Large-scale application of free energy perturbation calculations for antibody design
Zhu, Fangqiang, Bourguet, Feliza A., Bennett, William F. D., Lau, Edmond Y., Arrildt, Kathryn T., Segelke, Brent W., Zemla, Adam T., Desautels, Thomas A., Faissol, Daniel M.
Published in Scientific reports (21.07.2022)
Published in Scientific reports (21.07.2022)
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Journal Article
Differential laboratory passaging of SARS-CoV-2 viral stocks impacts the in vitro assessment of neutralizing antibodies
Avila-Herrera, Aram, Kimbrel, Jeffrey A, Manuel Martí, Jose, Thissen, James, Saada, Edwin A, Weisenberger, Tracy, Arrildt, Kathryn T, Segelke, Brent W, Allen, Jonathan E, Zemla, Adam, Borucki, Monica K
Published in PloS one (25.01.2024)
Published in PloS one (25.01.2024)
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Journal Article
PDBspheres: a method for finding 3D similarities in local regions in proteins
Zemla, Adam T, Allen, Jonathan E, Kirshner, Dan, Lightstone, Felice C
Published in NAR genomics and bioinformatics (01.12.2022)
Published in NAR genomics and bioinformatics (01.12.2022)
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Journal Article
Microbial mercury methylation in Antarctic sea ice
Gionfriddo, Caitlin M., Tate, Michael T., Wick, Ryan R., Schultz, Mark B., Zemla, Adam, Thelen, Michael P., Schofield, Robyn, Krabbenhoft, David P., Holt, Kathryn E., Moreau, John W.
Published in Nature microbiology (01.08.2016)
Published in Nature microbiology (01.08.2016)
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Journal Article
Single Amino Acid Mutations Affect Zika Virus Replication In Vitro and Virulence In Vivo
Collette, Nicole M, Lao, Victoria H I, Weilhammer, Dina R, Zingg, Barbara, Cohen, Shoshana D, Hwang, Mona, Coffey, Lark L, Grady, Sarah L, Zemla, Adam T, Borucki, Monica K
Published in Viruses (12.11.2020)
Published in Viruses (12.11.2020)
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Journal Article
Community Genomic and Proteomic Analyses of Chemoautotrophic Iron-Oxidizing “Leptospirillum rubarum” (Group II) and “Leptospirillum ferrodiazotrophum” (Group III) Bacteria in Acid Mine Drainage Biofilms
ALIAGA GOLTSMAN, Daniela S, DENEF, Vincent J, BAKER, Brett J, HAUSER, Loren, LAND, Miriam, SHAH, Manesh B, THELEN, Michael P, HETTICH, Robert L, BANFIELD, Jillian F, SINGER, Steven W, VERBERKMOES, Nathan C, LEFSRUD, Mark, MUELLER, Ryan S, DICK, Gregory J, SUN, Christine L, WHEELER, Korin E, ZEMLA, Adam
Published in Applied and Environmental Microbiology (01.07.2009)
Published in Applied and Environmental Microbiology (01.07.2009)
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Journal Article
Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction
Chaudhury, Sidhartha, Abdulhameed, Mohamed Diwan M, Singh, Narender, Tawa, Gregory J, D'haeseleer, Patrik M, Zemla, Adam T, Navid, Ali, Zhou, Carol E, Franklin, Matthew C, Cheung, Jonah, Rudolph, Michael J, Love, James, Graf, John F, Rozak, David A, Dankmeyer, Jennifer L, Amemiya, Kei, Daefler, Simon, Wallqvist, Anders
Published in PloS one (21.05.2013)
Published in PloS one (21.05.2013)
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Journal Article
A study of quality measures for protein threading models
Cristobal, S, Zemla, A, Fischer, D, Rychlewski, L, Elofsson, A
Published in BMC bioinformatics (01.08.2001)
Published in BMC bioinformatics (01.08.2001)
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Journal Article
The role of viral population diversity in adaptation of bovine coronavirus to new host environments
Borucki, Monica K, Allen, Jonathan E, Chen-Harris, Haiyin, Zemla, Adam, Vanier, Gilda, Mabery, Shalini, Torres, Clinton, Hullinger, Pamela, Slezak, Tom
Published in PloS one (07.01.2013)
Published in PloS one (07.01.2013)
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Journal Article
Identification of Genome-Wide Mutations in Ciprofloxacin-Resistant F. tularensis LVS Using Whole Genome Tiling Arrays and Next Generation Sequencing
Jaing, Crystal J, McLoughlin, Kevin S, Thissen, James B, Zemla, Adam, Gardner, Shea N, Vergez, Lisa M, Bourguet, Feliza, Mabery, Shalini, Fofanov, Viacheslav Y, Koshinsky, Heather, Jackson, Paul J
Published in PloS one (26.09.2016)
Published in PloS one (26.09.2016)
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Journal Article
Discovery of Small-Molecule Inhibitors of SARS-CoV-2 Proteins Using a Computational and Experimental Pipeline
Lau, Edmond Y., Negrete, Oscar A., Bennett, W. F. Drew, Bennion, Brian J., Borucki, Monica, Bourguet, Feliza, Epstein, Aidan, Franco, Magdalena, Harmon, Brooke, He, Stewart, Jones, Derek, Kim, Hyojin, Kirshner, Daniel, Lao, Victoria, Lo, Jacky, McLoughlin, Kevin, Mosesso, Richard, Murugesh, Deepa K., Saada, Edwin A., Segelke, Brent, Stefan, Maxwell A., Stevenson, Garrett A., Torres, Marisa W., Weilhammer, Dina R., Wong, Sergio, Yang, Yue, Zemla, Adam, Zhang, Xiaohua, Zhu, Fangqiang, Allen, Jonathan E., Lightstone, Felice C.
Published in Frontiers in molecular biosciences (09.07.2021)
Published in Frontiers in molecular biosciences (09.07.2021)
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Journal Article
Light Regimes Shape Utilization of Extracellular Organic C and N in a Cyanobacterial Biofilm
Stuart, Rhona K, Mayali, Xavier, Boaro, Amy A, Zemla, Adam, Everroad, R Craig, Nilson, Daniel, Weber, Peter K, Lipton, Mary, Bebout, Brad M, Pett-Ridge, Jennifer, Thelen, Michael P
Published in mBio (28.06.2016)
Published in mBio (28.06.2016)
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Journal Article
Identification of a novel drug lead that inhibits HCV infection and cell-to-cell transmission by targeting the HCV E2 glycoprotein
Al Olaby, Reem R, Cocquerel, Laurence, Zemla, Adam, Saas, Laure, Dubuisson, Jean, Vielmetter, Jost, Marcotrigiano, Joseph, Khan, Abdul Ghafoor, Vences Catalan, Felipe, Perryman, Alexander L, Freundlich, Joel S, Forli, Stefano, Levy, Shoshana, Balhorn, Rod, Azzazy, Hassan M
Published in PloS one (30.10.2014)
Published in PloS one (30.10.2014)
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A semi-quantitative, synteny-based method to improve functional predictions for hypothetical and poorly annotated bacterial and archaeal genes
Yelton, Alexis P, Thomas, Brian C, Simmons, Sheri L, Wilmes, Paul, Zemla, Adam, Thelen, Michael P, Justice, Nicholas, Banfield, Jillian F
Published in PLoS computational biology (01.10.2011)
Published in PLoS computational biology (01.10.2011)
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