Dewei Hu

Dewei Hu

PhD Fellow · NNF Center for Basic Metabolic Research, University of Copenhagen

I am a PhD fellow in Bioinformatics & Network Biology, supervised by Simon Rasmussen and Lars Juhl Jensen. My PhD is about "Representation learning for biological networks and multi-omics integration."

My research focuses on machine learning and network biology methods for understanding complex diseases. This involves integrating metabolomics, proteomics, and protein interaction networks at a population scale. I also develop cross-species protein embeddings built on the STRING database.

dewei.hu@sund.ku.dk GitHub Google Scholar LinkedIn

Education

University of Copenhagen

PhD in Bioinformatics & Network Biology
NNF Center for Protein Research / CBMR
2022 – 2026 · Copenhagen, Denmark

University of Copenhagen

MSc in Bioinformatics
2019 – 2021 · Copenhagen, Denmark

Southwest University of Science and Technology

BSc in Biotechnology
2015 – 2019 · Mianyang, China

Experience

PhD Fellow

NNF Center for Basic Metabolic Research, University of Copenhagen
Sep 2024 – Present · Copenhagen, Denmark

Visiting PhD Student

ZS Discovery (ZS Associates)
May – Aug 2025 · Kongens Lyngby, Denmark

PhD Fellow

NNF Center for Protein Research, University of Copenhagen
Aug 2022 – Dec 2024 · Copenhagen, Denmark

Bioinformatics Engineer

BioMap (BioMap Intelligent Technology Co., Ltd.)
Aug 2021 – Jun 2022 · Beijing, China

Publications

SLIM: A small linear model with STRING embeddings for single-cell genetic perturbation prediction
Hu D*, Pielies Avellí M*, Jensen LJ, Rasmussen S.
bioRxiv 2026.08.07.743481 (2026)
Preprint Preprint Code
Contrastive alignment transfers proteomic predictive signals to metabolomics data
Hu D, Rohrer C, Pielies Avellí M, Merino J, Jensen LJ, Rasmussen S.
medRxiv 2026.08.14.26360447 (2026)
Preprint Preprint Code
Molecular maps of diseases from omics data and network embeddings
Hu D*, Schaap-Johansen A-L*, Villarroel J, Ekebjærg C, Rasmussen S, Hansen DH, Wernersson R, Jensen LJ.
npj Systems Biology and Applications 12, 746 (2026)
Published Paper Code
SPACE: STRING proteins as complementary embeddings
Hu D, Szklarczyk D, von Mering C, Jensen LJ.
Bioinformatics 41(9):btaf496 (2025)
Published Paper Code
Genome-wide rules of transcription factor cooperativity revealed through in silico binding site ablation
He X, Einarsson H, Páleníková P, Rennie S, Hu D, Cui R, Vaagensø C, Lage K, Krautz R, Andersson R.
bioRxiv 2025.06.19.660093 — Under revision at Nature Communications
Under Revision Preprint
The STRING database in 2025: protein networks with directionality of regulation
Szklarczyk D, Nastou K, Koutrouli M, Kirsch R, Mehryary F, Hachilif R, …, Hu D, …, von Mering C.
Nucleic Acids Research 53(D1):D730–D737 (2025)
Published Paper