Lars Juhl Jensen
YOU?
Author Swipe
View article: Functional landscape of ubiquitin linkages couples K29-linked ubiquitylation to epigenome integrity
Functional landscape of ubiquitin linkages couples K29-linked ubiquitylation to epigenome integrity Open
Linkage-specific ubiquitin chains govern the outcome of numerous critical ubiquitin-dependent signaling processes, but their targets and functional impacts remain incompletely understood due to a paucity of tools for their specific detecti…
View article: SPACE: STRING proteins as complementary embeddings
SPACE: STRING proteins as complementary embeddings Open
Motivation Representation learning has revolutionized sequence-based prediction of protein function and subcellular localization. Protein networks are an important source of information complementary to sequences, but the use of protein ne…
View article: Enhancing dance learning by reducing cognitive load: A preregistered study on the effect of dancers’ viewing perspective and expertise
Enhancing dance learning by reducing cognitive load: A preregistered study on the effect of dancers’ viewing perspective and expertise Open
While movement sequences in choreography are often taught through instructor demonstrations, the influence of visual perspective on learning outcomes has received limited attention. Drawing on cognitive load theory, we investigated how per…
View article: The postbiotic ReFerm® versus standard nutritional support in advanced alcohol-related liver disease (GALA-POSTBIO): a randomized controlled phase 2 trial
The postbiotic ReFerm® versus standard nutritional support in advanced alcohol-related liver disease (GALA-POSTBIO): a randomized controlled phase 2 trial Open
Impaired gut barrier function may lead to progression of liver fibrosis in people with alcohol-related liver disease. The postbiotic ReFerm® can lower gut barrier permeability and may thereby reduce fibrosis formation. Here, we report the …
View article: Accurate plasmid reconstruction from metagenomics data using assembly-alignment graphs and contrastive learning
Accurate plasmid reconstruction from metagenomics data using assembly-alignment graphs and contrastive learning Open
Plasmids are extrachromosomal DNA molecules that enable horizontal gene transfer in bacteria, often conferring advantages such as antibiotic resistance. Despite their significance, plasmids are underrepresented in genomic databases due to …
View article: Epigenomic insights into extreme longevity in the world’s oldest terrestrial animal, Jonathan
Epigenomic insights into extreme longevity in the world’s oldest terrestrial animal, Jonathan Open
Giant tortoises exhibit exceptional longevity, often exceeding the human lifespan. To understand the genomic and epigenomic basis of their longevity, awe analyzed the DNA sequence and methylome of Jonathan, an Aldabra giant tortoise (Aldab…
View article: LSD600: the first corpus of biomedical abstracts annotated with lifestyle–disease relations
LSD600: the first corpus of biomedical abstracts annotated with lifestyle–disease relations Open
Lifestyle factors (LSFs) are increasingly recognized as instrumental in both the development and control of diseases. Despite their importance, there is a lack of methods to extract relations between LSFs and diseases from the literature, …
View article: SPACE: STRING proteins as complementary embeddings
SPACE: STRING proteins as complementary embeddings Open
Representation learning has revolutionized sequence-based prediction of protein function and subcellular localization. Protein networks are an important source of information complementary to sequences, but the use of protein networks has …
View article: The STRING database in 2025: protein networks with directionality of regulation
The STRING database in 2025: protein networks with directionality of regulation Open
Proteins cooperate, regulate and bind each other to achieve their functions. Understanding the complex network of their interactions is essential for a systems-level description of cellular processes. The STRING database compiles, scores a…
View article: Single-cell atlas of transcriptomic vulnerability across multiple neurodegenerative and neuropsychiatric diseases
Single-cell atlas of transcriptomic vulnerability across multiple neurodegenerative and neuropsychiatric diseases Open
Neurodegenerative and neuropsychiatric diseases impose a significant societal and public health burden. However, our understanding of the molecular mechanisms underlying these highly complex conditions remains limited. To gain deeper insig…
View article: Targeted disruption of linkage-specific ubiquitylation reveals a key role of K29-linked ubiquitylation in epigenome integrity
Targeted disruption of linkage-specific ubiquitylation reveals a key role of K29-linked ubiquitylation in epigenome integrity Open
Linkage-specific ubiquitin chains dictate the functional outcome of numerous critical ubiquitin-dependent signaling processes. However, the functions and targets of several poly-ubiquitin topologies remain poorly defined due to a paucity o…
View article: Streamlined analysis of drug targets by proteome integral solubility alteration indicates organ-specific engagement
Streamlined analysis of drug targets by proteome integral solubility alteration indicates organ-specific engagement Open
Proteins are the primary targets of almost all small molecule drugs. However, even the most selectively designed drugs can potentially target several unknown proteins. Identification of potential drug targets can facilitate design of new d…
View article: Lifestyle factors in the biomedical literature: an ontology and comprehensive resources for named entity recognition
Lifestyle factors in the biomedical literature: an ontology and comprehensive resources for named entity recognition Open
Motivation Despite lifestyle factors (LSFs) being increasingly acknowledged in shaping individual health trajectories, particularly in chronic diseases, they have still not been systematically described in the biomedical literature. This i…
View article: Graph databases in systems biology: a systematic review
Graph databases in systems biology: a systematic review Open
Graph databases are becoming increasingly popular across scientific disciplines, being highly suitable for storing and connecting complex heterogeneous data. In systems biology, they are used as a backend solution for biological data repos…
View article: STRING-ing together protein complexes: corpus and methods for extracting physical protein interactions from the biomedical literature
STRING-ing together protein complexes: corpus and methods for extracting physical protein interactions from the biomedical literature Open
Motivation Understanding biological processes relies heavily on curated knowledge of physical interactions between proteins. Yet, a notable gap remains between the information stored in databases of curated knowledge and the plethora of in…
View article: LSD600: the first corpus of biomedical abstracts annotated with lifestyle–disease relations
LSD600: the first corpus of biomedical abstracts annotated with lifestyle–disease relations Open
Lifestyle factors (LSFs) are increasingly recognized as instrumental in both the development and control of diseases. Despite their importance, there is a lack of methods to extract relations between LSFs and diseases from the literature, …
View article: TIN-X version 3: update with expanded dataset and modernized architecture for enhanced illumination of understudied targets
TIN-X version 3: update with expanded dataset and modernized architecture for enhanced illumination of understudied targets Open
TIN-X (Target Importance and Novelty eXplorer) is an interactive visualization tool for illuminating associations between diseases and potential drug targets and is publicly available at newdrugtargets.org . TIN-X uses natural language pro…
View article: Lifestyle factors in the biomedical literature: An ontology and comprehensive resources for named entity recognition
Lifestyle factors in the biomedical literature: An ontology and comprehensive resources for named entity recognition Open
Motivation Despite lifestyle factors (LSFs) being increasingly acknowledged in shaping individual health trajectories, particularly in chronic diseases, they have still not been systematically described in the biomedical literature. This i…
View article: Improving dictionary-based named entity recognition with deep learning
Improving dictionary-based named entity recognition with deep learning Open
Motivation Dictionary-based named entity recognition (NER) allows terms to be detected in a corpus and normalized to biomedical databases and ontologies. However, adaptation to different entity types requires new high-quality dictionaries …
View article: CoNECo: A Corpus for Named Entity recognition and normalization of protein Complexes
CoNECo: A Corpus for Named Entity recognition and normalization of protein Complexes Open
Motivation Despite significant progress in biomedical information extraction, there is a lack of resources for Named Entity Recognition (NER) and Normalization (NEN) of protein-containing complexes. Current resources inadequately address t…
View article: RegulaTome: a corpus of typed, directed, and signed relations between biomedical entities in the scientific literature
RegulaTome: a corpus of typed, directed, and signed relations between biomedical entities in the scientific literature Open
Motivation In the field of biomedical text mining, the ability to extract relations from literature is crucial for advancing both theoretical research and practical applications. There is a notable shortage of corpora designed to enhance t…
View article: The Use of Graph Databases in Systems Biology: A Systematic Review
The Use of Graph Databases in Systems Biology: A Systematic Review Open
Graph databases (GDBs) are becoming increasingly popular across scientific disciplines, being highly suitable to store and connect complex heterogeneous data. In systems biology, they are used as a backend solution for biological data repo…
View article: STREAMLINED PROTEOME-WIDE IDENTIFICATION OF DRUG TARGETS INDICATES ORGAN-SPECIFIC ENGAGEMENT
STREAMLINED PROTEOME-WIDE IDENTIFICATION OF DRUG TARGETS INDICATES ORGAN-SPECIFIC ENGAGEMENT Open
Proteins are the primary targets of almost all small molecule drugs. However, even the most selectively designed drugs can potentially target several unknown proteins. Identification of potential drug targets can facilitate design of new d…
View article: A quantitative and site-specific atlas of the citrullinome reveals widespread existence of citrullination and insights into PADI4 substrates
A quantitative and site-specific atlas of the citrullinome reveals widespread existence of citrullination and insights into PADI4 substrates Open
Despite the importance of citrullination in physiology and disease, global identification of citrullinated proteins, and the precise targeted sites, has remained challenging. Here we employed quantitative-mass-spectrometry-based proteomics…