Flux balance analysis with or without molecular crowding fails to predict two thirds of experimentally observed epistasis in yeast

Autor: Deya Alzoubi, Abdelmoneim Amer Desouki, Martin J. Lercher

Publikováno v: Scientific Reports, Vol 9, Iss 1, Pp 1-9 (2019)

Abstract Computational predictions of double gene knockout effects by flux balance analysis (FBA) have been used to characterized genome-wide patterns of epistasis in microorganisms. However, it is unclear how in silico predictions are related to in

Externí odkaz: https://doaj.org/article/c0f1bab04c3e40feba14e3a4d52be1dc

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

Autor: Colton J. Lloyd, Zachary B. Haiman, Daniel C. Zielinski, Martin J. Lercher, Nathan Mih, Abdelmoneim Amer Desouki, David Heckmann, Yuanchi Ha, Bernhard O. Palsson

Publikováno v: Nature Communications, Vol 9, Iss 1, Pp 1-10 (2018)
Heckmann, D, Lloyd, C J, Mih, N, Ha, Y, Zielinski, D C, Haiman, Z B, Desouki, A A, Lercher, M J & Palsson, B O 2018, ' Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models ', Nature Communications, vol. 9, 5252 . https://doi.org/10.1038/s41467-018-07652-6
Nature communications, vol 9, iss 1
Nature Communications

Knowing the catalytic turnover numbers of enzymes is essential for understanding the growth rate, proteome composition, and physiology of organisms, but experimental data on enzyme turnover numbers is sparse and noisy. Here, we demonstrate that machi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6bfa038068e6cf5b7d4f5904e6b70df5
http://link.springer.com/article/10.1038/s41467-018-07652-6

Alleles of a gene differ in pleiotropy, often mediated through currency metabolite production, in E. coli and yeast metabolic simulations

Autor: Deya Alzoubi, Martin J. Lercher, Abdelmoneim Amer Desouki

Publikováno v: Scientific Reports, Vol 8, Iss 1, Pp 1-9 (2018)
Scientific Reports

A major obstacle to the mapping of genotype-phenotype relationships is pleiotropy, the tendency of mutations to affect seemingly unrelated traits. Pleiotropy has major implications for evolution, development, ageing, and disease. Except for disease d

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7f0513d04906ffe2b2e3e8c8fbe02bc9
http://link.springer.com/article/10.1038/s41598-018-35092-1

ORCA: a Benchmark for Data Web Crawlers

Autor: Axel-Cyrille Ngonga Ngomo, Michael Röder, Geraldo de Souza, Abdelmoneim Amer Desouki, Denis Kuchelev

Publikováno v: ICSC

The number of RDF knowledge graphs available on the Web grows constantly. Gathering these graphs at large scale for downstream applications hence requires the use of crawlers. Although Data Web crawlers exist, and general Web crawlers could be adapte

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f52760fd01feccf16149de0f0a07e280

CycleFreeFlux: efficient removal of thermodynamically infeasible loops from flux distributions

Autor: Martin J. Lercher, Florian Jarre, Gabriel Gelius-Dietrich, Abdelmoneim Amer Desouki

Publikováno v: Bioinformatics. 31:2159-2165

Motivation: Constraint-based metabolic modeling methods such as Flux Balance Analysis (FBA) are routinely used to predict metabolic phenotypes, e.g. growth rates, ATP yield or the fitness of gene knockouts. One frequent difficulty of constraint-based

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::68fa1572573d388e9420ddf269e9e980
https://doi.org/10.1093/bioinformatics/btv096