Researchers: 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

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2021

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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

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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

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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

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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

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Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity, Daniel Peterson, Tang Li, Ana M. Calvo, and Yanbin Yin

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Output Consistency Scale to Standardize Ostomate Output Description in Clinical Practice and Studies, lisa Whisenhunt, Linda Xu, Fan Yang, and Jacques Izard

2020

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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

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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

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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

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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

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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

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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

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DNA Uptake by Type IV Filaments, Kurt H. Piepenbrink

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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

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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

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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

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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

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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

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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

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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

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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

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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

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Motility and adhesion through type IV pili in Gram-positive bacteria, Kurt H. Piepenbrink and Eric J. Sundberg

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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

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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

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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

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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

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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

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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

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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

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Methods for quantifying T cell receptor binding affinities and thermodynamics, Kurt H. Piepenbrink, Brian E. Gloor, Kathryn M. Armstrong, and Brian M. Baker

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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

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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

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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

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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

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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

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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

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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

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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

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Conformational changes and flexibility in T-cell receptor recognition of peptide–MHC complexes, Kathryn M. Armstrong, Kurt H. Piepenbrink, and Brian M. Baker