iModulonDB 2.0: dynamic tools to facilitate knowledge-mining and user-enabled analyses of curated transcriptomic datasets von Catoiu, Edward A, Krishnan, Jayanth, Li, Gaoyuan, Lou, Xuwen A, Rychel, Kevin, Yuan, Yuan, Bajpe, Heera, Patel, Arjun, Choe, Donghui, Shin, Jongoh, Burrows, Joshua, Phaneuf, Patrick V, Zielinski, Daniel C, Palsson, Bernhard O

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Whole-genome sequences from wild-type and laboratory-evolved strains define the alleleome and establish its hallmarks von Catoiu, Edward Alexander, Phaneuf, Patrick, Monk, Jonathan, Palsson, Bernhard O

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COBRAme: A computational framework for genome-scale models of metabolism and gene expression von Lloyd, Colton J, Ebrahim, Ali, Yang, Laurence, King, Zachary A, Catoiu, Edward, O'Brien, Edward J, Liu, Joanne K, Palsson, Bernhard O

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Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance von Kavvas, Erol S., Catoiu, Edward, Mih, Nathan, Yurkovich, James T., Seif, Yara, Dillon, Nicholas, Heckmann, David, Anand, Amitesh, Yang, Laurence, Nizet, Victor, Monk, Jonathan M., Palsson, Bernhard O.

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Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits von Seif, Yara, Kavvas, Erol, Lachance, Jean-Christophe, Yurkovich, James T., Nuccio, Sean-Paul, Fang, Xin, Catoiu, Edward, Raffatellu, Manuela, Palsson, Bernhard O., Monk, Jonathan M.

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Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes von Mih, Nathan, Monk, Jonathan M, Fang, Xin, Catoiu, Edward, Heckmann, David, Yang, Laurence, Palsson, Bernhard O

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OxyR Is a Convergent Target for Mutations Acquired during Adaptation to Oxidative Stress-Prone Metabolic States von Anand, Amitesh, Chen, Ke, Catoiu, Edward, Sastry, Anand V, Olson, Connor A, Sandberg, Troy E, Seif, Yara, Xu, Sibei, Szubin, Richard, Yang, Laurence, Feist, Adam M, Palsson, Bernhard O

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ssbio: a Python framework for structural systems biology von Mih, Nathan, Brunk, Elizabeth, Chen, Ke, Catoiu, Edward, Sastry, Anand, Kavvas, Erol, Monk, Jonathan M, Zhang, Zhen, Palsson, Bernhard O

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DatasetS1-UltraCompress_QSPACE_Ecoli.zip von Catoiu, Edward

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Pseudogene repair driven by selection pressure applied in experimental evolution von Anand, Amitesh, Olson, Connor A, Yang, Laurence, Sastry, Anand V, Catoiu, Edward, Choudhary, Kumari Sonal, Phaneuf, Patrick V, Sandberg, Troy E, Xu, Sibei, Hefner, Ying, Szubin, Richard, Feist, Adam M, Palsson, Bernhard O

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Reframing gene essentiality in terms of adaptive flexibility von Guzmán, Gabriela I, Olson, Connor A, Hefner, Ying, Phaneuf, Patrick V, Catoiu, Edward, Crepaldi, Lais B, Micas, Lucas Goldschmidt, Palsson, Bernhard O, Feist, Adam M

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Pseudogene repair driven by selection pressure applied in experimental evolution von Anand, Amitesh, Olson, Connor A., Yang, Laurence, Sastry, Anand V., Catoiu, Edward, Choudhary, Kumari Sonal, Phaneuf, Patrick V., Sandberg, Troy E., Xu, Sibei, Hefner, Ying, Szubin, Richard, Feist, Adam M., Palsson, Bernhard O.

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Additional file 1 of Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes von Mih, Nathan, Monk, Jonathan M., Fang, Xin, Catoiu, Edward, Heckmann, David, Yang, Laurence, Palsson, Bernhard O.

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Additional file 4 of Reframing gene essentiality in terms of adaptive flexibility von Guzmรกn, Gabriela I., Olson, Connor A., Hefner, Ying, Phaneuf, Patrick V., Catoiu, Edward, Lais B. Crepaldi, Micas, Lucas Goldschmidt, Palsson, Bernhard O., Feist, Adam M.

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