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Publications

Kostic Lab members underlined.

*equal contributor

corresponding author

E. coli Nissle 1917 modulates host glucose metabolism without directly acting on glucose

Scientific Reports, 2021

Chavkin TA, Pham LD, and Kostic AD. PMID: 34853343

Using Cartesian Doubt to build a sequencing-based view of microbiology

mSystems, 2021

Tierney BT, Szymanski E, Henriksen JR, Kostic AD, and Patel CJ†. PMID: 34636670

Leveraging vibration of effects analysis for robust discovery in observational biomedical data science

PLoS Biology, 2021

Tierney BT, Anderson E, Tan Y, Claypool K, Tangirala S, Kostic AD, Manrai AK, and Patel CJ. PMID: 34555021

Reconstruction of ancient microbial genomes from the human gut

Nature, 2021

Wibowo MC, Yang Z, Borry M, Hübner A, Huang KD, Tierney BT, Zimmerman S, Barajas-Olmos F, Contreras-Cubas C, García-Ortiz H, Martínez-Hernández A, Luber JM, Kirstahler P, Blohm T, Smiley FE, Arnold R, Ballal SA, Pamp SJ, Russ J, Maixner F, Rota-Stabelli O, Segata N, Reinhard K, Orozco L, Warinner C, Snow M, LeBlanc S, and Kostic AD†. PMID: 33981035

Gene-level metagenomic architectures across diseases yield high-resolution microbiome diagnostic indicators

Nature Communications, 2021

Tierney BT, Tan Y, Kostic AD†, and Patel CJ†. PMID: 34006865

 Mechanisms of microbial-neuronal interactions in pain and nociception

Neurobiology of Pain, 2021

Lagomarsino VN, Kostic AD†, and Chiu IM†. PMID: 33392418

A systematic machine learning and data type comparison yields metagenomic predictors of infant age, sex, breastfeeding, antibiotic usage, country of origin, and delivery type

PLoS Computational Biology, 2020

Le Goallec A*, Tierney BT*, Luber JM, Cofer EM, Kostic AD†, and Patel CJ†. PMID: 32392251

CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content

PeerJ, 2020

Borry M, Cordova B, Perri A, Wibowo M, Prasad Honap T, Ko J, Yu J, Britton K, Girdland-Flink L, Power RC, Stuijts I, Salazar-García DC, Hofman C, Hagan R, Samdapawindé Kagoné T, Meda N, Carabin H, Jacobson D, Reinhard K, Lewis C, Kostic AD, Jeong C, Herbig A, Hübner A, and Warinner C†. PMID: 32337106

The landscape of genetic content in the gut and oral human microbiome

Cell Host & Microbe, 2019

Tierney BT, Yang Z, Luber JM, Beaudin M, Wibowo MC, Baek C, Mehlenbacher E, Patel CJ†, and Kostic AD†. PMID: 31415755

Meta-omics analysis of elite athletes identifies a performance-enhancing microbe that functions via lactate metabolism

Nature Medicine, 2019

Scheiman J*, Luber JM*Chavkin TA*, MacDonald T, Tung A, Pham LD, Wibowo MC, Wurth RC, Punthambaker S, Tierney BT, Yang Z, Hattab MW, Avila-Pacheco J, Clish CB, Lessard S, Church GM†, and Kostic AD†. PMID: 31235964

Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing

Gigascience, 2018

Fang C, Zhong H, Lin Y, Chen B, Han M, Ren H, Lu H, Luber JM, Xia M, Li W, Stein S, Xu X, Zhang W, Drmanac R, Wang J, Yang H, Hammarström L, Kostic AD, Kristiansen K, and Li J. PMID: 29293960