Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates

מאת Heckmann, David, Zielinski, Daniel C., Palsson, Bernhard O.
הוצא לאור ב Nat Commun (2018)

BLISTER Regulates Polycomb-Target Genes, Represses Stress-Regulated Genes and Promotes Stress Responses in Arabidopsis thaliana

מאת Kleinmanns, Julia A., Schatlowski, Nicole, Heckmann, David, Schubert, Daniel
הוצא לאור ב Front Plant Sci (2017)

A biochemically-interpretable machine learning classifier for microbial GWAS

מאת Kavvas, Erol S., Yang, Laurence, Monk, Jonathan M., Heckmann, David, Palsson, Bernhard O.
הוצא לאור ב Nat Commun (2020)

Independent component analysis recovers consistent regulatory signals from disparate datasets

מאת Sastry, Anand V., Hu, Alyssa, Heckmann, David, Poudel, Saugat, Kavvas, Erol, Palsson, Bernhard O.
הוצא לאור ב PLoS Comput Biol (2021)

The role of photorespiration during the evolution of C(4) photosynthesis in the genus Flaveria

מאת Mallmann, Julia, Heckmann, David, Bräutigam, Andrea, Lercher, Martin J, Weber, Andreas PM, Westhoff, Peter, Gowik, Udo
יצא לאור 2014

Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes

מאת Mih, Nathan, Monk, Jonathan M., Fang, Xin, Catoiu, Edward, Heckmann, David, Yang, Laurence, Palsson, Bernhard O.
הוצא לאור ב BMC Bioinformatics (2020)

Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity

מאת Phaneuf, Patrick V., Yurkovich, James T., Heckmann, David, Wu, Muyao, Sandberg, Troy E., King, Zachary A., Tan, Justin, Palsson, Bernhard O., Feist, Adam M.
הוצא לאור ב BMC Genomics (2020)

Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

מאת Heckmann, David, Lloyd, Colton J., Mih, Nathan, Ha, Yuanchi, Zielinski, Daniel C., Haiman, Zachary B., Desouki, Abdelmoneim Amer, Lercher, Martin J., Palsson, Bernhard O.
הוצא לאור ב Nat Commun (2018)

Kinetic profiling of metabolic specialists demonstrates stability and consistency of in vivo enzyme turnover numbers

מאת Heckmann, David, Campeau, Anaamika, Lloyd, Colton J., Phaneuf, Patrick V., Hefner, Ying, Carrillo-Terrazas, Marvic, Feist, Adam M., Gonzalez, David J., Palsson, Bernhard O.
הוצא לאור ב Proc Natl Acad Sci U S A (2020)

Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance

מאת 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.
הוצא לאור ב Nat Commun (2018)

Cellular responses to reactive oxygen species are predicted from molecular mechanisms

מאת Yang, Laurence, Mih, Nathan, Anand, Amitesh, Park, Joon Ho, Tan, Justin, Yurkovich, James T., Monk, Jonathan M., Lloyd, Colton J., Sandberg, Troy E., Seo, Sang Woo, Kim, Donghyuk, Sastry, Anand V., Phaneuf, Patrick, Gao, Ye, Broddrick, Jared T., Chen, Ke, Heckmann, David, Szubin, Richard, Hefner, Ying, Feist, Adam M., Palsson, Bernhard O.
הוצא לאור ב Proc Natl Acad Sci U S A (2019)