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A. Murat Eren
PeerJ Editor, Author & Reviewer
2,150 Points

Contributions by role

Author 640
Preprint Author 70
Reviewer 35
Editor 1,405

Contributions by subject area

Bioinformatics
Biotechnology
Computational Biology
Genomics
Microbiology
Agricultural Science
Entomology
Plant Science
Ecology
Infectious Diseases
Respiratory Medicine
Dentistry
Rheumatology
Hematology
Environmental Sciences
Soil Science
Developmental Biology
Gastroenterology and Hepatology
Metabolic Sciences
Computational Science
Data Science
Graphics
Ecotoxicology
Environmental Impacts

A. Murat Eren

PeerJ Editor, Author & Reviewer

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

Editing Journals

PeerJ - the Journal of Life & Environmental Sciences

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

  • GitHub
  • Meren Lab
  • PubMed Search
  • LinkedIn

PeerJ Contributions

  • Articles 5
  • Preprints 2
  • Edited 10
  • Reviewed 1
August 27, 2019
Genome-resolved insights into a novel Spiroplasma symbiont of the Wheat Stem Sawfly (Cephus cinctus)
Carl J. Yeoman, Laura M. Brutscher, Özcan C. Esen, Furkan Ibaoglu, Curtis Fowler, A. Murat Eren, Kevin Wanner, David K. Weaver
https://doi.org/10.7717/peerj.7548 PubMed 31523509
July 12, 2018
Minimizing confounders and increasing data quality in murine models for studies of the gut microbiome
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Sarah L. Westcott, Patrick D. Schloss
https://doi.org/10.7717/peerj.1487 PubMed 26664811

Signed reviews submitted for articles published in PeerJ Note that some articles may not have the review itself made public unless authors have made them open as well.

September 20, 2016
A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq
Catherine M. Burke, Aaron E. Darling
https://doi.org/10.7717/peerj.2492 PubMed 27688981