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Academic Editor

A. Murat Eren

Summary

I am a computer scientist and a microbial ecologist. I develop algorithms and software platforms to make sense of the ecology of microbes through marker genes, metagenomes, and metatranscriptomes.

Bioinformatics Biotechnology Computational Biology Ecology Environmental Sciences Genomics Microbiology

Past or current institution affiliations

University of Chicago

Work details

Assistant Professor of Medicine

University of Chicago

October 2015

Department of Medicine

Dr. Eren’s research broadly focuses on the ecology of microbes. His group, which stands at the junction of computation, microbiology, and ecology, develops experimental approaches, algorithms, and software platforms to generate and make sense of high-throughput sequencing data, and to elucidate microbial community structure and/or functioning at the level of microbial marker genes, genomes, or pangenomes. Dr. Eren and his group create and utilize advanced visualization strategies and holistic approaches that combine multiple types of 'omics data to study complex medical and environmental questions.

Assistant Research Scientist

Marine Biological Laboratory

September 2013 - October 2015

Josephine Bay Paul Center

I have been working with multiple groups at the MBL and I plan to build even stronger bridges. In the long term, I wish to see the MBL as a hub for high-resolution microbiome research, where genome-resolved holistic computational approaches meet state-of-the-art molecular techniques and imaging to study microbes, and the environments in which they occur, at scales that would allow us to reach beyond “associations” and start investigating “mechanisms”. I wish to see the MBL become an authority on marine model organisms for microbiome research, and a frontier of host-microbe interactions, where the deep investigations of microbial communities are coupled with fundamental questions regarding the development, physiology, and the behavior of hosts with which they interact. Besides working towards these goals, I plan to continue teaching at MBL’s summer courses and explore ways to expand its course repertoire.

Websites

PeerJ Contributions

July 12, 2018

Minimizing confounders and increasing data quality in murine models for studies of the gut microbiome

3 citations

273 downloads

1,254 views

Jun Miyoshi, Vanessa Leone, Kentaro Nobutani, Mark W. Musch, Kristina Martinez-Guryn, Yunwei Wang, Sawako Miyoshi, Alexandria M. Bobe, A. Murat Eren, Eugene B. Chang

https://doi.org/10.7717/peerj.5166 PubMed 30013837

January 25, 2018

Linking pangenomes and metagenomes: the Prochlorococcus metapangenome

22 citations

1,409 downloads

7,968 views

Tom O. Delmont, A. Murat Eren

https://doi.org/10.7717/peerj.4320 PubMed 29423345

March 29, 2016

Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies

29 citations

1,064 downloads

7,609 views

Tom O. Delmont, A. Murat Eren

https://doi.org/10.7717/peerj.1839 PubMed 27069789

October 8, 2015

Anvi’o: an advanced analysis and visualization platform for ‘omics data

204 citations

3,400 downloads

20,380 views

A. Murat Eren, Özcan C. Esen, Christopher Quince, Joseph H. Vineis, Hilary G. Morrison, Mitchell L. Sogin, Tom O. Delmont

https://doi.org/10.7717/peerj.1319 PubMed 26500826

February 2, 2016 - Version: 1

Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies

1,323 downloads

3,548 views

Tom O Delmont, A. Murat Eren

https://doi.org/10.7287/peerj.preprints.1695v1

July 31, 2015 - Version: 1

Anvi’o: An advanced analysis and visualization platform for ‘omics data

1,715 downloads

2,886 views

A. Murat Eren, Özcan C Esen, Christopher Quince, Joseph H Vineis, Mitchell L Sogin, Tom O Delmont

https://doi.org/10.7287/peerj.preprints.1275v1

Academic Editor on

May 9, 2019

Optimizing de novo genome assembly from PCR-amplified metagenomes

258 downloads

1,291 views

Simon Roux, Gareth Trubl, Danielle Goudeau, Nandita Nath, Estelle Couradeau, Nathan A. Ahlgren, Yuanchao Zhan, David Marsan, Feng Chen, Jed A. Fuhrman, Trent R. Northen, Matthew B. Sullivan, Virginia I. Rich, Rex R. Malmstrom, Emiley A. Eloe-Fadrosh

https://doi.org/10.7717/peerj.6902 PubMed 31119088

September 26, 2017

Ananke: temporal clustering reveals ecological dynamics of microbial communities

4 citations

432 downloads

2,623 views

Michael W. Hall, Robin R. Rohwer, Jonathan Perrie, Katherine D. McMahon, Robert G. Beiko

https://doi.org/10.7717/peerj.3812 PubMed 28966891

September 12, 2017

Challenging a bioinformatic tool’s ability to detect microbial contaminants using in silico whole genome sequencing data

2 citations

335 downloads

1,494 views

Nathan D. Olson, Justin M. Zook, Jayne B. Morrow, Nancy J. Lin

https://doi.org/10.7717/peerj.3729 PubMed 28924496

April 25, 2017

Accumulation and expression of horizontally acquired genes in Arcobacter cryaerophilus that thrives in sewage

6 citations

484 downloads

1,710 views

Jess A. Millar, Rahul Raghavan

https://doi.org/10.7717/peerj.3269 PubMed 28462059

January 10, 2017

Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics

3 citations

383 downloads

3,487 views

Abraham G. Moller, Chun Liang

https://doi.org/10.7717/peerj.2844 PubMed 28097058

November 8, 2016

Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone

23 citations

847 downloads

3,796 views

Cristina N. Butterfield, Zhou Li, Peter F. Andeer, Susan Spaulding, Brian C. Thomas, Andrea Singh, Robert L. Hettich, Kenwyn B. Suttle, Alexander J. Probst, Susannah G. Tringe, Trent Northen, Chongle Pan, Jillian F. Banfield

https://doi.org/10.7717/peerj.2687 PubMed 27843720

August 11, 2016

Metabolomics of pulmonary exacerbations reveals the personalized nature of cystic fibrosis disease

21 citations

567 downloads

2,881 views

Robert A. Quinn, Yan Wei Lim, Tytus D. Mak, Katrine Whiteson, Mike Furlan, Douglas Conrad, Forest Rohwer, Pieter Dorrestein

https://doi.org/10.7717/peerj.2174 PubMed 27602256

June 9, 2016

The oral microbiome of patients with axial spondyloarthritis compared to healthy individuals

6 citations

407 downloads

2,128 views

Jordan E. Bisanz, Praema Suppiah, W. Murray Thomson, Trudy Milne, Nigel Yeoh, Anita Nolan, Grace Ettinger, Gregor Reid, Gregory B. Gloor, Jeremy P. Burton, Mary P. Cullinan, Simon M. Stebbings

https://doi.org/10.7717/peerj.2095 PubMed 27330858

June 1, 2016

Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes

14 citations

874 downloads

4,843 views

Branko Rihtman, Sean Meaden, Martha R.J. Clokie, Britt Koskella, Andrew D. Millard

https://doi.org/10.7717/peerj.2055 PubMed 27280068

December 8, 2015

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units

96 citations

1,923 downloads