Reply to: Erroneous predictions of auxotrophies by CarveMe
- Daniel Machado, Daniel Machado, Daniel Machado, Kiran R Patil
- Nat Ecol Evol, 10.1038/s41559-022-01939-0
Ecological modelling approaches for predicting emergent properties in microbial communities
- Naomi Iris van den Berg, Daniel Machado, Sophia Santos, …, William Harcombe, Sara Mitri, Kiran R Patil
- Nat Ecol Evol, 10.1038/s41559-022-01746-7
Metabolic memory underlying minimal residual disease in breast cancer
- Ksenija Radic Shechter, Eleni Kafkia, Katharina Zirngibl, …, Britta BrĂŒgger, Kiran R Patil, Martin Jechlinger
- Mol Syst Biol, 10.15252/msb.202010141
Co-evolution of strain design methods based on flux balance and elementary mode analysis
- Daniel Machado, Markus J HerrgÄrd
- Metab Eng, 10.1016/j.meteno.2015.04.001
Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community
- Sonja Blasche, Yongkyu Kim, Ruben A T Mars, …, Rute Neves, Uwe Sauer, Kiran Raosaheb Patil
- Nat Microbiol, 10.1038/s41564-020-00816-5
Polarization of microbial communities between competitive and cooperative metabolism
- Daniel Machado, Oleksandr M Maistrenko, Sergej Andrejev, …, Peer Bork, Kaustubh R Patil, Kiran R Patil
- Nat Ecol Evol, 10.1038/s41559-020-01353-4
MEMOTE for standardized genome-scale metabolic model testing
- Christian Lieven, Moritz E Beber, Brett G Olivier, …, Qianqian Yuan, Maksim Zakhartsev, Cheng Zhang
- Nat Biotechnol, 10.1038/s41587-020-0446-y
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
- Michael P Menden, Dennis Wang, Mike J Mason, …, Justin Guinney, Jonathan R Dry, Julio Saez-Rodriguez
- Nat Commun, 10.1038/s41467-019-09799-2
Linking genetic, metabolic, and phenotypic diversity among Saccharomyces cerevisiae strains using multi-omics associations
- Kang Kang, Basti Bergdahl, Daniel Machado, …, Markus J HerrgĂ„rd, Jochen Förster, Gianni Panagiotou
- Gigascience, 10.1093/gigascience/giz015
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities
- Daniel Machado, Sergej Andrejev, Melanie Tramontano, Kiran Raosaheb Patil
- Nucleic Acids Res, 10.1093/nar/gky537
Post-translational regulation of metabolism in fumarate hydratase deficient cancer cells
- Emanuel Gonçalves, Marco Sciacovelli, Ana S H Costa, …, Daniel Machado, Christian Frezza, Julio Saez-Rodriguez
- Metab Eng, 10.1016/j.ymben.2017.11.011
A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines
- Mehmet Gönen, Barbara A Weir, Glenn S Cowley, …, Gustavo Stolovitzky, William C Hahn, Adam A Margolin
- Cell Syst, 10.1016/j.cels.2017.09.004
Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes
- Jonathan M Monk, Anna Koza, Miguel A Campodonico, …, Bernhard O Palsson, Markus J HerrgĂ„rd, Adam M Feist
- Cell Syst, 10.1016/j.cels.2016.08.013
Current state and challenges for dynamic metabolic modeling
- Eleni Vasilakou, Daniel Machado, Axel Theorell, …, Katharina Nöh, Marco Oldiges, S Aljoscha Wahl
- Curr Opin Microbiol, 10.1016/j.mib.2016.07.008
Metabolomic and transcriptomic stress response of Escherichia coli
- Szymon Jozefczuk, Sebastian Klie, Gareth Catchpole, …, Dirk Steinhauser, Joachim Selbig, Lothar Willmitzer
- Mol Syst Biol, 10.1038/msb.2010.18