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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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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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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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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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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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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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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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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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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Discovery of Salmonella Virulence Factors Translocated via Outer Membrane Vesicles to Murine Macrophages von Yoon, Hyunjin, Ansong, Charles, Adkins, Joshua N, Heffron, Fred

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Phloem Exudate Protein Profiles during Drought and Recovery Reveal Abiotic Stress Responses in Tomato Vasculature von Ogden, Aaron J, Bhatt, Jishnu J, Brewer, Heather M, Kintigh, Jack, Kariuki, Samwel M, Rudrabhatla, Sairam, Adkins, Joshua N, Curtis, Wayne R

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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, Cullen, Daniel

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An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and specificity analysis von Kapp, Eugene A., Schütz, Frédéric, Connolly, Lisa M., Chakel, John A., Meza, Jose E., Miller, Christine A., Fenyo, David, Eng, Jimmy K., Adkins, Joshua N., Omenn, Gilbert S., Simpson, Richard J.

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Model‐driven multi‐omic data analysis elucidates metabolic immunomodulators of macrophage activation von Bordbar, Aarash, Mo, Monica L, Nakayasu, Ernesto S, Schrimpe‐Rutledge, Alexandra C, Kim, Young‐Mo, Metz, Thomas O, Jones, Marcus B, Frank, Bryan C, Smith, Richard D, Peterson, Scott N, Hyduke, Daniel R, Adkins, Joshua N, Palsson, Bernhard O

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Characterization of Local and Systemic Impact of Whitefly ( Bemisia tabaci ) Feeding and Whitefly-Transmitted Tomato Mottle Virus Infection on Tomato Leaves by Comprehensive Proteo... von Ogden, Aaron J, Boukari, Wardatou, Nava, Alba, Lucinda, Natalia, Sunter, Garry, Curtis, Wayne R, Adkins, Joshua N, Polston, Jane E

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Computational Prediction of Type III and IV Secreted Effectors in Gram-Negative Bacteria von McDermott, Jason E, Corrigan, Abigail, Peterson, Elena, Oehmen, Christopher, Niemann, George, Cambronne, Eric D, Sharp, Danna, Adkins, Joshua N, Samudrala, Ram, Heffron, Fred

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VIPER: an advanced software package to support high-throughput LC-MS peptide identification von Monroe, Matthew E., Tolić, Nikola, Jaitly, Navdeep, Shaw, Jason L., Adkins, Joshua N., Smith, Richard D.

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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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