Reading List

This page is a list of interesting papers that I’ve recently read.

7/29/18 - Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA

5/22/18 - Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

4/5/18 - Flux Imbalance Analysis and the Sensitivity of Cellular Growth to Changes in Metabolite Pools

2/15/18 - Functional integration of a metabolic network model and expression data without arbitrary thresholding

12/20/17 - Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission

12/18/17 - MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

12/15/17 - CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

6/4/16 - Genome characteristics of a generalist marine bacterial lineage

6/2/16 - Transfer of Viral Communities between Human Individuals during Fecal Microbiota Transplantation

4/9/16 - Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

3/23/16 - Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome

3/8/16 - An interactive reference framework for modeling a dynamic immune system

2/8/16 - Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation

2/2/16 - Microbiota-Dependent Sequelae of Acute Infection Compromise Tissue-Specific Immunity.

2/1/16 - Coculture of Escherichia coli O157:H7 with a Nonpathogenic E. coli Strain Increases Toxin Production and Virulence in a Germfree Mouse Model.

2/1/16 - Reverse Ecology: From Systems to Environments and Back

2/1/16 - Genome scale models of yeast: towards standardized evaluation and consistent omic integration

2/1/16 - The Last Word: Books as a Statistical Metaphor for Microbial Communities