Karsten Zengler

ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 39

Top Venues

Nature microbiology

Nature communications

bioRxiv : the preprint server for biology

PLoS computational biology

University of California, San Diego

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of California, San Diego

United States

Professor

Publications

Renee E Oles, Marvic Carrillo Terrazas, Luke R Loomis, Maxwell J Neal, Mousumi Paulchakrabarti, Simone Zuffa, Chia-Yun Hsu, Adriana Vasquez Ayala, Michael H Lee, Caitlin Tribelhorn, Pedro Belda Ferre, MacKenzie Bryant, Jasmine Zemlin, Jocelyn Young, Parambir Dulai, William J Sandborn, Mamata Sivagnanam, Manuela Raffatellu, David Pride, Pieter C Dorrestein, Karsten Zengler, Biswa Choudhury, Rob Knight, Hiutung Chu
Pathogenic Bacteroides fragilis strains can emerge from gut-resident commensals. bioRxiv : the preprint server for biology (2024)
Renee E Oles, Marvic Carrillo Terrazas, Luke R Loomis, Maxwell J Neal, Mousumi Paulchakrabarti, Simone Zuffa, Chia-Yun Hsu, Adriana Vasquez Ayala, Michael H Lee, Caitlin Tribelhorn, Pedro Belda Ferre, MacKenzie Bryant, Jasmine Zemlin, Jocelyn Young, Parambir Dulai, William J Sandborn, Mamata Sivagnanam, Manuela Raffatellu, David Pride, Pieter C Dorrestein, Karsten Zengler, Biswa Choudhury, Rob Knight, Hiutung Chu
Pathogenic Bacteroides fragilis strains can emerge from gut-resident commensals. bioRxiv : the preprint server for biology (2024)
Manish Kumar, Juan D Tibocha-Bonilla, Zoltan Fussy, Chloe Lieng, Sarah M Schwenck, Alice V Levesque, Mahmoud M Al-Bassam, Anurag Passi, Maxwell Neal, Cristal Zuñiga, Farrah Kaiyom, Josh L Espinoza, Hyun Gyu Lim, Shawn W Polson, Lisa Zeigler Allen, Karsten Zengler
Mixotrophic growth of a ubiquitous marine diatom. Science advances 10 (29) (2024)
Renee E Oles, Marvic Carrillo Terrazas, Luke R Loomis, Maxwell J Neal, Mousumi Paulchakrabarti, Simone Zuffa, Chia-Yun Hsu, Adriana Vasquez Ayala, Michael H Lee, Caitlin Tribelhorn, Pedro Belda Ferre, MacKenzie Bryant, Jasmine Zemlin, Jocelyn Young, Parambir Dulai, William J Sandborn, Mamata Sivagnanam, Manuela Raffatellu, David Pride, Pieter C Dorrestein, Karsten Zengler, Biswa Choudhury, Rob Knight, Hiutung Chu
Pathogenic Bacteroides fragilis strains can emerge from gut-resident commensals. bioRxiv : the preprint server for biology (2024)
Manish Kumar, Juan D Tibocha-Bonilla, Zoltan Fussy, Chloe Lieng, Sarah M Schwenck, Alice V Levesque, Mahmoud M Al-Bassam, Anurag Passi, Maxwell Neal, Cristal Zuñiga, Farrah Kaiyom, Josh L Espinoza, Hyun Gyu Lim, Shawn W Polson, Lisa Zeigler Allen, Karsten Zengler
Mixotrophic growth of a ubiquitous marine diatom. Science advances 10 (29) (2024)
Manish Kumar, Juan D Tibocha-Bonilla, Zoltan Fussy, Chloe Lieng, Sarah M Schwenck, Alice V Levesque, Mahmoud M Al-Bassam, Anurag Passi, Maxwell Neal, Cristal Zuñiga, Farrah Kaiyom, Josh L Espinoza, Hyun Gyu Lim, Shawn W Polson, Lisa Zeigler Allen, Karsten Zengler
Mixotrophic growth of a ubiquitous marine diatom. Science advances 10 (29) (2024)
Renee E Oles, Marvic Carrillo Terrazas, Luke R Loomis, Maxwell J Neal, Mousumi Paulchakrabarti, Simone Zuffa, Chia-Yun Hsu, Adriana Vasquez Ayala, Michael H Lee, Caitlin Tribelhorn, Pedro Belda Ferre, MacKenzie Bryant, Jasmine Zemlin, Jocelyn Young, Parambir Dulai, William J Sandborn, Mamata Sivagnanam, Manuela Raffatellu, David Pride, Pieter C Dorrestein, Karsten Zengler, Biswa Choudhury, Rob Knight, Hiutung Chu
Pathogenic Bacteroides fragilis strains can emerge from gut-resident commensals. bioRxiv : the preprint server for biology (2024)
Mahmoud M Al-Bassam, Karsten Zengler
Determination of the Chromatin Openness in Bacterial Genomes. Methods in molecular biology (Clifton, N.J.) 2611 (2023)
Mahmoud M Al-Bassam, Karsten Zengler
Determination of the Chromatin Openness in Bacterial Genomes. Methods in molecular biology (Clifton, N.J.) 2611 (2023)
Maxwell L Neal, Deepan Thiruppathy, Karsten Zengler
Genome-scale metabolic modeling of the human gut bacterium Bacteroides fragilis strain 638R. PLoS computational biology 19 (10) (2023)
Oriane Moyne, Mahmoud M Al-Bassam, Chloe Lieng, Deepan Thiruppathy, Grant J Norton, Manish Kumar, Eli Haddad, Livia S Zaramela, Karsten Zengler
Guild and Niche Determination Enable Targeted Alteration of the Microbiome. bioRxiv : the preprint server for biology (2023)
Diego Tec-Campos, Camila Posadas, Juan D Tibocha-Bonilla, Deepan Thiruppathy, Nathan Glonek, Cristal Zuñiga, Alejandro Zepeda, Karsten Zengler
The genome-scale metabolic model for the purple non-sulfur bacterium Rhodopseudomonas palustris Bis A53 accurately predicts phenotypes under chemoheterotrophic, chemoautotrophic, photoheterotrophic, and photoautotrophic growth conditions. PLoS computational biology 19 (8) (2023)
Joanna Coker, Kateryna Zhalnina, Clarisse Marotz, Deepan Thiruppathy, Megan Tjuanta, Gavin D'Elia, Rodas Hailu, Talon Mahosky, Meagan Rowan, Trent R Northen, Karsten Zengler
A Reproducible and Tunable Synthetic Soil Microbial Community Provides New Insights into Microbial Ecology. mSystems (2022)
Livia S Zaramela, Megan Tjuanta, Oriane Moyne, Maxwell Neal, Karsten Zengler
synDNA-a Synthetic DNA Spike-in Method for Absolute Quantification of Shotgun Metagenomic Sequencing. mSystems (2022)
Joanna K Coker, Oriane Moyne, Dmitry A Rodionov, Karsten Zengler
Carbohydrates great and small, from dietary fiber to sialic acids: How glycans influence the gut microbiome and affect human health. Gut microbes 13 (1) (2022)
Cameron Martino, Livia S Zaramela, Bei Gao, Mallory Embree, Janna Tarasova, Seth J Parker, Yanhan Wang, Huikuan Chu, Peng Chen, Kuei-Chuan Lee, Daniela Domingos Galzerani, Jivani M Gengatharan, Asama Lekbua, Maxwell Neal, Rob Knight, Hidekazu Tsukamoto, Christian M Metallo, Bernd Schnabl, Karsten Zengler
Acetate reprograms gut microbiota during alcohol consumption. Nature communications 13 (1) (2022)
Gabriela Canto-Encalada, Diego Tec-Campos, Juan D Tibocha-Bonilla, Karsten Zengler, Alejandro Zepeda, Cristal Zuñiga
Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds. PLoS computational biology 18 (2) (2022)
Juan D Tibocha-Bonilla, Cristal Zuñiga, Asama Lekbua, Colton Lloyd, Kevin Rychel, Katie Short, Karsten Zengler
Predicting stress response and improved protein overproduction in Bacillus subtilis. NPJ systems biology and applications 8 (1) (2022)
Juan D Tibocha-Bonilla, Cristal Zuñiga, Asama Lekbua, Colton Lloyd, Kevin Rychel, Katie Short, Karsten Zengler
Predicting stress response and improved protein overproduction in Bacillus subtilis. NPJ systems biology and applications 8 (1) (2022)
Juan D Tibocha-Bonilla, Cristal Zuñiga, Asama Lekbua, Colton Lloyd, Kevin Rychel, Katie Short, Karsten Zengler
Predicting stress response and improved protein overproduction in Bacillus subtilis. NPJ systems biology and applications 8 (1) (2022)
Joanna Coker, Livia S Zaramela, Karsten Zengler
Linking anaerobic gut bacteria and cardiovascular disease. Nature microbiology 7 (1) (2022)
Juan D Tibocha-Bonilla, Cristal Zuñiga, Asama Lekbua, Colton Lloyd, Kevin Rychel, Katie Short, Karsten Zengler
Predicting stress response and improved protein overproduction in Bacillus subtilis. NPJ systems biology and applications 8 (1) (2022)
Clarisse A Marotz, James T Morton, Perris Navarro, Joanna Coker, Pedro Belda-Ferre, Rob Knight, Karsten Zengler
Quantifying Live Microbial Load in Human Saliva Samples over Time Reveals Stable Composition and Dynamic Load. mSystems 6 (1) (2021)
Kunio Kawanishi, Joanna K Coker, Kaare V Grunddal, Chirag Dhar, Jason Hsiao, Karsten Zengler, Nissi Varki, Ajit Varki, Philip L S M Gordts
Dietary Neu5Ac Intervention Protects Against Atherosclerosis Associated With Human-Like Neu5Gc Loss-Brief Report. Arteriosclerosis, thrombosis, and vascular biology 41 (11) (2021)
Prerna Bali, Joanna K Coker, Ivonne Lozano-Pope, Karsten Zengler, Marygorret Obonyo
Microbiome Signatures in a Fast- and Slow-Progressing Gastric Cancer Murine Model and Their Contribution to Gastric Carcinogenesis. Microorganisms 9 (1) (2021)
Anurag Passi, Juan D Tibocha-Bonilla, Manish Kumar, Diego Tec-Campos, Karsten Zengler, Cristal Zuñiga
Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data. Metabolites 12 (1) (2021)
Debashis Sahoo, Livia S Zaramela, Gilberto E Hernandez, Uyen Mai, Sahar Taheri, Dharanidhar Dang, Ashley N Stouch, Rachel M Medal, Alyssa M McCoy, Judy L Aschner, Timothy S Blackwell, Karsten Zengler, Lawrence S Prince
Transcriptional profiling of lung macrophages identifies a predictive signature for inflammatory lung disease in preterm infants. Communications biology 3 (1) (2020)
Cristal Zuñiga, Tingting Li, Michael T Guarnieri, Jackson P Jenkins, Chien-Ting Li, Kerem Bingol, Young-Mo Kim, Michael J Betenbaugh, Karsten Zengler
Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth. Nature communications 11 (1) (2020)
Joanne K Liu, Colton Lloyd, Mahmoud M Al-Bassam, Ali Ebrahim, Ji-Nu Kim, Connor A Olson, Alexander Aksenov, Pieter Dorrestein, Karsten Zengler
Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen. PLoS computational biology 15 (3) (2019)
James T Morton, Clarisse A Marotz, Alex Washburne, Justin Silverman, Livia S Zaramela, Anna Edlund, Karsten Zengler, Rob Knight
Establishing microbial composition measurement standards with reference frames. Nature communications 10 (1) (2019)
Manish Kumar, Boyang Ji, Karsten Zengler, Jens B Nielsen
Modelling approaches for studying the microbiome. Nature microbiology 4 (8) (2019)
Cristal Zuñiga, Chien-Ting Li, Geng Yu, Mahmoud M Al-Bassam, Tingting Li, Liqun Jiang, Livia S Zaramela, Michael Guarnieri, Michael J Betenbaugh, Karsten Zengler
Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities. Nature microbiology 4 (12) (2019)
Karsten Zengler, Livia S Zaramela
The social network of microorganisms - how auxotrophies shape complex communities. Nature reviews. Microbiology 16 (6) (2019)
Boryoung Shin, Minjae Kim, Karsten Zengler, Kuk-Jeong Chin, Will A Overholt, Lisa M Gieg, Konstantinos T Konstantinidis, Joel E Kostka
Anaerobic degradation of hexadecane and phenanthrene coupled to sulfate reduction by enriched consortia from northern Gulf of Mexico seafloor sediment. Scientific reports 9 (1) (2019)
Livia S Zaramela, Cameron Martino, Frederico Alisson-Silva, Steven D Rees, Sandra L Diaz, Léa Chuzel, Mehul B Ganatra, Christopher H Taron, Patrick Secrest, Cristal Zuñiga, Jianbo Huang, Dionicio Siegel, Geoffrey Chang, Ajit Varki, Karsten Zengler
Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates. Nature microbiology 4 (12) (2019)
Mahmoud M Al-Bassam, Ji-Nu Kim, Livia S Zaramela, Benjamin P Kellman, Cristal Zuniga, Jacob M Wozniak, David J Gonzalez, Karsten Zengler
Optimization of carbon and energy utilization through differential translational efficiency. Nature communications 9 (1) (2018)
Philip Strandwitz, Ki Hyun Kim, Darya Terekhova, Joanne K Liu, Anukriti Sharma, Jennifer Levering, Daniel McDonald, David Dietrich, Timothy R Ramadhar, Asama Lekbua, Nader Mroue, Conor Liston, Eric J Stewart, Marc J Dubin, Karsten Zengler, Rob Knight, Jack A Gilbert, Jon Clardy, Kim Lewis
GABA-modulating bacteria of the human gut microbiota. Nature microbiology 4 (3) (2018)
Cristal Zuñiga, Jennifer Levering, Maciek R Antoniewicz, Michael T Guarnieri, Michael J Betenbaugh, Karsten Zengler
Predicting Dynamic Metabolic Demands in the Photosynthetic Eukaryote Chlorella vulgaris. Plant physiology 176 (1) (2017)
Scott D Wankel, Wiebke Ziebis, Carolyn Buchwald, Chawalit Charoenpong, Dirk de Beer, Jane Dentinger, Zhenjiang Xu, Karsten Zengler
Evidence for fungal and chemodenitrification based N2O flux from nitrogen impacted coastal sediments. Nature communications 8 (2017)

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Publication Activity (10 Years)

Top Topics

Top Venues

Karsten Zengler