Our People

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

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

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.

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

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

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.

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

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

Florian Trigodet Microbiologist using advanced computational strategies to make sense of the microbial ecology of complex habitats.

Number of changes in anvi'o code: 87

Most changes in: anvio/inversions.py

Latest commit: "Update log file" on 03 June 2025

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

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

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

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

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.

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

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

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

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

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.

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

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

Iva Veseli Computer scientist and biologist who leverages computational methods to study microbial metabolism in environmental metagenomes.

Number of changes in anvi'o code: 2214

Most changes in: anvio/kegg.py

Latest commit: "Set version requirement for meme" on 28 May 2025

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

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

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

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

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

Benjamin Luke Coltman Bioinformatician working on simplifying microbiome complexity

Number of changes in anvi'o code: 4

Most changes in: anvio/drivers/hmmer.py

Latest commit: "Rather than loading all hits into memory, this update chunks the processing. This is quicker than processing it a single line at a time, but will avoid overloading RAM. Related to PR #2423." on 03 June 2025

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

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

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

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: 7124

Most changes in: anvio/dbops.py

Latest commit: "update mini CV" on 12 June 2025

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

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

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.

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.

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

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

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.

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

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

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.

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

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

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

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.

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

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.