Optimization of a heterologous mevalonate pathway through the use of variant HMG-CoA reductases by Ma, Suzanne M., Garcia, David E., Redding-Johanson, Alyssa M., Friedland, Gregory D., Chan, Rossana, Batth, Tanveer S., Haliburton, John R., Chivian, Dylan, Keasling, Jay D., Petzold, Christopher J., Soon Lee, Taek, Chhabra, Swapnil R.

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Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth by Chivian, Dylan, Brodie, Eoin L, Alm, Eric J, Culley, David E, Dehal, Paramvir S, DeSantis, Todd Z, Gihring, Thomas M, Lapidus, Alla, Lin, Li-Hung, Lowry, Stephen R, Moser, Duane P, Richardson, Paul M, Southam, Gordon, Wanger, Greg, Pratt, Lisa M, Andersen, Gary L, Hazen, Terry C, Brockman, Fred J, Arkin, Adam P, Onstott, Tullis C

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Manipulation of the carbon storage regulator system for metabolite remodeling and biofuel production in Escherichia coli by McKee, Adrienne E, Rutherford, Becky J, Chivian, Dylan C, Baidoo, Edward K, Juminaga, Darmawi, Kuo, Dwight, Benke, Peter I, Dietrich, Jeffrey A, Ma, Suzanne M, Arkin, Adam P, Petzold, Christopher J, Adams, Paul D, Keasling, Jay D, Chhabra, Swapnil R

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Changes in microbial dynamics during long-term decomposition in tropical forests by DeAngelis, Kristen M., Chivian, Dylan, Fortney, Julian L., Arkin, Adam P., Simmons, Blake, Hazen, Terry C., Silver, Whendee L.

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Physically Realistic Homology Models Built with ROSETTA Can Be More Accurate than Their Templates by Misura, Kira M. S., Chivian, Dylan, Rohl, Carol A., Kim, David E., Baker, David

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Phylogenomically Guided Identification of Industrially Relevant GH1 β‑Glucosidases through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry by Heins, Richard A, Cheng, Xiaoliang, Nath, Sangeeta, Deng, Kai, Bowen, Benjamin P, Chivian, Dylan C, Datta, Supratim, Friedland, Gregory D, D’Haeseleer, Patrik, Wu, Dongying, Tran-Gyamfi, Mary, Scullin, Chessa S, Singh, Seema, Shi, Weibing, Hamilton, Matthew G, Bendall, Matthew L, Sczyrba, Alexander, Thompson, John, Feldman, Taya, Guenther, Joel M, Gladden, John M, Cheng, Jan-Fang, Adams, Paul D, Rubin, Edward M, Simmons, Blake A, Sale, Kenneth L, Northen, Trent R, Deutsch, Samuel

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De Novo Prediction of Three-dimensional Structures for Major Protein Families by Bonneau, Richard, Strauss, Charlie E.M, Rohl, Carol A, Chivian, Dylan, Bradley, Phillip, Malmström, Lars, Robertson, Tim, Baker, David

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Tracing Determinants of Dual Substrate Specificity in Glycoside Hydrolase Family 5 by Chen, Zhiwei, Friedland, Gregory D., Pereira, Jose H., Reveco, Sonia A., Chan, Rosa, Park, Joshua I., Thelen, Michael P., Adams, Paul D., Arkin, Adam P., Keasling, Jay D., Blanch, Harvey W., Simmons, Blake A., Sale, Kenneth L., Chivian, Dylan, Chhabra, Swapnil R.

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Automated prediction of CASP-5 structures using the Robetta server by Chivian, Dylan, Kim, David E., Malmström, Lars, Bradley, Philip, Robertson, Timothy, Murphy, Paul, Strauss, Charles E.M., Bonneau, Richard, Rohl, Carol A., Baker, David

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Prediction of CASP6 structures using automated robetta protocols by Chivian, Dylan, Kim, David E., Malmström, Lars, Schonbrun, Jack, Rohl, Carol A., Baker, David

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Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM by Kim, David E., Chivian, Dylan, Malmström, Lars, Baker, David

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Rosetta predictions in CASP5: Successes, failures, and prospects for complete automation by Bradley, Philip, Chivian, Dylan, Meiler, Jens, Misura, Kira M.S., Rohl, Carol A., Schief, William R., Wedemeyer, William J., Schueler-Furman, Ora, Murphy, Paul, Schonbrun, Jack, Strauss, Charles E.M., Baker, David

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Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection by Chivian, Dylan, Baker, David

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Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology by Malmström, Lars, Riffle, Michael, Strauss, Charlie E M, Chivian, Dylan, Davis, Trisha N, Bonneau, Richard, Baker, David

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Protein structure prediction and analysis using the Robetta server by Kim, David E., Chivian, Dylan, Baker, David

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KBase: The United States Department of Energy Systems Biology Knowledgebase by Arkin, Adam P, Cottingham, Robert W, Henry, Christopher S, Harris, Nomi L, Stevens, Rick L, Maslov, Sergei, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Canon, Shane, Sneddon, Michael W, Henderson, Matthew L, Riehl, William J, Murphy-Olson, Dan, Chan, Stephen Y, Kamimura, Roy T, Kumari, Sunita, Drake, Meghan M, Brettin, Thomas S, Glass, Elizabeth M, Chivian, Dylan, Gunter, Dan, Weston, David J, Allen, Benjamin H, Baumohl, Jason, Best, Aaron A, Bowen, Ben, Brenner, Steven E, Bun, Christopher C, Chandonia, John-Marc, Chia, Jer-Ming, Colasanti, Ric, Conrad, Neal, Davis, James J, Davison, Brian H, DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Dubchak, Inna, Edirisinghe, Janaka N, Fang, Gang, Faria, José P, Frybarger, Paul M, Gerlach, Wolfgang, Gerstein, Mark, Greiner, Annette, Gurtowski, James, Haun, Holly L, He, Fei, Jain, Rashmi, Joachimiak, Marcin P, Keegan, Kevin P, Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L, Meyer, Folker, Mills, Marissa, Novichkov, Pavel S, Oh, Taeyun, Olsen, Gary J, Olson, Robert, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S, Price, Gavin A, Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C, Schatz, Michael C, Seaver, Samuel M D, Shukla, Maulik, Sutormin, Roman A, Syed, Mustafa H, Thomason, James, Tintle, Nathan L, Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, Yoo, Shinjae, Yu, Dantong

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Assessment of predictions submitted for the CASP7 domain prediction category by Tress, Michael, Cheng, Jianlin, Baldi, Pierre, Joo, Keehyoung, Lee, Jinwoo, Seo, Joo-Hyun, Lee, Jooyoung, Baker, David, Chivian, Dylan, Kim, David, Ezkurdia, Iakes

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MicrobesOnline: an integrated portal for comparative and functional genomics by Dehal, Paramvir S, Joachimiak, Marcin P, Price, Morgan N, Bates, John T, Baumohl, Jason K, Chivian, Dylan, Friedland, Greg D, Huang, Katherine H, Keller, Keith, Novichkov, Pavel S, Dubchak, Inna L, Alm, Eric J, Arkin, Adam P

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Rosetta in CASP4: Progress in ab initio protein structure prediction by Bonneau, Richard, Tsai, Jerry, Ruczinski, Ingo, Chivian, Dylan, Rohl, Carol, Strauss, Charlie E. M., Baker, David

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In Vivo Oligomerization of the F Conjugative Coupling Protein TraD by HAFT, Rembrandt J. F, GACHELET, Eliora G, NGUYEN, Tran, TOUSSAINT, Luttrell, CHIVIAN, Dylan, TRAXLER, Beth

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