Our People
A randomly ordered, ever-growing list of 48 anvi’o developers and contributors.
Emily Fogarty
Microbiologist developing computational and wet lab strategies to study horizontal gene transfer in the human gut microbiome.
Number of changes in anvi'o code: 4
Most changes in: anvio/utils.py
Latest commit: "Added quince-mode flag" on 12 May 2020
A. Murat Eren (Meren)
Computer scientist and microbial ecologist interested in understanding mechanisms by which microbes interact with their surroundings, evolve, disperse, and respond to environmental change.
Number of changes in anvi'o code: 7120
Most changes in: anvio/dbops.py
Latest commit: "rogue git users identified." on 28 April 2025
Vini Salazar
Researcher, open-source developer and aspiring marine microbiologist.
Vini has not yet contributed to the codebase, but they are recognized for less tangible but equally valuable contributions, such as providing input to solve technical issues or lending their expertise to create new workflows in anvi'o.
Benjamin Luke Coltman
Bioinformatician working on simplifying microbiome complexity
Number of changes in anvi'o code: 3
Most changes in: anvio/drivers/hmmer.py
Latest commit: "Adding developer details" on 15 April 2025
Samuel Miller
Computational and molecular microbiologist studying how microbes function in their environments through tRNA-sequencing, proteomics, and metagenomics.
Number of changes in anvi'o code: 1499
Most changes in: anvio/biochemistry/reactionnetwork.py
Latest commit: "fix merging reaction network categories" on 23 January 2025
Elaina Graham
Elaina has not yet contributed to the codebase, but they are recognized for less tangible but equally valuable contributions, such as providing input to solve technical issues or lending their expertise to create new workflows in anvi'o.
Xabier Vázquez-Campos
Environmental microbiologist and bioinformatician - interested in all things 'omics, extremophiles, taxonomy and systematics, evolution...
Number of changes in anvi'o code: 5
Most changes in: sandbox/anvi-script-FASTA-to-contigs-db
Latest commit: "adding contributor info" on 15 March 2022
Hilary Morrison
A long and winding road to microbial ecology
Number of changes in anvi'o code: 2
Most changes in: anvio/data/misc/PEOPLE/CONTRIBUTORS.yaml
Latest commit: "Update CONTRIBUTORS.yaml" on 08 July 2022
Jessica Pan
Computer scientist interested in computational methods to investigate microbial ecosystems and making those techniques more accessible to others.
Number of changes in anvi'o code: 309
Most changes in: anvio/docs/__init__.py
Latest commit: "fixed a typo" on 07 January 2021
Kathryn Kananen
Bioinformatician and computational biologist interested in population genetics, automation, and genomic architecture exploration
Number of changes in anvi'o code: 4
Most changes in: anvio/data/misc/PEOPLE/AVATARS/KatKananen.jpg
Latest commit: "Removed image blur" on 15 February 2024
Antti Karkman
Computational microbiologist interested in antibiotic resistance in the environment
Number of changes in anvi'o code: 1
Most changes in: anvio/data/misc/PEOPLE/CONTRIBUTORS.yaml
Latest commit: "Update CONTRIBUTORS.yaml" on 14 January 2022
Evan Kiefl
Computational biologist and software developer. For my PhD I studied how selective pressures shape the evolution of proteins in naturally occurring microbial populations.
Number of changes in anvi'o code: 1746
Most changes in: anvio/variabilityops.py
Latest commit: "Update DEVELOPERS.yaml" on 06 December 2023
Patrick J. H. Bradley
Bioinformatician interested in Metagenomics, Statistical Modeling, Microbial Evolution, Functional Genomics and Metabolism
Patrick has not yet contributed to the codebase, but they are recognized for less tangible but equally valuable contributions, such as providing input to solve technical issues or lending their expertise to create new workflows in anvi'o.
Andrea Watson
Microbiologist interested in combining wet lab and computational methods in a complementary way to answer fundamental questions.
Number of changes in anvi'o code: 10
Most changes in: anvio/inversions.py
Latest commit: "cont only if contig stretches long enough #1970" on 22 August 2022
Antonio Fernandez-Guerra
Bioinformatician interested in development and application of new methodologies to analyze modern and ancient (meta)genomic data.
Antonio has not yet contributed to the codebase, but they are recognized for less tangible but equally valuable contributions, such as providing input to solve technical issues or lending their expertise to create new workflows in anvi'o.
Quentin Clayssen
Microbiologist and bioinformatician interested in metagenomics.
Number of changes in anvi'o code: 89
Most changes in: anvio/taxoestimation.py
Latest commit: "add some modifications lost during merging" on 16 September 2019
Daan R. Speth
Microbiologist and bioinformatician interested in understanding the metabolic and phylogenetic diversity of microorganisms through genomics and wet lab analyses
Number of changes in anvi'o code: 2
Most changes in: anvio/data/misc/PEOPLE/AVATARS/bio-daan.jpg
Latest commit: "add Daan Speth info to contributors" on 17 January 2022
Florian Trigodet
Microbiologist using advanced computational strategies to make sense of the microbial ecology of complex habitats.
Number of changes in anvi'o code: 86
Most changes in: anvio/inversions.py
Latest commit: "Check for unmapped reads" on 13 March 2025
Robert Murphy
Microbiologist and bioinformatician - intrested in microbial communites present in symbiosis as a source for novel secondary metabolites
Robert has not yet contributed to the codebase, but they are recognized for less tangible but equally valuable contributions, such as providing input to solve technical issues or lending their expertise to create new workflows in anvi'o.
Srinidhi Varadharajan
Number of changes in anvi'o code: 4
Most changes in: sandbox/anvi-script-variability-to-vcf
Latest commit: "Ordering sample IDs" on 06 December 2018
Alon Shaiber
Computational scientist previously studying microbial ecology, currently studying structural variation in cancer genomics, and what's next? Who knows?
Number of changes in anvi'o code: 892
Most changes in: anvio/workflows/metagenomics/Snakefile
Latest commit: "change Alon's bio" on 14 January 2022
Matthew Schechter
Microbiologist interested in combining comparative genomics and environmental metagenomics to identify genetic determinants of fitness in microbial populations in the human gut and ocean microbiome.
Number of changes in anvi'o code: 734
Most changes in: anvio/workflows/ecophylo/Snakefile
Latest commit: "mock dataset generation for ecophylo" on 16 December 2024
Moritz Buck
Number of changes in anvi'o code: 1
Most changes in: sandbox/anvi-script-compute-bayesian-pan-core
Latest commit: "added anvi-script-compute-bayesian-pan-core to the sandbox" on 12 July 2021
Oleg Vlasovets
Data Scientist studying bacteria in human gut.
Number of changes in anvi'o code: 3
Most changes in: anvio/data/misc/PEOPLE/DEVELOPERS.yaml
Latest commit: "fix the typo" on 15 March 2024
Ryan Moore
Number of changes in anvi'o code: 49
Most changes in: sandbox/anvi-script-visualize-split-coverages
Latest commit: "Add tests for xlim bug (#1481, #1482)" on 06 August 2020
Metehan Sever
Number of changes in anvi'o code: 460
Most changes in: anvio/data/interactive/index.html
Latest commit: "Add mode" on 10 March 2025
Chiara Vanni
Chiara has not yet contributed to the codebase, but they are recognized for less tangible but equally valuable contributions, such as providing input to solve technical issues or lending their expertise to create new workflows in anvi'o.
C. Titus Brown
Bioinformatics software developer and microbiome enthusiast.
Number of changes in anvi'o code: 6
Most changes in: anvio/data/misc/PEOPLE/DEVELOPERS.yaml
Latest commit: "fix typo" on 27 July 2023
Simon Roux
Viral ecologist and bioinformatician at the DOE JGI - interested in everything phage, 'omics, microbial and viral ecology and evolution, virus-host interactions, etc
Simon has not yet contributed to the codebase, but they are recognized for less tangible but equally valuable contributions, such as providing input to solve technical issues or lending their expertise to create new workflows in anvi'o.
Mahmoud Yousef
Computer scientist and medical student interested in exploring the intersection of bioinformatics and medicine, and how bioinformatic techniques can be used to advance the quality of medicine.
Number of changes in anvi'o code: 39
Most changes in: anvio/utils.py
Latest commit: "We can safely remove this now" on 06 February 2020
Jessika Fuessel
Biogeochemist and microbiologist intereted in understanding the production and fate of microbial metabolites within the context of changing environmental conditions using a multi-omics.
Number of changes in anvi'o code: 7
Most changes in: anvio/docs/programs/anvi-interactive.md
Latest commit: "Update anvi-interactive.md" on 25 April 2024
Mike Lee
Bioinformatician exploring microbial ecology and evolution in a wide range of environments.
Number of changes in anvi'o code: 23
Most changes in: sandbox/anvi-script-genbank-to-external-gene-calls
Latest commit: "Update DEVELOPERS.yaml" on 21 May 2024
Dan Utter
Microbial ecologist interested in the evolution and maintenance of diversity in complex natural communities, mostly using bioinformatics
Number of changes in anvi'o code: 4
Most changes in: anvio/data/misc/PEOPLE/AVATARS/bio-dutter.jpg
Latest commit: "add dutter to contributors" on 07 June 2022
Sebastian Cristian Treitli
Microbiologist and bioinformatician - interested in protists and symbiotic interactions between protists and bacteria.
Sebastian has not yet contributed to the codebase, but they are recognized for less tangible but equally valuable contributions, such as providing input to solve technical issues or lending their expertise to create new workflows in anvi'o.
Alexander Henoch
I am a biologist-turned-computer scientist interested in understanding the influence of the environmental change on the genetic composition of microbial populations.
Number of changes in anvi'o code: 1
Most changes in: requirements.txt
Latest commit: "added networkx for PanGraph extension" on 26 September 2023
Georges Kanaan
Oceanographer & Astrobiologist in training. Computer scientist. Studying sea-ice bacteria.
Number of changes in anvi'o code: 40
Most changes in: anvio/cogs.py
Latest commit: "Small bug fix in kaiju parser assuming 20 phylums" on 19 February 2025
Daniel Blankenberg
Number of changes in anvi'o code: 8
Most changes in: anvio/__init__.py
Latest commit: "Fix for LinkMers.list_contigs(). Since we require all BAMs to have the same contigs, we'll just use the values from the first BAM file." on 14 March 2019
Jarrod J. Scott
Microbiologist interested in understanding how bacteria and archaea coalesce into complex communities and how they affect host biology, biogeochemical cycles, and ecosystem-level processes in marine and terrestrial systems.
Jarrod has not yet contributed to the codebase, but they are recognized for less tangible but equally valuable contributions, such as providing input to solve technical issues or lending their expertise to create new workflows in anvi'o.
Tom O. Delmont
Microbial ecologist who seeks to understand small and large-scale ecological patterns in the microbial world.
Tom has not yet contributed to the codebase, but they are recognized for less tangible but equally valuable contributions, such as providing input to solve technical issues or lending their expertise to create new workflows in anvi'o.
Kathryn Lambert-Slosarska (Katy)
I am a marine (micro)biologist utilising computational approaches to understand the dynamism and impact of diversity-generating retroelements in microbial lifestyles within changing marine ecosystems.
Number of changes in anvi'o code: 3
Most changes in: anvio/data/misc/PEOPLE/DEVELOPERS.yaml
Latest commit: "Add files via upload" on 28 April 2025
Nick Youngblut
Microbiologist studying methanogens and host-microbiome coevolution
Number of changes in anvi'o code: 6
Most changes in: .github/workflows/ci.yml
Latest commit: "added avatar" on 10 April 2022
Özcan C. Esen
Computer engineer interested in developing tools for the visualization of complex data.
Number of changes in anvi'o code: 2088
Most changes in: anvio/data/interactive/js/main.js
Latest commit: "remove h5py dependency" on 07 January 2020
Isaac Fink
Computer scientist interested in enhancing the power and accessibility of computational strategies to study microbial life.
Number of changes in anvi'o code: 120
Most changes in: anvio/data/interactive/js/charts.js
Latest commit: "fix for manually colored genes" on 13 December 2022
Andrea Telatin
Senior Bioinformatician at the Quadram Institute Bioscience, Norwich, UK. Interested in metagenomics, microbial ecology, and open science.
Number of changes in anvi'o code: 8
Most changes in: sandbox/anvi-script-reformat-bam
Latest commit: "update docs" on 03 November 2023
Dylan Mankel
Geomicrobiologist studying the activity and distribution of life in extreme environments.
Number of changes in anvi'o code: 4
Most changes in: anvio/docs/programs/anvi-gen-variability-profile.md
Latest commit: "Update anvi-gen-variability-profile.md" on 11 May 2025
Iva Veseli
Computer scientist and biologist who leverages computational methods to study microbial metabolism in environmental metagenomes.
Number of changes in anvi'o code: 2213
Most changes in: anvio/kegg.py
Latest commit: "fix typo" on 28 April 2025
Matthew Lawrence Klein
Software developer interested in the role of technology in supporting a more equitable future on planet earth.
Number of changes in anvi'o code: 221
Most changes in: anvio/data/interactive/js/main.js
Latest commit: "better cotextual accordion show" on 14 April 2022
Amy D. Willis
Statistician and data scientist developing methods for the analysis of biodiversity, with a particular focus on the microbiome.
Number of changes in anvi'o code: 5
Most changes in: sandbox/anvi-script-run-functional-enrichment-stats
Latest commit: "address issue1828 with new lambda catches" on 10 November 2021