| Year |
Citation |
Score |
| 2024 |
Ning D, Wang Y, Fan Y, Wang J, Van Nostrand JD, Wu L, Zhang P, Curtis DJ, Tian R, Lui L, Hazen TC, Alm EJ, Fields MW, Poole F, Adams MWW, et al. Environmental stress mediates groundwater microbial community assembly. Nature Microbiology. PMID 38212658 DOI: 10.1038/s41564-023-01573-x |
0.453 |
|
| 2023 |
Zhang J, Huang Y, Trapecar M, Wright C, Schneider K, Kemmit J, Hernandez-Gordillo V, Griffith L, Alm E, Trumper D, Yoon JY, Breault D. An immune-competent human gut microphysiological system enables inflammation-modulation of Faecalibacterium prausnitzii. Research Square. PMID 37886530 DOI: 10.21203/rs.3.rs-3373576/v1 |
0.422 |
|
| 2022 |
Duvallet C, Wu F, McElroy KA, Imakaev M, Endo N, Xiao A, Zhang J, Floyd-O'Sullivan R, Powell MM, Mendola S, Wilson ST, Cruz F, Melman T, Sathyanarayana CL, Olesen SW, ... ... Alm EJ, et al. Nationwide Trends in COVID-19 Cases and SARS-CoV-2 RNA Wastewater Concentrations in the United States. Acs Es&T Water. 2: 1899-1909. PMID 36380771 DOI: 10.1021/acsestwater.1c00434 |
0.421 |
|
| 2022 |
Xiao A, Wu F, Bushman M, Zhang J, Imakaev M, Chai PR, Duvallet C, Endo N, Erickson TB, Armas F, Arnold B, Chen H, Chandra F, Ghaeli N, Gu X, ... ... Alm EJ, et al. Metrics to relate COVID-19 wastewater data to clinical testing dynamics. Water Research. 212: 118070. PMID 35101695 DOI: 10.1016/j.watres.2022.118070 |
0.427 |
|
| 2021 |
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 RNA concentrations in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases. The Science of the Total Environment. 805: 150121. PMID 34534872 DOI: 10.1016/j.scitotenv.2021.150121 |
0.577 |
|
| 2021 |
Paradis CJ, Miller JI, Moon JW, Spencer SJ, Lui LM, Van Nostrand JD, Ning D, Steen AD, McKay LD, Arkin AP, Zhou J, Alm EJ, Hazen TC. Sustained ability of a natural microbial community to remove nitrate from groundwater. Ground Water. PMID 34490626 DOI: 10.1111/gwat.13132 |
0.44 |
|
| 2021 |
Gurry T, Nguyen LTT, Yu X, Alm EJ. Functional heterogeneity in the fermentation capabilities of the healthy human gut microbiota. Plos One. 16: e0254004. PMID 34288919 DOI: 10.1371/journal.pone.0254004 |
0.599 |
|
| 2021 |
Chu ND, Crothers JW, Nguyen LTT, Kearney SM, Smith MB, Kassam Z, Collins C, Xavier R, Moses PL, Alm EJ. Dynamic Colonization of Microbes and Their Functions after Fecal Microbiota Transplantation for Inflammatory Bowel Disease. Mbio. e0097521. PMID 34281401 DOI: 10.1128/mBio.00975-21 |
0.698 |
|
| 2021 |
Wu F, Xiao A, Zhang J, Moniz K, Endo N, Armas F, Bushman M, Chai PR, Duvallet C, Erickson TB, Foppe K, Ghaeli N, Gu X, Hanage WP, Huang KH, ... ... Alm EJ, et al. Wastewater surveillance of SARS-CoV-2 across 40 U.S. states from February to June 2020. Water Research. 202: 117400. PMID 34274898 DOI: 10.1016/j.watres.2021.117400 |
0.435 |
|
| 2021 |
Kothari A, Roux S, Zhang H, Prieto A, Soneja D, Chandonia JM, Spencer S, Wu X, Altenburg S, Fields MW, Deutschbauer AM, Arkin AP, Alm EJ, Chakraborty R, Mukhopadhyay A. Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance. Msystems. e0053721. PMID 34184913 DOI: 10.1128/mSystems.00537-21 |
0.507 |
|
| 2021 |
Xiao A, Wu F, Bushman M, Zhang J, Imakaev M, Chai PR, Duvallet C, Endo N, Erickson TB, Armas F, Arnold B, Chen H, Chandra F, Ghaeli N, Gu X, ... ... Alm EJ, et al. Metrics to relate COVID-19 wastewater data to clinical testing dynamics. Medrxiv : the Preprint Server For Health Sciences. PMID 34159339 DOI: 10.1101/2021.06.10.21258580 |
0.413 |
|
| 2021 |
Groussin M, Poyet M, Sistiaga A, Kearney SM, Moniz K, Noel M, Hooker J, Gibbons SM, Segurel L, Froment A, Mohamed RS, Fezeu A, Juimo VA, Lafosse S, Tabe FE, ... ... Alm EJ, et al. Elevated rates of horizontal gene transfer in the industrialized human microbiome. Cell. PMID 33794144 DOI: 10.1016/j.cell.2021.02.052 |
0.784 |
|
| 2021 |
Wu F, Xiao A, Zhang J, Moniz K, Endo N, Armas F, Bushman M, Chai PR, Duvallet C, Erickson TB, Foppe K, Ghaeli N, Gu X, Hanage WP, Huang KH, ... ... Alm EJ, et al. Wastewater Surveillance of SARS-CoV-2 across 40 U.S. states. Medrxiv : the Preprint Server For Health Sciences. PMID 33758888 DOI: 10.1101/2021.03.10.21253235 |
0.435 |
|
| 2020 |
Diener C, Reyes-Escogido ML, Jimenez-Ceja LM, Matus M, Gomez-Navarro CM, Chu ND, Zhong V, Tejero ME, Alm E, Resendis-Antonio O, Guardado-Mendoza R. Progressive Shifts in the Gut Microbiome Reflect Prediabetes and Diabetes Development in a Treatment-Naive Mexican Cohort. Frontiers in Endocrinology. 11: 602326. PMID 33488518 DOI: 10.3389/fendo.2020.602326 |
0.669 |
|
| 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 |
0.628 |
|
| 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 |
0.451 |
|
| 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 |
0.353 |
|
| 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 |
0.58 |
|
| 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 |
0.767 |
|
| 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 |
0.3 |
|
| 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 |
0.52 |
|
| 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 |
0.359 |
|
| 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 |
0.792 |
|
| 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 |
0.75 |
|
| 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 |
0.745 |
|
| 2019 |
Díaz-Sánchez S, Perrotta AR, Rockafellow I, Alm EJ, Okimoto R, Hawken R, Hanning I. Using fecal microbiota as biomarkers for predictions of performance in the selective breeding process of pedigree broiler breeders. Plos One. 14: e0216080. PMID 31063485 DOI: 10.1371/Journal.Pone.0216080 |
0.344 |
|
| 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 |
0.66 |
|
| 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 |
0.315 |
|
| 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 |
0.738 |
|
| 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 |
0.338 |
|
| 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 |
0.328 |
|
| 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 |
0.302 |
|
| 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 |
0.783 |
|
| 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 |
0.78 |
|
| 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 |
0.77 |
|
| 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 |
0.791 |
|
| 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 |
0.612 |
|
| 2018 |
Yona AH, Alm EJ, Gore J. Random sequences rapidly evolve into de novo promoters. Nature Communications. 9: 1530. PMID 29670097 DOI: 10.1038/S41467-018-04026-W |
0.306 |
|
| 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 |
0.788 |
|
| 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 |
0.535 |
|
| 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 |
0.753 |
|
| 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 |
0.775 |
|
| 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 |
0.617 |
|
| 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 |
0.693 |
|
| 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 |
0.622 |
|
| 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 |
0.386 |
|
| 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 |
0.79 |
|
| 2017 |
Perrotta AR, Kumaraswamy R, Bastidas-Oyanedel JR, Alm EJ, Rodríguez J. Inoculum composition determines microbial community and function in an anaerobic sequential batch reactor. Plos One. 12: e0171369. PMID 28196102 DOI: 10.1371/Journal.Pone.0171369 |
0.349 |
|
| 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 |
0.605 |
|
| 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 |
0.33 |
|
| 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 |
0.753 |
|
| 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 |
0.779 |
|
| 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 |
0.714 |
|
| 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 |
0.353 |
|
| 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 |
0.641 |
|
| 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 |
0.347 |
|
| 2016 |
Fondi M, Karkman A, Tamminen MV, Bosi E, Virta M, Fani R, Alm E, McInerney JO. "Every Gene Is Everywhere but the Environment Selects": Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis. Genome Biology and Evolution. 8: 1388-400. PMID 27190206 DOI: 10.1093/Gbe/Evw077 |
0.352 |
|
| 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 |
0.305 |
|
| 2016 |
Allegretti JR, Kearney S, Li N, Bogart E, Bullock K, Gerber GK, Bry L, Clish CB, Alm E, Korzenik JR. Recurrent Clostridium difficile infection associates with distinct bile acid and microbiome profiles. Alimentary Pharmacology & Therapeutics. PMID 27086647 DOI: 10.1111/Apt.13616 |
0.686 |
|
| 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 |
0.338 |
|
| 2016 |
Allegretti JR, Storm M, Smith M, Kelly CR, Kearney S, Perrotta A, Elliott RJ, Swanson P, Kassam Z, Alm E. Su1739 Strain-Level Analysis of Microbial Engraftment Associated With Resolution of Recurrent Clostridium difficile Following Fecal Microbiota Transplantation Gastroenterology. 150: S540-S541. DOI: 10.1016/S0016-5085(16)31856-X |
0.695 |
|
| 2016 |
Allegretti JR, Kearney S, Li N, Bogart E, Bullock K, Gerber G, Bry L, Clish CB, Alm E, Korzenik JR. 95 Clostridium difficile Infection Associates With Distinct Bile Acid and Microbiome Profiles Gastroenterology. 150: S24. DOI: 10.1016/S0016-5085(16)30206-2 |
0.678 |
|
| 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 |
0.731 |
|
| 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 |
0.324 |
|
| 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 |
0.76 |
|
| 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 |
0.665 |
|
| 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 |
0.691 |
|
| 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 |
0.357 |
|
| 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 |
0.678 |
|
| 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 |
0.664 |
|
| 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 |
0.694 |
|
| 2013 |
Preheim SP, Perrotta AR, Friedman J, Smilie C, Brito I, Smith MB, Alm E. Computational methods for high-throughput comparative analyses of natural microbial communities. Methods in Enzymology. 531: 353-70. PMID 24060130 DOI: 10.1016/B978-0-12-407863-5.00018-6 |
0.735 |
|
| 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 |
0.714 |
|
| 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 |
0.768 |
|
| 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 |
0.345 |
|
| 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 |
0.737 |
|
| 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 |
0.639 |
|
| 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 |
0.359 |
|
| 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 |
0.775 |
|
| 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 |
0.357 |
|
| 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 |
0.598 |
|
| 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 |
0.765 |
|
| 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 |
0.368 |
|
| 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 |
0.373 |
|
| 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 |
0.776 |
|
| 2012 |
Fournier GP, Andam CP, Alm EJ, Gogarten JP. Erratum to: Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life Origins of Life and Evolution of Biospheres. 42: 377-377. DOI: 10.1007/S11084-012-9294-1 |
0.732 |
|
| 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 |
0.747 |
|
| 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 |
0.697 |
|
| 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 |
0.604 |
|
| 2011 |
David LA, Alm EJ. Rapid evolutionary innovation during an Archaean genetic expansion. Nature. 469: 93-6. PMID 21170026 DOI: 10.1038/Nature09649 |
0.676 |
|
| 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 |
0.792 |
|
| 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 |
0.5 |
|
| 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 |
0.765 |
|
| 2010 |
Timberlake S, Joachimiak M, Joyner D, Chakraborty R, Baumohl J, Dehal P, Arkin A, Hazen T, Alm E. Conservation of Modules but not Phenotype in Bacterial Response to Environmental Stress Lawrence Berkeley National Laboratory. DOI: 10.2172/985921 |
0.521 |
|
| 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 |
0.341 |
|
| 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 |
0.704 |
|
| 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 |
0.308 |
|
| 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 |
0.604 |
|
| 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 |
0.525 |
|
| 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 |
0.74 |
|
| 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 |
0.787 |
|
| 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 |
0.358 |
|
| 2007 |
Stolyar S, He Q, Joachimiak MP, He Z, Yang ZK, Borglin SE, Joyner DC, Huang K, Alm E, Hazen TC, Zhou J, Wall JD, Arkin AP, Stahl DA. Response of Desulfovibrio vulgaris to alkaline stress. Journal of Bacteriology. 189: 8944-52. PMID 17921288 DOI: 10.1128/Jb.00284-07 |
0.491 |
|
| 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 |
0.491 |
|
| 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 |
0.54 |
|
| 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 |
0.527 |
|
| 2006 |
Price MN, Arkin AP, Alm EJ. The life-cycle of operons. Plos Genetics. 2: e96. PMID 16789824 DOI: 10.1371/Journal.Pgen.0020096 |
0.527 |
|
| 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 |
0.513 |
|
| 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 |
0.49 |
|
| 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 |
0.438 |
|
| 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 |
0.523 |
|
| 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 |
0.495 |
|
| 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 |
0.493 |
|
| 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 |
0.494 |
|
| 2006 |
Price MN, Arkin AP, Alm EJ. Correction: The Life-Cycle of Operons Plos Genetics. 2: e126. DOI: 10.1371/Journal.Pgen.0020126 |
0.47 |
|
| 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 |
0.522 |
|
| 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 |
0.535 |
|
| 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 |
0.499 |
|
| 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 |
0.519 |
|
| 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 |
0.52 |
|
| 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 |
0.52 |
|
| 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 DOI: 10.1186/Gb-2004-5-11-R90 |
0.506 |
|
| 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 |
0.518 |
|
| 2003 |
Ivankov DN, Garbuzynskiy SO, Alm E, Plaxco KW, Baker D, Finkelstein AV. Contact order revisited: influence of protein size on the folding rate. Protein Science : a Publication of the Protein Society. 12: 2057-62. PMID 12931003 DOI: 10.1110/Ps.0302503 |
0.547 |
|
| 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 |
0.403 |
|
| 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 |
0.692 |
|
| 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 |
0.749 |
|
| 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 |
0.36 |
|
| 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 |
0.363 |
|
| 1999 |
Riddle DS, Grantcharova VP, Santiago JV, Alm E, Ruczinski I, Baker D. Experiment and theory highlight role of native state topology in SH3 folding. Nature Structural Biology. 6: 1016-24. PMID 10542092 DOI: 10.1038/14901 |
0.747 |
|
| 1999 |
Alm E, Baker D. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Proceedings of the National Academy of Sciences of the United States of America. 96: 11305-10. PMID 10500172 DOI: 10.1073/Pnas.96.20.11305 |
0.375 |
|
| 1999 |
Alm E, Baker D. Matching theory and experiment in protein folding. Current Opinion in Structural Biology. 9: 189-96. PMID 10322214 DOI: 10.1016/S0959-440X(99)80027-X |
0.38 |
|
| 1998 |
Cardullo RA, Alm EJ. Introduction to image processing. Methods in Cell Biology. 56: 91-115. PMID 9500134 DOI: 10.1016/S0091-679X(08)60422-7 |
0.625 |
|
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