Deep learning allows genome-scale prediction of Michaelis constants from structural features
Kroll, Alexander, Engqvist, Martin K M, Heckmann, David, Lercher, Martin J
Published in PLoS biology (19.10.2021)
Published in PLoS biology (19.10.2021)
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Journal Article
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models
Heckmann, David, Lloyd, Colton J., Mih, Nathan, Ha, Yuanchi, Zielinski, Daniel C., Haiman, Zachary B., Desouki, Abdelmoneim Amer, Lercher, Martin J., Palsson, Bernhard O.
Published in Nature communications (07.12.2018)
Published in Nature communications (07.12.2018)
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Journal Article
A biochemically-interpretable machine learning classifier for microbial GWAS
Kavvas, Erol S., Yang, Laurence, Monk, Jonathan M., Heckmann, David, Palsson, Bernhard O.
Published in Nature communications (22.05.2020)
Published in Nature communications (22.05.2020)
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Journal Article
Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance
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.
Published in Nature communications (17.10.2018)
Published in Nature communications (17.10.2018)
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Journal Article
Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers
Heckmann, David, Campeau, Anaamika, Lloyd, Colton J., Phaneuf, Patrick V., Hefner, Ying, Carrillo-Terrazas, Marvic, Feist, Adam M., Gonzalez, David J., Palsson, Bernhard O.
Published in Proceedings of the National Academy of Sciences - PNAS (15.09.2020)
Published in Proceedings of the National Academy of Sciences - PNAS (15.09.2020)
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Journal Article
Modeling photosynthetic resource allocation connects physiology with evolutionary environments
Sundermann, Esther M., Lercher, Martin J., Heckmann, David
Published in Scientific reports (05.08.2021)
Published in Scientific reports (05.08.2021)
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Journal Article
A generic avian physiologically-based kinetic (PBK) model and its application in three bird species
Baier, Vanessa, Paini, Alicia, Schaller, Stephan, Scanes, Colin G., Bone, Audrey J., Ebeling, Markus, Preuss, Thomas G., Witt, Johannes, Heckmann, David
Published in Environment international (01.11.2022)
Published in Environment international (01.11.2022)
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Journal Article
The role of photorespiration during the evolution of C4 photosynthesis in the genus Flaveria
Mallmann, Julia, Heckmann, David, Bräutigam, Andrea, Lercher, Martin J, Weber, Andreas P M, Westhoff, Peter, Gowik, Udo
Published in eLife (16.06.2014)
Published in eLife (16.06.2014)
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Journal Article
Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates
Heckmann, David, Zielinski, Daniel C., Palsson, Bernhard O.
Published in Nature communications (10.12.2018)
Published in Nature communications (10.12.2018)
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Journal Article
Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity
Phaneuf, Patrick V, Yurkovich, James T, Heckmann, David, Wu, Muyao, Sandberg, Troy E, King, Zachary A, Tan, Justin, Palsson, Bernhard O, Feist, Adam M
Published in BMC genomics (25.07.2020)
Published in BMC genomics (25.07.2020)
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Journal Article
Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes
Mih, Nathan, Monk, Jonathan M, Fang, Xin, Catoiu, Edward, Heckmann, David, Yang, Laurence, Palsson, Bernhard O
Published in BMC bioinformatics (29.04.2020)
Published in BMC bioinformatics (29.04.2020)
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Journal Article
Quantitative Morphometric, Physiological, and Metabolic Characteristics of Chickens and Mallards for Physiologically Based Kinetic Model Development
Scanes, Colin G, Witt, Johannes, Ebeling, Markus, Schaller, Stephan, Baier, Vanessa, Bone, Audrey J, Preuss, Thomas G, Heckmann, David
Published in Frontiers in physiology (06.04.2022)
Published in Frontiers in physiology (06.04.2022)
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Journal Article
Quantitative Comparison of Avian and Mammalian Physiologies for Parameterization of Physiologically Based Kinetic Models
Scanes, Colin G, Witt, Johannes, Ebeling, Markus, Schaller, Stephan, Baier, Vanessa, Bone, Audrey J, Preuss, Thomas G, Heckmann, David
Published in Frontiers in physiology (05.04.2022)
Published in Frontiers in physiology (05.04.2022)
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Journal Article