Avlant Nilsson

About me
Publications
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About me

Assistant Professor, Department of Cell and Molecular Biology (CMB),
Karolinska Institutet, Sweden 2023-PRES.
Postdoc, Massachusetts Institute of Technology (MIT), Cambridge, US 2019 -
2023.
PhD, Department of Biology and Biological Engineering, Chalmers University of
Technology, Sweden 2014 – 2019.
M.S. Engineering Physics, Chalmers University of Technology, Sweden 2012 –
2014.
B.S. Biological Engineering, Chalmers University of Technology, Sweden 2009
– 2012.

Articles

Article: ISCIENCE. 2024;27(4):109509

Inference of drug off-target effects on cellular signaling using interactome-based deep learning.

Meimetis N; Lauffenburger DA; Nilsson A
Article: NPJ SYSTEMS BIOLOGY AND APPLICATIONS. 2024;10(1):13

AutoTransOP: translating omics signatures without orthologue requirements using deep learning.

Meimetis N; Pullen KM; Zhu DY; Nilsson A; Hoang TN; Magliacane S; Lauffenburger DA
Article: CELL REPORTS. 2023;42(4):112402

Antibodies against the Ebola virus soluble glycoprotein are associated with long-term vaccine-mediated protection of non-human primates.

Gunn BM; McNamara RP; Wood L; Taylor S; Devadhasan A; Guo W; Das J; Nilsson A; Shurtleff A; Dubey S; Eichberg M; Suscovich TJ; Saphire EO; Lauffenburger D; Coller B-A; Simon JK; Alter G
Article: NATURE COMMUNICATIONS. 2022;13(1):3069

Artificial neural networks enable genome-scale simulations of intracellular signaling.

Nilsson A; Peters JM; Meimetis N; Bryson B; Lauffenburger DA
Article: FRONTIERS IN ONCOLOGY. 2022;12:878920

Cancer-Associated Fibroblasts and Squamous Epithelial Cells Constitute a Unique Microenvironment in a Mouse Model of Inflammation-Induced Colon Cancer.

Vega PN; Nilsson A; Kumar MP; Niitsu H; Simmons AJ; Ro J; Wang J; Chen Z; Joughin BA; Li W; McKinley ET; Liu Q; Roland JT; Washington MK; Coffey RJ; Lauffenburger DA; Lau KS
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2020;117(19):10294-10304

Quantitative analysis of amino acid metabolism in liver cancer links glutamate excretion to nucleotide synthesis.

Nilsson A; Haanstra JR; Engqvist M; Gerding A; Bakker BM; Klingmüller U; Teusink B; Nielsen J
Article: SCIENCE SIGNALING. 2020;13(624):eaaz1482

An atlas of human metabolism.

Robinson JL; Kocabaş P; Wang H; Cholley P-E; Cook D; Nilsson A; Anton M; Ferreira R; Domenzain I; Billa V; Limeta A; Hedin A; Gustafsson J; Kerkhoven EJ; Svensson LT; Palsson BO; Mardinoglu A; Hansson L; Uhlén M; Nielsen J
Article: NATURE COMMUNICATIONS. 2019;10(1):5072

Complex I is bypassed during high intensity exercise.

Nilsson A; Björnson E; Flockhart M; Larsen FJ; Nielsen J
Article: NATURE BIOTECHNOLOGY. 2018;36(3):272-281

Recon3D enables a three-dimensional view of gene variation in human metabolism.

Brunk E; Sahoo S; Zielinski DC; Altunkaya A; Dräger A; Mih N; Gatto F; Nilsson A; Preciat Gonzalez GA; Aurich MK; Prlić A; Sastry A; Danielsdottir AD; Heinken A; Noronha A; Rose PW; Burley SK; Fleming RMT; Nielsen J; Thiele I; Palsson BO
Article: CELL SYSTEMS. 2017;5(6):538-541

Metabolic Models of Protein Allocation Call for the Kinetome.

Nilsson A; Nielsen J; Palsson BO
Article: METABOLIC ENGINEERING. 2017;43(Pt B):103-112

Genome scale metabolic modeling of cancer.

Nilsson A; Nielsen J
Article: MOLECULAR SYSTEMS BIOLOGY. 2017;13(8):935

Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints.

Sánchez BJ; Zhang C; Nilsson A; Lahtvee P-J; Kerkhoven EJ; Nielsen J
Article: NPJ SYSTEMS BIOLOGY AND APPLICATIONS. 2017;3:3

Predicting growth of the healthy infant using a genome scale metabolic model.

Nilsson A; Mardinoglu A; Nielsen J
Article: SCIENTIFIC REPORTS. 2016;6:22264

Metabolic Trade-offs in Yeast are Caused by F1F0-ATP synthase.

Nilsson A; Nielsen J
Article: NUCLEIC ACIDS RESEARCH. 2014;42(Web Server issue):W175-W181

BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data.

Garcia-Albornoz M; Thankaswamy-Kosalai S; Nilsson A; Väremo L; Nookaew I; Nielsen J
Article: SOURCE CODE FOR BIOLOGY AND MEDICINE. 2014;9:17

A dedicated database system for handling multi-level data in systems biology.

Pornputtapong N; Wanichthanarak K; Nilsson A; Nookaew I; Nielsen J

All other publications

Preprint: BIORXIV. 2023

Inference of drug off-target effects on cellular signaling using Interactome-Based Deep Learning

Meimetis N; Lauffenburger D; Nilsson A
Preprint: BIORXIV. 2023

Autoencoder Model for Translating Omics Signatures

Meimetis N; Pullen K; Zhu D; Nilsson A; Hoang TN; Magliacane S; Lauffenburger D
Editorial comment: TRENDS IN BIOCHEMICAL SCIENCES. 2018;43(6):395-397

Metabolite Depletion Affects Flux Profiling of Cell Lines.

Nilsson A; Haanstra JR; Teusink B; Nielsen J

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