6.047 / 6.878 Computational Biology: Genomes, Networks, Evolution, Fall 2008 by Kellis, Manolis, Galagan, James

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Positive selection for unpreferred codon usage in eukaryotic genomes by Neafsey, Daniel E., Galagan, James E.

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Mechanisms of intron gain and loss in Cryptococcus by Neafsey, Daniel E., Galagan, James E., Sharpton, Thomas J., Taylor, John W.

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Cross-kingdom patterns of alternative splicing and splice recognition by McGuire, Abigail Manson, Pearson, Matthew D., Neafsey, Daniel E., Galagan, James E.

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How accurate can genetic predictions be? by Dreyfuss, Jonathan M., Levner, Daniel, Galagan, James E., Church, George M., Ramoni, Marco F.

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Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models by Brandes, Aaron, Lun, Desmond S., Ip, Kuhn, Zucker, Jeremy, Colijn, Caroline, Weiner, Brian, Galagan, James E.

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Large-scale identification of genetic design strategies using local search by Lun, Desmond S., Rockwell, Graham, Guido, Nicholas J., Baym, Michael Hartmann, Kelner, Jonathan Adam, Berger, Bonnie, Galagan, James E., Church, George M.

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Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production by Murray, Megan B., Moody, D. Branch, Cheng, Tan-Yun, Farhat, Maha R., Galagan, James E., Weiner, Brian, Lun, Desmond S., Brandes, Aaron, Colijn, Caroline, Zucker, Jeremy

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Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria by Wu, Xiaolin, Cao, Bo, Aquino, Patricia, Chiu, Tsu-Pei, Chen, Chao, Jiang, Susu, Deng, Zixin, Chen, Shi, Rohs, Remo, Wang, Lianrong, Galagan, James E, Dedon, Peter C

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Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria by Wu, Xiaolin, Cao, Bo, Aquino, Patricia, Chiu, Tsu-Pei, Chen, Chao, Jiang, Susu, Deng, Zixin, Chen, Shi, Rohs, Remo, Wang, Lianrong, Galagan, James E, Dedon, Peter C

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Short-term genome evolution of Listeria monocytogenes in a non-controlled environment by Orsi, Renato H., Borowsky, Mark L., Lauer, Peter, Young, Sarah K., Nusbaum, Chad, Galagan, James E., Birren, Bruce W., Ivy, Reid A., Sun, Qi, Graves, Lewis M., Swaminathan, Bala, Wiedmann, Martin

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Comparative analysis of mycobacterium and related actinomycetes yields insight into the evolution of mycobacterium tuberculosis pathogenesis by McGuire, Abigail, Weiner, Brian, Park, Sang, Raman, Sahadevan, Dolganov, Gregory, Peterson, Matthew, Riley, Robert, Zucker, Jeremy, Stolte, Christian, Koehrsen, Mike, Yamamoto, Robert T, Iacobelli-Martinez, Milena, Kidd, Matthew J, Maer, Andreia M, Schoolnik, Gary K, Wapinski, Ilan Neustat, Abeel, Thomas, White, Jared, Sisk, Peter, Regev, Aviv, Galagan, James E.

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Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis by Farhat, Maha R., Shapiro, B. Jesse, Kieser, Karen J., Sultana, Razvan, Jacobson, Karen R., Victor, Thomas C., Warren, Robin M., Streicher, Elizabeth M., Calver, Alistair, Sloutsky, Alex, Kaur, Devinder, Posey, Jamie E., Plikaytis, Bonnie, Oggioni, Marco R., Gardy, Jennifer L., Johnston, James C., Rodrigues, Mabel, Tang, Patrick K. C., Kato-Maeda, Midori, Borowsky, Mark L., Muddukrishna, Bhavana, Kreiswirth, Barry N., Kurepina, Natalia, Galagan, James E., Gagneux, Sebastien, Birren, Bruce W., Rubin, Eric J., Sabeti, Pardis C., Murray, Megan B., Lander, Eric Steven

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