Jennifer Auchtung
Andy Benson
Siddappa Byrareddy
Edgar Cahoon
Jennifer Clarke
Jonathan B. Clayton
Tom Clemente
Samodha Fernando
Jeffrey A. French
Corrine Hanson
Robert Hutkins
David Hyten
Jacques Izard
Tricia LeVan
Peter Mannon
Etsuko Moriyama
Robert Norgren
Kurt Piepenbrink
Amanda Ramer-Tait
Heather Rasmussen
Devin Rose
James Schnable
Hyun-Seob Song
Harkamal Walia
Yanbin Yin
2023
Antibiotic-induced gut dysbiosis and cognitive, emotional, and behavioral changes in rodents: a systematic review and meta-analysis, Shivdeep S. Hayer, Soonjo Hwang, and Jonathan B. Clayton
Antibiotic-induced gut dysbiosis and cognitive, emotional, and behavioral changes in rodents: a systematic review and meta-analysis, Shivdeep S. Hayer, Soonjo Hwang, and Jonathan B. Clayton
Distinct gene expression profiles between human preterm-derived and adult-derived intestinal organoids exposed to Enterococcus faecalis: a pilot study, Andrea C. Masi, Tatiana Y. Fofanova, Christopher A. Lamb, Jennifer Auchtung, Robert A. Britton, Mary K. Estes, Sasirekha Ramani, Simon J. Cockell, Jonathan Coxhead, Nicholas D. Embleton, Janet E. Berrington, Joseph F. Petrosino, and Christopher J. Stewart
Homeobox transcription factor HbxA influences expression of over one thousand genes in the model fungus Aspergillus nidulans, Sandesh S. Pandit, Jinfang Zheng, Yanbin Yan, Sophie Lorber, Olivier Puel, Sourabh Dhingra, Eduardo A. Espeso, and Ana M. Calvo
The Inherited Intestinal Microbiota from Myeloid-Specific ZIP8KO Mice Impairs Pulmonary Host Defense against Pneumococcal Pneumonia, Derrick R. Samuelson, Deandra R. Smith, Kelly C. Cunningham, Sabah Haq, Daniel N. Villageliú, Christi Christi Ellis, Niaz Bahar Chowdhury, Amanda E. Ramer-Tait, Jeff Price, and Daren L. Knoell
2022
The Unique Seed Protein Composition of Quality Protein Popcorn Promotes Growth of Beneficial Bacteria From the Human Gut Microbiome, Nate Korth, Leandra Parsons, Mallory J. Van Haute, Qinnan Yang, Preston Hurst, James C. Schnable, David R. Holding, and Andrew K. Benson
AcaFinder: Genome Mining for Anti-CRISPR-Associated Genes, Bowen Yang, Jinfang Zheng, and Yanbin Yin
The chromosome-level rambutan genome reveals a significant role of segmental duplication in the expansion of resistance genes, Jinfang Zheng1, Lyndel W. Meinhardt, Ricardo Goenaga, Tracie Matsumoto, Dapeng Zhang, and Yanbin Yin
2021
Characterization of Two Zygnema Strains (Zygnema circumcarinatum SAG 698-1a and SAG 698-1b) and a Rapid Method to Estimate Nuclear Genome Size of Zygnematophycean Green Algae, Xuehuan Feng, Andreas Holzinger, Charlotte Permann, Dirk Anderson, and Yanbin Yin
Characterization of Two Zygnema Strains (Zygnema circumcarinatum SAG 698-1a and SAG 698-1b) and a Rapid Method to Estimate Nuclear Genome Size of Zygnematophycean Green Algae, Xuehuan Feng, Andreas Holzinger, Charlotte Permann, Dirk Anderson, and Yanbin Yin
Characterization of Two Zygnema Strains (Zygnema circumcarinatum SAG 698-1a and SAG 698-1b) and a Rapid Method to Estimate Nuclear Genome Size of Zygnematophycean Green Algae, Xuehuan Feng, Andreas Holzinger, Charlotte Permann, Dirk Anderson, and Yanbin Yin
The Sulfur Microbial Diet Is Associated With Increased Risk of Early-Onset Colorectal Cancer Precursors, Long H. Nguyen, Yin Cao, Jinhee Hur, Raaj S. Mehta, Daniel R. Sikavi, Yiqing Wang, Wenjie Ma, Kana Wu, Mingyang Song, Edward L. Giovannucci, Eric B. Rimm, Walter C. Willett, Wendy S. Garrett, Jacques Izard, Curtis Huttenhower, and Andrew T. Chan
Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity, Daniel Peterson, Tang Li, Ana M. Calvo, and Yanbin Yin
Output Consistency Scale to Standardize Ostomate Output Description in Clinical Practice and Studies, lisa Whisenhunt, Linda Xu, Fan Yang, and Jacques Izard
The chromosome-level genome of dragon fruit reveals whole-genome duplication and chromosomal co-localization of betacyanin biosynthetic genes, Jinfang Zheng, Lyndel W. Meinhardt, Ricardo Goenaga, Dapeng Zhang, and Yanbin Yin
2020
Point-of-Decision Prompts Increase Dietary Fiber Content of Consumers’ Food Choices in an Online Grocery Shopping Simulation, Kristina Arslain, Christopher Gustafson, and Devin J. Rose
The Trait Repertoire Enabling Cyanobacteria to Bloom Assessed through Comparative Genomic Complexity and Metatranscriptomics, Huansheng Cao, Yohei Shimura, Morgan M. Steffen, Zhou Yang, Jingrang Lu, Allen Joel, Landon Jenkins, Masanobu Kawachi, Yanbin Yin, and Ferran Garcia-Pichel
Alteration of the Gut Microbiome in Normal and Overweight School Children from Selangor with Lactobacillus Fermented Milk Administration, Narcisse Joseph, Jonathan B. Clayton, Susan L. Hoops, Carter A. Linhardt, Amalia Mohd Hashim, Barakatun Nisak Mohd Yusof, Suresh Kumar, and Syafinaz Amin Nordin
Stool microbiome, pH and short/branched chain fatty acids in infants receiving extensively hydrolyzed formula, amino acid formula, or human milk through two months of age, Car Reen Kok, Bradford Brabec, Maciej Chichlowski, Cheryl L. Harris, Nancy Moore, Jennifer L. Wampler, Jon Vanderhoof, Devin Rose, and Robert Hutkins
A mouse model of human TLR4 D299G/T399I SNPs reveals mechanisms of altered LPS and pathogen responses, Katharina Richard, Kurt H. Piepenbrink, Kari Ann Shirey, Archana Gopalakrishnan, Shreeram Nallar, Daniel J. Prantner, Darren J. Perkins, Wendy Lai, Alexandra Vik, Vladimir Y. Toshchakov, Chiguang Feng, Rachel Fanaroff, Andrei E. Medvedev, Jorge C.G. Blanco, and Stefanie N. Vogel
2019
An In Vitro Enrichment Strategy for Formulating Synergistic Synbiotics, Car Reen Kok, David Fabian Gomez Quintero, Clement Niyirora, Devin Rose, Amanda Li, and Robert Hutkins
DNA Uptake by Type IV Filaments, Kurt H. Piepenbrink
The structure of PilA from Acinetobacter baumannii AB5075 suggests a mechanism for functional specialization in Acinetobacter type IV pili, Leslie A. Ronish, Erik Lillehoj, James K. Fields, Eric J. Sundberg, and Kurt Piepenbrink
Candida albicans quorum-sensing molecule farnesol modulates staphyloxanthin production and activates the thiol-based oxidative-stress response in Staphylococcus aureus, Taissa Vila, Eric F. Kong, Ahmed Ibrahim, Kurt Piepenbrink, Amol C. Shetty, Carrie McCracken, Vincent Bruno, and Mary Ann Jabra-Rizk
2018
Considerations for best practices in studies of fiber or other dietary components and the intestinal microbiome, David M. Klurfeld, Cindy D. Davis, Robert W. Karp, Emma Allen-Vercoe, Eugene B. Chang, Benoit Chassaing, George C. Fahey Jr, Bruce R. Hamaker, Hannah D. Holscher, Johanna W. Lampe, Andre Marette, Eric Martens, Stephen J. O'Keefe, Devin J. Rose, Maria Saarela, Barbara O. Schneeman, Joanne L. Slavin, Justin L. Sonnenburg, Kelly S. Swanson, Gary D. Wu, and Christopher J. Lynch
2017
Structure-Based Design of Hepatitis C Virus Vaccines That Elicit Neutralizing Antibody Responses to a Conserved Epitope, Brian G. Pierce, Elisabeth N. Boucher, Kurt H. Piepenbrink, Monir Ejemal, Chelsea A. Rapp, William D. Thomas Jr, Eric J. Sundberg, Zhiping Weng, and Yang Wang
How an alloreactive T-cell receptor achieves peptide and MHC specificity, Yuan Wang, Nishant K. Singh, Timothy T. Spear, Lance M. Hellman, Kurt H. Piepenbrink, Rachel H. McMahan, Hugo R. Rosen, Craig W. Vander Kooi, Michael I. Nishimura, and Brian M. Baker
2016
The NEU1-selective sialidase inhibitor, C9- butyl-amide-DANA, blocks sialidase activity and NEU1-mediated bioactivities in human lung in vitro and murine lung in vivo, Sang W. Hyun, Anguo Liu, Zhenguo Liu, Alan S. Cross, Avelino C. Verceles, Sadagopan Magesh, Yadagiri Kommagalla, Chandrababunaidu Kona, Hiromune Ando, Irina G. Luzina, Sergei P. Atamas, Kurt H. Piepenbrink, Eric J. Sundberg, Wei Guang, Hideharu Ishida, Erik P. Lillehoj, and Simeon E. Goldblum
Type IV pili promote early biofilm formation by Clostridium difficile, Grace A. Maldarelli, Kurt H. Piepenbrink, Alison J. Scott, Jeffrey A. Freiberg, Yang Song, Yvonee Achermann, Robert K. Ernst, Mark E. Shirtliff, Eric J. Sundberg, Michael S. Donnenberg, and Erik C. von Rosenvinge
Structural Diversity in the Type IV Pili of Multidrug-resistant Acinetobacter, Kurt H. Piepenbrink, Erik Lillehoj, Christian M. Harding, Jason W. Labonte, Xiaotong Zuo, Chelsea A. Rapp, Robert S. Munson Jr, Simeon E. Goldblum, Mario F. Feldman, Jeffrey J. Gray, and Eric J. Sundberg
Structural and Evolutionary Analyses Show Unique Stabilization Strategies in the Type IV Pili of Clostridium difficile, Kurt H. Piepenbrink, Grace A. Maldarelli, Claudia F. Martinez de la Pena, Tanis C. Dingle, George L. Mulvey, Amanda Lee, Erik von Rosenvinge, Glen D. Armstrong, Michael S. Donnenberg, and Eric J. Sundberg
Motility and adhesion through type IV pili in Gram-positive bacteria, Kurt H. Piepenbrink and Eric J. Sundberg
A generalized framework for computational design and mutational scanning of T-cell receptor binding interfaces, Timothy P. Riley, Cory M. Ayres, Lance M. Hellman, Nishant K. Singh, Michael Cosiano, Jennifer M. Cimons, Michael J. Anderson, Kurt H. Piepenbrink, Brian G. Pierce, Zhiping Weng, and Brian M. Baker
2015
Some of the most interesting CASP11 targets through the eyes of their authors, Andriy Kryshtafovych, John Moult, Arnaud Basle, Alex Burgin, Timonthy K. Craig, Robert A. Edwards, Deborah Fass, Marcus D. Hartmann, Mateusz Korycinski, Richard J. Lewis, Donald Lorimer, Andrei N. Lupas, Janet Newman, Thomas S. Peat, Kurt H. Piepenbrink, Janani Prahlad, Mark J. van Raaij, Forest Rohwer, Anca M. Segall, Victor Seguritan, Eric J. Sundberg, Abhimanyu K. Singh, Mark A. Wilson, and Torsten Schwede
2014
Structure of Clostridium difficile PilJ Exhibits Unprecedented Divergence from Known Type IV Pilins, Kurt H. Piepenbrink, Grace A. Maldarelli, Claudia F. Martinez de la Pena, George L. Mulvey, Greg A. Snyder, Leon De Masi, Erik C. von Rosenvinge, Sebastian Gunther, Glen D. Armstrong, Michael S. Donnenberg, and Eric J. Sundberg
Plasticity in the contribution of T cell receptor variable region residues to binding of peptide-HLA-A2 complexes, Sheena N. Smith, Daniel Sommermeyer, Kurt H. Piepenbrink, Sydney J. Blevins, Helga Bernhard, Wolfgang Uckert, Brian M. Baker, and David M. Kranz
A Novel Multivalent, Single-Domain Antibody Targeting TcdA and TcdB Prevents Fulminant Clostridium difficile Infection in Mice, Zhiyong Yang, Diane Schmidt, Weilong Liu, Shan Li, Lianfa Shi, Jinliang Sheng, Kevin Chen, Hua Yu, Jacqueline M. Tremblay, Xinhua Chen, Kurt H. Piepenbrink, Eric J. Sundberg, Ciaran P. Kelly, Guang Bai, Charles B. Shoemaker, and Hanping Feng
2013
Recruitment of TLR adapter TRIF to TLR4 signaling complex is mediated by the second helical region of TRIF TIR domain, Wenji Piao, Lisa W. Ru, Kurt H. Piepenbrink, Eric J. Sundberg, Stefanie N. Vogel, and Vladimir Y. Toshchakov
The basis for limited specificity and MHC restriction in a T cell receptor interface, Kurt H. Piepenbrink, Sydney J. Blevins, Daniel R. Scott, and Brian M. Baker
Methods for quantifying T cell receptor binding affinities and thermodynamics, Kurt H. Piepenbrink, Brian E. Gloor, Kathryn M. Armstrong, and Brian M. Baker
Holobiont nutrition: Considering the role of the gastrointestinal microbiota in the health benefits of whole grains, Jens Walter, Ines Martinez, and Devin J. Rose
2012
Single-Chain VαVβ T Cell Receptors Function Without Mispairing With Endogenous TCR Chains1, David H. Aggen, Adam S. Chervin, Thomas M. Schmitt, Boris Engels, Jennifer D. Stone, Sarah A. Richman, Kurt H. Piepenbrink, Brian M. Baker, Philip D. Greenberg, Hans Schreiber, and David M. Kranz
Conformational melding permits a conserved binding geometry in TCR recognition of foreign and self molecular mimics, Oleg Y. Borbulevych, Kurt H. Piepenbrink, and Brian M. Baker
Gut microbiome composition is linked to whole grain-induced immunological improvements, Ines Martinez, James M. Lattimer, Kelcie L. Hubach, Jennifer A. Case, Junyi Yang, Casey G. Weber, Julie A. Louk, Devin J. Rose, Gayaneh Kyureghian, Daniel A. Peterson, Mark D. Haub, and Jens Walter
2011
Identification and engineering of human variable regions that allow expression of stable single-chain T cell receptors, David H. Aggen, Adam S. Chervin, Francis K. Insaidoo, Kurt H. Piepenbrink, Brian M. Baker, and David M. Kranz
Fluorine substitutions in an antigenic peptide selectively modulate T cell receptor binding in a minimally perturbing manner, Kurt H. Piepenbrink, Oleg Y. Borbulevych, Ruth F. Sommese, John Clemens, Kathrynq M. Armstrong, Clare Desmond, Priscilla Do, and Brian M. Baker
Disparate degrees of hypervariable loop flexibility control T cell receptor cross-reactivity, specificity, and binding mechanism, Daniel R. Scott, Oleg Y. Borbulevych, Kurt H. Piepenbrink, Steven A. Corcelli, and Brian M. Baker
2009
T cell receptor cross-reactivity directed by antigen-dependent tuning of peptide-MHC molecular flexibility, Oleg Y. Borbulevych, Kurt H. Piepenbrink, Brian E. Gloor, Daniel R. Scott, Ruth F. Sommese, David K. Cole, Andrew K. Sewell, and Brian M. Baker
2008
Conformational changes and flexibility in T-cell receptor recognition of peptide–MHC complexes, Kathryn M. Armstrong, Kurt H. Piepenbrink, and Brian M. Baker