Works matching AU Zengler, Karsten

Results: 63

A road map for the development of community systems (CoSy) biology.

Published in:

Nature Reviews Microbiology, 2012, v. 10, n. 5, p. 366, doi. 10.1038/nrmicro2763

By:

Zengler, Karsten;
Palsson, Bernhard O.

Publication type:

Article

Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states.

Published in:

BMC Biology, 2014, v. 12, n. 1, p. 2, doi. 10.1186/1741-7007-12-4

By:

Byung-Kwan Cho;
Donghyuk Kim;
Knight, Eric M.;
Zengler, Karsten;
Palsson, Bernhard O.

Publication type:

Article

Anoxybacillus kamchatkensis sp. nov., a novel thermophilic facultative aerobic bacterium with a broad pH optimum from the Geyser valley, Kamchatka.

Published in:

Extremophiles, 2005, v. 9, n. 5, p. 391, doi. 10.1007/s00792-005-0479-7

By:

Kevbrin, Vadim V.;
Zengler, Karsten;
Lysenko, Anatolii M.;
Wiegel, Juergen

Publication type:

Article

Spatial chemistry of citrus reveals molecules bactericidal to Candidatus Liberibacter asiaticus.

Published in:

Scientific Reports, 2024, v. 14, n. 1, p. 1, doi. 10.1038/s41598-024-70499-z

By:

A. Aksenov, Alexander;
Blacutt, Alex;
Ginnan, Nichole;
Rolshausen, Philippe E.;
V. Melnik, Alexey;
Lotfi, Ali;
C. Gentry, Emily;
Ramasamy, Manikandan;
Zuniga, Cristal;
Zengler, Karsten;
Mandadi, Kranthi K.;
Dorrestein, Pieter C.;
Roper, M. Caroline

Publication type:

Article

Functional and Proteomic Analysis of Streptococcus pyogenes Virulence Upon Loss of Its Native Cas9 Nuclease.

Published in:

Frontiers in Microbiology, 2019, p. 1, doi. 10.3389/fmicb.2019.01967

By:

Gao, Nina J.;
Al-Bassam, Mahmoud M.;
Poudel, Saugat;
Wozniak, Jacob M.;
Gonzalez, David J.;
Olson, Joshua;
Zengler, Karsten;
Nizet, Victor;
Valderrama, J. Andrés

Publication type:

Article

Determining the Control Circuitry of Redox Metabolism at the Genome-Scale.

Published in:

PLoS Genetics, 2014, v. 10, n. 4, p. 1, doi. 10.1371/journal.pgen.1004264

By:

Federowicz, Stephen;
Kim, Donghyuk;
Ebrahim, Ali;
Lerman, Joshua;
Nagarajan, Harish;
Cho, Byung-kwan;
Zengler, Karsten;
Palsson, Bernhard

Publication type:

Article

The Genome Organization of Thermotoga maritima Reflects Its Lifestyle.

Published in:

PLoS Genetics, 2013, v. 9, n. 4, p. 1, doi. 10.1371/journal.pgen.1003485

By:

Latif, Haythem;
Lerman, Joshua A.;
Portnoy, Vasiliy A.;
Tarasova, Yekaterina;
Nagarajan, Harish;
Schrimpe-Rutledge, Alexandra C.;
Smith, Richard D.;
Adkins, Joshua N.;
Dae-Hee Lee;
Yu Qiu;
Zengler, Karsten

Publication type:

Article

A genome-scale metabolic model for the denitrifying bacterium Thauera sp. MZ1T accurately predicts degradation of pollutants and production of polymers.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012736

By:

Tec-Campos, Diego;
Tibocha-Bonilla, Juan D.;
Jiang, Celina;
Passi, Anurag;
Thiruppathy, Deepan;
Zuñiga, Cristal;
Posadas, Camila;
Zepeda, Alejandro;
Zengler, Karsten

Publication type:

Article

Transcriptional profiling of lung macrophages identifies a predictive signature for inflammatory lung disease in preterm infants.

Published in:

Communications Biology, 2020, v. 3, n. 1, p. 1, doi. 10.1038/s42003-020-0985-2

By:

Sahoo, Debashis;
Zaramela, Livia S.;
Hernandez, Gilberto E.;
Mai, Uyen;
Taheri, Sahar;
Dang, Dharanidhar;
Stouch, Ashley N.;
Medal, Rachel M.;
McCoy, Alyssa M.;
Aschner, Judy L.;
Blackwell, Timothy S.;
Zengler, Karsten;
Prince, Lawrence S.

Publication type:

Article

Linking metabolic phenotypes to pathogenic traits among "Candidatus Liberibacter asiaticus" and its hosts.

Published in:

NPJ Systems Biology & Applications, 2020, v. 6, n. 1, p. 1, doi. 10.1038/s41540-020-00142-w

By:

Zuñiga, Cristal;
Peacock, Beth;
Liang, Bo;
McCollum, Greg;
Irigoyen, Sonia C.;
Tec-Campos, Diego;
Marotz, Clarisse;
Weng, Nien-Chen;
Zepeda, Alejandro;
Vidalakis, Georgios;
Mandadi, Kranthi K.;
Borneman, James;
Zengler, Karsten

Publication type:

Article

Dynamic resource allocation drives growth under nitrogen starvation in eukaryotes.

Published in:

NPJ Systems Biology & Applications, 2020, v. 6, n. 1, p. 1, doi. 10.1038/s41540-020-0135-y

By:

Tibocha-Bonilla, Juan D.;
Kumar, Manish;
Richelle, Anne;
Godoy-Silva, Rubén D.;
Zengler, Karsten;
Zuñiga, Cristal

Publication type:

Article

Utilizing genome-scale models to optimize nutrient supply for sustained algal growth and lipid productivity.

Published in:

NPJ Systems Biology & Applications, 2019, v. 5, n. 1, p. N.PAG, doi. 10.1038/s41540-019-0110-7

By:

Li, Chien-Ting;
Yelsky, Jacob;
Chen, Yiqun;
Zuñiga, Cristal;
Eng, Richard;
Jiang, Liqun;
Shapiro, Alison;
Huang, Kai-Wen;
Zengler, Karsten;
Betenbaugh, Michael J.

Publication type:

Article

Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data.

Published in:

Metabolites (2218-1989), 2022, v. 12, n. 1, p. 14, doi. 10.3390/metabo12010014

By:

Passi, Anurag;
Tibocha-Bonilla, Juan D.;
Kumar, Manish;
Tec-Campos, Diego;
Zengler, Karsten;
Zuniga, Cristal

Publication type:

Article

A c-type cytochrome and a transcriptional regulator responsible for enhanced extracellular electron transfer in Geobacter sulfurreducens revealed by adaptive evolution.

Published in:

Environmental Microbiology, 2011, v. 13, n. 1, p. 13, doi. 10.1111/j.1462-2920.2010.02302.x

By:

Tremblay, Pier-Luc;
Summers, Zarath M.;
Glaven, Richard H.;
Nevin, Kelly P.;
Zengler, Karsten;
Barrett, Christian L.;
Qiu, Yu;
Palsson, Bernhard O.;
Lovley, Derek R.

Publication type:

Article

Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom.

Published in:

PLoS ONE, 2016, v. 11, n. 5, p. 1, doi. 10.1371/journal.pone.0155038

By:

Levering, Jennifer;
Broddrick, Jared;
Dupont, Christopher L.;
Peers, Graham;
Beeri, Karen;
Mayers, Joshua;
Gallina, Alessandra A.;
Allen, Andrew E.;
Palsson, Bernhard O.;
Zengler, Karsten

Publication type:

Article

Elucidation of complexity and prediction of interactions in microbial communities.

Published in:

Microbial Biotechnology, 2017, v. 10, n. 6, p. 1500, doi. 10.1111/1751-7915.12855

By:

Zuñiga, Cristal;
Zaramela, Livia;
Zengler, Karsten

Publication type:

Article

Crystal ball - 2013.

Published in:

Microbial Biotechnology, 2013, v. 6, n. 1, p. 3, doi. 10.1111/1751-7915.12014

By:

Curtis, Tom;
Daran, Jean-Marc;
Pronk, Jack T.;
Frey, Joachim;
Jansson, Janet K.;
Robbins-Pianka, Adam;
Knight, Rob;
Schnürer, Anna;
Smets, Barth F.;
Smid, E. J.;
Abee, T.;
Vicente, Miguel;
Zengler, Karsten

Publication type:

Article

Unraveling interactions in microbial communities - from co-cultures to microbiomes.

Published in:

Journal of Microbiology, 2015, v. 53, n. 5, p. 295, doi. 10.1007/s12275-015-5060-1

By:

Tan, Justin;
Zuniga, Cristal;
Zengler, Karsten

Publication type:

Article

Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009828

By:

Canto-Encalada, Gabriela;
Tec-Campos, Diego;
Tibocha-Bonilla, Juan D.;
Zengler, Karsten;
Zepeda, Alejandro;
Zuñiga, Cristal

Publication type:

Article

Acetate reprograms gut microbiota during alcohol consumption.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-31973-2

By:

Martino, Cameron;
Zaramela, Livia S.;
Gao, Bei;
Embree, Mallory;
Tarasova, Janna;
Parker, Seth J.;
Wang, Yanhan;
Chu, Huikuan;
Chen, Peng;
Lee, Kuei-Chuan;
Galzerani, Daniela Domingos;
Gengatharan, Jivani M.;
Lekbua, Asama;
Neal, Maxwell;
Knight, Rob;
Tsukamoto, Hidekazu;
Metallo, Christian M.;
Schnabl, Bernd;
Zengler, Karsten

Publication type:

Article

Carbohydrates great and small, from dietary fiber to sialic acids: How glycans influence the gut microbiome and affect human health.

Published in:

Gut Microbes, 2021, v. 13, n. 1, p. 1, doi. 10.1080/19490976.2020.1869502

By:

Coker, Joanna K;
Moyne, Oriane;
Rodionov, Dmitry A.;
Zengler, Karsten

Publication type:

Article

ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions.

Published in:

PLoS ONE, 2018, v. 13, n. 5, p. 1, doi. 10.1371/journal.pone.0197272

By:

Latif, Haythem;
Federowicz, Stephen;
Ebrahim, Ali;
Tarasova, Janna;
Szubin, Richard;
Utrilla, Jose;
Zengler, Karsten;
Palsson, Bernhard O.

Publication type:

Article

Model of metabolism and gene expression predicts proteome allocation in Pseudomonas putida.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00521-1

By:

Tibocha-Bonilla, Juan D.;
Gandhi, Vishant;
Lieng, Chloe;
Moyne, Oriane;
Santibáñez-Palominos, Rodrigo;
Zengler, Karsten

Publication type:

Article

Optimization of nutrient utilization efficiency and productivity for algal cultures under light and dark cycles using genome-scale model process control.

Published in:

NPJ Systems Biology & Applications, 2023, v. 9, n. 1, p. 1, doi. 10.1038/s41540-022-00260-7

By:

Li, Chien-Ting;
Eng, Richard;
Zuniga, Cristal;
Huang, Kai-Wen;
Chen, Yiqun;
Zengler, Karsten;
Betenbaugh, Michael J.

Publication type:

Article

Predicting stress response and improved protein overproduction in Bacillus subtilis.

Published in:

NPJ Systems Biology & Applications, 2022, v. 8, n. 1, p. 1, doi. 10.1038/s41540-022-00259-0

By:

Tibocha-Bonilla, Juan D.;
Zuñiga, Cristal;
Lekbua, Asama;
Lloyd, Colton;
Rychel, Kevin;
Short, Katie;
Zengler, Karsten

Publication type:

Article

Biocontrol in built environments to reduce pathogen exposure and infection risk.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2024, v. 18, n. 1, p. 1, doi. 10.1093/ismejo/wrad024

By:

Gottel, Neil R;
Hill, Megan S;
Neal, Maxwell J;
Allard, Sarah M;
Zengler, Karsten;
Gilbert, Jack A

Publication type:

Article

Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2014, v. 8, n. 4, p. 757, doi. 10.1038/ismej.2013.187

By:

Embree, Mallory;
Nagarajan, Harish;
Movahedi, Narjes;
Chitsaz, Hamidreza;
Zengler, Karsten

Publication type:

Article

Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale.

Published in:

BMC Systems Biology, 2014, v. 8, n. 1, p. 1, doi. 10.1186/s12918-014-0110-6

By:

Liu, Joanne K.;
O'Brien, Edward J.;
Lerman, Joshua A.;
Zengler, Karsten;
Palsson, Bernhard O.;
Feist, Adam M.

Publication type:

Article

Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii.

Published in:

Microbial Cell Factories, 2013, v. 12, n. 1, p. 1, doi. 10.1186/1475-2859-12-118

By:

Nagarajan, Harish;
Sahin, Merve;
Nogales, Juan;
Latif, Haythem;
Lovley, Derek R.;
Ebrahim, Ali;
Zengler, Karsten

Publication type:

Article

The impact of skin care products on skin chemistry and microbiome dynamics.

Published in:

BMC Biology, 2019, v. 17, n. 1, p. 1, doi. 10.1186/s12915-019-0660-6

By:

Bouslimani, Amina;
da Silva, Ricardo;
Kosciolek, Tomasz;
Janssen, Stefan;
Callewaert, Chris;
Amir, Amnon;
Dorrestein, Kathleen;
Melnik, Alexey V.;
Zaramela, Livia S.;
Kim, Ji-Nu;
Humphrey, Gregory;
Schwartz, Tara;
Sanders, Karenina;
Brennan, Caitriona;
Luzzatto-Knaan, Tal;
Ackermann, Gail;
McDonald, Daniel;
Zengler, Karsten;
Knight, Rob;
Dorrestein, Pieter C.

Publication type:

Article

Anaerobic degradation of hexadecane and phenanthrene coupled to sulfate reduction by enriched consortia from northern Gulf of Mexico seafloor sediment.

Published in:

Scientific Reports, 2019, v. 9, n. 1, p. 1, doi. 10.1038/s41598-018-36567-x

By:

Shin, Boryoung;
Kim, Minjae;
Zengler, Karsten;
Chin, Kuk-Jeong;
Overholt, Will A.;
Gieg, Lisa M.;
Konstantinidis, Konstantinos T.;
Kostka, Joel E.

Publication type:

Article

Evidence for fungal and chemodenitrification based N<sub>2</sub>O flux from nitrogen impacted coastal sediments.

Published in:

Nature Communications, 2017, v. 8, n. 6, p. 15595, doi. 10.1038/ncomms15595

By:

Wankel, Scott D.;
Ziebis, Wiebke;
Buchwald, Carolyn;
Charoenpong, Chawalit;
de Beer, Dirk;
Dentinger, Jane;
Xu, Zhenjiang;
Zengler, Karsten

Publication type:

Article

Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association.

Published in:

Nature Communications, 2013, v. 4, n. 11, p. 2809, doi. 10.1038/ncomms3809

By:

Nagarajan, Harish;
Embree, Mallory;
Rotaru, Amelia-Elena;
Shrestha, Pravin M.;
Feist, Adam M.;
Palsson, Bernhard Ø;
Lovley, Derek R.;
Zengler, Karsten

Publication type:

Article

Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks.

Published in:

Nature Communications, 2013, v. 4, n. 4, p. 1755, doi. 10.1038/ncomms2743

By:

Qiu, Yu;
Nagarajan, Harish;
Embree, Mallory;
Shieu, Wendy;
Abate, Elisa;
Juárez, Katy;
Cho, Byung-Kwan;
Elkins, James G.;
Nevin, Kelly P.;
Barrett, Christian L.;
Lovley, Derek R.;
Palsson, Bernhard O.;
Zengler, Karsten

Publication type:

Article

The microbiome extends to subepidermal compartments of normal skin.

Published in:

Nature Communications, 2013, v. 4, n. 2, p. 1431, doi. 10.1038/ncomms2441

By:

Nakatsuji, Teruaki;
Chiang, Hsin-I.;
Jiang, Shangi B.;
Nagarajan, Harish;
Zengler, Karsten;
Gallo, Richard L.

Publication type:

Article

Predicting Dynamic Metabolic Demands in the Photosynthetic Eukaryote Chlorella vulgaris.

Published in:

Plant Physiology, 2018, v. 176, n. 1, p. 450, doi. 10.1104/pp.17.00605

By:

Zuñiga, Cristal;
Levering, Jennifer;
Antoniewicz, Maciek R.;
Guarnieri, Michael T.;
Betenbaugh, Michael J.;
Zengler, Karsten

Publication type:

Article

Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions.

Published in:

Plant Physiology, 2016, v. 172, n. 1, p. 589, doi. 10.1104/pp.16.00593

By:

Zuñiga, Cristal;
Chien-Ting Li;
Huelsman, Tyler;
Levering, Jennifer;
Zielinski, Daniel C.;
McConnell, Brian O.;
Long, Christopher P.;
Knoshaug, Eric P.;
Guarnieri, Michael T.;
Antoniewicz, Maciek R.;
Betenbaugh, Michael J.;
Zengler, Karsten

Publication type:

Article

Constraint-Based Modeling of Carbon Fixation and the Energetics of Electron Transfer in <i>Geobacter metallireducens</i>.

Published in:

PLoS Computational Biology, 2014, v. 10, n. 4, p. 1, doi. 10.1371/journal.pcbi.1003575

By:

Feist, Adam M.;
Nagarajan, Harish;
Rotaru, Amelia-Elena;
Tremblay, Pier-Luc;
Zhang, Tian;
Nevin, Kelly P.;
Lovley, Derek R.;
Zengler, Karsten

Publication type:

Article

Erratum: Arch Microbiol (1999) 172: 204–212.

Published in:

2000

By:

Zengler, Karsten;
Heider, Johann;
Rosselló-Mora, Ramon;
Widdel, Friedrich

Publication type:

Erratum

Improving saliva shotgun metagenomics by chemical host DNA depletion.

Published in:

Microbiome, 2018, v. 6, p. 1, doi. 10.1186/s40168-018-0426-3

By:

Marotz, Clarisse A.;
Sanders, Jon G.;
Zuniga, Cristal;
Zaramela, Livia S.;
Knight, Rob;
Zengler, Karsten

Publication type:

Article

Metabolic capability and in situ activity of microorganisms in an oil reservoir.

Published in:

Microbiome, 2018, v. 6, p. 1, doi. 10.1186/s40168-017-0392-1

By:

Yi-Fan Liu;
Galzerani, Daniela Domingos;
Mbadinga, Serge Maurice;
Zaramela, Livia S.;
Ji-Dong Gu;
Bo-Zhong Mu;
Zengler, Karsten

Publication type:

Article

Optimization of carbon and energy utilization through differential translational efficiency.

Published in:

Nature Communications, 2018, v. 9, p. 1, doi. 10.1038/s41467-018-06993-6

By:

Al-Bassam, Mahmoud M.;
Kim, Ji-Nu;
Zaramela, Livia S.;
Kellman, Benjamin P.;
Zuniga, Cristal;
Wozniak, Jacob M.;
Gonzalez, David J.;
Zengler, Karsten

Publication type:

Article

Group B Streptococcus Biofilm Regulatory Protein A Contributes to Bacterial Physiology and Innate Immune Resistance.

Published in:

2018

By:

Patras, Kathryn A;
Derieux, Jaclyn;
Al-Bassam, Mahmoud M;
Adiletta, Nichole;
Vrbanac, Alison;
Lapek, John D;
Zengler, Karsten;
Gonzalez, David J;
Nizet, Victor

Publication type:

journal article

ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualization.

Published in:

BMC Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s12859-022-05056-4

By:

Tamasco, Gustavo;
Kumar, Manish;
Zengler, Karsten;
Silva-Rocha, Rafael;
da Silva, Ricardo Roberto

Publication type:

Article

Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006848

By:

Liu, Joanne K.;
Lloyd, Colton;
Al-Bassam, Mahmoud;
Ebrahim, Ali;
Kim, Ji-Nu;
Olson, Connor;
Aksenov, Alexander;
Dorrestein, Pieter;
Zengler, Karsten

Publication type:

Article

A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 01, p. 1, doi. 10.1371/journal.pcbi.1006644

By:

Seif, Yara;
Monk, Jonathan M.;
Mih, Nathan;
Tsunemoto, Hannah;
Poudel, Saugat;
Zuniga, Cristal;
Broddrick, Jared;
Zengler, Karsten;
Palsson, Bernhard O.

Publication type:

Article

Methane formation from long-chain alkanes by anaerobic microorganisms.

Published in:

Nature, 1999, v. 401, n. 6750, p. 266, doi. 10.1038/45777

By:

Zengler, Karsten;
Richnow, Hans H.;
Rossello-Mora, Ramon;
Michaelis, Walter;
Widdel, Friedrich

Publication type:

Article

FRT - FONDATION RENE TOURAINE.

Published in:

Experimental Dermatology, 2016, v. 25, n. 11, p. 917, doi. 10.1111/exd.13160

By:

Bosch, Thomas C. G.;
Zengler, Karsten;
Naik, Shruti;
Biedermann, Tilo;
Kong, Heidi H.;
Loser, Karin;
Brüggeman, Holger;
Calleawert, Chris;
Lambert, Jo;
Van de Wiele, Tom

Publication type:

Article

Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-17612-8

By:

Zuñiga, Cristal;
Li, Tingting;
Guarnieri, Michael T.;
Jenkins, Jackson P.;
Li, Chien-Ting;
Bingol, Kerem;
Kim, Young-Mo;
Betenbaugh, Michael J.;
Zengler, Karsten

Publication type:

Article

Investigating Moorella thermoacetica metabolism with a genome-scale constraint-based metabolic model.

Published in:

Integrative Biology, 2015, v. 7, n. 8, p. 869, doi. 10.1039/c5ib00095e

By:

Islam, M. Ahsanul;
Zengler, Karsten;
Edwards, Elizabeth A.;
Mahadevan, Radhakrishnan;
Stephanopoulos, Gregory

Publication type:

Article