NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes.

by Gabriel A Al-Ghalith, Emmanuel Montassier, Henry N Ward, Dan Knights
Published 2016-01-01

SHI7 Is a Self-Learning Pipeline for Multipurpose Short-Read DNA Quality Control

by Gabriel A. Al-Ghalith, Benjamin Hillmann, Kaiwei Ang, Robin Shields-Cutler, Dan Knights
Published 2018-04-01

Evaluating the Information Content of Shallow Shotgun Metagenomics

by Benjamin Hillmann, Gabriel A. Al-Ghalith, Robin R. Shields-Cutler, Qiyun Zhu, Daryl M. Gohl, Kenneth B. Beckman, Rob Knight, Dan Knights
Published 2018-11-01

CLOUD: a non-parametric detection test for microbiome outliers

by Emmanuel Montassier, Gabriel A. Al-Ghalith, Benjamin Hillmann, Kimberly Viskocil, Amanda J. Kabage, Christopher E. McKinlay, Michael J. Sadowsky, Alexander Khoruts, Dan Knights
Published 2018-08-01

High-Throughput flaA Short Variable Region Sequencing to Assess Campylobacter Diversity in Fecal Samples From Birds

by Qian Zhang, Gabriel A. Al-Ghalith, Mayumi Kobayashi, Takahiro Segawa, Takahiro Segawa, Mitsuto Maeda, Satoshi Okabe, Dan Knights, Dan Knights, Dan Knights, Satoshi Ishii, Satoshi Ishii, Satoshi Ishii
Published 2018-09-01

Wild primate microbiomes prevent weight gain in germ-free mice

by Dimitrios N. Sidiropoulos, Gabriel A. Al-Ghalith, Robin R. Shields-Cutler, Tonya L. Ward, Abigail J. Johnson, Pajau Vangay, Dan Knights, Purna C. Kashyap, Yibo Xian, Amanda E. Ramer-Tait, Jonathan B. Clayton
Published 2020-05-01

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

by Qiyun Zhu, Uyen Mai, Wayne Pfeiffer, Stefan Janssen, Francesco Asnicar, Jon G. Sanders, Pedro Belda-Ferre, Gabriel A. Al-Ghalith, Evguenia Kopylova, Daniel McDonald, Tomasz Kosciolek, John B. Yin, Shi Huang, Nimaichand Salam, Jian-Yu Jiao, Zijun Wu, Zhenjiang Z. Xu, Kalen Cantrell, Yimeng Yang, Erfan Sayyari, Maryam Rabiee, James T. Morton, Sheila Podell, Dan Knights, Wen-Jun Li, Curtis Huttenhower, Nicola Segata, Larry Smarr, Siavash Mirarab, Rob Knight
Published 2019-12-01

Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity

by Xue-Song Zhang, Jackie Li, Kimberly A Krautkramer, Michelle Badri, Thomas Battaglia, Timothy C Borbet, Hyunwook Koh, Sandy Ng, Rachel A Sibley, Yuanyuan Li, Wimal Pathmasiri, Shawn Jindal, Robin R Shields-Cutler, Ben Hillmann, Gabriel A Al-Ghalith, Victoria E Ruiz, Alexandra Livanos, Angélique B van ‘t Wout, Nabeetha Nagalingam, Arlin B Rogers, Susan Jenkins Sumner, Dan Knights, John M Denu, Huilin Li, Kelly V Ruggles, Richard Bonneau, R Anthony Williamson, Marcus Rauch, Martin J Blaser
Published 2018-07-01

Distribution of Bacterial α1,3-Galactosyltransferase Genes in the Human Gut Microbiome

by Emmanuel Montassier, Emmanuel Montassier, Emmanuel Montassier, Gabriel A. Al-Ghalith, Camille Mathé, Camille Mathé, Quentin Le Bastard, Quentin Le Bastard, Venceslas Douillard, Venceslas Douillard, Venceslas Douillard, Abel Garnier, Abel Garnier, Abel Garnier, Rémi Guimon, Rémi Guimon, Rémi Guimon, Bastien Raimondeau, Bastien Raimondeau, Yann Touchefeu, Yann Touchefeu, Emilie Duchalais, Emilie Duchalais, Nicolas Vince, Nicolas Vince, Sophie Limou, Sophie Limou, Pierre-Antoine Gourraud, Pierre-Antoine Gourraud, Pierre-Antoine Gourraud, David A. Laplaud, David A. Laplaud, Arnaud B. Nicot, Arnaud B. Nicot, Jean-Paul Soulillou, Jean-Paul Soulillou, Laureline Berthelot, Laureline Berthelot
Published 2020-01-01