Microbial 'omics


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2020 | 2019

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.

Abigail Schmid bio photo

Abigail Schmid (Undergraduate Researcher)

I am interested in using applied mathematics and computational techniques to answer questions about microbial life.

Andrea Watson bio photo

Andrea Watson (Graduate Student)

I am interested in combining wet lab and computational methods in a complementary way to answer microbiological questions.

Emily Fogarty bio photo

Emily Fogarty (Graduate Student)

I am interested in developing computational and wet lab strategies to study horizontal gene transfer in the human gut microbiome.

Evan Kiefl bio photo

Evan Kiefl (Graduate Student)

I am interested in uncovering how single nucleotide variants map to functional variation in the genes of naturally-occuring microbial populations.

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.

Ibrahim Mohamed bio photo

Ibrahim Mohamed (Undergraduate Researcher)

“I am a student researcher interested in applying concepts from mathematics and computer science to understand and analyze metagenomes.”

Isaac Fink bio photo

Isaac Fink (Undergraduate Researcher)

“I am interested in enhancing the power and accessibility of computational tools that analyze the microbiome.”

Iva Veseli bio photo

Iva Veseli (Graduate Student)

I am a computer scientist/biologist who likes leveraging computational methods to explore biological data. Currently, I am studying biogeography and ecology of the gut microbiome.

Jessica Pan bio photo

Jessica Pan (Undergraduate Researcher)

I am interested in using computational strategies to investigate microbial ecosystems and working to make those techniques more accessible to others.

Karen Lolans bio photo

Karen Lolans (Senior Research Technician)

As a molecular microbiologist, I am interested in the potential that interwoven wet lab and computational strategies play in elucidating complex microbial interactions and processes.

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. I am often quite busy, but if you need to schedule a meeting with me for my services, you can ask anyone in the lab to have access to my calendar.

  • Therapy Dog.
Matthew Lawrence Klein bio photo

Matthew Lawrence Klein (Programmer)

“I am interested in technology's role in supporting a more equitable future on planet earth.”

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.

Rebecca Xiong bio photo

Rebecca Xiong (Undergraduate Researcher)

I am a student researcher interested in unraveling the intricate connections between microbial ecology and the human body.

Samuel Miller bio photo

Samuel Miller (Post-doctoral Scientist)

I study how microbes function in their environments by developing and applying computational tools to interpret data from approaches such as tRNA-sequencing, proteomics, and metagenomics.

Those we miss (sorted by date) 

Joe Runde bio photo

Joe Runde

Joe was a Physician Researcher with us between 07/2018 and 07/202. 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, Joe was an Assistant Professor at the Section of Gastroenterology, Hepatology and Nutrition of , an affiliate of the Northwestern University.

Alon Shaiber bio photo

Alon Shaiber

Alon was a Graduate Student with us 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, Alon was a Genomics Data Scientist at Weill Cornell Medicine.

Özcan C. Esen bio photo

Özcan C. Esen

Ozcan was a Programmer with us 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 with us 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, 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 with us 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, 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 with us 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, 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 with us 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, Tom was a CNRS scientist studying microbial life at the Genoscope in France.

Steven Cui bio photo

Steven Cui

Steven was a Summer Student with us 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, Steven was a Software Engineer at Capital One.

Meren's note on our struggle with the lack of gender diversity in the lab: This is something we are quite aware and upset about, and I finally decided to put a note about the issue on this page to make sure it is clear to everyone. I see the gender imbalance in our lab as my failure, and I am looking forward to fixing it. I advertised only one postdoc position so far, which was the only time I had the opportunity to ameliorate the lack of diversity, however, I wasn't lucky enough to get enough number of applications from women. When I mentioned our struggle with attracting applications from women to the lab to Rika Anderson, she speculated that it might be because there is a major gender imbalance in computer science. Although that is true, I would like to mention that I am interested in working with highly qualified women in both microbiology and/or computer science. I also am suggested to put photos of my collaborators on this page, since a very large fraction of the people I collaborate with are women, to make sure people are not discouraged by the current representation of women in the lab. Although I understand the good intention, I don't want to use names or photos of my friends and colleagues as a part of an apology for something we have to fix. Throughout my life I was very critical of cultural and political practices that make people feel comfortable with the lack of diversity, and this note is not my attempt to excuse myself form this responsibility, but to communicate my discomfort with where we are in our lab. If you are a woman, or any other poorly represented part of the society in science considering applying to our lab, please don't let the current situation stop you from doing it. Thank you!