Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks. - Dmitry A. Rodionov; Inna Dubchak; Adam P. Arkin; Eric J. Alm; Mikhail S. Gelfand (PLoS Comput. Biol., 2005)

OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments. - Morgan N. Price; Adam P. Arkin; Eric J. Alm (BMC Bioinform., 2006)

The Evolution of Two-Component Systems in Bacteria Reveals Different Strategies for Niche Adaptation. - Eric J. Alm; Katherine H. Huang; Adam P. Arkin (PLoS Comput. Biol., 2006)

MicrobesOnline: an integrated portal for comparative and functional genomics. - Paramvir S. Dehal; Marcin P. Joachimiak; Morgan N. Price; John T. Bates; Jason K. Baumohl; Dylan Chivian; Greg D. Friedland; Katherine H. Huang; Keith Keller; Pavel S. Novichkov; Inna Dubchak; Eric J. Alm; et al. (Nucleic Acids Res., 2010)

Local Gene Regulation Details a Recognition Code within the LacI Transcriptional Factor Family. - Francisco M. Camas; Eric J. Alm; Juan F. Poyatos (PLoS Comput. Biol., 2010)

Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss. - Mukul S. Bansal; Eric J. Alm; Manolis Kellis (Bioinform., 2012)

Inferring Correlation Networks from Genomic Survey Data. - Jonathan Friedman; Eric J. Alm (PLoS Comput. Biol., 2012)

Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss. - Mukul S. Bansal; Eric J. Alm; Manolis Kellis (J. Comput. Biol., 2013)

Improved gene tree error correction in the presence of horizontal gene transfer. - Mukul S. Bansal; Yi-Chieh Wu; Eric J. Alm; Manolis Kellis (Bioinform., 2015)

Mobile genes in the human microbiome are structured from global to individual scales. - Ilana L. Brito; Suzan A. Yilmaz; K. Huang; Liyi Xu; Stacy D. Jupiter; Aaron P. Jenkins; Waisea Naisilisili; Manu V. Tamminen; Chris S. Smillie; Jennifer R. Wortman; Bruce W. Birren; Ramnik J. Xavier; et al. (Nat., 2016)

Two dynamic regimes in the human gut microbiome. - Sean M. Gibbons; Sean M. Kearney; Chris S. Smillie; Eric J. Alm (PLoS Comput. Biol., 2017)

Correcting for batch effects in case-control microbiome studies. - Sean M. Gibbons; Claire Duvallet; Eric J. Alm (PLoS Comput. Biol., 2018)

Longitudinal wastewater sampling in buildings reveals temporal dynamics of metabolites. - Ethan D. Evans; Chengzhen Dai; Siavash Isazadeh; Shinkyu Park; Carlo Ratti; Eric J. Alm (PLoS Comput. Biol., 2020)

MicrobiomeCensus estimates human population sizes from wastewater samples based on inter-individual variability in gut microbiomes. - Lin Zhang; Likai Chen; Xiaoqian (annie) Yu; Claire Duvallet; Siavash Isazadeh; Chengzhen Dai; Shinkyu Park; Katya Frois-Moniz; Fabio Duarte; Carlo Ratti; Eric J. Alm; Fangqiong Ling (PLoS Comput. Biol., 2022)