Draft Genome Sequence of Enterobacter sp. Strain A8, a Carbazole-Degrading Bacterium

por Gupta, Nidhi, Skinner, Kelly A., Khan, Samiya, Edirisinghe, Janaka N., Henry, Christopher S.
Publicado 2019

From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model

por Cuevas, Daniel A., Edirisinghe, Janaka, Henry, Chris S., Overbeek, Ross, O’Connell, Taylor G., Edwards, Robert A.
Publicado 2016

Modeling central metabolism and energy biosynthesis across microbial life

por Edirisinghe, Janaka N., Weisenhorn, Pamela, Conrad, Neal, Xia, Fangfang, Overbeek, Ross, Stevens, Rick L., Henry, Christopher S.
Publicado 2016

Comparative Genomics of Cultured and Uncultured Strains Suggests Genes Essential for Free-Living Growth of Liberibacter

por Fagen, Jennie R., Leonard, Michael T., McCullough, Connor M., Edirisinghe, Janaka N., Henry, Christopher S., Davis, Michael J., Triplett, Eric W.
Publicado 2014

Metabolic Reconstruction and Modeling Microbial Electrosynthesis

por Marshall, Christopher W., Ross, Daniel E., Handley, Kim M., Weisenhorn, Pamela B., Edirisinghe, Janaka N., Henry, Christopher S., Gilbert, Jack A., May, Harold D., Norman, R. Sean
Publicado 2017

Enabling comparative modeling of closely related genomes: example genus Brucella

por Faria, José P., Edirisinghe, Janaka N., Davis, James J., Disz, Terrence, Hausmann, Anna, Henry, Christopher S., Olson, Robert, Overbeek, Ross A., Pusch, Gordon D., Shukla, Maulik, Vonstein, Veronika, Wattam, Alice R.
Publicado 2014

Draft Genome Sequence of Rhodococcus sp. Strain ATCC 49988, a Quinoline-Degrading Bacterium

por Gupta, Nidhi, Skinner, Kelly A., Summers, Zarath M., Edirisinghe, Janaka N., Faria, José P., Marshall, Christopher W., Sharma, Anukriti, Gottel, Neil R., Gilbert, Jack A., Henry, Christopher S., O’Loughlin, Edward J.
Publicado 2019

Draft Genome Sequence of 2-Methylpyridine-, 2-Ethylpyridine-, and 2-Hydroxypyridine-Degrading Arthrobacter sp. Strain ATCC 49987

por Gupta, Nidhi, Skinner, Kelly A., Summers, Zarath M., Edirisinghe, Janaka N., Faria, José P., Marshall, Christopher W., Sharma, Anukriti, Gottel, Neil R., Gilbert, Jack A., Henry, Christopher S., O’Loughlin, Edward J.
Publicado 2020

Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine

por Heinken, Almut, Hertel, Johannes, Acharya, Geeta, Ravcheev, Dmitry A., Nyga, Malgorzata, Okpala, Onyedika Emmanuel, Hogan, Marcus, Magnúsdóttir, Stefanía, Martinelli, Filippo, Nap, Bram, Preciat, German, Edirisinghe, Janaka N., Henry, Christopher S., Fleming, Ronan M. T., Thiele, Ines
Publicado 2023

Draft Genome Sequence of Pseudarthrobacter sp. Strain ATCC 49442 (Formerly Micrococcus luteus), a Pyridine-Degrading Bacterium

por Gupta, Nidhi, Skinner, Kelly A., Summers, Zarath M., Edirisinghe, Janaka N., Weisenhorn, Pamela B., Faria, José P., Marshall, Christopher W., Sharma, Anukriti, Gottel, Neil R., Gilbert, Jack A., Henry, Christopher S., O’Loughlin, Edward J.
Publicado 2020

kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase

por Shaffer, Michael, Borton, Mikayla A, Bolduc, Ben, Faria, José P, Flynn, Rory M, Ghadermazi, Parsa, Edirisinghe, Janaka N, Wood-Charlson, Elisha M, Miller, Christopher S, Chan, Siu Hung Joshua, Sullivan, Matthew B, Henry, Christopher S, Wrighton, Kelly C
Publicado 2023

Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation

por Faria, José P., Davis, James J., Edirisinghe, Janaka N., Taylor, Ronald C., Weisenhorn, Pamela, Olson, Robert D., Stevens, Rick L., Rocha, Miguel, Rocha, Isabel, Best, Aaron A., DeJongh, Matthew, Tintle, Nathan L., Parrello, Bruce, Overbeek, Ross, Henry, Christopher S.
Publicado 2016

Evolution of substrate specificity in a retained enzyme driven by gene loss

por Juárez-Vázquez, Ana Lilia, Edirisinghe, Janaka N, Verduzco-Castro, Ernesto A, Michalska, Karolina, Wu, Chenggang, Noda-García, Lianet, Babnigg, Gyorgy, Endres, Michael, Medina-Ruíz, Sofía, Santoyo-Flores, Julián, Carrillo-Tripp, Mauricio, Ton-That, Hung, Joachimiak, Andrzej, Henry, Christopher S, Barona-Gómez, Francisco
Publicado 2017

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

por Seaver, Samuel M D, Liu, Filipe, Zhang, Qizhi, Jeffryes, James, Faria, José P, Edirisinghe, Janaka N, Mundy, Michael, Chia, Nicholas, Noor, Elad, Beber, Moritz E, Best, Aaron A, DeJongh, Matthew, Kimbrel, Jeffrey A, D’haeseleer, Patrik, McCorkle, Sean R, Bolton, Jay R, Pearson, Erik, Canon, Shane, Wood-Charlson, Elisha M, Cottingham, Robert W, Arkin, Adam P, Henry, Christopher S
Publicado 2020

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

por Seaver, Samuel M D, Liu, Filipe, Zhang, Qizhi, Jeffryes, James, Faria, José P, Edirisinghe, Janaka N, Mundy, Michael, Chia, Nicholas, Noor, Elad, Beber, Moritz E, Best, Aaron A, DeJongh, Matthew, Kimbrel, Jeffrey A, D’haeseleer, Patrik, McCorkle, Sean R, Bolton, Jay R, Pearson, Erik, Canon, Shane, Wood-Charlson, Elisha M, Cottingham, Robert W, Arkin, Adam P, Henry, Christopher S
Publicado 2020

Author Correction: A genomic catalog of Earth’s microbiomes

por Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I-Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B. K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Woyke, Tanja, Mouncey, Nigel J., Ivanova, Natalia N., Kyrpides, Nikos C., Eloe-Fadrosh, Emiley A.
Publicado 2021

Publisher Correction: A genomic catalog of Earth’s microbiomes

por Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I-Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B. K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Woyke, Tanja, Mouncey, Nigel J., Ivanova, Natalia N., Kyrpides, Nikos C., Eloe-Fadrosh, Emiley A.
Publicado 2020

A genomic catalog of Earth’s microbiomes

por Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I-Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B. K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Woyke, Tanja, Mouncey, Nigel J., Ivanova, Natalia N., Kyrpides, Nikos C., Eloe-Fadrosh, Emiley A.
Publicado 2020

MEMOTE for standardized genome-scale metabolic model testing

por Lieven, Christian, Beber, Moritz E., Olivier, Brett G., Bergmann, Frank T., Ataman, Meric, Babaei, Parizad, Bartell, Jennifer A., Blank, Lars M., Chauhan, Siddharth, Correia, Kevin, Diener, Christian, Dräger, Andreas, Ebert, Birgitta E., Edirisinghe, Janaka N., Faria, José P., Feist, Adam M., Fengos, Georgios, Fleming, Ronan M. T., García-Jiménez, Beatriz, Hatzimanikatis, Vassily, van Helvoirt, Wout, Henry, Christopher S., Hermjakob, Henning, Herrgård, Markus J., Kaafarani, Ali, Kim, Hyun Uk, King, Zachary, Klamt, Steffen, Klipp, Edda, Koehorst, Jasper J., König, Matthias, Lakshmanan, Meiyappan, Lee, Dong-Yup, Lee, Sang Yup, Lee, Sunjae, Lewis, Nathan E., Liu, Filipe, Ma, Hongwu, Machado, Daniel, Mahadevan, Radhakrishnan, Maia, Paulo, Mardinoglu, Adil, Medlock, Gregory L., Monk, Jonathan M., Nielsen, Jens, Nielsen, Lars Keld, Nogales, Juan, Nookaew, Intawat, Palsson, Bernhard O., Papin, Jason A., Patil, Kiran R., Poolman, Mark, Price, Nathan D., Resendis-Antonio, Osbaldo, Richelle, Anne, Rocha, Isabel, Sánchez, Benjamín J., Schaap, Peter J., Malik Sheriff, Rahuman S., Shoaie, Saeed, Sonnenschein, Nikolaus, Teusink, Bas, Vilaça, Paulo, Vik, Jon Olav, Wodke, Judith A. H., Xavier, Joana C., Yuan, Qianqian, Zakhartsev, Maksim, Zhang, Cheng
Publicado 2020

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

por Lieven, Christian, Beber, Moritz E., Olivier, Brett G., Bergmann, Frank T., Ataman, Meric, Babaei, Parizad, Bartell, Jennifer A., Blank, Lars M., Chauhan, Siddharth, Correia, Kevin, Diener, Christian, Dräger, Andreas, Ebert, Birgitta E., Edirisinghe, Janaka N., Faria, José P., Feist, Adam M., Fengos, Georgios, Fleming, Ronan M. T., García-Jiménez, Beatriz, Hatzimanikatis, Vassily, van Helvoirt, Wout, Henry, Christopher S., Hermjakob, Henning, Herrgård, Markus J., Kaafarani, Ali, Kim, Hyun Uk, King, Zachary, Klamt, Steffen, Klipp, Edda, Koehorst, Jasper J., König, Matthias, Lakshmanan, Meiyappan, Lee, Dong-Yup, Lee, Sang Yup, Lee, Sunjae, Lewis, Nathan E., Liu, Filipe, Ma, Hongwu, Machado, Daniel, Mahadevan, Radhakrishnan, Maia, Paulo, Mardinoglu, Adil, Medlock, Gregory L., Monk, Jonathan M., Nielsen, Jens, Nielsen, Lars Keld, Nogales, Juan, Nookaew, Intawat, Palsson, Bernhard O., Papin, Jason A., Patil, Kiran R., Poolman, Mark, Price, Nathan D., Resendis-Antonio, Osbaldo, Richelle, Anne, Rocha, Isabel, Sánchez, Benjamín J., Schaap, Peter J., Sheriff, Rahuman S. Malik, Shoaie, Saeed, Sonnenschein, Nikolaus, Teusink, Bas, Vilaça, Paulo, Vik, Jon Olav, Wodke, Judith A. H., Xavier, Joana C., Yuan, Qianqian, Zakhartsev, Maksim, Zhang, Cheng
Publicado 2020