Works by Alm, Eric

Results: 96

Gut microbiota profiles of peninsular Malaysian populations are associated with urbanization and lifestyle.

Published in:

Scientific Reports, 2025, v. 15, n. 1, p. 1, doi. 10.1038/s41598-025-07117-z

By:

Jamaluddin, Nurul Fauzani;
Brovkina, Olga;
Nor Rashid, Nurshamimi;
Al-Maleki, Anis Rageh;
Lim, Yvonne Ai-Lian;
Tan, Maw Pin;
Lee, Soo Ching;
Duvallet, Claire;
Corzett, Christopher H.;
Alm, Eric;
Groussin, Mathieu;
Poyet, Mathilde;
Ibrahim, Fatimah

Publication type:

Article

Erratum to: Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life.

Published in:

2012

By:

Fournier, Gregory;
Andam, Cheryl;
Alm, Eric;
Gogarten, J.

Publication type:

Correction Notice

Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life.

Published in:

Origins of Life & Evolution of the Biosphere, 2011, v. 41, n. 6, p. 621, doi. 10.1007/s11084-011-9261-2

By:

Fournier, Gregory;
Andam, Cheryl;
Alm, Eric;
Gogarten, J.

Publication type:

Article

A practical guide to methods controlling false discoveries in computational biology.

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1716-1

By:

Korthauer, Keegan;
Kimes, Patrick K.;
Duvallet, Claire;
Reyes, Alejandro;
Subramanian, Ayshwarya;
Teng, Mingxiang;
Shukla, Chinmay;
Alm, Eric J.;
Hicks, Stephanie C.

Publication type:

Article

The Histidine Operon Is Ancient.

Published in:

Journal of Molecular Evolution, 2006, v. 62, n. 6, p. 807, doi. 10.1007/s00239-005-0191-3

By:

Price, Morgan N.;
Alm, Eric J.;
Arkin, Adam P.

Publication type:

Article

MicrobesOnline: an integrated portal for comparative and functional genomics.

Published in:

Nucleic Acids Research, 2010, v. 38, p. D396, doi. 10.1093/nar/gkp919

By:

Dehal, Paramvir S.;
Joachimiak, Marcin P.;
Price, Morgan N.;
Bates, John T.;
Baumohl, Jason K.;
Chivian, Dylan;
Friedland, Greg D.;
Huang, Katherine H.;
Keller, Keith;
Novichkov, Pavel S.;
Dubchak, Inna L.;
Alm, Eric J.;
Arkin, Adam P.

Publication type:

Article

Engineering transcription factors with novel DNA-binding specificity using comparative genomics.

Published in:

Nucleic Acids Research, 2009, v. 37, n. 8, p. 2493, doi. 10.1093/nar/gkp079

By:

Desai, Tasha A.;
Rodionov, Dmitry A.;
Gelfand, Mikhail S.;
Alm, Eric J.;
Rao, Christopher V.

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2005, v. 33, n. 10, p. 3224, doi. 10.1093/nar/gki638

By:

Price, Morgan N.;
Alm, Eric J.;
Arkin, Adam P.

Publication type:

Article

A novel method for accurate operon predictions in all sequenced prokaryotes.

Published in:

Nucleic Acids Research, 2005, v. 33, n. 3, p. 880, doi. 10.1093/nar/gki232

By:

Price, Morgan N.;
Huang, Katherine H.;
Alm, Eric J.;
Arkin, Adam P.

Publication type:

Article

An omics-based framework for assessing the health risk of antimicrobial resistance genes.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-25096-3

By:

Zhang, An-Ni;
Gaston, Jeffry M.;
Dai, Chengzhen L.;
Zhao, Shijie;
Poyet, Mathilde;
Groussin, Mathieu;
Yin, Xiaole;
Li, Li-Guan;
van Loosdrecht, Mark C. M.;
Topp, Edward;
Gillings, Michael R.;
Hanage, William P.;
Tiedje, James M.;
Moniz, Katya;
Alm, Eric J.;
Zhang, Tong

Publication type:

Article

Author Correction: X-Mapper: fast and accurate sequence alignment via gapped x-mers.

Published in:

2025

By:

Gaston, Jeffry M.;
Alm, Eric J.;
Zhang, An-Ni

Publication type:

Correction Notice

X-Mapper: fast and accurate sequence alignment via gapped x-mers.

Published in:

Genome Biology, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s13059-024-03473-7

By:

Gaston, Jeffry M.;
Alm, Eric J.;
Zhang, An-Ni

Publication type:

Article

Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools.

Published in:

PLoS ONE, 2019, v. 14, n. 12, p. 1, doi. 10.1371/journal.pone.0223680

By:

Jiang, Xiaofang;
Hall, Andrew Brantley;
Xavier, Ramnik J.;
Alm, Eric J.

Publication type:

Article

Framework for rational donor selection in fecal microbiota transplant clinical trials.

Published in:

PLoS ONE, 2019, v. 14, n. 10, p. 1, doi. 10.1371/journal.pone.0222881

By:

Duvallet, Claire;
Zellmer, Caroline;
Panchal, Pratik;
Budree, Shrish;
Osman, Majdi;
Alm, Eric J.

Publication type:

Article

Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors.

Published in:

BMC Immunology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s12865-019-0300-5

By:

Chu, Nathaniel D.;
Bi, Haixin Sarah;
Emerson, Ryan O.;
Sherwood, Anna M.;
Birnbaum, Michael E.;
Robins, Harlan S.;
Alm, Eric J.

Publication type:

Article

Comparing Patterns of Natural Selection across Species Using Selective Signatures.

Published in:

PLoS Genetics, 2008, v. 4, n. 2, p. 1, doi. 10.1371/journal.pgen.0040023

By:

Shapiro, B. Jesse;
Alm, Eric J.

Publication type:

Article

Correction: The Life-Cycle of Operons.

Published in:

2006

By:

Price, Morgan N.;
Arkin, Adam P.;
Alm, Eric J.

Publication type:

Correction Notice

The Life-Cycle of Operons.

Published in:

PLoS Genetics, 2006, v. 2, n. 6, p. e96, doi. 10.1371/journal.pgen.0020096

By:

Price, Morgan N.;
Arkin, Adam P.;
Alm, Eric J.

Publication type:

Article

Two dynamic regimes in the human gut microbiome.

Published in:

PLoS Computational Biology, 2017, v. 13, n. 2, p. 1, doi. 10.1371/journal.pcbi.1005364

By:

Gibbons, Sean M.;
Kearney, Sean M.;
Smillie, Chris S.;
Alm, Eric J.

Publication type:

Article

Culturing of "Unculturable" Subsurface Microbes: Natural Organic Carbon Source Fuels the Growth of Diverse and Distinct Bacteria From Groundwater.

Published in:

Frontiers in Microbiology, 2020, v. 11, p. N.PAG, doi. 10.3389/fmicb.2020.610001

By:

Wu, Xiaoqin;
Spencer, Sarah;
Gushgari-Doyle, Sara;
Yee, Mon Oo;
Voriskova, Jana;
Li, Yifan;
Alm, Eric J.;
Chakraborty, Romy

Publication type:

Article

Metapopulation structure of Vibrionaceae among coastal marine invertebrates.

Published in:

Environmental Microbiology, 2011, v. 13, n. 1, p. 265, doi. 10.1111/j.1462-2920.2010.02328.x

By:

Preheim, Sarah P.;
Boucher, Yan;
Wildschutte, Hans;
David, Lawrence A.;
Veneziano, Daniele;
Alm, Eric J.;
Polz, Martin F.

Publication type:

Article

Maternal Microbiota Modulate a Fragile X-like Syndrome in Offspring Mice.

Published in:

Genes, 2022, v. 13, n. 8, p. 1409, doi. 10.3390/genes13081409

By:

Varian, Bernard J.;
Weber, Katherine T.;
Kim, Lily J.;
Chavarria, Tony E.;
Carrasco, Sebastian E.;
Muthupalani, Sureshkumar;
Poutahidis, Theofilos;
Zafarullah, Marwa;
Al Olaby, Reem R.;
Barboza, Mariana;
Solakyildirim, Kemal;
Lebrilla, Carlito;
Tassone, Flora;
Wu, Fuqing;
Alm, Eric J.;
Erdman, Susan E.

Publication type:

Article

"Every Gene Is Everywhere but the Environment Selects": Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis.

Published in:

Genome Biology & Evolution, 2016, v. 8, n. 5, p. 1388, doi. 10.1093/gbe/evw077

By:

Fondi, Marco;
Karkman, Antti;
Tamminen, Manu V.;
Bosi, Emanuele;
Virta, Marko;
Fani, Renato;
Alm, Eric;
McInerney, James O.

Publication type:

Article

Inoculum composition determines microbial community and function in an anaerobic sequential batch reactor.

Published in:

PLoS ONE, 2017, v. 12, n. 2, p. 1, doi. 10.1371/journal.pone.0171369

By:

Perrotta, Allison R.;
Kumaraswamy, Rajkumari;
Bastidas-Oyanedel, Juan R.;
Alm, Eric J.;
Rodríguez, Jorge

Publication type:

Article

Profiling Living Bacteria Informs Preparation of Fecal Microbiota Transplantations.

Published in:

PLoS ONE, 2017, v. 12, n. 1, p. 1, doi. 10.1371/journal.pone.0170922

By:

Chu, Nathaniel D.;
Smith, Mark B.;
Perrotta, Allison R.;
Kassam, Zain;
Alm, Eric J.

Publication type:

Article

A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments.

Published in:

PLoS ONE, 2016, v. 11, n. 5, p. 1, doi. 10.1371/journal.pone.0154804

By:

Olesen, Scott W.;
Vora, Suhani;
Techtmann, Stephen M.;
Fortney, Julian L.;
Bastidas-Oyanedel, Juan R.;
Rodríguez, Jorge;
Hazen, Terry C.;
Alm, Eric J.

Publication type:

Article

MicrobiomeCensus estimates human population sizes from wastewater samples based on inter-individual variability in gut microbiomes.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 9, p. 1, doi. 10.1371/journal.pcbi.1010472

By:

Zhang, Lin;
Chen, Likai;
Yu, Xiaoqian;
Duvallet, Claire;
Isazadeh, Siavash;
Dai, Chengzhen;
Park, Shinkyu;
Frois-Moniz, Katya;
Duarte, Fabio;
Ratti, Carlo;
Alm, Eric J.;
Ling, Fangqiong

Publication type:

Article

Effect of antibiotic pretreatment on bacterial engraftment after Fecal Microbiota Transplant (FMT) in IBS-D.

Published in:

Gut Microbes, 2022, v. 14, n. 1, p. 1, doi. 10.1080/19490976.2021.2020067

By:

Singh, Prashant;
Alm, Eric J.;
Kelley, John M.;
Cheng, Vivian;
Smith, Mark;
Kassam, Zain;
Nee, Judy;
Iturrino, Johanna;
Lembo, Anthony

Publication type:

Article

16S rRNA sequencing analysis: the devil is in the details.

Published in:

Gut Microbes, 2020, v. 11, n. 5, p. 1139, doi. 10.1080/19490976.2020.1747336

By:

Tsou, Amy M.;
Olesen, Scott W.;
Alm, Eric J.;
Snapper, Scott B.

Publication type:

Article

Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles.

Published in:

Gut Microbes, 2019, v. 10, n. 3, p. 358, doi. 10.1080/19490976.2018.1528822

By:

Sinha, Trishla;
Vich Vila, Arnau;
Garmaeva, Sanzhima;
Jankipersadsing, Soesma A.;
Imhann, Floris;
Collij, Valerie;
Bonder, Marc Jan;
Jiang, Xiaofang;
Gurry, Thomas;
Alm, Eric J.;
D'Amato, Mauro;
Weersma, Rinse K.;
Scherjon, Sicco;
Wijmenga, Cisca;
Fu, Jingyuan;
Kurilshikov, Alexander;
Zhernakova, Alexandra

Publication type:

Article

dbOTU3: A new implementation of distribution-based OTU calling.

Published in:

PLoS ONE, 2017, v. 12, n. 5, p. 1, doi. 10.1371/journal.pone.0176335

By:

Olesen, Scott W.;
Duvallet, Claire;
Alm, Eric J.

Publication type:

Article

Contact order revisited: Influence of protein size on the folding rate.

Published in:

Protein Science: A Publication of the Protein Society, 2003, v. 12, n. 9, p. 2057, doi. 10.1110/ps.0302503

By:

Ivankov, Dmitry N.;
Garbuzynskiy, Sergiy O.;
Alm, Eric;
Plaxco, Kevin W.;
Baker, David;
Finkelstein, Alexei V.

Publication type:

Article

The Evolution of Two-Component Systems in Bacteria Reveals Different Strategies for Niche Adaptation.

Published in:

PLoS Computational Biology, 2006, v. 2, n. 11, p. 1329, doi. 10.1371/journal.pcbi.0020143

By:

Alm, Eric;
Huang, Katherine;
Arkin, Adam

Publication type:

Article

Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks.

Published in:

PLoS Computational Biology, 2005, v. 1, n. 5, p. 415, doi. 10.1371/journal.pcbi.0010055

By:

Rodionov, Dmitry A.;
Dubchak, Inna L.;
Arkin, Adam P.;
Alm, Eric J.;
Gelfand, Mikhail S.;
Miyano, Satoru

Publication type:

Article

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

Published in:

Bioinformatics, 2015, v. 31, n. 8, p. 1211, doi. 10.1093/bioinformatics/btu806

By:

Bansa, Mukul S.;
Yi-Chieh Wu;
Alm, Eric J.;
Kellis, Manolis

Publication type:

Article

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

Published in:

Bioinformatics, 2015, v. 31, n. 7, p. 1211, doi. 10.1093/bioinformatics/btu806

By:

Bansal, Mukul S.;
Yi-Chieh Wu;
Alm, Eric J.;
Kellis, Manolis

Publication type:

Article

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

Published in:

Bioinformatics, 2012, v. 28, n. 12, p. i283, doi. 10.1093/bioinformatics/bts225

By:

Bansal, Mukul S.;
Alm, Eric J.;
Kellis, Manolis

Publication type:

Article

Tracking Strains in the Microbiome: Insights from Metagenomics and Models.

Published in:

Frontiers in Microbiology, 2016, p. 1, doi. 10.3389/fmicb.2016.00712

By:

Brito, Ilana L.;
Alm, Eric J.;
Brown, C. Titus;
Badger, Jonathan

Publication type:

Article

Fecal Microbiota Transplant for Relapsing Clostridium difficile Infection Using a Frozen Inoculum From Unrelated Donors: A Randomized, Open-Label, Controlled Pilot Study.

Published in:

Clinical Infectious Diseases, 2014, v. 58, n. 11, p. 1515, doi. 10.1093/cid/ciu135

By:

Youngster, Ilan;
Sauk, Jenny;
Pindar, Christina;
Wilson, Robin G.;
Kaplan, Jess L.;
Smith, Mark B.;
Alm, Eric J.;
Gevers, Dirk;
Russell, George H.;
Hohmann, Elizabeth L.

Publication type:

Article

Low-level resource partitioning supports coexistence among functionally redundant bacteria during successional dynamics.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2024, v. 18, n. 1, p. 1, doi. 10.1093/ismejo/wrad013

By:

Yu, Xiaoqian Annie;
McLean, Craig;
Hehemann, Jan-Hendrik;
Angeles-Albores, David;
Wu, Fuqing;
Muszyński, Artur;
Corzett, Christopher H;
Azadi, Parastoo;
Kujawinski, Elizabeth B;
Alm, Eric J;
Polz, Martin F

Publication type:

Article

Genome and sequence determinants governing the expression of horizontally acquired DNA in bacteria.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2020, v. 14, n. 9, p. 2347, doi. 10.1038/s41396-020-0696-1

By:

Gomes, Antonio L. C.;
Johns, Nathan I.;
Yang, Anthony;
Velez-Cortes, Florencia;
Smillie, Christopher S.;
Smith, Mark B.;
Alm, Eric J.;
Wang, Harris H.

Publication type:

Article

Interactions in self-assembled microbial communities saturate with diversity.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2019, v. 13, n. 6, p. 1602, doi. 10.1038/s41396-019-0356-5

By:

Yu, Xiaoqian;
Polz, Martin F.;
Alm, Eric J.

Publication type:

Article

Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2018, v. 12, n. 10, p. 2403, doi. 10.1038/s41396-018-0192-z

By:

Kearney, Sean M.;
Gibbons, Sean M.;
Poyet, Mathilde;
Gurry, Thomas;
Bullock, Kevin;
Allegretti, Jessica R.;
Clish, Clary B.;
Alm, Eric J.

Publication type:

Article

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2016, v. 10, n. 7, p. 1669, doi. 10.1038/ismej.2015.235

By:

Weiss, Sophie;
Van Treuren, Will;
Lozupone, Catherine;
Faust, Karoline;
Friedman, Jonathan;
Deng, Ye;
Xia, Li Charlie;
Xu, Zhenjiang Zech;
Ursell, Luke;
Alm, Eric J;
Birmingham, Amanda;
Cram, Jacob A;
Fuhrman, Jed A;
Raes, Jeroen;
Sun, Fengzhu;
Zhou, Jizhong;
Knight, Rob

Publication type:

Article

Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2016, v. 10, n. 2, p. 427, doi. 10.1038/ismej.2015.124

By:

Spencer, Sarah J;
Tamminen, Manu V;
Preheim, Sarah P;
Guo, Mira T;
Briggs, Adrian W;
Brito, Ilana L;
A Weitz, David;
Pitkänen, Leena K;
Vigneault, Francois;
Virta, Marko PJuhani;
Alm, Eric J

Publication type:

Article

Reproducibility of Vibrionaceae population structure in coastal bacterioplankton.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2013, v. 7, n. 3, p. 509, doi. 10.1038/ismej.2012.134

By:

Szabo, Gitta;
Preheim, Sarah P;
Kauffman, Kathryn M;
David, Lawrence A;
Shapiro, Jesse;
Alm, Eric J;
Polz, Martin F

Publication type:

Article

Shape and evolution of the fundamental niche in marine Vibrio.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2012, v. 6, n. 12, p. 2168, doi. 10.1038/ismej.2012.65

By:

Materna, Arne C;
Friedman, Jonathan;
Bauer, Claudia;
David, Christina;
Chen, Sara;
Huang, Ivy B;
Gillens, April;
Clarke, Sean A;
Polz, Martin F;
Alm, Eric J

Publication type:

Article

The slow:fast substitution ratio reveals changing patterns of natural selection in γ-proteobacterial genomes.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2009, v. 3, n. 10, p. 1180, doi. 10.1038/ismej.2009.51

By:

Shapiro, B. Jesse;
Alm, Eric

Publication type:

Article

An immune-competent human gut microphysiological system enables inflammation-modulation by Faecalibacterium prausnitzii.

Published in:

NPJ Biofilms & Microbiomes, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41522-024-00501-z

By:

Zhang, Jianbo;
Huang, Yu-Ja;
Trapecar, Martin;
Wright, Charles;
Schneider, Kirsten;
Kemmitt, John;
Hernandez-Gordillo, Victor;
Yoon, Jun Young;
Poyet, Mathilde;
Alm, Eric J.;
Breault, David T.;
Trumper, David L.;
Griffith, Linda G.

Publication type:

Article

Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort.

Published in:

Scientific Reports, 2018, v. 8, n. 1, p. 1, doi. 10.1038/s41598-018-30783-1

By:

Gurry, Thomas;
HST Microbiome Consortium*;
Gibbons, Sean M.;
Nguyen, Le Thanh Tu;
Kearney, Sean M.;
Ananthakrishnan, Ashwin;
Jiang, Xiaofang;
Duvallet, Claire;
Kassam, Zain;
Alm, Eric J.

Publication type:

Article