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Capturing sequence ambiguity among taxa in a primer-specific manner to improve taxonomic classification of amplicon sequencing Nearing, Jacob T.; Thompson, Kelsey N.; Kuntz, Thomas; Louyakis, Artemis S.; Bhosle, Amrisha; Branck, Tobyn; Badri, Dayakar, V; Franzosa, Eric A.; Brockel, Christoph; Huttenhower, Curtis; Short, Meghan, I Share Save
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A Small-Molecule Inhibitor of Gut Bacterial Urease Protects the Host from Liver Injury Richards-Corke, Khyle C.; Jiang, Yindi; Yeliseyev, Vladimir; Zhang, Yancong; Franzosa, Eric A.; Wang, Zhipeng A.; Abeywardana, Maheeshi Yapa; Cole, Phillip A.; Huttenhower, Curtis; Bry, Lynn; Balskus, Emily P. Share Save
Optimized model architectures for deep learning on genomic data (vol 7, 516, 2024) Guenduez, Hueseyin Anil; Mreches, Rene; Moosbauer, Julia; Robertson, Gary; To, Xiao-Yin; Franzosa, Eric A.; Huttenhower, Curtis; Rezaei, Mina; McHardy, Alice C.; Bischl, Bernd; Muench, Philipp C.; Binder, Martin Share Save
Optimized model architectures for deep learning on genomic data Guenduez, Hueseyin Anil; Mreches, Rene; Moosbauer, Julia; Robertson, Gary; To, Xiao-Yin; Franzosa, Eric A.; Huttenhower, Curtis; Rezaei, Mina; Mchardy, Alice C.; Bischl, Bernd; Muench, Philipp C.; Binder, Martin Share Save
Integrated annotation prioritizes metabolites with bioactivity in inflammatory bowel disease Bhosle, Amrisha; Bae, Sena; Zhang, Yancong; Chun, Eunyoung; Avila-Pacheco, Julian; Geistlinger, Ludwig; Pishchany, Gleb; Glickman, Jonathan N.; Michaud, Monia; Waldron, Levi; Clish, Clary B.; Xavier, Ramnik J.; Vlamakis, Hera; Franzosa, Eric A.; Garrett, Wendy S.; Huttenhower, Curtis Share Save
BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures Geistlinger, Ludwig; Mirzayi, Chloe; Zohra, Fatima; Azhar, Rimsha; Elsafoury, Shaimaa; Grieve, Clare; Wokaty, Jennifer; Gamboa-Tuz, Samuel David; Sengupta, Pratyay; Hecht, Issac; Ravikrishnan, Aarthi; Goncalves, Rafael S.; Franzosa, Eric; Raman, Karthik; Carey, Vincent; Dowd, Jennifer B.; Jones, Heidi E.; Davis, Sean; Segata, Nicola; Huttenhower, Curtis; Waldron, Levi Share Save
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Gut microbial metabolism of 5-ASA diminishes its clinical efficacy in inflammatory bowel disease Mehta, Raaj S.; Mayers, Jared R.; Zhang, Yancong; Bhosle, Amrisha; Glasser, Nathaniel R.; Nguyen, Long H.; Ma, Wenjie; Bae, Sena; Branck, Tobyn; Song, Kijun; Sebastian, Luke; Pacheco, Julian Avila; Seo, Hyuk-Soo; Clish, Clary; Dhe-Paganon, Sirano; Ananthakrishnan, Ashwin N.; Franzosa, Eric A.; Balskus, Emily P.; Chan, Andrew T.; Huttenhower, Curtis Share Save
Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4 Blanco-Miguez, Aitor; Beghini, Francesco; Cumbo, Fabio; McIver, Lauren J.; Thompson, Kelsey N.; Zolfo, Moreno; Manghi, Paolo; Dubois, Leonard; Huang, Kun D.; Thomas, Andrew Maltez; Nickols, William A.; Piccinno, Gianmarco; Piperni, Elisa; Puncochar, Michal; Valles-Colomer, Mireia; Tett, Adrian; Giordano, Francesca; Davies, Richard; Wolf, Jonathan; Berry, Sarah E.; Spector, Tim D.; Franzosa, Eric A.; Pasolli, Edoardo; Asnicar, Francesco; Huttenhower, Curtis; Segata, Nicola Share Save
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Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin Ma, Siyuan; Shungin, Dmitry; Mallick, Himel; Schirmer, Melanie; Nguyen, Long H.; Kolde, Raivo; Franzosa, Eric; Vlamakis, Hera; Xavier, Ramnik; Huttenhower, Curtis Share Save
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Dietary fiber intake, the gut microbiome, and chronic systemic inflammation in a cohort of adult men Ma, Wenjie; Nguyen, Long H.; Song, Mingyang; Wang, Dong D.; Franzosa, Eric A.; Cao, Yin; Joshi, Amit; Drew, David A.; Mehta, Raaj; Ivey, Kerry L.; Strate, Lisa L.; Giovannucci, Edward L.; Izard, Jacques; Garrett, Wendy; Rimm, Eric B.; Huttenhower, Curtis; Chan, Andrew T. Share Save
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