across habitats, geography, and phylogeny. Enables researchers to explore the global microbiome with unprecedented scope and consistency.

Impact

Integrated data from thousands of metagenomes worldwide
Unified interface for exploring microbial diversity across ecosystems
Consistent processing enables cross-study comparisons
Published in Nucleic Acids Research (2024)

Metagenomics pipelines Database architecture Web development Data integration

Website Paper

Research Impact

68 Publications • 5,214 Citations

Featured First Author

GUNC: detection of chimerism and contamination in prokaryotic genomes

Genome Biology • 2021

270+ citations

Paper Code DOI

Featured First Author

proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes

Nucleic Acids Research • 2023

65+ citations

Paper Database DOI

Featured First Author

SPIRE: a Searchable, Planetary-scale mIcrobiome REsource

Nucleic Acids Research • 2024

75+ citations

Paper DOI

Featured First Author

VIRE: a metagenome-derived, planetary-scale virome resource with environmental context

Nucleic Acids Research • 2025

New citations

Paper DOI

Featured First Author

proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes

Nucleic Acids Research • 2025

New citations

Paper Database DOI

Drivers and determinants of strain dynamics following fecal microbiota transplantation

Nature Medicine • 2022

205+ citations

Paper DOI

A faecal microbiota signature with high specificity for pancreatic cancer

Gut • 2022

265+ citations

Paper DOI

Discovery of antimicrobial peptides in the global microbiome with machine learning

Cell • 2024

280+ citations

Paper DOI

Technical Expertise

Skills and technologies for bioinformatics research and software development

Bioinformatics & Genomics

Expertise in computational analysis of biological data

Prokaryotic Genomics expert

Genome assembly, annotation, quality control
Metagenomics expert

MAG recovery, taxonomic profiling, functional analysis
Genome Quality Control expert

Contamination detection, chimera identification
Phylogenomics advanced

Phylogenetic analysis, taxonomic classification
Comparative Genomics expert

Cross-genome analysis, functional prediction
Sequence Analysis expert

Alignment, annotation, homology detection

Software Development

Building robust, scalable bioinformatics tools

Python expert

Primary language for bioinformatics pipelines and tools

Biopython NumPy Pandas Click
Nextflow advanced

Workflow management and pipeline development
Bash/Shell Scripting expert

Automation, data processing, system administration
R intermediate

Statistical analysis and visualization
Git/Version Control expert

Collaborative development, code review
Software Design advanced

API design, modular architecture, testing

Data Science & Analysis

Large-scale data processing and analysis

Statistical Analysis advanced

Hypothesis testing, modeling, interpretation
Data Visualization advanced

Creating clear, informative scientific visualizations

matplotlib ggplot2 plotly
Database Management advanced

SQL, database design, query optimization
Large-scale Data Processing expert

Processing millions of genomes and metagenomes

Infrastructure & DevOps

Deploying and maintaining bioinformatics infrastructure

High-Performance Computing expert

SLURM, PBS, parallel processing
Containerization advanced

Reproducible software environments

Docker Singularity
CI/CD advanced

Automated testing and deployment

GitHub Actions GitLab CI
Linux Systems expert

Server administration, optimization
Cloud Computing intermediate

Cloud-based bioinformatics workflows

AWS GCP

Developed Tools

GUNC

Genome quality control

proGenomes

Genome database

Professional Experience

Building impactful bioinformatics tools and contributing to scientific research

2019-05 – Present

Senior Bioinformatics Software Engineer

EMBL

Bork Group

Heidelberg, Germany

academic

Leading development of bioinformatics tools and databases for genome quality assessment and prokaryotic genomics research. Building software used by thousands of researchers worldwide.

Developed GUNC tool for genome contamination detection (260+ citations)
Led proGenomes database evolution from 87K to 2 million genomes
Co-developed SPIRE and VIRE planetary-scale microbiome resources

Python Nextflow HPC Metagenomics Database development

Bork Group → EMBL →

2017-05 – 2019-04

Bioinformatician

German Cancer Research Center (DKFZ)

Genomics and Proteomics Core Facility

Heidelberg, Germany

industry

Contributed bioinformatics expertise to cancer genomics research, supporting core facility operations and collaborative research projects.

Supported genomics and proteomics analysis workflows
Collaborated on cancer genomics projects

Bioinformatics pipelines Genomics Core facility operations

DKFZ →

2014-03 – 2017-04

Postdoctoral Fellow

Wellcome Trust Sanger Institute

Cancer Genome Project

Hinxton, Cambridge, UK

academic

Postdoctoral research in cancer genomics within the Cancer Genome Project under Dr. Peter Campbell. Conducted computational analysis of cancer genomes and contributed to understanding somatic mutations in cancer.

Co-authored research on mitochondrial DNA transfer in cancer cells
Contributed to Cancer Genome Project initiatives
Developed computational methods for cancer genomics analysis

Cancer genomics Bioinformatics Genomic analysis Python R

Sanger Institute → Cancer Genome Project →

2009-09 – 2013-12

PhD - Post-Graduate Researcher

NUI Maynooth

Host-Pathogen Interaction Laboratory

Maynooth, Ireland

academic

Doctoral research on "The role of the human DEAD-box protein DDX3 in type I interferon induction" under Dr. Martina Schroeder. Investigated host-pathogen interactions and innate immune responses at the molecular level.

Characterized DDX3 protein's role in antiviral immune responses
Developed expertise in molecular biology and cell signaling
Published findings on interferon induction mechanisms

Cell culture Co-Immunoprecipitation Molecular Cloning qRT-PCR Confocal Microscopy siRNA Knockdown Luciferase Reporter Assays

Maynooth University →