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; 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 (NAR). 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. 2024;BIORXIV
Library-based single-cell analysis of CAR signaling reveals drivers of in vivo persistence.
Perez CR; Garmilla A; Nilsson A; Baghdassarian HM; Gordon KS; Lima LG; Smith BE; Maus MV; Lauffenburger DA; Birnbaum ME
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

Grants

DDLS Fellow in Precision Medicine & Diagnostics
Knut and Alice Wallenberg Foundation
1 May 2024 - 30 April 2029
Data driven modeling of the tumor microenvironment
The Swedish Cancer Society
1 January 2024 - 31 December 2026
Deep learning models of cancer mechanisms
The Swedish Cancer Society
1 July 2023 - 30 June 2029
Deep learning the Immune System
Vetenskapsrådet
1 January 2020 - 31 December 2022

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