Distance restraints from crosslinking mass spectrometry: Mining a molecular dynamics simulation database to evaluate lysine–lysine distances von Merkley, Eric D., Rysavy, Steven, Kahraman, Abdullah, Hafen, Ryan P., Daggett, Valerie, Adkins, Joshua N.

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Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data von Jaitly, Navdeep, Mayampurath, Anoop, Littlefield, Kyle, Adkins, Joshua N, Anderson, Gordon A, Smith, Richard D

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Guided construction of single cell reference for human and mouse lung von Guo, Minzhe, Morley, Michael P., Jiang, Cheng, Wu, Yixin, Li, Guangyuan, Du, Yina, Zhao, Shuyang, Wagner, Andrew, Cakar, Adnan Cihan, Kouril, Michal, Jin, Kang, Gaddis, Nathan, Kitzmiller, Joseph A., Stewart, Kathleen, Basil, Maria C., Lin, Susan M., Ying, Yun, Babu, Apoorva, Wikenheiser-Brokamp, Kathryn A., Mun, Kyu Shik, Naren, Anjaparavanda P., Clair, Geremy, Adkins, Joshua N., Pryhuber, Gloria S., Misra, Ravi S., Aronow, Bruce J., Tickle, Timothy L., Salomonis, Nathan, Sun, Xin, Morrisey, Edward E., Whitsett, Jeffrey A., Xu, Yan

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High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labeling in a Nanodroplet Sample Preparation Platform von Dou, Maowei, Clair, Geremy, Tsai, Chia-Feng, Xu, Kerui, Chrisler, William B, Sontag, Ryan L, Zhao, Rui, Moore, Ronald J, Liu, Tao, Pasa-Tolic, Ljiljana, Smith, Richard D, Shi, Tujin, Adkins, Joshua N, Qian, Wei-Jun, Kelly, Ryan T, Ansong, Charles, Zhu, Ying

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High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip von Woo, Jongmin, Williams, Sarah M., Markillie, Lye Meng, Feng, Song, Tsai, Chia-Feng, Aguilera-Vazquez, Victor, Sontag, Ryan L., Moore, Ronald J., Hu, Dehong, Mehta, Hardeep S., Cantlon-Bruce, Joshua, Liu, Tao, Adkins, Joshua N., Smith, Richard D., Clair, Geremy C., Pasa-Tolic, Ljiljana, Zhu, Ying

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Stochastic Variation in Expression of the Tricarboxylic Acid Cycle Produces Persister Cells von Zalis, Eliza A, Nuxoll, Austin S, Manuse, Sylvie, Clair, Geremy, Radlinski, Lauren C, Conlon, Brian P, Adkins, Joshua, Lewis, Kim

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Comprehensive computational design of ordered peptide macrocycles von Hosseinzadeh, Parisa, Bhardwaj, Gaurav, Mulligan, Vikram Khipple, Shortridge, Matthew D., Craven, Timothy W., Pardo-Avila, Fátima, Rettie, Stephen A., Kim, David E., Silva, Daniel-Adriano, Ibrahim, Yehia M., Webb, Ian K., Cort, John R., Adkins, Joshua N., Varani, Gabriele, Baker, David

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Lignin induced iron reduction by novel sp., Tolumonas lignolytic BRL6-1 von Chaput, Gina, Billings, Andrew F., DeDiego, Lani, Orellana, Roberto, Adkins, Joshua N., Nicora, Carrie D., Kim, Young-Mo, Chu, Rosalie, Simmons, Blake, DeAngelis, Kristen M.

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Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models von Palsson, Bernhard Ø, Lewis, Nathan E, Hixson, Kim K, Conrad, Tom M, Lerman, Joshua A, Charusanti, Pep, Polpitiya, Ashoka D, Adkins, Joshua N, Schramm, Gunnar, Purvine, Samuel O, Lopez-Ferrer, Daniel, Weitz, Karl K, Eils, Roland, König, Rainer, Smith, Richard D

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Phage-specific metabolic reprogramming of virocells von Howard-Varona, Cristina, Lindback, Morgan M., Bastien, G. Eric, Solonenko, Natalie, Zayed, Ahmed A., Jang, HoBin, Andreopoulos, Bill, Brewer, Heather M., Glavina del Rio, Tijana, Adkins, Joshua N., Paul, Subhadeep, Sullivan, Matthew B., Duhaime, Melissa B.

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In silico method for modelling metabolism and gene product expression at genome scale von Lerman, Joshua A., Hyduke, Daniel R., Latif, Haythem, Portnoy, Vasiliy A., Lewis, Nathan E., Orth, Jeffrey D., Schrimpe-Rutledge, Alexandra C., Smith, Richard D., Adkins, Joshua N., Zengler, Karsten, Palsson, Bernhard O.

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DAnTE: a statistical tool for quantitative analysis of -omics data von Polpitiya, Ashoka D., Qian, Wei-Jun, Jaitly, Navdeep, Petyuk, Vladislav A., Adkins, Joshua N., Camp, David G., Anderson, Gordon A., Smith, Richard D.

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Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typhimurium in response to infection-like conditions von Ansong, Charles, Wu, Si, Da Meng, Liu, Xiaowen, Brewer, Heather M., Kaiser, Brooke L. Deatherage, Nakayasu, Ernesto S., Cort, John R., Pevzner, Pavel, Smith, Richard D., Heffron, Fred, Adkins, Joshua N., Paša-Tolić, Ljiljana

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A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection von Deatherage Kaiser, Brooke L, Li, Jie, Sanford, James A, Kim, Young-Mo, Kronewitter, Scott R, Jones, Marcus B, Peterson, Christine T, Peterson, Scott N, Frank, Bryan C, Purvine, Samuel O, Brown, Joseph N, Metz, Thomas O, Smith, Richard D, Heffron, Fred, Adkins, Joshua N

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New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells von Couvillion, Sneha P, Zhu, Ying, Nagy, Gabe, Adkins, Joshua N, Ansong, Charles, Renslow, Ryan S, Piehowski, Paul D, Ibrahim, Yehia M, Kelly, Ryan T, Metz, Thomas O

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Distinct cerebrospinal fluid proteomes differentiate post-treatment lyme disease from chronic fatigue syndrome von Schutzer, Steven E, Angel, Thomas E, Liu, Tao, Schepmoes, Athena A, Clauss, Therese R, Adkins, Joshua N, Camp, David G, Holland, Bart K, Bergquist, Jonas, Coyle, Patricia K, Smith, Richard D, Fallon, Brian A, Natelson, Benjamin H

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The Campylobacter jejuni CiaD effector co-opts the host cell protein IQGAP1 to promote cell entry von Negretti, Nicholas M., Gourley, Christopher R., Talukdar, Prabhat K., Clair, Geremy, Klappenbach, Courtney M., Lauritsen, Cody J., Adkins, Joshua N., Konkel, Michael E.

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Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella: implications for virulence and global protein translation von Ansong, Charles, Yoon, Hyunjin, Porwollik, Steffen, Mottaz-Brewer, Heather, Petritis, Brianne O, Jaitly, Navdeep, Adkins, Joshua N, McClelland, Michael, Heffron, Fred, Smith, Richard D

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The genome organization of Thermotoga maritima reflects its lifestyle von Latif, Haythem, Lerman, Joshua A, Portnoy, Vasiliy A, Tarasova, Yekaterina, Nagarajan, Harish, Schrimpe-Rutledge, Alexandra C, Smith, Richard D, Adkins, Joshua N, Lee, Dae-Hee, Qiu, Yu, Zengler, Karsten

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efam: an expanded, metaproteome-supported HMM profile database of viral protein families von Zayed, Ahmed A, Lücking, Dominik, Mohssen, Mohamed, Cronin, Dylan, Bolduc, Ben, Gregory, Ann C, Hargreaves, Katherine R, Piehowski, Paul D, White III, Richard A, Huang, Eric L, Adkins, Joshua N, Roux, Simon, Moraru, Cristina, Sullivan, Matthew B

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