Our People

Antti Karkman Computational microbiologist interested in antibiotic resistance in the environment

Number of changes in anvi'o code: 2

Most changes in: anvio/cli/process_genbank.py

Latest commit: "anvi-process-genbank now also includes the tRNA and rRNA, and non-coding features (pseudogenes)" on 20 May 2026

Isa Wilkie Marine microbiologist specialising in bioinformatic analysis of microbial populations, with experience developing pipelines for metagenomics, structural annotation, and population-level variation.

Isa 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.

Metehan Sever

Number of changes in anvi'o code: 534

Most changes in: anvio/data/interactive/index.html

Latest commit: "Add mode" on 10 March 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: 749

Most changes in: anvio/workflows/ecophylo/Snakefile

Latest commit: "fix" on 31 July 2025

Mateu Menendez-Serra Computational ecologist integrating ancient environmental genomics, microbial ecology, and statistical modeling to reconstruct past ecosystems and study long-term ecosystem dynamics.

Mateu 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.

Sarah Tucker I am a marine microbiologist interested in the genomic, metabolic, and physiological diversity of microorganisms and how this diversity impacts ecological interactions and ocean processes.

Number of changes in anvi'o code: 2

Most changes in: anvio/data/misc/PEOPLE/CONTRIBUTORS.yaml

Latest commit: "Add git_records for Sarah Tucker" on 15 December 2025

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: 34

Most changes in: anvio/data/misc/PEOPLE/DEVELOPERS.yaml

Latest commit: "fix cazyme description" on 28 January 2026

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

María Alejandra Valdez Cabrera Mathematical statistician developing methods for complex data structures arising in health and biological sciences

María 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.

Luigi Gallucci Microbial ecologist exploring deep-sea environments to study microbial evolution and the dispersion patterns connecting hydrothermal vents with the open ocean.

Luigi 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.

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

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

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: 8041

Most changes in: anvio/dbops.py

Latest commit: "detail can use / can provide usatge" on 27 May 2026

Avril Hoyningen-Huene I am a microbial ecologist delving into the dynamics of phytoplankton functional changes in response to saesonal environmental changes.

Number of changes in anvi'o code: 1

Most changes in: anvio/data/misc/PEOPLE/AVATARS/avrilhoyningen.jpg

Latest commit: "add avril and xixi to contributors.yaml" on 20 May 2026

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

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

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.

Moritz Buck

Number of changes in anvi'o code: 3

Most changes in: anvio/drivers/metabat2.py

Latest commit: "Fixed metbat2 parser" on 21 June 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

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

Bastien Camillo PhD Student in Multi-Species Comparative Genomics on Diatoms, also interested in Exobiology & Synthetic Biology

Bastien 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

Ahmed Belfaqih Microbiology master's student with a growing focus on bioinformatics

Number of changes in anvi'o code: 16

Most changes in: anvio/panrep.py

Latest commit: "added logging and simplified sanity_check" on 25 May 2026

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

Blandine Trouche Microbial ecologist studying the biogeography and adaptation of microbial life to the greatest ocean depths

Number of changes in anvi'o code: 2

Most changes in: anvio/data/misc/PEOPLE/AVATARS/btrouche.png

Latest commit: "added picture btrouche" on 20 May 2026

Xabier Vázquez-Campos Environmental microbiologist and bioinformatician - interested in all things 'omics, extremophiles, taxonomy and systematics, evolution...

Number of changes in anvi'o code: 9

Most changes in: anvio/clustering.py

Latest commit: "remove dup hamming" on 06 January 2026

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.

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.

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

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

Number of changes in anvi'o code: 361

Most changes in: anvio/profiler.py

Latest commit: "update doc for gene highlight" on 29 May 2026

Sarah Teichman Biostatistician interested in differential abundance methodology and statistical education

Number of changes in anvi'o code: 1

Most changes in: anvio/data/misc/PEOPLE/AVATARS/MariaAVC.png

Latest commit: "add maria valdez cabrera and sarah teichman to contributors, associated with statdivlab tutorials" on 05 December 2025

Dylan Mankel Geomicrobiologist studying the activity and distribution of life in extreme environments.

Number of changes in anvi'o code: 5

Most changes in: anvio/docs/artifacts/variability-profile-txt.md

Latest commit: "Update variability-profile-txt.md" on 17 February 2026

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.

Eeva Eronen-Rasimus Microbial ecologist interested in how bacteria survive in ice, their coupling with sea-ice algae and ultimately, their contribution to carbon cycling in the oceans and the consequences of diminishing sea ice for bacteria mediated processes.

Eeva 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.

Sarahi L. Garcia Microbial ecologist studying interactions at different levels of microbial organization.

Number of changes in anvi'o code: 3

Most changes in: anvio/docs/programs/anvi-gen-pan-representative.md

Latest commit: "updated documentation for pan representative" on 21 May 2026

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

Igor S. Pessi Microbiologist specialized in the study of polar microbial communities, with a focus on the use of molecular ecology methods such as metagenomics and metatranscriptomics.

Number of changes in anvi'o code: 3

Most changes in: anvio/cli/kofam_accessions_to_hmms_directory.py

Latest commit: "fixed __authors__" on 21 May 2026

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

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: 2355

Most changes in: anvio/biochemistry/reactionnetwork.py

Latest commit: "remove unreachable except block, since missing reference isoacceptors have already been filtered" on 28 May 2026

Kathryn Kananen Bioinformatician and computational biologist interested in population genetics, automation, and genomic architecture exploration

Number of changes in anvi'o code: 22

Most changes in: anvio/tests/unit/workflows/test_manifest.py

Latest commit: "Fixed workflow -pan.db ending error; fixed component test json reference" on 21 May 2026

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

Chiara Vanni Bioinformatician interested in making sense of the functional unknowns in meta(genomes). Recently experimenting with ancient metagenomics.

Number of changes in anvi'o code: 1

Most changes in: anvio/data/misc/PEOPLE/CONTRIBUTORS.yaml

Latest commit: "update contributor info for Chiara Vanni" on 20 May 2026

Benjamin Luke Coltman Bioinformatician working on simplifying microbiome complexity

Number of changes in anvi'o code: 11

Most changes in: anvio/drivers/hmmer.py

Latest commit: "Fixes #2539 by adding a simple fix for backward compatibility" on 11 February 2026

Andrea Telatin Head of Bioinformatics at the Quadram Institute Bioscience, Norwich, UK. Interested in metagenomics, microbial ecology, and open science.

Number of changes in anvi'o code: 13

Most changes in: sandbox/anvi-script-reformat-bam

Latest commit: "This was not using the class but relied on argparse.ArgumentParser" on 21 May 2026

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

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.

Georges Kanaan (Gio) Oceanographer & Astrobiologist. Computer scientist. Studying sea-ice bacteria.

Number of changes in anvi'o code: 38

Most changes in: anvio/cogs.py

Latest commit: "Small bug fix in kaiju parser assuming 20 phylums" on 19 February 2025

Guillermo Rangel-Pineros I am a microbiologist and bioinformatician interested in the development of computational workflows for the analysis of ancient microbial DNA

Number of changes in anvi'o code: 1

Most changes in: anvio/data/misc/PEOPLE/AVATARS/anvio-yunjeong.png

Latest commit: "added contributors details Guillermo, Mateu, Yunjeong" on 20 May 2026

Xi Chen (Xixi) I am a bioinformatician and microbial ecologist. I enjoy tailoring computational methods to explore the diversity and dynamics of microbes. My current focus is on those that live in the ocean.

Number of changes in anvi'o code: 2

Most changes in: anvio/docs/programs/anvi-split.md

Latest commit: "Update anvi-split docs to reflect contig-only split mode. See issue 2605." on 20 May 2026

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.

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

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.

Joseph Nesme Microbial ecologist studying plasmid diversity in the environment

Number of changes in anvi'o code: 4

Most changes in: anvio/workflows/pangenomics/Snakefile

Latest commit: "Add support for --I-know-this-is-not-a-good-idea flag in pangenomics workflow" on 27 January 2026

Yunjeong So Microbiome researcher specialising in the functional analysis of modern and ancient microbial communities, using computational approaches to study microbial functions relevant to human health and the environment

Yunjeong 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: 313

Most changes in: anvio/panops.py

Latest commit: "get-sequences-for-genecalls fix when using genomes.db" on 05 May 2026

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

Number of changes in anvi'o code: 2544

Most changes in: anvio/kegg.py

Latest commit: "add to the docs" on 26 May 2026

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: 4

Most changes in: anvio/data/misc/PEOPLE/AVATARS/bio-daan.jpg

Latest commit: "updated the GlobDB functions documentation markdown file" on 22 May 2026

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.

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.

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

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

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

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

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