Ainonen S, Tejesvi MV, Mahmud MR, Paalanne N, Pokka T, Li W, Nelson KE, Salo J, Renko M, Vänni P, Pirttilä AM, Tapiainen T
Antibiotics at birth and later antibiotic courses: effects on gut microbiota.
Pediatric research. 2021-04-06;
PMID: 33824448
Gut microbiome differences between amyotrophic lateral sclerosis patients and spouse controls.
Amyotrophic lateral sclerosis & frontotemporal degeneration. 2021-04-05; 1-9.
PMID: 33818222
Espinoza JL, Dupont CL, O'Rourke A, Beyhan S, Morales P, Spoering A, Meyer KJ, Chan AP, Choi Y, Nierman WC, Lewis K, Nelson KE
Predicting antimicrobial mechanism-of-action from transcriptomes: A generalizable explainable artificial intelligence approach.
PLoS computational biology. 2021-03-29; 17.3: e1008857.
PMID: 33780444
Forensic Microbiome Database: A Tool for Forensic Geolocation Meta-Analysis Using Publicly Available 16S rRNA Microbiome Sequencing.
Frontiers in microbiology. 2021-03-23; 12.644861.
PMID: 33833745
Gomez A, Sharma AK, Mallott EK, Petrzelkova KJ, Jost Robinson CA, Yeoman CJ, Carbonero F, Pafco B, Rothman JM, Ulanov A, Vlckova K, Amato KR, Schnorr SL, Dominy NJ, Modry D, Todd A, Torralba M, Nelson KE, Burns MB, Blekhman R, Remis M, Stumpf RM, Wilson BA, Gaskins HR, Garber PA, White BA, Leigh SR
Erratum for Gomez et al., "Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints".
mSphere. 2021-03-17; 6.2:
PMID: 33731474
Advances in Microbiome Research for Animal Health.
Annual review of animal biosciences. 2021-02-16; 9.289-311.
PMID: 33317323
Microbial Species that Initially Colonize the Human Gut at Birth or in Early Childhood Can Stay in Human Body for Lifetime.
Microbial ecology. 2021-01-07;
PMID: 33410935
Sharma AK, Petrzelkova K, Pafco B, Jost Robinson CA, Fuh T, Wilson BA, Stumpf RM, Torralba MG, Blekhman R, White B, Nelson KE, Leigh SR, Gomez A
Traditional Human Populations and Nonhuman Primates Show Parallel Gut Microbiome Adaptations to Analogous Ecological Conditions.
mSystems. 2020-12-22; 5.6:
PMID: 33361321
The Oral Host-Microbial Interactome: An Ecological Chronometer of Health?
Trends in microbiology. 2020-12-02;
PMID: 33279381
Torralba MG, Aleti G, Li W, Moncera KJ, Lin YH, Yu Y, Masternak MM, Golusinski W, Golusinski P, Lamperska K, Edlund A, Freire M, Nelson KE
Correction to: Oral Microbial Species and Virulence Factors Associated with Oral Squamous Cell Carcinoma.
Microbial ecology. 2020-11-20;
PMID: 33219400
Torralba MG, Aleti G, Li W, Moncera KJ, Lin YH, Yu Y, Masternak MM, Golusinski W, Golusinski P, Lamperska K, Edlund A, Freire M, Nelson KE
Oral Microbial Species and Virulence Factors Associated with Oral Squamous Cell Carcinoma.
Microbial ecology. 2020-11-06;
PMID: 33155101
Protein signatures from blood plasma and urine suggest changes in vascular function and IL-12 signaling in elderly with a history of chronic diseases compared with an age-matched healthy cohort.
GeroScience. 2020-09-24;
PMID: 32974878
Inflammatory Networks Linking Oral Microbiome with Systemic Health and Disease.
Journal of dental research. 2020-09-01; 99.10: 1131-1139.
PMID: 32459164
Predictive Signatures of 19 Antibiotic-Induced Escherichia coli Proteomes.
ACS infectious diseases. 2020-08-14; 6.8: 2120-2129.
PMID: 32673475
Applications of weighted association networks applied to compositional data in biology.
Environmental microbiology. 2020-08-01; 22.8: 3020-3038.
PMID: 32436334
Kaul D, Rathnasinghe R, Ferres M, Tan GS, Barrera A, Pickett BE, Methe BA, Das SR, Budnik I, Halpin RA, Wentworth D, Schmolke M, Mena I, Albrecht RA, Singh I, Nelson KE, García-Sastre A, Dupont CL, Medina RA
Author Correction: Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection.
Nature communications. 2020-06-16; 11.1: 3132.
PMID: 32546784
Kaul D, Rathnasinghe R, Ferres M, Tan GS, Barrera A, Pickett BE, Methe BA, Das SR, Das S, Budnik I, Halpin RA, Wentworth D, Schmolke M, Mena I, Albrecht RA, Singh I, Nelson KE, García-Sastre A, Dupont CL, Medina RA
Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection.
Nature communications. 2020-05-21; 11.1: 2537.
PMID: 32439901
Characterizing Microbial Signatures on Sculptures and Paintings of Similar Provenance.
Microbial ecology. 2020-05-21;
PMID: 32440698
Freire M, Moustafa A, Harkins DM, Torralba MG, Zhang Y, Leong P, Saffery R, Bockmann M, Kuelbs C, Hughes T, Craig JM, Nelson KE
Longitudinal Study of Oral Microbiome Variation in Twins.
Scientific reports. 2020-05-14; 10.1: 7954.
PMID: 32409670
Persistent Gut Microbial Dysbiosis in Children with Acute Lymphoblastic Leukemia (ALL) During Chemotherapy.
Microbial ecology. 2020-05-01; 79.4: 1034-1043.
PMID: 31754744
Vertical transmission of gut microbiome and antimicrobial resistance genes in infants exposed to antibiotics at birth.
The Journal of infectious diseases. 2020-04-02;
PMID: 32239170
Imai Y, Meyer KJ, Iinishi A, Favre-Godal Q, Green R, Manuse S, Caboni M, Mori M, Niles S, Ghiglieri M, Honrao C, Ma X, Guo JJ, Makriyannis A, Linares-Otoya L, Böhringer N, Wuisan ZG, Kaur H, Wu R, Mateus A, Typas A, Savitski MM, Espinoza JL, O'Rourke A, Nelson KE, Hiller S, Noinaj N, Schäberle TF, D'Onofrio A, Lewis K
Author Correction: A new antibiotic selectively kills Gram-negative pathogens.
Nature. 2020-04-01; 580.7802: E3.
PMID: 32269338
Vuillermin PJ, O'Hely M, Collier F, Allen KJ, Tang MLK, Harrison LC, Carlin JB, Saffery R, Ranganathan S, Sly PD, Gray L, Molloy J, Pezic A, Conlon M, Topping D, Nelson K, Mackay CR, Macia L, Koplin J, Dawson SL, Moreno-Betancur M, Ponsonby AL, J. Craig Venter Institute, BIS Investigator Group
Maternal carriage of Prevotella during pregnancy associates with protection against food allergy in the offspring.
Nature communications. 2020-03-24; 11.1: 1452.
PMID: 32210229
O'Rourke A, Beyhan S, Choi Y, Morales P, Chan AP, Espinoza JL, Dupont CL, Meyer KJ, Spoering A, Lewis K, Nierman WC, Nelson KE
Mechanism-of-Action Classification of Antibiotics by Global Transcriptome Profiling.
Antimicrobial agents and chemotherapy. 2020-02-21; 64.3:
PMID: 31907190
Shomorony I, Cirulli ET, Huang L, Napier LA, Heister RR, Hicks M, Cohen IV, Yu HC, Swisher CL, Schenker-Ahmed NM, Li W, Nelson KE, Brar P, Kahn AM, Spector TD, Caskey CT, Venter JC, Karow DS, Kirkness EF, Shah N
An unsupervised learning approach to identify novel signatures of health and disease from multimodal data.
Genome medicine. 2020-01-10; 12.1: 7.
PMID: 31924279
Long-term impact of oral surgery with or without amoxicillin on the oral microbiome-A prospective cohort study.
Scientific reports. 2019-12-10; 9.1: 18761.
PMID: 31822712
Gastro-intestinal and oral microbiome signatures associated with healthy aging.
GeroScience. 2019-12-01; 41.6: 907-921.
PMID: 31620923
Imai Y, Meyer KJ, Iinishi A, Favre-Godal Q, Green R, Manuse S, Caboni M, Mori M, Niles S, Ghiglieri M, Honrao C, Ma X, Guo J, Guo JJ, Makriyannis A, Linares-Otoya L, Böhringer N, Wuisan ZG, Kaur H, Wu R, Mateus A, Mateus A, Typas A, Savitski MM, Espinoza JL, O'Rourke A, Nelson KE, Hiller S, Noinaj N, Schäberle TF, D'Onofrio A, Lewis K
A new antibiotic selectively kills Gram-negative pathogens.
Nature. 2019-12-01; 576.7787: 459-464.
PMID: 31747680
Pessoa L, Aleti G, Choudhury S, Nguyen D, Yaskell T, Zhang Y, Li W, Nelson KE, Neto LLS, Sant'Ana ACP, Freire M
Host-Microbial Interactions in Systemic Lupus Erythematosus and Periodontitis.
Frontiers in immunology. 2019-11-12; 10.2602.
PMID: 31781106
Visconti A, Le Roy CI, Rosa F, Rossi N, Martin TC, Mohney RP, Li W, de Rinaldis E, Bell JT, Venter JC, Nelson KE, Spector TD, Falchi M
Interplay between the human gut microbiome and host metabolism.
Nature communications. 2019-10-03; 10.1: 4505.
PMID: 31582752
Loomba R, Seguritan V, Li W, Long T, Klitgord N, Bhatt A, Dulai PS, Caussy C, Bettencourt R, Highlander SK, Jones MB, Sirlin CB, Schnabl B, Brinkac L, Schork N, Chen CH, Brenner DA, Biggs W, Yooseph S, Venter JC, Nelson KE
Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease.
Cell metabolism. 2019-09-03; 30.3: 607.
PMID: 31484056
Gomez A, Sharma AK, Mallott EK, Petrzelkova KJ, Jost Robinson CA, Yeoman CJ, Carbonero F, Pafco B, Rothman JM, Ulanov A, Vlckova K, Amato KR, Schnorr SL, Dominy NJ, Modry D, Todd A, Torralba M, Nelson KE, Burns MB, Blekhman R, Remis M, Stumpf RM, Wilson BA, Gaskins HR, Garber PA, White BA, Leigh SR
Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints.
mSphere. 2019-07-31; 4.4:
PMID: 31366708
Tapiainen T, Koivusaari P, Brinkac L, Lorenzi HA, Salo J, Renko M, Pruikkonen H, Pokka T, Li W, Nelson K, Pirttilä AM, Tejesvi MV
Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants.
Scientific reports. 2019-07-23; 9.1: 10635.
PMID: 31337807
Pafčo B, Sharma AK, Petrželková KJ, Vlčková K, Todd A, Yeoman CJ, Wilson BA, Stumpf R, White BA, Nelson KE, Leigh S, Gomez A
Gut microbiome composition of wild western lowland gorillas is associated with individual age and sex factors.
American journal of physical anthropology. 2019-07-01; 169.3: 575-585.
PMID: 31025322
Lin YH, Eguez RV, Torralba MG, Singh H, Golusinski P, Goliusinski W, Golusinski W, Masternak M, Nelson KE, Freire M, Yu Y
Self-Assembled STrap for Global Proteomics and Salivary Biomarker Discovery.
Journal of proteome research. 2019-04-05; 18.4: 1907-1915.
PMID: 30848925
Choi Y, Banerjee A, McNish S, Couch KS, Torralba MG, Lucas S, Tovchigrechko A, Madupu R, Yooseph S, Nelson KE, Shanmugam VK, Chan AP
Co-occurrence of Anaerobes in Human Chronic Wounds.
Microbial ecology. 2019-04-01; 77.3: 808-820.
PMID: 30141127
Amato KR, G Sanders J, Song SJ, Nute M, Metcalf JL, Thompson LR, Morton JT, Amir A, J McKenzie V, Humphrey G, Gogul G, Gaffney J, L Baden A, A O Britton G, P Cuozzo F, Di Fiore A, J Dominy N, L Goldberg T, Gomez A, Kowalewski MM, J Lewis R, Link A, L Sauther M, Tecot S, A White B, E Nelson K, M Stumpf R, Knight R, R Leigh S
Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes.
The ISME journal. 2019-03-01; 13.3: 576-587.
PMID: 29995839
A novel approach for the identification and phylogenetic delineation of human Mycoplasma species and strains using genomic segment sequence analysis.
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases. 2019-03-01; 68.68-76.
PMID: 30529087
OMeta: an ontology-based, data-driven metadata tracking system.
BMC bioinformatics. 2019-01-07; 20.1: 8.
PMID: 30612540
Xylitol and sorbitol effects on the microbiome of saliva and plaque.
Journal of oral microbiology. 2019-01-01; 11.1: 1536181.
PMID: 30598728
The Airplane Cabin Microbiome.
Microbial ecology. 2019-01-01; 77.1: 87-95.
PMID: 29876609
Li X, Rensing C, Taylor WL, Costelle C, Brejnrod AD, Ferry RJ, Higgins PB, Folli F, Kottapalli KR, Hubbard GB, Dick EJ, Yooseph S, Nelson KE, Schlabritz-Loutsevitch N
Papio spp. Colon microbiome and its link to obesity in pregnancy.
Journal of medical primatology. 2018-12-01; 47.6: 393-401.
PMID: 30039863
Espinoza JL, Harkins DM, Torralba M, Gomez A, Highlander SK, Jones MB, Leong P, Saffery R, Bockmann M, Kuelbs C, Inman JM, Hughes T, Craig JM, Nelson KE, Dupont CL
Supragingival Plaque Microbiome Ecology and Functional Potential in the Context of Health and Disease.
mBio. 2018-11-27; 9.6:
PMID: 30482830
Rosas-Salazar C, Shilts MH, Tovchigrechko A, Schobel S, Chappell JD, Larkin EK, Gebretsadik T, Halpin RA, Nelson KE, Moore ML, Anderson LJ, Peebles RS, Das SR, Hartert TV
Nasopharyngeal Lactobacillus is associated with a reduced risk of childhood wheezing illnesses following acute respiratory syncytial virus infection in infancy.
The Journal of allergy and clinical immunology. 2018-11-01; 142.5: 1447-1456.e9.
PMID: 29330010
Vlčková K, Pafčo B, Petrželková KJ, Modrý D, Todd A, Yeoman CJ, Torralba M, Wilson BA, Stumpf RM, White BA, Nelson KE, Leigh SR, Gomez A
Relationships Between Gastrointestinal Parasite Infections and the Fecal Microbiome in Free-Ranging Western Lowland Gorillas.
Frontiers in microbiology. 2018-06-15; 9.1202.
PMID: 29963018
Spatial and Environmental Variation of the Human Hair Microbiota.
Scientific reports. 2018-06-13; 8.1: 9017.
PMID: 29899411
Moustafa A, Li W, Singh H, Moncera KJ, Torralba MG, Yu Y, Manuel O, Biggs W, Venter JC, Nelson KE, Pieper R, Telenti A
Microbial metagenome of urinary tract infection.
Scientific reports. 2018-03-12; 8.1: 4333.
PMID: 29531289
Raulo A, Ruokolainen L, Lane A, Amato K, Knight R, Leigh S, Stumpf R, White B, Nelson KE, Baden AL, Tecot SR
Social behaviour and gut microbiota in red-bellied lemurs (Eulemur rubriventer): In search of the role of immunity in the evolution of sociality.
The Journal of animal ecology. 2018-03-01; 87.2: 388-399.
PMID: 29205327
Bacterial Species Identified on the Skin of Bottlenose Dolphins Off Southern California via Next Generation Sequencing Techniques.
Microbial ecology. 2018-02-01; 75.2: 303-309.
PMID: 29080910
Moustafa A, Li W, Anderson EL, Wong EHM, Dulai PS, Sandborn WJ, Biggs W, Yooseph S, Jones MB, Venter JC, Nelson KE, Chang JT, Telenti A, Boland BS
Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease.
Clinical and translational gastroenterology. 2018-01-18; 9.1: e132.
PMID: 29345635
Vlčková K, Shutt-Phillips K, Heistermann M, Pafčo B, Petrželková KJ, Todd A, Modrý D, Nelson KE, Wilson BA, Stumpf RM, White BA, Leigh SR, Gomez A
Impact of stress on the gut microbiome of free-ranging western lowland gorillas.
Microbiology (Reading, England). 2018-01-01; 164.1: 40-44.
PMID: 29205130
Comparative genomics of four Mycoplasma species of the human urogenital tract: Analysis of their core genomes and virulence genes.
International journal of medical microbiology : IJMM. 2017-12-01; 307.8: 508-520.
PMID: 28927691
Brim H, Yooseph S, Lee E, Sherif ZA, Abbas M, Laiyemo AO, Varma S, Torralba M, Dowd SE, Nelson KE, Pathmasiri W, Sumner S, de Vos W, Liang Q, Yu J, Zoetendal E, Ashktorab H
A Microbiomic Analysis in African Americans with Colonic Lesions Reveals Streptococcus sp.VT162 as a Marker of Neoplastic Transformation.
Genes. 2017-11-09; 8.11:
PMID: 29120399
The Threat of Antimicrobial Resistance on the Human Microbiome.
Microbial ecology. 2017-11-01; 74.4: 1001-1008.
PMID: 28492988
Llorente C, Jepsen P, Inamine T, Wang L, Bluemel S, Wang HJ, Loomba R, Bajaj JS, Schubert ML, Sikaroodi M, Gillevet PM, Xu J, Kisseleva T, Ho SB, Depew J, Du X, Sørensen HT, Vilstrup H, Nelson KE, Brenner DA, Fouts DE, Schnabl B
Gastric acid suppression promotes alcoholic liver disease by inducing overgrowth of intestinal Enterococcus.
Nature communications. 2017-10-16; 8.1: 837.
PMID: 29038503
Gomez A, Espinoza JL, Harkins DM, Leong P, Saffery R, Bockmann M, Torralba M, Kuelbs C, Kodukula R, Inman J, Hughes T, Craig JM, Highlander SK, Jones MB, Dupont CL, Nelson KE
Host Genetic Control of the Oral Microbiome in Health and Disease.
Cell host & microbe. 2017-09-13; 22.3: 269-278.e3.
PMID: 28910633
Wright MS, McCorrison J, Gomez AM, Beck E, Harkins D, Shankar J, Mounaud S, Segubre-Mercado E, Mojica AMR, Bacay B, Nzenze SA, Kimaro SZM, Adrian P, Klugman KP, Lucero MG, Nelson KE, Madhi S, Sutton GG, Nierman WC, Losada L
Strain Level Streptococcus Colonization Patterns during the First Year of Life.
Frontiers in microbiology. 2017-09-06; 8.1661.
PMID: 28932211
Integrating the microbiome as a resource in the forensics toolkit.
Forensic science international. Genetics. 2017-09-01; 30.141-147.
PMID: 28728057
Singh H, Yu Y, Suh MJ, Torralba MG, Stenzel RD, Tovchigrechko A, Thovarai V, Harkins DM, Rajagopala SV, Osborne W, Cogen FR, Kaplowitz PB, Nelson KE, Madupu R, Pieper R
Type 1 Diabetes: Urinary Proteomics and Protein Network Analysis Support Perturbation of Lysosomal Function.
Theranostics. 2017-07-07; 7.10: 2704-2717.
PMID: 28819457
Patterns in Gut Microbiota Similarity Associated with Degree of Sociality among Sex Classes of a Neotropical Primate.
Microbial ecology. 2017-07-01; 74.1: 250-258.
PMID: 28124727
Loomba R, Seguritan V, Li W, Long T, Klitgord N, Bhatt A, Dulai PS, Caussy C, Bettencourt R, Highlander SK, Jones MB, Sirlin CB, Schnabl B, Brinkac L, Schork N, Chen CH, Brenner DA, Biggs W, Yooseph S, Venter JC, Nelson KE
Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease.
Cell metabolism. 2017-05-02; 25.5: 1054-1062.e5.
PMID: 28467925
Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies.
BMC genomics. 2017-04-13; 18.1: 296.
PMID: 28407798
HSV-1 clinical isolates with unique in vivo and in vitro phenotypes and insight into genomic differences.
Journal of neurovirology. 2017-04-01; 23.2: 171-185.
PMID: 27739035
The Human Microbiome and Cancer.
Cancer prevention research (Philadelphia, Pa.). 2017-04-01; 10.4: 226-234.
PMID: 28096237
Reducing the Bottleneck in Discovery of Novel Antibiotics.
Microbial ecology. 2017-04-01; 73.3: 658-667.
PMID: 27896376
Moustafa A, Xie C, Kirkness E, Biggs W, Wong E, Turpaz Y, Bloom K, Delwart E, Nelson KE, Venter JC, Telenti A
The blood DNA virome in 8,000 humans.
PLoS pathogens. 2017-03-22; 13.3: e1006292.
PMID: 28328962
The Oral Microbiome of Children: Development, Disease, and Implications Beyond Oral Health.
Microbial ecology. 2017-02-01; 73.2: 492-503.
PMID: 27628595
Characterization of Early-Phase Neutrophil Extracellular Traps in Urinary Tract Infections.
PLoS pathogens. 2017-01-27; 13.1: e1006151.
PMID: 28129394
Effect of Macondo Prospect 252 Oil on Microbiota Associated with Pelagic Sargassum in the Northern Gulf of Mexico.
Microbial ecology. 2017-01-01; 73.1: 91-100.
PMID: 27815589
Comprehensive Metaproteomic Analyses of Urine in the Presence and Absence of Neutrophil-Associated Inflammation in the Urinary Tract.
Theranostics. 2017-01-01; 7.2: 238-252.
PMID: 28042331
Rosas-Salazar C, Shilts MH, Tovchigrechko A, Schobel S, Chappell JD, Larkin EK, Shankar J, Yooseph S, Nelson KE, Halpin RA, Moore ML, Anderson LJ, Peebles RS, Das SR, Hartert TV
Differences in the Nasopharyngeal Microbiome During Acute Respiratory Tract Infection With Human Rhinovirus and Respiratory Syncytial Virus in Infancy.
The Journal of infectious diseases. 2016-12-15; 214.12: 1924-1928.
PMID: 27923952
Cui J, Chen CH, Lo MT, Schork N, Bettencourt R, Gonzalez MP, Bhatt A, Hooker J, Shaffer K, Nelson KE, Long MT, Brenner DA, Sirlin CB, Loomba R, For The Genetics Of Nafld In Twins Consortium
Shared genetic effects between hepatic steatosis and fibrosis: A prospective twin study.
Hepatology (Baltimore, Md.). 2016-11-01; 64.5: 1547-1558.
PMID: 27315352
Vlčková K, Gomez A, Petrželková KJ, Whittier CA, Todd AF, Yeoman CJ, Nelson KE, Wilson BA, Stumpf RM, Modrý D, White BA, Leigh SR
Effect of Antibiotic Treatment on the Gastrointestinal Microbiome of Free-Ranging Western Lowland Gorillas (Gorilla g. gorilla).
Microbial ecology. 2016-11-01; 72.4: 943-954.
PMID: 26984253
Anderson EL, Li W, Klitgord N, Highlander SK, Dayrit M, Seguritan V, Yooseph S, Biggs W, Venter JC, Nelson KE, Jones MB
A robust ambient temperature collection and stabilization strategy: Enabling worldwide functional studies of the human microbiome.
Scientific reports. 2016-08-25; 6.31731.
PMID: 27558918
Rajagopala SV, Yooseph S, Harkins DM, Moncera KJ, Zabokrtsky KB, Torralba MG, Tovchigrechko A, Highlander SK, Pieper R, Sender L, Nelson KE
Gastrointestinal microbial populations can distinguish pediatric and adolescent Acute Lymphoblastic Leukemia (ALL) at the time of disease diagnosis.
BMC genomics. 2016-08-15; 17.1: 635.
PMID: 27527070
Host age, social group, and habitat type influence the gut microbiota of wild ring-tailed lemurs (Lemur catta).
American journal of primatology. 2016-08-01; 78.8: 883-92.
PMID: 27177345
Microbial diversity in individuals and their household contacts following typical antibiotic courses.
Microbiome. 2016-07-30; 4.1: 39.
PMID: 27473422
Nasopharyngeal Microbiome in Respiratory Syncytial Virus Resembles Profile Associated with Increased Childhood Asthma Risk.
American journal of respiratory and critical care medicine. 2016-05-15; 193.10: 1180-3.
PMID: 27174483
Gomez A, Petrzelkova KJ, Burns MB, Yeoman CJ, Amato KR, Vlckova K, Modry D, Todd A, Jost Robinson CA, Remis MJ, Torralba MG, Morton E, Umaña JD, Carbonero F, Gaskins HR, Nelson KE, Wilson BA, Stumpf RM, White BA, Leigh SR, Blekhman R
Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns.
Cell reports. 2016-03-08; 14.9: 2142-2153.
PMID: 26923597
Amato KR, Martinez-Mota R, Righini N, Raguet-Schofield M, Corcione FP, Marini E, Humphrey G, Gogul G, Gaffney J, Lovelace E, Williams L, Luong A, Dominguez-Bello MG, Stumpf RM, White B, Nelson KE, Knight R, Leigh SR
Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species.
Oecologia. 2016-03-01; 180.3: 717-33.
PMID: 26597549
Fouts DE, Matthias MA, Adhikarla H, Adler B, Amorim-Santos L, Berg DE, Bulach D, Buschiazzo A, Chang YF, Galloway RL, Haake DA, Haft DH, Hartskeerl R, Ko AI, Levett PN, Matsunaga J, Mechaly AE, Monk JM, Nascimento AL, Nelson KE, Palsson B, Peacock SJ, Picardeau M, Ricaldi JN, Thaipandungpanit J, Wunder EA, Yang XF, Zhang JJ, Vinetz JM
What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira.
PLoS neglected tropical diseases. 2016-02-18; 10.2: e0004403.
PMID: 26890609
Gulia-Nuss M, Nuss AB, Meyer JM, Sonenshine DE, Roe RM, Waterhouse RM, Sattelle DB, de la Fuente J, Ribeiro JM, Megy K, Thimmapuram J, Miller JR, Walenz BP, Koren S, Hostetler JB, Thiagarajan M, Joardar VS, Hannick LI, Bidwell S, Hammond MP, Young S, Zeng Q, Abrudan JL, Almeida FC, Ayllón N, Bhide K, Bissinger BW, Bonzon-Kulichenko E, Buckingham SD, Caffrey DR, Caimano MJ, Croset V, Driscoll T, Gilbert D, Gillespie JJ, Giraldo-Calderón GI, Grabowski JM, Jiang D, Khalil SM, Khalil SMS, Kim D, Kocan KM, Koči J, Kuhn RJ, Kurtti TJ, Lees K, Lang EG, Kennedy RC, Kwon H, Perera R, Qi Y, Radolf JD, Sakamoto JM, Sánchez-Gracia A, Severo MS, Silverman N, Šimo L, Tojo M, Tornador C, Van Zee JP, Vázquez J, Vieira FG, Villar M, Wespiser AR, Yang Y, Zhu J, Arensburger P, Pietrantonio PV, Barker SC, Shao R, Zdobnov EM, Hauser F, Grimmelikhuijzen CJ, Grimmelikhuijzen CJP, Park Y, Rozas J, Benton R, Pedra JH, Pedra JHF, Nelson DR, Unger MF, Tubio JM, Tubio JMC, Tu Z, Robertson HM, Shumway M, Sutton G, Wortman JR, Lawson D, Wikel SK, Nene VM, Fraser CM, Collins FH, Birren B, Nelson KE, Caler E, Hill CA
Genomic insights into the Ixodes scapularis tick vector of Lyme disease.
Nature communications. 2016-02-09; 7.10507.
PMID: 26856261
Gomez A, Rothman JM, Petrzelkova K, Yeoman CJ, Vlckova K, Umaña JD, Carr M, Modry D, Todd A, Torralba M, Nelson KE, Stumpf RM, Wilson BA, Blekhman R, White BA, Leigh SR
Temporal variation selects for diet-microbe co-metabolic traits in the gut of Gorilla spp.
The ISME journal. 2016-02-01; 10.2: 514-26.
PMID: 26315972
Shilts MH, Rosas-Salazar C, Tovchigrechko A, Larkin EK, Torralba M, Akopov A, Halpin R, Peebles RS, Moore ML, Anderson LJ, Nelson KE, Hartert TV, Das SR
Minimally Invasive Sampling Method Identifies Differences in Taxonomic Richness of Nasal Microbiomes in Young Infants Associated with Mode of Delivery.
Microbial ecology. 2016-01-01; 71.1: 233-42.
PMID: 26370110
Loomba R, Schork N, Chen CH, Bettencourt R, Bhatt A, Ang B, Nguyen P, Hernandez C, Richards L, Salotti J, Lin S, Seki E, Nelson KE, Sirlin CB, Brenner D, Genetics of NAFLD in Twins Consortium
Heritability of Hepatic Fibrosis and Steatosis Based on a Prospective Twin Study.
Gastroenterology. 2015-12-01; 149.7: 1784-93.
PMID: 26299412
Edlund A, Yang Y, Yooseph S, Hall AP, Nguyen DD, Dorrestein PC, Nelson KE, He X, Lux R, Shi W, McLean JS
Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism.
The ISME journal. 2015-12-01; 9.12: 2605-19.
PMID: 26023872
Amato KR, Yeoman CJ, Cerda G, Schmitt CA, Cramer JD, Miller ME, Gomez A, Turner TR, Wilson BA, Stumpf RM, Nelson KE, White BA, Knight R, Leigh SR
Variable responses of human and non-human primate gut microbiomes to a Western diet.
Microbiome. 2015-11-16; 3.53.
PMID: 26568112
Jones MB, Highlander SK, Anderson EL, Li W, Dayrit M, Klitgord N, Fabani MM, Seguritan V, Green J, Pride DT, Yooseph S, Biggs W, Nelson KE, Venter JC
Library preparation methodology can influence genomic and functional predictions in human microbiome research.
Proceedings of the National Academy of Sciences of the United States of America. 2015-11-10; 112.45: 14024-9.
PMID: 26512100
Alivisatos AP, Alivisatos AP, Blaser MJ, Balskus EP, Biteen JS, Brodie EL, Chun M, Blaser MJ, Dangl JL, Brodie EL, Donohue TJ, Browning ND, Dorrestein PC, Cardon ZG, Cavanaugh CM, Gilbert JA, Green JL, Chun M, Jansson JK, Cliffel DE, Colwell RR, Knight R, Dangl JL, Maxon ME, McFall-Ngai MJ, Donohue TJ, Miller JF, Dorrestein PC, Pollard KS, Fraser SE, Ruby EG, Friesen ML, Gilbert JA, Taha SA, Gilbert SF, Unified Microbiome Initiative Consortium, Green JL, Harwood CS, Henriksen JR, Highlander SK, Huang Y, Jansson JK, Johnson AT, Kasper DL, Knight R, Kujawinski EB, Martin CL, Maxon ME, McFall-Ngai MJ, Miller JF, Moran MA, Nelson KE, Orphan VJ, Ozcan A, Paša-Tolić L, Pollard KS, Regev A, Rubin EM, Ruby EG, Segre JA, Silver PA, Taha SA, Vivanco JM, Weinstock GM, Weiss PS, Yang P
MICROBIOME. A unified initiative to harness Earth's microbiomes.
Science (New York, N.Y.). 2015-10-30; 350.6260: 507-8.
PMID: 26511287
Similar Neutrophil-Driven Inflammatory and Antibacterial Responses in Elderly Patients with Symptomatic and Asymptomatic Bacteriuria.
Infection and immunity. 2015-10-01; 83.10: 4142-53.
PMID: 26238715
Yooseph S, Kirkness EF, Tran TM, Harkins DM, Jones MB, Torralba MG, O'Connell E, Nutman TB, Doumbo S, Doumbo OK, Traore B, Crompton PD, Nelson KE
Stool microbiota composition is associated with the prospective risk of Plasmodium falciparum infection.
BMC genomics. 2015-08-22; 16.631.
PMID: 26296559
Suh MJ, Tovchigrechko A, Thovarai V, Rolfe MA, Torralba MG, Wang J, Adkins JN, Webb-Robertson BJ, Osborne W, Cogen FR, Kaplowitz PB, Metz TO, Nelson KE, Madupu R, Pieper R
Quantitative Differences in the Urinary Proteome of Siblings Discordant for Type 1 Diabetes Include Lysosomal Enzymes.
Journal of proteome research. 2015-08-07; 14.8: 3123-35.
PMID: 26143644
High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae.
Standards in genomic sciences. 2015-07-18; 10.37.
PMID: 26221418
Gomez A, Petrzelkova K, Yeoman CJ, Vlckova K, Mrázek J, Koppova I, Carbonero F, Ulanov A, Modry D, Todd A, Torralba M, Nelson KE, Gaskins HR, Wilson B, Stumpf RM, White BA, Leigh SR
Gut microbiome composition and metabolomic profiles of wild western lowland gorillas (Gorilla gorilla gorilla) reflect host ecology.
Molecular ecology. 2015-05-01; 24.10: 2551-65.
PMID: 25846719
Diagnosing inflammation and infection in the urinary system via proteomics.
Journal of translational medicine. 2015-04-08; 13.111.
PMID: 25889401
Waldor MK, Tyson G, Borenstein E, Ochman H, Moeller A, Finlay BB, Kong HH, Gordon JI, Nelson KE, Dabbagh K, Smith H
Where next for microbiome research?
PLoS biology. 2015-01-20; 13.1: e1002050.
PMID: 25602283
An Update on the Status of Current Research on the Mammalian Microbiome.
ILAR journal. 2015-01-01; 56.2: 163-8.
PMID: 26323626
Chen P, Torralba M, Tan J, Embree M, Zengler K, Stärkel P, van Pijkeren JP, Depew J, Loomba R, Ho SB, Bajaj JS, Mutlu EA, Keshavarzian A, Tsukamoto H, Nelson KE, Fouts DE, Schnabl B
Supplementation of saturated long-chain fatty acids maintains intestinal eubiosis and reduces ethanol-induced liver injury in mice.
Gastroenterology. 2015-01-01; 148.1: 203-214.e16.
PMID: 25239591
Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH
Standardized metadata for human pathogen/vector genomic sequences.
PloS one. 2014-06-17; 9.6: e99979.
PMID: 24936976
Pregnancy's stronghold on the vaginal microbiome.
PloS one. 2014-06-04; 9.6: e98514.
PMID: 24896831
O Cuív P, Klaassens ES, Smith WJ, Mondot S, Durkin AS, Harkins DM, Foster L, McCorrison J, Torralba M, Nelson KE, Morrison M
Draft Genome Sequence of Enterococcus faecium PC4.1, a Clade B Strain Isolated from Human Feces.
Genome announcements. 2014-02-06; 2.1:
PMID: 24503986
Microbiome analysis of stool samples from African Americans with colon polyps.
PloS one. 2013-12-20; 8.12: e81352.
PMID: 24376500
O Cuív P, Klaassens ES, Smith WJ, Mondot S, Durkin AS, Harkins DM, Foster L, McCorrison J, Torralba M, Nelson KE, Morrison M
Draft Genome Sequence of Enterococcus faecalis PC1.1, a Candidate Probiotic Strain Isolated from Human Feces.
Genome announcements. 2013-02-21; 1.1:
PMID: 23469340
Microbiome in human health and disease.
Science progress. 2013-01-01; 96.Pt 2: 153-70.
PMID: 23901633
Yeoman CJ, Thomas SM, Miller ME, Ulanov AV, Torralba M, Lucas S, Gillis M, Cregger M, Gomez A, Ho M, Leigh SR, Stumpf R, Creedon DJ, Smith MA, Weisbaum JS, Nelson KE, Wilson BA, White BA
A multi-omic systems-based approach reveals metabolic markers of bacterial vaginosis and insight into the disease.
PloS one. 2013-01-01; 8.12: e56111.
PMID: 23405259
The Human Microbiome Project: a community resource for the healthy human microbiome.
PLoS biology. 2012-08-14; 10.8: e1001377.
PMID: 22904687
Jeraldo P, Sipos M, Chia N, Brulc JM, Dhillon AS, Konkel ME, Larson CL, Nelson KE, Qu A, Schook LB, Yang F, White BA, Goldenfeld N
Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes.
Proceedings of the National Academy of Sciences of the United States of America. 2012-06-19; 109.25: 9692-8.
PMID: 22615407
Bacterial translocation and changes in the intestinal microbiome in mouse models of liver disease.
Journal of hepatology. 2012-06-01; 56.6: 1283-92.
PMID: 22326468
Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community.
BMC bioinformatics. 2012-03-19; 13.42.
PMID: 22429538
Ampofo WK, Bachtiar NS, Bakamutumaho B, Barr I, Baylor N, Bedford T, Bernat J, Blayer S, Bourrier M, Boye CS, Bresee J, Broberg E, Brytting M, Bucher D, Cassels FJ, Cebedzic R, Chadha M, Chittakanpitch M, Cobey S, Colegate T, Costa JA, Cox NJ, Daves S, Do MH, Diep Ldo T, Edwards S, Eichelberger M, El Aouad R, El Kholy N, Engelhardt O, Fathalla F, Ferguson N, Franks J, Giovanni MY, Gog J, Grohmann G, Gupta S, Hachid A, Hay A, Heraud JM, Hidayati N, Howard K, Huang S, Hungnes O, Jernigan D, Kadjo H, Kang C, Katz J, Kelso A, Kiselev OI, Kistner O, Kullabutr K, Lambert L, Le M, Leung-Tack P, Levandowski R, Li Y, Lim W, Locher OK, López-Martínez I, Louwerens J, Maharani, McCauley J, Mefed K, Miller JD, Mishra AC, Mokhtari-Azad T, Monto A, Nelson K, Nelson M, Neumeier E, Njouom R, Ochieng WO, Odagiri T, Paiva TM, Pechirra P, Poon L, Prosenc K, Rambaut A, Riayati EE, Rimmelzwaan G, Russell C, Salisbury D, Sampurno OD, Savy V, Schoofs P, Schweiger B, Selleck P, Shaw M, Shay D, Sheibani A, Siqueira M, Slim A, Smith D, Spiro D, Stevens J, Sturm-Ramirez KM, Tada Y, Takizawa K, Tashiro M, Taylor B, Thomas Y, Van der Werf S, Waddell AL, Wang D, Webby R, Weber S, Weir JP, Win N, Wood J, Wu A, Zahoor Zaidi SS, Zambon M
Improving influenza vaccine virus selection: report of a WHO informal consultation held at WHO headquarters, Geneva, Switzerland, 14-16 June 2010.
Influenza and other respiratory viruses. 2012-03-01; 6.2: 142-52, e1-5.
PMID: 21819547
Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis.
BMC genomics. 2010-09-07; 11.488.
PMID: 20819230
Bacterial diversity in the oral cavity of 10 healthy individuals.
The ISME journal. 2010-08-01; 4.8: 962-74.
PMID: 20336157
Antimicrobial resistance of the coral pathogen Vibrio coralliilyticus and Caribbean sister phylotypes isolated from a diseased octocoral.
Microbial ecology. 2010-05-01; 59.4: 646-57.
PMID: 20309538
Microbial fuel cells and microbial ecology: applications in ruminant health and production research.
Microbial ecology. 2010-04-01; 59.3: 415-27.
PMID: 20024685
Chain PS, Grafham DV, Fulton RS, FitzGerald MG, Hostetler J, Muzny D, Ali J, Birren B, Bruce DC, Buhay C, Cole JR, Ding Y, Dugan S, Field D, Garrity GM, Gibbs R, Graves T, Han CS, Harrison SH, Highlander S, Hugenholtz P, Khouri HM, Kodira CD, Kolker E, Kyrpides NC, Lang D, Lapidus A, Malfatti SA, Markowitz V, Metha T, Nelson KE, Parkhill J, Pitluck S, Qin X, Read TD, Schmutz J, Sozhamannan S, Sterk P, Strausberg RL, Sutton G, Thomson NR, Tiedje JM, Weinstock G, Wollam A, Genomic Standards Consortium Human Microbiome Project Jumpstart Consortium, Detter JC
Genomics. Genome project standards in a new era of sequencing.
Science (New York, N.Y.). 2009-10-09; 326.5950: 236-7.
PMID: 19815760
Deboy RT, Mongodin EF, Fouts DE, Tailford LE, Khouri H, Emerson JB, Mohamoud Y, Watkins K, Henrissat B, Gilbert HJ, Nelson KE
Insights into plant cell wall degradation from the genome sequence of the soil bacterium Cellvibrio japonicus.
Journal of bacteriology. 2008-08-01; 190.15: 5455-63.
PMID: 18556790
Population diversity and dynamics of Streptococcus mitis, Streptococcus oralis, and Streptococcus infantis in the upper respiratory tracts of adults, determined by a nonculture strategy.
Infection and immunity. 2008-05-01; 76.5: 1889-96.
PMID: 18316382
Metagenomic analysis of the human distal gut microbiome.
Science (New York, N.Y.). 2006-06-02; 312.5778: 1355-9.
PMID: 16741115
Chromosome evolution in the Thermotogales: large-scale inversions and strain diversification of CRISPR sequences.
Journal of bacteriology. 2006-04-01; 188.7: 2364-74.
PMID: 16547022
Molecular analysis of the bacterial microbiota in the human stomach.
Proceedings of the National Academy of Sciences of the United States of America. 2006-01-17; 103.3: 732-7.
PMID: 16407106
Diversity of the human intestinal microbial flora.
Science (New York, N.Y.). 2005-06-10; 308.5728: 1635-8.
PMID: 15831718
Fouts DE, Mongodin EF, Mandrell RE, Miller WG, Rasko DA, Ravel J, Brinkac LM, Deboy RT, Parker CT, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Sullivan SA, Shetty JU, Ayodeji MA, Shvartsbeyn A, Schatz MC, Badger JH, Fraser CM, Nelson KE
Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species.
PLoS biology. 2005-01-01; 3.1: e15.
PMID: 15660156
Nelson KE, Fouts DE, Mongodin EF, Ravel J, Deboy RT, Kolonay JF, Rasko DA, Angiuoli SV, Gill SR, Paulsen IT, Peterson J, White O, Nelson WC, Nierman W, Beanan MJ, Brinkac LM, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Haft DH, Selengut J, Van Aken S, Khouri H, Fedorova N, Forberger H, Tran B, Kathariou S, Wonderling LD, Uhlich GA, Bayles DO, Luchansky JB, Fraser CM
Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species.
Nucleic acids research. 2004-01-01; 32.8: 2386-95.
PMID: 15115801
Heidelberg JF, Paulsen IT, Nelson KE, Gaidos EJ, Nelson WC, Read TD, Eisen JA, Seshadri R, Ward N, Methe B, Clayton RA, Meyer T, Tsapin A, Scott J, Beanan M, Brinkac L, Daugherty S, Deboy RT, Dodson RJ, Durkin AS, Haft DH, Kolonay JF, Madupu R, Peterson JD, Umayam LA, White O, Wolf AM, Vamathevan J, Weidman J, Impraim M, Lee K, Berry K, Lee C, Mueller J, Khouri H, Gill J, Utterback TR, McDonald LA, Feldblyum TV, Smith HO, Venter JC, Nealson KH, Fraser CM
Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis.
Nature biotechnology. 2002-11-01; 20.11: 1118-23.
PMID: 12368813
Heidelberg JF, Eisen JA, Nelson WC, Clayton RA, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Umayam L, Gill SR, Nelson KE, Read TD, Tettelin H, Richardson D, Ermolaeva MD, Vamathevan J, Bass S, Qin H, Dragoi I, Sellers P, McDonald L, Utterback T, Fleishmann RD, Nierman WC, White O, Salzberg SL, Smith HO, Colwell RR, Mekalanos JJ, Venter JC, Fraser CM
DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae.
Nature. 2000-08-03; 406.6795: 477-83.
PMID: 10952301
Tettelin H, Saunders NJ, Heidelberg J, Jeffries AC, Nelson KE, Eisen JA, Ketchum KA, Hood DW, Peden JF, Dodson RJ, Nelson WC, Gwinn ML, DeBoy R, Peterson JD, Hickey EK, Haft DH, Salzberg SL, White O, Fleischmann RD, Dougherty BA, Mason T, Ciecko A, Parksey DS, Blair E, Cittone H, Clark EB, Cotton MD, Utterback TR, Khouri H, Qin H, Vamathevan J, Gill J, Scarlato V, Masignani V, Pizza M, Grandi G, Sun L, Smith HO, Fraser CM, Moxon ER, Rappuoli R, Venter JC
Complete genome sequence of Neisseria meningitidis serogroup B strain MC58.
Science (New York, N.Y.). 2000-03-10; 287.5459: 1809-15.
PMID: 10710307
White O, Eisen JA, Heidelberg JF, Hickey EK, Peterson JD, Dodson RJ, Haft DH, Gwinn ML, Nelson WC, Richardson DL, Moffat KS, Qin H, Jiang L, Pamphile W, Crosby M, Shen M, Vamathevan JJ, Lam P, McDonald L, Utterback T, Zalewski C, Makarova KS, Aravind L, Daly MJ, Minton KW, Fleischmann RD, Ketchum KA, Nelson KE, Salzberg S, Smith HO, Venter JC, Fraser CM
Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1.
Science (New York, N.Y.). 1999-11-19; 286.5444: 1571-7.
PMID: 10567266
Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, McDonald L, Utterback TR, Malek JA, Linher KD, Garrett MM, Stewart AM, Cotton MD, Pratt MS, Phillips CA, Richardson D, Heidelberg J, Sutton GG, Fleischmann RD, Eisen JA, White O, Salzberg SL, Smith HO, Venter JC, Fraser CM
Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima.
Nature. 1999-05-27; 399.6734: 323-9.
PMID: 10360571