Latest research projects, publications, and talks
Heterogeneous Molecular Graph Neural Networks for Predicting Molecule Properties [preprint]
Posted
Zeren Shui (Ph.D. student), George Karypis (professor)
Longitudinal multi-omics reveals subset-specific mechanisms underlying irritable bowel syndrome [journal]
Posted
Ruben AT Mars, Yi Yang, Tonya Ward, Mo Houtti (Ph.D. student), Sambhawa Priya, Heather R Lekatz, Xiaojia Tang, Zhifu Sun, Krishna R Kalari, Tal Korem, Yogesh Bhattarai, Tenghao Zheng, Noam Bar, Gary Frost, Abigail J Johnson, Will van Treuren, Shuo Han, Tamas Ordog, Madhusudan Grover, Justin Sonnenburg, Mauro D’Amato, Michael Camilleri, Eran Elinav, Eran Segal, Ran Blekhman, Gianrico Farrugia, Jonathan R Swann, Dan Knights (professor), Purna C Kashyap
Cell
Systematic analysis of bypass suppression of essential genes [journal]
Posted
Jolanda van Leeuwen, Carles Pons, Guihong Tan, Jason Zi Wang, Jing Hou, Jochen Weile, Marinella Gebbia, Wendy Liang, Ermira Shuteriqi, Zhijian Li, Maykel Lopes, Matej Ušaj, Andreia Dos Santos Lopes, Natascha van Lieshout, Chad L Myers (professor), Frederick P Roth, Patrick Aloy, Brenda J Andrews, Charles Boone
Molecular Systems Biology
Major functional bias for mitochondrial complexes in genome-wide CRISPR screens [preprint]
Posted
Mahfuzur Rahman (Ph.D. student), Maximilian Billmann (post-doctoral associate), Michael Costanzo, Michael Aregger, Amy Tong, Katherine Chan, Henry N. Ward (Ph.D. student), Kevin R. Brown, Brenda J. Andrews, Charles Boone, Jason Moffat, Chad L. Myers (professor)
Randomised clinical study: oral aspirin 325 mg daily vs placebo alters gut microbial composition and bacterial taxa associated with colorectal cancer risk [journal]
Posted
Anna E Prizment, Christopher Staley, Guillaume C Onyeaghala, Sithara Vivek, Bharat Thyagarajan, Robert J Straka, Ryan T Demmer, Dan Knights (professor), Katie A Meyer, Aasma Shaukat, Michael J Sadowsky, Timothy R Church
Alimentary Pharmacology & Therapeutics
Computational Methods for Mapping Genetic Interactions in Human Cells [research project]
Posted
Chad L. Myers (professor)
National Institute of Health (NIH) National Human Genome Research Institute
Gut microbiome signatures of nursing home residents carrying Enterobacteria Producing Extended-spectrum β-lactamases [journal]
Posted
Quentin Le Bastard, Guillaume Chapelet, Gabriel Birgand, Benjamin M Hillmann (Ph.D. student), François Javaudin, Niki Hayatgheib, Céline Bourigault, Pascale Bemer, Laure De Decker, Eric Batard, Didier Lepelletier, Emmanuel Montassier
Antimicrobial Resistance & Infection Control
Repurpose open data to discover therapeutics for COVID-19 using deep learning [journal]
Posted
Xiangxiang Zeng, Xiang Song, Tengfei Ma, Xiaoqin Pan, Yadi Zhou, Yuan Hou, Zheng Zhang, Kenli Li, George Karypis (professor), Feixiong Cheng
Journal of Proteome Research
US immigration is associated with rapid and persistent acquisition of antibiotic resistance genes in the gut [journal]
Posted
Quentin Le Bastard, Pajau Vangay, Eric Batard, Dan Knights (professor), Emmanuel Montassier
Clinical Infectious Diseases
SHOGUN: a modular, accurate and scalable framework for microbiome quantification [journal]
Posted
Benjamin Hillmann (Ph.D. student), Gabriel A Al-Ghalith, Robin R Shields-Cutler, Qiyun Zhu, Rob Knight, Dan Knights (professor)
Bioinformatics