Inferring Correlation Networks from Genomic Survey Data

by Friedman, Jonathan, Alm, Eric J.
Published 2012

Comparing Patterns of Natural Selection across Species Using Selective Signatures

by Shapiro, B. Jesse, Alm, Eric J
Published 2008

Correction: Comparing Patterns of Natural Selection across Species Using Selective Signatures

by Shapiro, B. Jesse, Alm, Eric J
Published 2008

Tracking Strains in the Microbiome: Insights from Metagenomics and Models

by Brito, Ilana L., Alm, Eric J.
Published in Front Microbiol (2016)

Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss

by Bansal, Mukul S., Alm, Eric J., Kellis, Manolis
Published 2012

Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss

by Bansal, Mukul S., Alm, Eric J., Kellis, Manolis
Published 2013

Sympatric Speciation: When Is It Possible in Bacteria?

by Friedman, Jonathan, Alm, Eric J., Shapiro, B. Jesse
Published 2013

dbOTU3: A new implementation of distribution-based OTU calling

by Olesen, Scott W., Duvallet, Claire, Alm, Eric J.
Published in PLoS One (2017)

Random sequences rapidly evolve into de novo promoters

by Yona, Avihu H., Alm, Eric J., Gore, Jeff
Published in Nat Commun (2018)

Correcting for batch effects in case-control microbiome studies

by Gibbons, Sean M., Duvallet, Claire, Alm, Eric J.
Published in PLoS Comput Biol (2018)

Interactions in self-assembled microbial communities saturate with diversity

by Yu, Xiaoqian, Polz, Martin F., Alm, Eric J.
Published in ISME J (2019)

Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication

by Price, Morgan N., Alm, Eric J., Arkin, Adam P.
Published 2005

OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments

by Price, Morgan N, Arkin, Adam P, Alm, Eric J
Published 2006

The Life-Cycle of Operons

by Price, Morgan N, Arkin, Adam P, Alm, Eric J
Published 2006

Correction: The Life-Cycle of Operons

by Price, Morgan N, Arkin, Adam P, Alm, Eric J
Published 2006

Local Gene Regulation Details a Recognition Code within the LacI Transcriptional Factor Family

by Camas, Francisco M., Alm, Eric J., Poyatos, Juan F.
Published 2010

Horizontal Gene Transfer and the Evolution of Bacterial and Archaeal Population Structure

by Polz, Martin F., Alm, Eric J., Hanage, William P.
Published 2013

Improved gene tree error correction in the presence of horizontal gene transfer

by Bansal, Mukul S., Wu, Yi-Chieh, Alm, Eric J., Kellis, Manolis
Published in Bioinformatics (2015)

Virtual Microfluidics for digital quantification and single-cell sequencing

by Xu, Liyi, Brito, Ilana L., Alm, Eric J., Blainey, Paul C.
Published in Nat Methods (2016)

Two dynamic regimes in the human gut microbiome

by Gibbons, Sean M., Kearney, Sean M., Smillie, Chris S., Alm, Eric J.
Published in PLoS Comput Biol (2017)