Avlant Nilsson

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Primary: Shown in the list of current labels.

Year 2026

PubMed DOI Crossref
Biologically informed neural network models are robust to spurious interactions via self-pruning.
Nordenstorm O, Baghdassarian H, Xu X, Lauffenburger DA, Nilsson A
Bioinformatics 42 (8) - [2026-08-03; online 2026-07-26]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
Zero-shot prediction of drug responses using biologically informed neural networks trained on phosphoproteomic timeseries.
Antonopoulos K, Nordenstorm O, Nilsson A
PLoS Comput Biol 22 (3) e1014100 [2026-03-00; online 2026-03-18]
Avlant Nilsson DDLS Fellow

Year 2025

PubMed DOI Crossref
Library-based single-cell analysis of CAR signaling reveals drivers of in vivo persistence.
Perez CR, Garmilla A, Nilsson A, ..., Lauffenburger DA, Birnbaum ME
Cell Syst 16 (5) 101260 [2025-05-21; online 2025-04-10]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
Towards an interpretable deep learning model of cancer.
Nilsson A, Meimetis N, Lauffenburger DA
NPJ Precis Oncol 9 (1) 46 [2025-02-14; online 2025-02-14]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
Protocol to infer off-target effects of drugs on cellular signaling using interactome-based deep learning.
Meimetis N, Lauffenburger DA, Nilsson A
STAR Protoc 6 (1) 103573 [2025-01-16; online 2025-01-16]
Avlant Nilsson DDLS Fellow

Year 2024

PubMed DOI Crossref
Author Correction: AutoTransOP: translating omics signatures without orthologue requirements using deep learning.
Meimetis N, Pullen KM, Zhu DY, ..., Magliacane S, Lauffenburger DA
NPJ Syst Biol Appl 10 (1) 148 [2024-12-13; online 2024-12-13]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
Inference of drug off-target effects on cellular signaling using interactome-based deep learning.
Meimetis N, Lauffenburger DA, Nilsson A
iScience 27 (4) 109509 [2024-04-19; online 2024-03-14]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
AutoTransOP: translating omics signatures without orthologue requirements using deep learning.
Meimetis N, Pullen KM, Zhu DY, ..., Magliacane S, Lauffenburger DA
NPJ Syst Biol Appl 10 (1) 13 [2024-01-29; online 2024-01-29]
Avlant Nilsson DDLS Fellow

Year 2023

DOI Crossref
Autoencoder Model for Translating Omics Signatures
Meimetis N, Pullen KM, Zhu DY, ..., Magliacane S, Lauffenburger DA
- - (-) - [2023-06-11; online 2023-06-11]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
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, ..., Simon JK, Alter G
Cell Reports 42 (4) 112402 [2023-04-25; online 2023-04-15]
Avlant Nilsson DDLS Fellow

Year 2022

PubMed DOI Crossref
Artificial neural networks enable genome-scale simulations of intracellular signaling.
Nilsson A, Peters JM, Meimetis N, Bryson B, Lauffenburger DA
Nat Commun 13 (1) 3069 [2022-06-02; online 2022-06-02]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
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, ..., Lauffenburger DA, Lau KS
Front Oncol 12 (-) 878920 [2022-05-04; online 2022-05-04]
Avlant Nilsson DDLS Fellow

Year 2020

PubMed DOI Crossref
Quantitative analysis of amino acid metabolism in liver cancer links glutamate excretion to nucleotide synthesis.
Nilsson A, Haanstra JR, Engqvist M, ..., Teusink B, Nielsen J
Proc. Natl. Acad. Sci. U.S.A. 117 (19) 10294-10304 [2020-05-12; online 2020-04-27]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
An atlas of human metabolism.
Robinson JL, Kocabaş P, Wang H, ..., Uhlén M, Nielsen J
Sci Signal 13 (624) eaaz1482 [2020-03-24; online 2020-03-24]
Adil Mardinoglu Avlant Nilsson SciLifeLab Fellow

Year 2019

PubMed DOI Crossref
Complex I is bypassed during high intensity exercise.
Nilsson A, Björnson E, Flockhart M, Larsen FJ, Nielsen J
Nat Commun 10 (1) 5072 [2019-11-07; online 2019-11-07]
Avlant Nilsson DDLS Fellow

Year 2018

PubMed DOI Crossref
Metabolite Depletion Affects Flux Profiling of Cell Lines.
Nilsson A, Haanstra JR, Teusink B, Nielsen J
Trends Biochem. Sci. 43 (6) 395-397 [2018-06-00; online 2018-04-12]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
Recon3D enables a three-dimensional view of gene variation in human metabolism.
Brunk E, Sahoo S, Zielinski DC, ..., Thiele I, Palsson BO
Nat. Biotechnol. 36 (3) 272-281 [2018-03-00; online 2018-02-19]
Avlant Nilsson DDLS Fellow

Year 2017

PubMed DOI Crossref
Metabolic Models of Protein Allocation Call for the Kinetome.
Nilsson A, Nielsen J, Palsson BO
Cell Systems 5 (6) 538-541 [2017-12-27; online 2017-12-29]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
Genome scale metabolic modeling of cancer.
Nilsson A, Nielsen J
Metab. Eng. 43 (Pt B) 103-112 [2017-09-00; online 2016-11-04]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints.
Sánchez BJ, Zhang C, Nilsson A, ..., Kerkhoven EJ, Nielsen J
Mol Syst Biol 13 (8) 935 [2017-08-03; online 2017-08-03]
Affiliated researcher Avlant Nilsson
PubMed DOI Crossref
Predicting growth of the healthy infant using a genome scale metabolic model.
Nilsson A, Mardinoglu A, Nielsen J
NPJ Syst Biol Appl 3 (1) 3 [2017-01-31; online 2017-01-31]
Adil Mardinoglu Avlant Nilsson SciLifeLab Fellow

Year 2016

PubMed DOI Crossref
Metabolic Trade-offs in Yeast are Caused by F1F0-ATP synthase.
Nilsson A, Nielsen J
Sci Rep 6 (-) 22264 [2016-03-01; online 2016-03-01]
Avlant Nilsson DDLS Fellow

Year 2014

PubMed DOI Crossref
A dedicated database system for handling multi-level data in systems biology.
Pornputtapong N, Wanichthanarak K, Nilsson A, Nookaew I, Nielsen J
Source Code Biol Med 9 (-) 17 [2014-07-10; online 2014-07-10]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data.
Garcia-Albornoz M, Thankaswamy-Kosalai S, Nilsson A, ..., Nookaew I, Nielsen J
Nucleic Acids Res. 42 (Web Server issue) W175-W181 [2014-07-00; online 2014-05-03]
Avlant Nilsson DDLS Fellow
SciLifeLab Data Centre
Publications 9.5.1