Zelezniak, Aleksej

Metabolic dependencies drive species co-occurrence in diverse microbial communities

Zelezniak, A., Andrejev, S., Ponomarova, O., Mende, D. R., Bork, P., & Patil, K. R. (2015) · Proceedings of the National Academy of Sciences

Microbial Metabolic Engineering and BioproductionMicrobial Community Ecology and Physiology

Cited by 930

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

Messner, C. B., Demichev, V., Wendisch, D., Michalick, L., White, M., Freiwald, A., Textoris-Taube, K., Vernardis, S. I., Egger, A.-S., Kreidl, M., et al. (2020) · Cell Systems

Advanced Proteomics Techniques and ApplicationsCOVID-19 Clinical Research Studies

Cited by 561

Expanding functional protein sequence spaces using generative adversarial networks

Repecka, D., Jauniskis, V., Karpus, L., Rembeza, E., Rokaitis, I., Zrimec, J., Poviloniene, S., Laurynenas, A., Viknander, S., Abuajwa, W., et al. (2021) · Nature Machine Intelligence

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 388

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies

Tramontano, M., Andrejev, S., Pruteanu, M., Klünemann, M., Kuhn, M., Galardini, M., Jouhten, P., Zelezniak, A., Zeller, G., Bork, P., et al. (2018) · Nature Microbiology

Gut microbiota and healthMicrobial Metabolic Engineering and Bioproduction

Cited by 295

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

Demichev, V., Tober-Lau, P., Lemke, O., Nazarenko, T., Thibeault, C., Whitwell, H., Röhl, A., Freiwald, A., Szyrwiel, L., Ludwig, D., et al. (2021) · Cell Systems

COVID-19 Clinical Research StudiesSARS-CoV-2 and COVID-19 Research

Cited by 200

Functional Metabolomics Describes the Yeast Biosynthetic Regulome

Mülleder, M., Calvani, E., Alam, M. T., Wang, R. K., Eckerstorfer, F., Zelezniak, A., & Ralser, M. (2016) · Cell

Fungal and yeast genetics researchMicrobial Metabolic Engineering and Bioproduction

Cited by 178

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

Zrimec, J., Börlin, C. S., Buric, F., Muhammad, A. S., Chen, R., Siewers, V., Verendel, V., Nielsen, J., Töpel, M., & Zelezniak, A. (2020) · Nature Communications

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 174

Gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure

Zrimec, J., Buric, F., Muhammad, A. S., Chen, R., Verendel, V., Töpel, M., & Zelezniak, A. (2019) · Nature Communications

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 173

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

Haas, R., Zelezniak, A., Iacovacci, J., Kamrad, S., Townsend, S., & Ralser, M. (2017) · Current Opinion in Systems Biology

Bioinformatics and Genomic NetworksGene Regulatory Network Analysis

Cited by 131

Computational scoring and experimental evaluation of enzymes generated by neural networks

Johnson, S. R., Fu, X., Viknander, S., Goldin, C., Monaco, S., Zelezniak, A., & Yang, K. K. (2025) · Nature Biotechnology

Protein Structure and DynamicsEnzyme Catalysis and Immobilization

Cited by 99

Precise label-free quantitative proteomes in high-throughput by microLC and data-independent SWATH acquisition

Vowinckel, J., Zelezniak, A., Kibler, A., Bruderer, R., Muelleder, M., Reiter, L., & Ralser, M. (2016) · Scientific Reports

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 81

Bayesian genome scale modelling identifies thermal determinants of yeast metabolism

Li, G., Hu, Y., Zrimec, J., Luo, H., Wang, H., Zelezniak, A., Ji, B., & Nielsen, J. (2021) · Nature Communications

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 57

The Role of Metabolism in Shaping Enzyme Structures Over 400 Million Years of Evolution

Lemke, O., Heineike, B. M., Viknander, S., Cohen, N., Steenwyk, J. L., Spranger, L., Li, F., Agostini, F., Lee, C. T., Aulakh, S. K., et al. (2024) · Nature

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 28

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

Sánchez, B. J., Lahtvee, P., Campbell, K., Kasvandik, S., Yu, R., Domenzain, I., Zelezniak, A., & Nielsen, J. (2021) · PROTEOMICS

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 18

The amino acid sequence determines protein abundance through its conformational stability and reduced synthesis cost

Buric, F., Viknander, S., Fu, X., Lemke, O., Zrimec, J., Szyrwiel, L., Mueleder, M., Ralser, M., & Zelezniak, A. (2023) · Protein Science

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 12