Aleksej Zelezniak

Associate Professor at Systems and Synthetic Biology

Source: chalmers.se
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Showing 27 publications

2023

Cell-cell metabolite exchange creates a pro-survival metabolic environment that extends lifespan

Clara Correia-Melo, Stephan Kamrad, Roland Tengölics et al
Cell. Vol. 186 (1), p. 63-79.e21
Journal article
2022

Learning deep representations of enzyme thermal adaptation

Gang Li, Filip Buric, Jan Zrimec et al
Protein Science. Vol. 31 (12)
Journal article
2022

Enhanced metabolism and negative regulation of ER stress support higher erythropoietin production in HEK293 cells

Rasool Saghaleyni, Magdalena Malm, Noah Moruzzi et al
Cell Reports. Vol. 39 (11)
Journal article
2022

Toward learning the principles of plant gene regulation

Jan Zrimec, Aleksej Zelezniak, Kristina Gruden
Trends in Plant Science. Vol. In Press
Other text in scientific journal
2022

Data mining of Saccharomyces cerevisiae mutants engineered for increased tolerance towards inhibitors in lignocellulosic hydrolysates

Elena Cámara, Lisbeth Olsson, Jan Zrimec et al
Biotechnology Advances. Vol. 57
Review article
2022

Controlling gene expression with deep generative design of regulatory DNA

Jan Zrimec, Xiaozhi Fu, Muhammad Azam Sheikh et al
Nature Communications. Vol. 13 (1), p. 5099-
Journal article
2021

Performance of Regression Models as a Function of Experiment Noise

Gang Li, Jan Zrimec, Boyang Ji et al
Bioinformatics and Biology Insights. Vol. 15
Journal article
2021

Plastic-Degrading Potential across the Global Microbiome Correlates with Recent Pollution Trends

Jan Zrimec, Mariia Kokina, Sara Jonasson et al
mBio. Vol. 12 (5)
Journal article
2021

Potential for improved retention rate by personalized antiseizure medication selection: A register-based analysis

Samuel Håkansson, Markus Karlander, David Larsson et al
Epilepsia. Vol. 62 (9), p. 2123-2132
Journal article
2021

metaGEM: reconstruction of genome scale metabolic models directly from metagenomes

Francisco Zorrilla, Filip Buric, K. R. Patil et al
Nucleic Acids Research. Vol. 49 (21)
Journal article
2021

Benchmarking accuracy and precision of intensity-based absolute quantification of protein abundances in Saccharomyces cerevisiae

Benjamín José Sánchez, Petri-Jaan Lahtvee, Kate Campbell et al
Proteomics. Vol. 21 (6)
Journal article
2021

A time-resolved proteomic and prognostic map of COVID-19

Vadim Demichev, Pinkus Tober-Lau, Oliver Lemke et al
Cell Systems. Vol. 12 (8), p. 780-794.e7
Journal article
2021

Learning the Regulatory Code of Gene Expression

Jan Zrimec, Filip Buric, Mariia Kokina et al
Frontiers in Molecular Biosciences. Vol. 8
Review article
2021

Bayesian genome scale modelling identifies thermal determinants of yeast metabolism

Gang Li, Yating Hu, Jan Zrimec et al
Nature Communications. Vol. 12 (1)
Journal article
2021

Ultra-fast proteomics with Scanning SWATH

Christoph B. Messner, Vadim Demichev, Nic Bloomfield et al
Nature Biotechnology. Vol. 39 (7), p. 846-854
Journal article
2021

Expanding functional protein sequence spaces using generative adversarial networks

Donatas Repecka, Vykintas Jauniskis, Laurynas Karpus et al
Nature Machine Intelligence. Vol. 3 (4), p. 324-333
Journal article
2021

Optimizing epilepsy treatment: big data from population-wide registers suggest room for improvement in drug selection

Samuel Hakansson, Markus Karlander, David Larsson et al
Epilepsia. Vol. 62, p. 168-168
Other conference contribution
2020

Parallel Factor Analysis Enables Quantification and Identification of Highly Convolved Data-Independent-Acquired Protein Spectra

Filip Buric, Jan Zrimec, Aleksej Zelezniak
Patterns. Vol. 1 (9)
Journal article
2020

Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure

Jan Zrimec, Christoph Sebastian Börlin, Filip Buric et al
Nature Communications. Vol. 11 (1)
Journal article
2020

Ultra-High-Throughput Clinical Proteomics Reveals Classifiers of COVID-19 Infection

Christoph B. Messner, Vadim Demichev, Daniel Wendisch et al
Cell Systems. Vol. 11 (1), p. 11-24.E4
Journal article
2019

Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity

Toni I. Gossmann, Achchuthan Shanmugasundram, Stefan Börno et al
Current Biology. Vol. 29 (10), p. 1712-1720.e7
Journal article
2018

Cost-effective generation of precise label-free quantitative proteomes in high-throughput by microLC and data-independent acquisition

Jakob Vowinckel, Aleksej Zelezniak, Roland Bruderer et al
Scientific Reports. Vol. 8 (1)
Journal article
2018

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies

Melanie Tramontano, Sergej Andrejev, Mihaela Pruteanu et al
Nature Microbiology. Vol. 3 (4), p. 514-522
Journal article
2018

Biochemical principles enabling metabolic cooperativity and phenotypic heterogeneity at the single cell level

Kate Campbell, Lucia Herrera-Dominguez, Clara Correia-Melo et al
Current Opinion in Systems Biology. Vol. 8, p. 97-108
Review article
2018

Machine Learning Predicts the Yeast Metabolome from the Quantitative Proteome of Kinase Knockouts

Aleksej Zelezniak, Jakob Vowinckel, Floriana Capuano et al
Cell Systems. Vol. 7 (3), p. 269-283
Journal article
2017

Designing and interpreting 'multi-omic' experiments that may change our understanding of biology

Robert Haas, Aleksej Zelezniak, Jacopo Iacovacci et al
Current Opinion in Systems Biology. Vol. 6, p. 37-45
Review article
2017

The self-inhibitory nature of metabolic networks and its alleviation through compartmentalization

M. T. Alam, V. Olin-Sandoval, A. Stincone et al
Nature Communications. Vol. 8, p. Article no 16018-
Journal article

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