Table of Contents

Interested in joining? Please consider reading the lab culture and expectations first. Some information on our location and space is here. Interested in visiting? Please do! We welcome visitors and short-term research stays as long as we are able -- please send an email to any of us to start the conversation.

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This is the most current one. We have an archive of them here.

From left-bottom of the photo to the top of the stairs: Alex Henoch, Iva Veseli, Florian Trigodet, Xixi Chen, Kathryn Lambert-Slosarska (Katy), Metehan Sever. The bottom pair, left-to-right: Avril von Hoyningen-Huene, Chris Robinson (who happened to be visiting our group from the University of Indiana at the time). The top pair: Raïssa Meyer, Sarah Tucker. The photograph is missing our colleagues Samuel Miller, Matthew Schechter, Jessika Fuessel, Amy Willis, and Marie Carstensen who couldn't make it for various reasons.

Current Members (sorted by name)

A. Murat Eren (Meren) bio photo

A. Murat Eren (Meren) (PI)

I am a computer scientist with a deep appreciation for the complexity of life. I design algorithms and experiments to better understand microbes and their ecology.

Affiliations Papers Blog posts
Alexander Henoch bio photo

Alexander Henoch (Graduate Student)

I am a biologist-turned-computer scientist interested in understanding the influence of the environmental change on the genetic composition of microbial populations.

Avril von Hoyningen-Huene bio photo

Avril von Hoyningen-Huene (Post-doctoral Scientist)

I am a microbiologist and bioinformatician delving into the dynamics of phytoplankton communities in response to environmental changes.

Florian Trigodet bio photo

Florian Trigodet (Senior Scientist)

I am a microbiologist by training, and as a postdoctoral researcher I am using advanced computational strategies to make sense of the microbial ecology of complex habitats.

Iva Veseli bio photo

Iva Veseli (Post-doctoral Scientist)

I am a computer scientist/biologist who leverages computational methods to explore biological data. Currently, I am studying microbial metabolism in environmental metagenomes.

Kathryn Lambert-Slosarska (Katy) bio photo

Kathryn Lambert-Slosarska (Katy) (Graduate Student)

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.

Affiliations
Raïssa Meyer bio photo

Raïssa Meyer (Post-doctoral Scientist)

I am a marine microbiologist interested in data interoperability. I work with (meta)data, people, and the systems and standards needed for global 'omics observing of marine microbes.

Sarah Tucker bio photo

Sarah Tucker (Post-doctoral Scientist)

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. Currently, I am using computational approaches to examine how marine microbes respond to environmental change.

Xi Chen (Xixi) bio photo

Xi Chen (Xixi) (Post-doctoral Scientist)

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.

Honorary Members

Kiki Füßel bio photo

Kiki Füßel (Mood Regulator)

I am an environmental scientist and a passionate anthropologist who has mastered the use of somatosensory, olfactory, and gustatory systems. If you need to schedule a meeting with me for my services, feel free to reach my personal assistant, Meren.

Affiliations
  • current Therapy Dog.

Collaborators

Those who work closely and actively with our group. It is a fact that we collaborate with many more researchers than what is shown below. The individuals below are those with whom we interact almost daily, who publish with our group very frequently, and with whom we always have something active. They are almost a member of our group with their contributions to our work, but they are just elsewhere.

Jessika Füssel bio photo

Jessika Füssel

My aim is to understand the production and fate of microbial metabolites within the context of changing environmental conditions using multi-omics approaches.

Alumni (sorted by date)

Those who were officiallly affiliated with our group and continued their career elsewhere. If you see yourself or someone else below with outdated information, please edit this file.

Matthew Schechter bio photo

Matthew Schechter

Matt was a Graduate Student in our group between 10/2019 and 02/2025. During his time with our group, he developed methods to leverage the growing number of environmental genomes and metagenomes to study the phylogeography of individual proteins. His work led to the creation of EcoPhylo, an easy-to-use computational workflow that integrates ecological and evolutionary perspectives on gene families de novo. The last time we checked (which was in 2025), Matt was A postdoctoral researcher in Luis Barreiro's group at UChicago.

Metehan Sever bio photo

Metehan Sever

Mete was a Scientific Programmer in our group between 10/2022 and 02/2025. Mete worked on improving anvi'o interactive interfaces by finetuning existing features or adding new ones. Some of his work, especially on how to display and work with phylogenetic trees made anvi'o much more suitable for such applications. The last time we checked (which was in 2025), Mete was A MSc student at the University of Oldenburg.

Cynthia Wang bio photo

Cynthia Wang

Cynthia was a Fulbright Scholar in our group between 09/2022 and 07/2023. She investigated computational means to study the interplay between codon composition in genomes and their metabolic priorities. The last time we checked (which was in 2024), Cynthia was A graduate student at the Biophysical Sciences Graduate Program at the University of Chicago.

Emily Fogarty bio photo

Emily Fogarty

Emily was a Graduate Student in our group between 06/2018 and 06/2023. Emily put an effort into understanding the ecology and evolution of naturally occurring plasmids of the human gut microbiome. Her work described the ecology of pBI143, a cryptic plasmid that happens to be one of the most prevalent and numerous extrachromosomal circular elements of the human gut. The last time we checked (which was in 2024), Emily was a Clinical Affairs Associate at the Theralink Technologies, Inc..

Isaac Fink bio photo

Isaac Fink

Isaac was a Undergraduate Researcher in our group between 04/2020 and 01/2023. Isaac worked on implementing new capabilities for anvi'o to visualize genomic contexts interactively, and contributed code to improve interactive interfaces of anvi'o. The last time we checked (which was in 2024), Isaac was an Associate Software Engineer at Veeva Systems.

Samuel Miller bio photo

Samuel Miller

Sam was a Post-doctoral Scientist in our group between 11/2019 and 9/2022. Sam took on one of the most exciting challenges our group had to offer at that time: taking advantage of the recent advances in high-throughput sequencing of short RNA molecules to make sense of microbial tRNA transcripts in complex habitats. Towards this goal, he developed novel and advanced open-source software tools to study all aspects of chemical modification and relative abundance analysis of tRNA transcripts, and combining them with tRNA genes, codons, and metabolisms found in genomes and metagenomes. The last time we checked (which was in 2024), Sam was a Scientific Programmer for the Center for Chemical Currencies of a Microbial Planet at the Marine Biological Laboratory.

Matthew Lawrence Klein bio photo

Matthew Lawrence Klein

Matthew was a Programmer in our group between 11/2020 and 10/2022. Matthew focused on improving the anvi'o interactive interface. He has made numerous significant contributions to anvi'o that improved the responsiveness of the interactive interface, addressed many bugs, and added most needed features. The last time we checked (which was in 2024), Matthew was a Software Developer in Los Angeles.

Evan Kiefl bio photo

Evan Kiefl

Evan was a Graduate Student in our group between 04/2017 and 06/2022. Evan has made technical and intellectual contributions that allowed us to interpret the genetic diversity within naturally occuring microbial populations in the context of their predicted protein structures. The last time we checked (which was in 2024), Evan was a Protein Bioinformatician at Arcadia Science.

Karen Lolans bio photo

Karen Lolans

Karen was a Senior Research Technician in our group between 07/2018 and 10/2021. Karen has made significant contributons to the wet-lab branch of our group at the University of Chicago by creating and benchmarking protocols for tRNA sequencing and high molecular weight DNA extraction for long-read sequencing even from most challenging samples of low-biomass and host contamination. The last time we checked (which was in 2024), Karen was a Senior Technician at the University of Chicago.

Andrea Watson bio photo

Andrea Watson

Andrea was a Graduate Student in our group between 06/2017 and 09/2021. Throughout her graduate work, Andrea investigated the determinants of microbial colonization in the human gut, a critical question of the human microbiome research that has been beyond our reach outside of simplified model systems. Using genome-resolved metagenomics and fecal microbiota transplantation experiments, Andrea has found some answers to discuss the factors that influence microbial biodiversity in stressful gut environments. The last time we checked (which was in 2024), Andrea was a Bioinformatics Scientist II at Vedanta Biosciences.

Jessica Pan bio photo

Jessica Pan

Jessica was a Undergraduate Researcher in our group between 06/2019 and 09/2020. Jessica has joined our lab as a high-school student and made significant contributions to the completely brand-new anvi'o help system. The last time we checked (which was in 2024), Jessica was a Computer Science Master's Student at the Massachusetts Institute of Technology.

Abigail Schmid bio photo

Abigail Schmid

Abby was a Undergraduate Researcher in our group between 10/2017 and 09/2020. Abby joined our group as an undergraduate researcher and used pangenomics and metagenomics for high-throughput characterization on hypervariable genomic islands of some of the most prevalent members of the human microbiome. Her work left behind a treasure trove of insights into some of the most interesting parts of microbial genomes. The last time we checked (which was in 2024), Abby was an Engineering Science PhD student at the University of Colorado Boulder.

Joe Runde bio photo

Joe Runde

Joe was a Physician Researcher in our group between 07/2018 and 07/2020. In addition to serving as a Physician Researcher at the University of Chicago Medicine, Joe joined our group to study with us the microbial community dynamics in Chron's disease during Exclusive Enteral Nutrition therapy. His dedication and passion had a huge influence on our lab culture and dynamics. The last time we checked (which was in 2023), Joe was an Assistant Professor at the Lurie Children's Hospital, Northwestern University.

Alon Shaiber bio photo

Alon Shaiber

Alon was a Graduate Student in our group between 10/2016 and 02/2020. Throughout his studies of the human oral cavity microbiome and its enigmatic members via genome-resolved metagenomics, he served the community with his open code and tutorials. Alon, the very first graduate student to join our group, dramatically influenced the trajectory of our science. The last time we checked (which was in 2024), Alon was the Computational Biology Team Lead at Immunai.

Özcan C. Esen bio photo

Özcan C. Esen

Ozcan was a Programmer in our group between 02/2016 and 02/2020. Ozcan worked on anvi'o since it was nothing more than an idea, and has been one of the most prolific developers of it during the last five years. His remarkable contributions to the interactive capabilities of anvi'o has always been a critical component of the platform, and will continue to help many life scientists who use anvi'o.

Mahmoud Yousef bio photo

Mahmoud Yousef

Mahmoud was a Undergraduate Researcher in our group between 05/2017 and 02/2020. Focusing on pangenomics, he developed functional and geometric homogeneity indices so we can interpret the heterogeneity within gene clusters. The last time we checked (which was in 2024), Mahmoud was an MD/PhD student at the Pritzker School of Medicine, University of Chicago.

Quentin Clayssen bio photo

Quentin Clayssen

Quentin was a FACCTS Visiting Scientist in our group between 04/2019 and 10/2019. He contributed to the development of an anvi'o framework for the rapid determination of genome taxonomy. The last time we checked (which was in 2024), Quentin was a Bioinformatician at DNA Script.

Sonny T. M. Lee bio photo

Sonny T. M. Lee

Sonny was a Post-doctoral Scientist in our group between 05/2016 and 05/2018. He took the responsibility of leading the Fecal Microbiota Transplantation work in our lab. Sonny also was the driving force behind setting up the wet-lab component of our group. The last time we checked (which was in 2024), Sonny was an Associate Professor of Microbial Ecology (http://www.the-lee-lab.com) at the Kansas State University, Division of Biology.

Steven Cui bio photo

Steven Cui

Steven was a Summer Student in our group between 07/2016 and 10/2016. He contributed to the development of tRNA-seq tools, a project that bridged Meren's and Tao Pan's interests. The last time we checked (which was in 2024), Steven was a Principal Associate and a Senior Software Engineer Capital One.

Tom O. Delmont bio photo

Tom O. Delmont

Tom was a Post-doctoral Scientist in our group between 10/2015 and 05/2018. He contributed to the development of anvi'o and its application to the ocean and gut metagenomes. Tom was the very first member of our lab, and Meren and Tom have spent lots of time together thinking about new ways to make sense of metagenomic data. The last time we checked (which was in 2024), Tom was a CNRS scientist at the Genoscope in France.

Community

Those who generously shared their experiences, opinions and/or computational expertise with us and others through blog posts that appeared on our web pages. If you see yourself or someone else below with outdated information, please edit this file.

Michael Yu bio photo

Michael Yu

I develop new machine learning methods and algorithms to study large biomedical datasets. I'm interested in transferring techniques in computational biology to other fields, including natural language processing.

Blair G. Paul bio photo

Blair G. Paul

Our lab investigates the influence of genetic variation on physical and chemical interactions among microorganisms, with additional interest in microbe-virus dynamics.

Affiliation at the time of their contributions Papers
Antonio Fernandez-Guerra bio photo

Antonio Fernandez-Guerra

My group and I develop and apply new methodologies to analyze modern and ancient (meta)genomic data. We like to use ancient microbes to reconstruct past environments and make sense of the genes of unknown function in genomes and metagenomes.

Affiliation at the time of their contributions Papers Blog posts
Mike Lee bio photo

Mike Lee

Affiliation at the time of their contributions Papers Blog posts
Veronika Kivenson bio photo

Veronika Kivenson

Affiliation at the time of their contributions Papers Blog posts
Antti Karkman bio photo

Antti Karkman

Affiliation at the time of their contributions Papers Blog posts
Elaina Graham bio photo

Elaina Graham

Affiliation at the time of their contributions Blog posts
Bryan Merrill bio photo

Bryan Merrill

Affiliation at the time of their contributions Papers Blog posts
Vincent J. Denef bio photo

Vincent J. Denef

Affiliation at the time of their contributions Blog posts
Jacob T. Evans bio photo

Jacob T. Evans

Affiliation at the time of their contributions Blog posts
Jarrod J. Scott bio photo

Jarrod J. Scott

Affiliation at the time of their contributions Papers Blog posts

Visitors

Those who visited our laboratory for a period of a week or longer.

Amy D Willis

Amy, who was a Professor at Department of Biostatistics, University of Washington 🇺🇸, arrived on 09/2024 and stayed with us for about 9 months. Amy's visit was more than a visit -- it was a true sabbatical during which we took advantage of the new genomes in public databases to investigate the codon variation landscape throughout the tree of life as a function of microbial ecology, evolution, and metabolism. Members of our group is forever thankful to the members of Amy's group for sharing her with us.

Siyu Mei

Mei, who was a Graduate Student at Groningen Institute for Evolutionary Life Science, University of Groningen 🇳🇱, arrived on 03/2025 and stayed with us for about 1 month.

Chris Robinson

Chris, who was a Graduate Student at Department of Biology, Indiana University 🇺🇸, arrived on 11/2024 and stayed with us for about 6 weeks.

Eeva Eronen-Rasimus

Eeva, who was a Senior Researcher at Marine Reserach Center, Finnish Environmental Institute 🇫🇮, arrived on 10/2024 and stayed with us for about 10 days.

Eeva, Igor, and Tommi during a lunch meeting with the rest of the group :)

Tommi Välikangas

Tommi, who was a Postdoctoral Scientist at , Natural Resources Institute Finland 🇫🇮, arrived on 10/2024 and stayed with us for about 10 days.

Igor Pessi

Igor, who was a Postdoctoral Scientist at , Finnish Environment Institute 🇫🇮, arrived on 10/2024 and stayed with us for about 10 days.

Stephen J Giovannoni

Steve, who was a Professor at Department of Microbiology, Oregon State University 🇺🇸, arrived on 07/2024 and stayed with us for about 3 months. A large proportion of the logistics of Steve's visit was coordinated by the Hanse-Wissenschaftskolleg (HWK), an independent institute for advanced study and a non-profit foundation. We are extremely lucky in Oldenburg that such an institute exists and supports international collaborators who wish to visit a lab in the region. If you are thinking about coming here for a sabbatical or a for a few months of research stay, please consider visiting the HWK web page.

Journal Club with Steve.

Arthur Cousson

Arthur, who was a Graduate Student at EcoSols Joint Research Unit, Institut Agro Montpellier 🇫🇷, arrived on 05/2024 and stayed with us for about 8 weeks.

Arthur and others.

Oleg Vlasovets

Oleg, who was a Graduate Student at , Helmholtz Zentrum München 🇩🇪, arrived on 01/2024 and stayed with us for about 3 months.

Lunch meeting with Oleg (on the most left), Daan Speth, Tom Delmont, Sarahi Garcia, and others in the lab.

Mary Ann Moran

Mary Ann, who was a Professor at Department of Marine Sciences, University of Georgia 🇺🇸, arrived on 10/2023 and stayed with us for about a week.

Sarahi Garcia, Sandra McLellan, Jessika Fuessel, Meren, and Mary Ann Moran in Bremen.

Sandra McLellan

Sandra, who was a Professor at School of Freshwater Sciences, University of Wisconsin-Milwaukee 🇺🇸, arrived on 10/2023 and stayed with us for about a week.

Jed Fuhrman

Jed, who was a Professor at Wrigley Institute for Environmental Studies, University of Southern California 🇺🇸, arrived on 09/2022 and stayed with us for about a week.

Tom Delmont, Jed Fuhrman, Meren, and all the carboard boxes.