Eric J. Alm, PhD - Publications

Biological Engineering Massachusetts Institute of Technology, Cambridge, MA, United States 
Ecology, Microbiology, Genomics

135 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Yu X, Gurry T, Nguyen LTT, Richardson HS, Alm EJ. Prebiotics and Community Composition Influence Gas Production of the Human Gut Microbiota. Mbio. 11. PMID 32900799 DOI: 10.1128/mBio.00217-20  0.92
2020 Wu F, Zhang J, Xiao A, Gu X, Lee WL, Armas F, Kauffman K, Hanage W, Matus M, Ghaeli N, Endo N, Duvallet C, Poyet M, Moniz K, Washburne AD, ... ... Alm EJ, et al. SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases. Msystems. 5. PMID 32694130 DOI: 10.1128/mSystems.00614-20  0.64
2020 Groussin M, Mazel F, Alm EJ. Co-evolution and Co-speciation of Host-Gut Bacteria Systems. Cell Host & Microbe. 28: 12-22. PMID 32645351 DOI: 10.1016/j.chom.2020.06.013  0.36
2020 Wu F, Xiao A, Zhang J, Moniz K, Endo N, Armas F, Bonneau R, Brown MA, Bushman M, Chai PR, Duvallet C, Erickson TB, Foppe K, Ghaeli N, Gu X, ... ... Alm EJ, et al. SARS-CoV-2 titers in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases. Medrxiv : the Preprint Server For Health Sciences. PMID 32607521 DOI: 10.1101/2020.06.15.20117747  0.68
2020 Gomes ALC, Johns NI, Yang A, Velez-Cortes F, Smillie CS, Smith MB, Alm EJ, Wang HH. Genome and sequence determinants governing the expression of horizontally acquired DNA in bacteria. The Isme Journal. PMID 32514119 DOI: 10.1038/s41396-020-0696-1  0.76
2020 Tsou AM, Olesen SW, Alm EJ, Snapper SB. 16S rRNA sequencing analysis: the devil is in the details. Gut Microbes. 1-4. PMID 32329652 DOI: 10.1080/19490976.2020.1747336  0.44
2020 Tian R, Ning D, He Z, Zhang P, Spencer SJ, Gao S, Shi W, Wu L, Zhang Y, Yang Y, Adams BG, Rocha AM, Detienne BL, Lowe KA, Joyner DC, ... ... Alm EJ, et al. Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity. Microbiome. 8: 51. PMID 32252814 DOI: 10.1186/s40168-020-00825-w  0.76
2019 Jiang X, Hall AB, Xavier RJ, Alm EJ. Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools. Plos One. 14: e0223680. PMID 31830054 DOI: 10.1371/journal.pone.0223680  0.36
2019 Duvallet C, Zellmer C, Panchal P, Budree S, Osman M, Alm EJ. Framework for rational donor selection in fecal microbiota transplant clinical trials. Plos One. 14: e0222881. PMID 31600222 DOI: 10.1371/journal.pone.0222881  0.64
2019 Poyet M, Groussin M, Gibbons SM, Avila-Pacheco J, Jiang X, Kearney SM, Perrotta AR, Berdy B, Zhao S, Lieberman TD, Swanson PK, Smith M, Roesemann S, Alexander JE, Rich SA, ... ... Alm EJ, et al. A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research. Nature Medicine. PMID 31477907 DOI: 10.1038/s41591-019-0559-3  0.76
2019 Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, et al. Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology. PMID 31399723 DOI: 10.1038/s41587-019-0252-6  0.76
2019 Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology. PMID 31341288 DOI: 10.1038/s41587-019-0209-9  0.76
2019 Chu ND, Bi HS, Emerson RO, Sherwood AM, Birnbaum ME, Robins HS, Alm EJ. Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors. Bmc Immunology. 20: 19. PMID 31226930 DOI: 10.1186/s12865-019-0300-5  0.4
2019 Korthauer K, Kimes PK, Duvallet C, Reyes A, Subramanian A, Teng M, Shukla C, Alm EJ, Hicks SC. A practical guide to methods controlling false discoveries in computational biology. Genome Biology. 20: 118. PMID 31164141 DOI: 10.1186/s13059-019-1716-1  0.64
2019 Miller JI, Techtmann S, Fortney J, Mahmoudi N, Joyner D, Liu J, Olesen S, Alm E, Fernandez A, Gardinali P, GaraJayeva N, Askerov FS, Hazen TC. Oil Hydrocarbon Degradation by Caspian Sea Microbial Communities. Frontiers in Microbiology. 10: 995. PMID 31143165 DOI: 10.3389/fmicb.2019.00995  0.44
2019 Duvallet C, Larson K, Snapper S, Iosim S, Lee A, Freer K, May K, Alm E, Rosen R. Aerodigestive sampling reveals altered microbial exchange between lung, oropharyngeal, and gastric microbiomes in children with impaired swallow function. Plos One. 14: e0216453. PMID 31107879 DOI: 10.1371/journal.pone.0216453  0.64
2019 Zhao S, Lieberman TD, Poyet M, Kauffman KM, Gibbons SM, Groussin M, Xavier RJ, Alm EJ. Adaptive Evolution within Gut Microbiomes of Healthy People. Cell Host & Microbe. PMID 31028005 DOI: 10.1016/j.chom.2019.03.007  0.76
2019 Brito IL, Gurry T, Zhao S, Huang K, Young SK, Shea TP, Naisilisili W, Jenkins AP, Jupiter SD, Gevers D, Alm EJ. Transmission of human-associated microbiota along family and social networks. Nature Microbiology. PMID 30911128 DOI: 10.1038/s41564-019-0409-6  0.6
2019 Yu X, Polz MF, Alm EJ. Interactions in self-assembled microbial communities saturate with diversity. The Isme Journal. PMID 30809013 DOI: 10.1038/s41396-019-0356-5  0.92
2019 Jiang X, Hall AB, Arthur TD, Plichta DR, Covington CT, Poyet M, Crothers J, Moses PL, Tolonen AC, Vlamakis H, Alm EJ, Xavier RJ. Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut. Science (New York, N.Y.). 363: 181-187. PMID 30630933 DOI: 10.1126/science.aau5238  0.4
2018 Vich Vila A, Imhann F, Collij V, Jankipersadsing SA, Gurry T, Mujagic Z, Kurilshikov A, Bonder MJ, Jiang X, Tigchelaar EF, Dekens J, Peters V, Voskuil MD, Visschedijk MC, van Dullemen HM, ... ... Alm EJ, et al. Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome. Science Translational Medicine. 10. PMID 30567928 DOI: 10.1126/scitranslmed.aap8914  0.56
2018 Sinha T, Vich Vila A, Garmaeva S, Jankipersadsing SA, Imhann F, Collij V, Bonder MJ, Jiang X, Gurry T, Alm EJ, D'Amato M, Weersma RK, Scherjon S, Wijmenga C, Fu J, et al. Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles. Gut Microbes. 1-9. PMID 30373468 DOI: 10.1080/19490976.2018.1528822  0.56
2018 Gurry T, Gibbons SM, Nguyen LTT, Kearney SM, Ananthakrishnan A, Jiang X, Duvallet C, Kassam Z, Alm EJ. Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort. Scientific Reports. 8: 12699. PMID 30139999 DOI: 10.1038/s41598-018-30783-1  0.76
2018 Kearney SM, Gibbons SM, Erdman SE, Alm EJ. Orthogonal Dietary Niche Enables Reversible Engraftment of a Gut Bacterial Commensal. Cell Reports. 24: 1842-1851. PMID 30110640 DOI: 10.1016/j.celrep.2018.07.032  0.76
2018 Johns NI, Gomes ALC, Yim SS, Yang A, Blazejewski T, Smillie CS, Smith MB, Alm EJ, Kosuri S, Wang HH. Metagenomic mining of regulatory elements enables programmable species-selective gene expression. Nature Methods. 15: 323-329. PMID 30052624 DOI: 10.1038/nmeth.4633  0.76
2018 Kearney SM, Gibbons SM, Poyet M, Gurry T, Bullock K, Allegretti JR, Clish CB, Alm EJ. Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota. The Isme Journal. PMID 29899513 DOI: 10.1038/s41396-018-0192-z  0.76
2018 Olesen SW, Leier MM, Alm EJ, Kahn SA. Searching for superstool: maximizing the therapeutic potential of FMT. Nature Reviews. Gastroenterology & Hepatology. PMID 29703976 DOI: 10.1038/s41575-018-0019-4  0.44
2018 Gibbons SM, Duvallet C, Alm EJ. Correcting for batch effects in case-control microbiome studies. Plos Computational Biology. 14: e1006102. PMID 29684016 DOI: 10.1371/journal.pcbi.1006102  0.76
2018 Corzett CH, Elsherbini J, Chien DM, Hehemann JH, Henschel A, Preheim SP, Yu X, Alm EJ, Polz MF. Evolution of a Vegetarian : Metabolic Specialization of to Macroalgal Substrates. Journal of Bacteriology. PMID 29632094 DOI: 10.1128/JB.00020-18  0.92
2018 He Z, Zhang P, Wu L, Rocha AM, Tu Q, Shi Z, Wu B, Qin Y, Wang J, Yan Q, Curtis D, Ning D, Van Nostrand JD, Wu L, Yang Y, ... ... Alm EJ, et al. Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning. Mbio. 9. PMID 29463661 DOI: 10.1128/mBio.02435-17  0.76
2018 Smillie CS, Sauk J, Gevers D, Friedman J, Sung J, Youngster I, Hohmann EL, Staley C, Khoruts A, Sadowsky MJ, Allegretti JR, Smith MB, Xavier RJ, Alm EJ. Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation. Cell Host & Microbe. 23: 229-240.e5. PMID 29447696 DOI: 10.1016/j.chom.2018.01.003  0.76
2018 Martin-Platero AM, Cleary B, Kauffman K, Preheim SP, McGillicuddy DJ, Alm EJ, Polz MF. High resolution time series reveals cohesive but short-lived communities in coastal plankton. Nature Communications. 9: 266. PMID 29348571 DOI: 10.1038/s41467-017-02571-4  0.92
2017 Duvallet C, Gibbons SM, Gurry T, Irizarry RA, Alm EJ. Meta-analysis of gut microbiome studies identifies disease-specific and shared responses. Nature Communications. 8: 1784. PMID 29209090 DOI: 10.1038/s41467-017-01973-8  0.76
2017 Duvallet C, Gibbons SM, Gurry T, Irizarry RA, Alm EJ. Meta-analysis of gut microbiome studies identifies disease-specific and shared responses. Nature Communications. 8: 1784. PMID 29209090 DOI: 10.1038/s41467-017-01973-8  0.76
2017 Duvallet C, Gibbons SM, Gurry T, Irizarry RA, Alm EJ. Meta-analysis of gut microbiome studies identifies disease-specific and shared responses. Nature Communications. 8: 1784. PMID 29209090 DOI: 10.1038/s41467-017-01973-8  0.76
2017 Duvallet C, Gibbons SM, Gurry T, Irizarry RA, Alm EJ. Meta-analysis of gut microbiome studies identifies disease-specific and shared responses. Nature Communications. 8: 1784. PMID 29209090 DOI: 10.1038/s41467-017-01973-8  0.76
2017 Wilck N, Matus MG, Kearney SM, Olesen SW, Forslund K, Bartolomaeus H, Haase S, Mähler A, Balogh A, Markó L, Vvedenskaya O, Kleiner FH, Tsvetkov D, Klug L, Costea PI, ... ... Alm EJ, et al. Salt-responsive gut commensal modulates TH17 axis and disease. Nature. PMID 29143823 DOI: 10.1038/nature24628  0.76
2017 Pakpour S, Bhanvadia A, Zhu R, Amarnani A, Gibbons SM, Gurry T, Alm EJ, Martello LA. Identifying predictive features of Clostridium difficile infection recurrence before, during, and after primary antibiotic treatment. Microbiome. 5: 148. PMID 29132405 DOI: 10.1186/s40168-017-0368-1  0.76
2017 Bajaj JS, Kassam Z, Cox IJ, Gurry T, Williams R, Alm E, John B, Smith M, Taylor-Robinson SD, Gillevet PM. Reply to HEP-17-1121. Hepatology (Baltimore, Md.). PMID 28714102 DOI: 10.1002/hep.29368  0.56
2017 Bajaj JS, Kassam Z, Fagan A, Gavis EA, Liu E, Cox IJ, Kheradman R, Heuman D, Wang J, Gurry T, Williams R, Sikaroodi M, Fuchs M, Alm E, John B, et al. Fecal Microbiota Transplant from a Rational Stool Donor Improves Hepatic Encephalopathy: A Randomized Clinical Trial. Hepatology (Baltimore, Md.). PMID 28586116 DOI: 10.1002/hep.29306  0.56
2017 Olesen SW, Duvallet C, Alm EJ. dbOTU3: A new implementation of distribution-based OTU calling. Plos One. 12: e0176335. PMID 28472072 DOI: 10.1371/journal.pone.0176335  0.64
2017 Park SH, Perrotta A, Hanning I, Diaz-Sanchez S, Pendleton S, Alm E, Ricke SC. Pasture flock chicken cecal microbiome responses to prebiotics and plum fiber feed amendments. Poultry Science. PMID 28339946 DOI: 10.3382/ps/pew441  0.4
2017 Brito IL, Yilmaz S, Huang K, Xu L, Jupiter SD, Jenkins AP, Naisilisili W, Tamminen M, Smillie CS, Wortman JR, Birren BW, Xavier RJ, Blainey PC, Singh AK, Gevers D, ... Alm EJ, et al. Corrigendum: Mobile genes in the human microbiome are structured from global to individual scales. Nature. PMID 28329759 DOI: 10.1038/nature20774  0.76
2017 Groussin M, Mazel F, Sanders JG, Smillie CS, Lavergne S, Thuiller W, Alm EJ. Unraveling the processes shaping mammalian gut microbiomes over evolutionary time. Nature Communications. 8: 14319. PMID 28230052 DOI: 10.1038/ncomms14319  0.76
2017 Gibbons SM, Kearney SM, Smillie CS, Alm EJ. Two dynamic regimes in the human gut microbiome. Plos Computational Biology. 13: e1005364. PMID 28222117 DOI: 10.1371/journal.pcbi.1005364  0.76
2017 Olesen SW, Gurry T, Alm EJ. Designing fecal microbiota transplant trials that account for differences in donor stool efficacy. Statistical Methods in Medical Research. 962280216688502. PMID 28178876 DOI: 10.1177/0962280216688502  0.56
2017 Chu ND, Clarke SA, Timberlake S, Polz MF, Grossman AD, Alm EJ. A Mobile Element in mutS Drives Hypermutation in a Marine Vibrio. Mbio. 8. PMID 28174306 DOI: 10.1128/mBio.02045-16  0.92
2017 Chu ND, Smith MB, Perrotta AR, Kassam Z, Alm EJ. Profiling Living Bacteria Informs Preparation of Fecal Microbiota Transplantations. Plos One. 12: e0170922. PMID 28125667 DOI: 10.1371/journal.pone.0170922  0.56
2017 King AJ, Preheim SP, Bailey KL, Robeson MS, Roy Chowdhury T, Crable BR, Hurt RA, Mehlhorn TL, Lowe KA, Phelps TJ, Palumbo AV, Brandt CC, Brown SD, Podar M, Zhang P, ... ... Alm EJ, et al. Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation. Environmental Science & Technology. PMID 28112946 DOI: 10.1021/acs.est.6b04751  0.76
2016 Olesen SW, Alm EJ. Dysbiosis is not an answer. Nature Microbiology. 1: 16228. PMID 27886190 DOI: 10.1038/nmicrobiol.2016.228  0.44
2016 Varian BJ, Poutahidis T, DiBenedictis BT, Levkovich T, Ibrahim Y, Didyk E, Shikhman L, Cheung HK, Hardas A, Ricciardi CE, Kolandaivelu K, Veenema AH, Alm EJ, Erdman SE. Microbial lysate upregulates host oxytocin. Brain, Behavior, and Immunity. PMID 27825953 DOI: 10.1016/j.bbi.2016.11.002  0.56
2016 Hehemann JH, Arevalo P, Datta MS, Yu X, Corzett CH, Henschel A, Preheim SP, Timberlake S, Alm EJ, Polz MF. Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes. Nature Communications. 7: 12860. PMID 27653556 DOI: 10.1038/ncomms12860  0.8
2016 Preheim SP, Olesen SW, Spencer SJ, Materna A, Varadharajan C, Blackburn M, Friedman J, Rodríguez J, Hemond H, Alm EJ. Surveys, simulation and single-cell assays relate function and phylogeny in a lake ecosystem. Nature Microbiology. 1: 16130. PMID 27562262 DOI: 10.1038/nmicrobiol.2016.130  0.8
2016 Xu L, Brito IL, Alm EJ, Blainey PC. Virtual microfluidics for digital quantification and single-cell sequencing. Nature Methods. PMID 27479330 DOI: 10.1038/nmeth.3955  0.8
2016 Brito IL, Yilmaz S, Huang K, Xu L, Jupiter SD, Jenkins AP, Naisilisili W, Tamminen M, Smillie CS, Wortman JR, Birren BW, Xavier RJ, Blainey PC, Singh AK, Gevers D, ... Alm EJ, et al. Mobile genes in the human microbiome are structured from global to individual scales. Nature. PMID 27409808 DOI: 10.1038/nature18927  0.8
2016 David LA, Materna AC, Friedman J, Baptista MI, Blackburn MC, Perrotta A, Erdman SE, Alm EJ. Erratum to: Host lifestyle affects human microbiota on daily timescales. Genome Biology. 17: 117. PMID 27246704 DOI: 10.1186/s13059-016-0988-y  0.88
2016 Brito IL, Alm EJ. Tracking Strains in the Microbiome: Insights from Metagenomics and Models. Frontiers in Microbiology. 7: 712. PMID 27242733 DOI: 10.3389/fmicb.2016.00712  0.8
2016 Olesen SW, Vora S, Techtmann SM, Fortney JL, Bastidas-Oyanedel JR, Rodríguez J, Hazen TC, Alm EJ. A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments. Plos One. 11: e0154804. PMID 27152415 DOI: 10.1371/journal.pone.0154804  0.44
2016 Weiss S, Van Treuren W, Lozupone C, Faust K, Friedman J, Deng Y, Xia LC, Xu ZZ, Ursell L, Alm EJ, Birmingham A, Cram JA, Fuhrman JA, Raes J, Sun F, et al. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. The Isme Journal. PMID 26905627 DOI: 10.1038/ismej.2015.235  0.64
2016 Kassam Z, Cribb Fabersunne C, Smith MB, Alm EJ, Kaplan GG, Nguyen GC, Ananthakrishnan AN. Clostridium difficile associated risk of death score (CARDS): a novel severity score to predict mortality among hospitalised patients with C. difficile infection. Alimentary Pharmacology & Therapeutics. PMID 26849527 DOI: 10.1111/apt.13546  0.8
2015 Spencer SJ, Tamminen MV, Preheim SP, Guo MT, Briggs AW, Brito IL, A Weitz D, Pitkänen LK, Vigneault F, Virta MP, Alm EJ. Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers. The Isme Journal. PMID 26394010 DOI: 10.1038/ismej.2015.124  0.6
2015 Cleary B, Brito IL, Huang K, Gevers D, Shea T, Young S, Alm EJ. Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning. Nature Biotechnology. PMID 26368049 DOI: 10.1038/nbt.3329  0.8
2015 Smith MB, Rocha AM, Smillie CS, Olesen SW, Paradis C, Wu L, Campbell JH, Fortney JL, Mehlhorn TL, Lowe KA, Earles JE, Phillips J, Techtmann SM, Joyner DC, Elias DA, ... ... Alm EJ, et al. Natural bacterial communities serve as quantitative geochemical biosensors. Mbio. 6: e00326-15. PMID 25968645 DOI: 10.1128/mBio.00326-15  0.8
2015 Stollman N, Smith M, Giovanelli A, Mendolia G, Burns L, Didyk E, Burgess J, Noh A, Edelstein C, Alm E, Kassam Z. Frozen encapsulated stool in recurrent Clostridium difficile: exploring the role of pills in the treatment hierarchy of fecal microbiota transplant nonresponders. The American Journal of Gastroenterology. 110: 600-1. PMID 25853204 DOI: 10.1038/ajg.2015.81  0.8
2015 Fournier GP, Alm EJ. Ancestral Reconstruction of a Pre-LUCA Aminoacyl-tRNA Synthetase Ancestor Supports the Late Addition of Trp to the Genetic Code. Journal of Molecular Evolution. 80: 171-85. PMID 25791872 DOI: 10.1007/s00239-015-9672-1  1
2015 Poutahidis T, Varian BJ, Levkovich T, Lakritz JR, Mirabal S, Kwok C, Ibrahim YM, Kearney SM, Chatzigiagkos A, Alm EJ, Erdman SE. Dietary microbes modulate transgenerational cancer risk. Cancer Research. 75: 1197-204. PMID 25716681 DOI: 10.1158/0008-5472.CAN-14-2732  0.8
2015 Bansal MS, Wu YC, Alm EJ, Kellis M. Improved gene tree error correction in the presence of horizontal gene transfer. Bioinformatics (Oxford, England). 31: 1211-8. PMID 25481006 DOI: 10.1093/bioinformatics/btu806  0.8
2014 Levkovich T, Poutahidis T, Cappelle K, Smith MB, Perrotta A, Alm EJ, Erdman SE. 'Hygienic' lymphocytes convey increased cancer risk. Journal of Analytical Oncology. 3: 113-121. PMID 25722756 DOI: 10.6000/1927-7229.2014.03.03.1  0.56
2014 Oren Y, Smith MB, Johns NI, Kaplan Zeevi M, Biran D, Ron EZ, Corander J, Wang HH, Alm EJ, Pupko T. Transfer of noncoding DNA drives regulatory rewiring in bacteria. Proceedings of the National Academy of Sciences of the United States of America. 111: 16112-7. PMID 25313052 DOI: 10.1073/pnas.1413272111  0.8
2014 Smith M, Kassam Z, Edelstein C, Burgess J, Alm E. OpenBiome remains open to serve the medical community. Nature Biotechnology. 32: 867. PMID 25203030 DOI: 10.1038/nbt.3006  0.36
2014 David LA, Materna AC, Friedman J, Campos-Baptista MI, Blackburn MC, Perrotta A, Erdman SE, Alm EJ. Host lifestyle affects human microbiota on daily timescales. Genome Biology. 15: R89. PMID 25146375 DOI: 10.1186/gb-2014-15-7-r89  0.8
2014 Youngster I, Sauk J, Pindar C, Wilson RG, Kaplan JL, Smith MB, Alm EJ, Gevers D, Russell GH, Hohmann EL. Fecal microbiota transplant for relapsing Clostridium difficile infection using a frozen inoculum from unrelated donors: a randomized, open-label, controlled pilot study. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. 58: 1515-22. PMID 24762631 DOI: 10.1093/cid/ciu135  0.8
2014 Rothman DH, Fournier GP, French KL, Alm EJ, Boyle EA, Cao C, Summons RE. Methanogenic burst in the end-Permian carbon cycle. Proceedings of the National Academy of Sciences of the United States of America. 111: 5462-7. PMID 24706773 DOI: 10.1073/pnas.1318106111  0.8
2014 Poutahidis T, Springer A, Levkovich T, Qi P, Varian BJ, Lakritz JR, Ibrahim YM, Chatzigiagkos A, Alm EJ, Erdman SE. Probiotic microbes sustain youthful serum testosterone levels and testicular size in aging mice. Plos One. 9: e84877. PMID 24392159 DOI: 10.1371/journal.pone.0084877  0.8
2014 Lakritz JR, Poutahidis T, Levkovich T, Varian BJ, Ibrahim YM, Chatzigiagkos A, Mirabal S, Alm EJ, Erdman SE. Beneficial bacteria stimulate host immune cells to counteract dietary and genetic predisposition to mammary cancer in mice. International Journal of Cancer. Journal International Du Cancer. 135: 529-40. PMID 24382758 DOI: 10.1002/ijc.28702  0.8
2014 Levkovich T, Poutahidis T, Cappelle K, Smith MB, Perrotta A, Alm EJ, Erdman SE. 'Hygienic' lymphocytes convey increased cancer risk Journal of Analytical Oncology. 3: 113-121.  0.8
2013 Poutahidis T, Kearney SM, Levkovich T, Qi P, Varian BJ, Lakritz JR, Ibrahim YM, Chatzigiagkos A, Alm EJ, Erdman SE. Microbial symbionts accelerate wound healing via the neuropeptide hormone oxytocin. Plos One. 8: e78898. PMID 24205344 DOI: 10.1371/journal.pone.0078898  0.8
2013 Bansal MS, Alm EJ, Kellis M. Reconciliation revisited: handling multiple optima when reconciling with duplication, transfer, and loss. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 738-54. PMID 24033262 DOI: 10.1089/cmb.2013.0073  0.8
2013 Preheim SP, Perrotta AR, Martin-Platero AM, Gupta A, Alm EJ. Distribution-based clustering: using ecology to refine the operational taxonomic unit. Applied and Environmental Microbiology. 79: 6593-603. PMID 23974136 DOI: 10.1128/AEM.00342-13  0.8
2013 Poutahidis T, Kleinewietfeld M, Smillie C, Levkovich T, Perrotta A, Bhela S, Varian BJ, Ibrahim YM, Lakritz JR, Kearney SM, Chatzigiagkos A, Hafler DA, Alm EJ, Erdman SE. Microbial reprogramming inhibits Western diet-associated obesity. Plos One. 8: e68596. PMID 23874682 DOI: 10.1371/journal.pone.0068596  0.8
2013 Friedman J, Alm EJ, Shapiro BJ. Sympatric speciation: when is it possible in bacteria? Plos One. 8: e53539. PMID 23349716 DOI: 10.1371/journal.pone.0053539  0.8
2013 Levkovich T, Poutahidis T, Smillie C, Varian BJ, Ibrahim YM, Lakritz JR, Alm EJ, Erdman SE. Probiotic bacteria induce a 'glow of health'. Plos One. 8: e53867. PMID 23342023 DOI: 10.1371/journal.pone.0053867  0.8
2013 Polz MF, Alm EJ, Hanage WP. Horizontal gene transfer and the evolution of bacterial and archaeal population structure. Trends in Genetics : Tig. 29: 170-5. PMID 23332119 DOI: 10.1016/j.tig.2012.12.006  0.8
2013 Park SH, Hanning I, Perrota A, Bench BJ, Alm E, Ricke SC. Modifying the gastrointestinal ecology in alternatively raised poultry and the potential for molecular and metabolomic assessment. Poultry Science. 92: 546-61. PMID 23300323 DOI: 10.3382/ps.2012-02734  0.8
2013 Szabo G, Preheim SP, Kauffman KM, David LA, Shapiro J, Alm EJ, Polz MF. Reproducibility of Vibrionaceae population structure in coastal bacterioplankton. The Isme Journal. 7: 509-19. PMID 23178668 DOI: 10.1038/ismej.2012.134  0.92
2012 Friedman J, Alm EJ. Inferring correlation networks from genomic survey data. Plos Computational Biology. 8: e1002687. PMID 23028285 DOI: 10.1371/journal.pcbi.1002687  0.8
2012 Materna AC, Friedman J, Bauer C, David C, Chen S, Huang IB, Gillens A, Clarke SA, Polz MF, Alm EJ. Shape and evolution of the fundamental niche in marine Vibrio. The Isme Journal. 6: 2168-77. PMID 22832347 DOI: 10.1038/ismej.2012.65  0.8
2012 Papa E, Docktor M, Smillie C, Weber S, Preheim SP, Gevers D, Giannoukos G, Ciulla D, Tabbaa D, Ingram J, Schauer DB, Ward DV, Korzenik JR, Xavier RJ, Bousvaros A, ... Alm EJ, et al. Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease. Plos One. 7: e39242. PMID 22768065 DOI: 10.1371/journal.pone.0039242  0.8
2012 Methé BA, Nelson KE, Pop M, Creasy HH, Giglio MG, Huttenhower C, Gevers D, Petrosino JF, Abubucker S, Badger JH, Chinwalla AT, Earl AM, Fitzgerald MG, Fulton RS, Hallsworth-Pepin K, ... ... Alm EJ, et al. A framework for human microbiome research Nature. 486: 215-221. PMID 22699610 DOI: 10.1038/nature11209  0.8
2012 Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT, Creasy HH, Earl AM, Fitzgerald MG, Fulton RS, Giglio MG, Hallsworth-Pepin K, Lobos EA, Madupu R, Magrini V, ... ... Alm EJ, et al. Structure, function and diversity of the healthy human microbiome Nature. 486: 207-214. PMID 22699609 DOI: 10.1038/nature11234  0.8
2012 Bansal MS, Alm EJ, Kellis M. Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss. Bioinformatics (Oxford, England). 28: i283-91. PMID 22689773 DOI: 10.1093/bioinformatics/bts225  0.8
2012 Shapiro BJ, Friedman J, Cordero OX, Preheim SP, Timberlake SC, Szabó G, Polz MF, Alm EJ. Population genomics of early events in the ecological differentiation of bacteria. Science (New York, N.Y.). 336: 48-51. PMID 22491847 DOI: 10.1126/science.1218198  0.92
2011 Fournier GP, Andam CP, Alm EJ, Gogarten JP. Molecular evolution of aminoacyl tRNA synthetase proteins in the early history of life. Origins of Life and Evolution of the Biosphere : the Journal of the International Society For the Study of the Origin of Life. 41: 621-32. PMID 22200905 DOI: 10.1007/s11084-011-9261-2  1
2011 Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, Alm EJ. Ecology drives a global network of gene exchange connecting the human microbiome. Nature. 480: 241-4. PMID 22037308 DOI: 10.1038/nature10571  0.8
2011 Wang L, Chen S, Vergin KL, Giovannoni SJ, Chan SW, DeMott MS, Taghizadeh K, Cordero OX, Cutler M, Timberlake S, Alm EJ, Polz MF, Pinhassi J, Deng Z, Dedon PC. DNA phosphorothioation is widespread and quantized in bacterial genomes. Proceedings of the National Academy of Sciences of the United States of America. 108: 2963-8. PMID 21285367 DOI: 10.1073/pnas.1017261108  0.8
2011 David LA, Alm EJ. Rapid evolutionary innovation during an Archaean genetic expansion. Nature. 469: 93-6. PMID 21170026 DOI: 10.1038/nature09649  0.88
2011 Preheim SP, Boucher Y, Wildschutte H, David LA, Veneziano D, Alm EJ, Polz MF. Metapopulation structure of Vibrionaceae among coastal marine invertebrates. Environmental Microbiology. 13: 265-75. PMID 20819104 DOI: 10.1111/j.1462-2920.2010.02328.x  0.8
2010 Camas FM, Alm EJ, Poyatos JF. Local gene regulation details a recognition code within the LacI transcriptional factor family. Plos Computational Biology. 6: e1000989. PMID 21085639 DOI: 10.1371/journal.pcbi.1000989  0.8
2010 Rodrigue S, Materna AC, Timberlake SC, Blackburn MC, Malmstrom RR, Alm EJ, Chisholm SW. Unlocking short read sequencing for metagenomics. Plos One. 5: e11840. PMID 20676378 DOI: 10.1371/journal.pone.0011840  0.8
2010 He Z, Zhou A, Baidoo E, He Q, Joachimiak MP, Benke P, Phan R, Mukhopadhyay A, Hemme CL, Huang K, Alm EJ, Fields MW, Wall J, Stahl D, Hazen TC, et al. Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation. Applied and Environmental Microbiology. 76: 1574-86. PMID 20038696 DOI: 10.1128/AEM.02141-09  0.8
2010 Dehal PS, Joachimiak MP, Price MN, Bates JT, Baumohl JK, Chivian D, Friedland GD, Huang KH, Keller K, Novichkov PS, Dubchak IL, Alm EJ, Arkin AP. MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Research. 38: D396-400. PMID 19906701 DOI: 10.1093/nar/gkp919  0.8
2009 Shapiro BJ, Alm E. The slow:fast substitution ratio reveals changing patterns of natural selection in γ-proteobacterial genomes Isme Journal. 3: 1180-1192. PMID 19458656 DOI: 10.1038/ismej.2009.51  0.8
2009 Shapiro BJ, David LA, Friedman J, Alm EJ. Looking for Darwin's footprints in the microbial world. Trends in Microbiology. 17: 196-204. PMID 19375326 DOI: 10.1016/j.tim.2009.02.002  0.88
2009 Desai TA, Rodionov DA, Gelfand MS, Alm EJ, Rao CV. Engineering transcription factors with novel DNA-binding specificity using comparative genomics. Nucleic Acids Research. 37: 2493-503. PMID 19264798 DOI: 10.1093/nar/gkp079  0.8
2009 Fraser C, Alm EJ, Polz MF, Spratt BG, Hanage WP. The bacterial species challenge: making sense of genetic and ecological diversity. Science (New York, N.Y.). 323: 741-6. PMID 19197054 DOI: 10.1126/science.1159388  0.8
2009 Kazakov AE, Rodionov DA, Alm E, Arkin AP, Dubchak I, Gelfand MS. Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria Journal of Bacteriology. 91: 52-64. PMID 18820024 DOI: 10.1128/JB.01175-08  0.8
2008 Chivian D, Brodie EL, Alm EJ, Culley DE, Dehal PS, DeSantis TZ, Gihring TM, Lapidus A, Lin LH, Lowry SR, Moser DP, Richardson PM, Southam G, Wanger G, Pratt LM, et al. Environmental genomics reveals a single-species ecosystem deep within Earth. Science (New York, N.Y.). 322: 275-8. PMID 18845759 DOI: 10.1126/science.1155495  0.8
2008 Hunt DE, David LA, Gevers D, Preheim SP, Alm EJ, Polz MF. Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science (New York, N.Y.). 320: 1081-5. PMID 18497299 DOI: 10.1126/science.1157890  0.8
2008 Shapiro BJ, Alm EJ. Comparing patterns of natural selection across species using selective signatures. Plos Genetics. 4: e23. PMID 18266472 DOI: 10.1371/journal.pgen.0040023  0.8
2007 Bender KS, Yen HC, Hemme CL, Yang Z, He Z, He Q, Zhou J, Huang KH, Alm EJ, Hazen TC, Arkin AP, Wall JD. Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough. Applied and Environmental Microbiology. 73: 5389-400. PMID 17630305 DOI: 10.1128/AEM.00276-07  0.8
2006 Alm E, Huang K, Arkin A. The evolution of two-component systems in bacteria reveals different strategies for niche adaptation Plos Computational Biology. 2: 1329-1342. PMID 17083272 DOI: 10.1371/journal.pcbi.0020143  0.8
2006 Clark ME, He Q, He Z, Huang KH, Alm EJ, Wan XF, Hazen TC, Arkin AP, Wall JD, Zhou JZ, Fields MW. Temporal transcriptomic analysis as Desulfovibrio vulgaris Hildenborough transitions into stationary phase during electron donor depletion. Applied and Environmental Microbiology. 72: 5578-88. PMID 16885312 DOI: 10.1128/AEM.00284-06  0.8
2006 Price MN, Arkin AP, Alm EJ. The life-cycle of operons. Plos Genetics. 2: e96. PMID 16789824 DOI: 10.1371/journal.pgen.0020096  0.8
2006 He Q, Huang KH, He Z, Alm EJ, Fields MW, Hazen TC, Arkin AP, Wall JD, Zhou J. Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis. Applied and Environmental Microbiology. 72: 4370-81. PMID 16751553 DOI: 10.1128/AEM.02609-05  0.8
2006 Mukhopadhyay A, He Z, Alm EJ, Arkin AP, Baidoo EE, Borglin SC, Chen W, Hazen TC, He Q, Holman HY, Huang K, Huang R, Joyner DC, Katz N, Keller M, et al. Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach. Journal of Bacteriology. 188: 4068-78. PMID 16707698 DOI: 10.1128/JB.01921-05  0.8
2006 Price MN, Alm EJ, Arkin AP. The histidine operon is ancient. Journal of Molecular Evolution. 62: 807-8. PMID 16612542 DOI: 10.1007/s00239-005-0191-3  0.8
2006 Chhabra SR, He Q, Huang KH, Gaucher SP, Alm EJ, He Z, Hadi MZ, Hazen TC, Wall JD, Zhou J, Arkin AP, Singh AK. Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough. Journal of Bacteriology. 188: 1817-28. PMID 16484192 DOI: 10.1128/JB.188.5.1817-1828.2006  0.8
2006 Leaphart AB, Thompson DK, Huang K, Alm E, Wan XF, Arkin A, Brown SD, Wu L, Yan T, Liu X, Wickham GS, Zhou J. Transcriptome profiling of Shewanella oneidensis gene expression following exposure to acidic and alkaline pH. Journal of Bacteriology. 188: 1633-42. PMID 16452448 DOI: 10.1128/JB.188.4.1633-1642.2006  0.8
2006 Price MN, Arkin AP, Alm EJ. OpWise: operons aid the identification of differentially expressed genes in bacterial microarray experiments. Bmc Bioinformatics. 7: 19. PMID 16412220 DOI: 10.1186/1471-2105-7-19  0.8
2006 Brown SD, Martin M, Deshpande S, Seal S, Huang K, Alm E, Yang Y, Wu L, Yan T, Liu X, Arkin A, Chourey K, Zhou J, Thompson DK. Cellular response of Shewanella oneidensis to strontium stress Applied and Environmental Microbiology. 72: 890-900. PMID 16391131 DOI: 10.1128/AEM.72.1.890-900.2006  0.8
2005 Rodionov DA, Dubchak IL, Arkin AP, Alm EJ, Gelfand MS. Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks. Plos Computational Biology. 1: e55. PMID 16261196 DOI: 10.1371/journal.pcbi.0010055  0.8
2005 Alm EJ, Huang KH, Price MN, Koche RP, Keller K, Dubchak IL, Arkin AP. The MicrobesOnline Web site for comparative genomics. Genome Research. 15: 1015-22. PMID 15998914 DOI: 10.1101/gr.3844805  0.8
2005 Price MN, Alm EJ, Arkin AP. Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication. Nucleic Acids Research. 33: 3224-34. PMID 15942025 DOI: 10.1093/nar/gki638  0.8
2005 Price MN, Huang KH, Arkin AP, Alm EJ. Operon formation is driven by co-regulation and not by horizontal gene transfer. Genome Research. 15: 809-19. PMID 15930492 DOI: 10.1101/gr.3368805  0.8
2005 Liu Y, Gao W, Wang Y, Wu L, Liu X, Yan T, Alm E, Arkin A, Thompson DK, Fields MW, Zhou J. Transcriptome analysis of Shewanella oneidensis MR-1 in response to elevated salt conditions Journal of Bacteriology. 187: 2501-2507. PMID 15774893 DOI: 10.1128/JB.187.7.2501-2507.2005  0.8
2005 Price MN, Huang KH, Alm EJ, Arkin AP. A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Research. 33: 880-92. PMID 15701760 DOI: 10.1093/nar/gki232  0.8
2004 Rodionov DA, Dubchak I, Arkin A, Alm E, Gelfand MS. Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria Genome Biology. 5: R90. PMID 15535866  0.8
2004 Gao H, Wang Y, Liu X, Yan T, Wu L, Alm E, Arkin A, Thompson DK, Zhou J. Global transcriptome analysis of the heat shock response of Shewanella oneidensis. Journal of Bacteriology. 186: 7796-803. PMID 15516594 DOI: 10.1128/JB.186.22.7796-7803.2004  0.8
2003 Alm E, Arkin AP. Biological networks Current Opinion in Structural Biology. 13: 193-202. PMID 12727512 DOI: 10.1016/S0959-440X(03)00031-9  0.8
2002 Alm E, Morozov AV, Kortemme T, Baker D. Simple physical models connect theory and experiment in protein folding kinetics. Journal of Molecular Biology. 322: 463-76. PMID 12217703 DOI: 10.1016/S0022-2836(02)00706-4  0.8
2001 Grantcharova V, Alm EJ, Baker D, Horwich AL. Mechanisms of protein folding. Current Opinion in Structural Biology. 11: 70-82. PMID 11179895 DOI: 10.1016/S0959-440X(00)00176-7  0.8
2000 McCallister EL, Alm E, Baker D. Critical role of β-hairpin formation in protein G folding Nature Structural Biology. 7: 669-673. PMID 10932252 DOI: 10.1038/77971  0.8
2000 Yi Q, Scalley-Kim ML, Alm EJ, Baker D. NMR characterization of residual structure in the denatured state of protein L. Journal of Molecular Biology. 299: 1341-51. PMID 10873457 DOI: 10.1006/jmbi.2000.3816  0.8
2000 Alonso DO, Alm E, Daggett V. Characterization of the unfolding pathway of the cell-cycle protein p13suc1 by molecular dynamics simulations: implications for domain swapping. Structure (London, England : 1993). 8: 101-10. PMID 10673427 DOI: 10.1016/S0969-2126(00)00083-6  0.8
1998 Cardullo RA, Alm EJ. Introduction to image processing. Methods in Cell Biology. 56: 91-115. PMID 9500134  1
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