2019 | 2020 | (dark COVID years) | 2023

Interested in joining? Please consider reading the lab culture and expectations first. Some information on our location and space is also here.

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. [photos: 1, 2, 3].

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, HIPP)

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

Cynthia Wang bio photo

Cynthia Wang (Fulbright Scholar)

A recent computer science B.S. who is exploring the association between sequence composition and metabolism.

Florian Trigodet bio photo

Florian Trigodet (Post-doctoral 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) (Master's Student)

I am a marine (micro)biologist trying to utilise computational approaches to understand the dynamism and impact of diversity generating retroelements in microbial lifestyles within changing marine ecosystems.

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.

  • current Therapy Dog.
Matthew Schechter bio photo

Matthew Schechter (Graduate Student)

I am interested in combining comparative genomics and environmental metagenomics to identify genetic determinants of fitness in microbial populations in the human gut and ocean microbiome.

Metehan Sever bio photo

Metehan Sever (Scientific Programmer)

I am a computer scientist and UX designer who loves to design and develop user interfaces.

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 <a href=https://www.howtopronounce.com/xixi target=_blank>🔊</a>) bio photo

Xi Chen (Xixi 🔊) (Post-doctoral Scientist, HIPP)

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.

Previous Members (sorted by date) 

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 If you see yourself or someone else below with outdated information, please edit this file.

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 2023), 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..

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 has to offer: 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 2023), 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..

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 2022), Evan was a Bioinformatician at AbCellera.

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 2023), 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 2023), Andrea was a Bioinformatics Scientist 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 2022), Jessica was an undergraduate 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 2022), 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 2023), Alon was a Senior Computational Biologist 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 2023), Mahmoud was a medical 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 2020), Quentin was a graduate student at the ETH Zurich.

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 2023), Sonny was an Assistant Professor of Microbial Ecology (http://www.the-lee-lab.com) at the Kansas State University, Division of Biology.

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 2023), Tom was a CNRS scientist at the Genoscope in France.

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 2021), Steven was a Software Engineer at Capital One.

Collaborators and Partners in Science 

Our partners in science who work closely and actively with our group. Undoubtedly, this list will forever be incomplete. We collaborate with many more scientists and we benefit from the guidance of many of our senior colleagues. This dynamic list is meant to mention our most active collaborators with whom we interact almost daily to weekly (sorted by name, please edit this file if updates necessary).

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.

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.

Jessika Fuessel bio photo

Jessika Fuessel

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

Amy D. Willis bio photo

Amy D. Willis

My lab and I develop statistical and computational methods for the analysis of biodiversity data, with a particular focus on the microbiome. Like the Meren lab, I'm passionate about reproducible science, meaningful data analysis, ecosystem and host health, outreach and education, and collaborating with scientists who share these values.


Members of our community who generously shared their experiences, opinions and/or computational expertise with others through blog posts. If you see yourself or someone else below with outdated information, please edit this file.

Veronika Kivenson bio photo

Veronika Kivenson

Papers Blog posts
Antti Karkman bio photo

Antti Karkman

Papers Blog posts
Elaina Graham bio photo

Elaina Graham

Vincent J. Denef bio photo

Vincent J. Denef

Jacob T. Evans bio photo

Jacob T. Evans