Eric J. Alm

Publication Activity (10 Years)

Years Active: 2005-2022
Publications (10 Years): 6

Top Topics

Sampling Strategies

Horizontal Gene Transfer

Sequenced Genomes

Top Venues

PLoS Comput. Biol.

J. Comput. Biol.

Publications

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
MicrobiomeCensus estimates human population sizes from wastewater samples based on inter-individual variability in gut microbiomes. PLoS Comput. Biol. 18 (9) (2022)
Ethan D. Evans, Chengzhen Dai, Siavash Isazadeh, Shinkyu Park, Carlo Ratti, Eric J. Alm
Longitudinal wastewater sampling in buildings reveals temporal dynamics of metabolites. PLoS Comput. Biol. 16 (6) (2020)
Sean M. Gibbons, Claire Duvallet, Eric J. Alm
Correcting for batch effects in case-control microbiome studies. PLoS Comput. Biol. 14 (4) (2018)
Sean M. Gibbons, Sean M. Kearney, Chris S. Smillie, Eric J. Alm
Two dynamic regimes in the human gut microbiome. PLoS Comput. Biol. 13 (2) (2017)
Ilana L. Brito, Suzan A. Yilmaz, K. Huang, Liyi Xu, Stacy D. Jupiter, Aaron P. Jenkins, Waisea Naisilisili, Manu V. Tamminen, Chris S. Millie, Jennifer R. Wortman, Bruce W. Birren, Ramnik J. Xavier, Paul C. Blainey, A. K. Singh, Dirk Gevers, Eric J. Alm
Mobile genes in the human microbiome are structured from global to individual scales. Nat. 535 (7612) (2016)
Mukul S. Bansal, Yi-Chieh Wu, Eric J. Alm, Manolis Kellis
Improved gene tree error correction in the presence of horizontal gene transfer. Bioinform. 31 (8) (2015)
Mukul S. Bansal, Eric J. Alm, Manolis Kellis
Reconciliation Revisited: Handling Multiple Optima When Reconciling with Duplication, Transfer, and Loss. RECOMB (2013)
Mukul S. Bansal, Eric J. Alm, Manolis Kellis
Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss. J. Comput. Biol. 20 (10) (2013)
Jonathan Friedman, Eric J. Alm
Inferring Correlation Networks from Genomic Survey Data. PLoS Comput. Biol. 8 (9) (2012)
Mukul S. Bansal, Eric J. Alm, Manolis Kellis
Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss. Bioinform. 28 (12) (2012)
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, Adam P. Arkin
MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Res. 38 (Database-Issue) (2010)
Francisco M. Camas, Eric J. Alm, Juan F. Poyatos
Local Gene Regulation Details a Recognition Code within the LacI Transcriptional Factor Family. PLoS Comput. Biol. 6 (11) (2010)
Eric J. Alm, Katherine H. Huang, Adam P. Arkin
The Evolution of Two-Component Systems in Bacteria Reveals Different Strategies for Niche Adaptation. PLoS Comput. Biol. 2 (11) (2006)
Morgan N. Price, Adam P. Arkin, Eric J. Alm
OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments. BMC Bioinform. 7 (2006)
Dmitry A. Rodionov, Inna Dubchak, Adam P. Arkin, Eric J. Alm, Mikhail S. Gelfand
Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks. PLoS Comput. Biol. 1 (5) (2005)