Avlant Nilsson

About me
Publications
Public outreach and news

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; Klingmueller U; Teusink B; Nielsen J
Article: SCIENCE SIGNALING. 2020;13(624):eaaz1482
An atlas of human metabolism
Robinson JL; Kocabas 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; Uhlen M; Nielsen J
Article: NATURE COMMUNICATIONS. 2019;10(1):5072
Complex I is bypassed during high intensity exercise
Nilsson A; Bjornson 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; Drager A; Mih N; Gatto F; Nilsson A; Gonzalez GAP; Aurich MK; Prlic 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
Sanchez 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(W1):W175-W181
BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data
Garcia-Albornoz M; Thankaswamy-Kosalai S; Nilsson A; Varemo 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
Preprint: BIORXIV. 2021
Artificial neural networks enable genome-scale simulations of intracellular signaling
Nilsson A; Peters JM; Bryson B; Lauffenburger DA
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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