Erik L. L. Sonnhammer
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View article: GeneSNAKE: a Python package for benchmarking and simulation of gene regulatory networks and perturbation-induced expression data
GeneSNAKE: a Python package for benchmarking and simulation of gene regulatory networks and perturbation-induced expression data Open
Understanding how genes interact with and regulate each other is a key challenge in systems biology. One of the primary methods to study this is through gene regulatory networks (GRNs). The field of GRN inference however faces many challen…
View article: Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration
Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration Open
The rapid advancement of DNA sequencing technologies and computational algorithms has led to an unprecedented surge in genomic data, driven by several large-scale sequencing projects worldwide. Orthology plays a crucial role in understandi…
View article: BiGSM: Bayesian inference of gene regulatory network via sparse modelling
BiGSM: Bayesian inference of gene regulatory network via sparse modelling Open
Motivation Inference of gene regulatory network (GRN) is challenging due to the inherent sparsity of the GRN matrix and noisy expression data, often leading to a high possibility of false positive or negative predictions. To address this, …
View article: Topology-based metrics for finding the optimal sparsity in gene regulatory network inference
Topology-based metrics for finding the optimal sparsity in gene regulatory network inference Open
Motivation Gene regulatory network (GRN) inference is a complex task aiming to unravel regulatory interactions between genes in a cell. A major shortcoming of most GRN inference methods is that they do not attempt to find the optimal spars…
View article: The FunCoup Cytoscape App: multi-species network analysis and visualization
The FunCoup Cytoscape App: multi-species network analysis and visualization Open
Summary Functional association networks, such as FunCoup, are crucial for analyzing complex gene interactions. To facilitate the analysis and visualization of such genome-wide networks, there is a need for seamless integration with powerfu…
View article: Comprehensive analysis of the RBP regulome reveals functional modules and drug candidates in liver cancer
Comprehensive analysis of the RBP regulome reveals functional modules and drug candidates in liver cancer Open
RNA binding proteins (RBPs) are essential components of the transcriptomic regulome. Identifying the RBP regulome in cancer cells is crucial to discovering and understanding carcinogenesis mechanisms and providing new therapeutic targets. …
View article: GeneSPIDER2: large scale GRN simulation and benchmarking with perturbed single-cell data
GeneSPIDER2: large scale GRN simulation and benchmarking with perturbed single-cell data Open
Single-cell data is increasingly used for gene regulatory network (GRN) inference, and benchmarks for this have been developed based on simulated data. However, existing single-cell simulators cannot model the effects of gene perturbations…
View article: Benchmarking enrichment analysis methods with the disease pathway network
Benchmarking enrichment analysis methods with the disease pathway network Open
Enrichment analysis (EA) is a common approach to gain functional insights from genome-scale experiments. As a consequence, a large number of EA methods have been developed, yet it is unclear from previous studies which method is the best f…
View article: Data from A Novel ACKR2-Dependent Role of Fibroblast-Derived CXCL14 in Epithelial-to-Mesenchymal Transition and Metastasis of Breast Cancer
Data from A Novel ACKR2-Dependent Role of Fibroblast-Derived CXCL14 in Epithelial-to-Mesenchymal Transition and Metastasis of Breast Cancer Open
Purpose:Fibroblasts expressing the orphan chemokine CXCL14 have been previously shown to associate with poor breast cancer prognosis and promote cancer growth. This study explores the mechanism underlying the poor survival associations of …
View article: Supplementary Figure Legends from A Novel ACKR2-Dependent Role of Fibroblast-Derived CXCL14 in Epithelial-to-Mesenchymal Transition and Metastasis of Breast Cancer
Supplementary Figure Legends from A Novel ACKR2-Dependent Role of Fibroblast-Derived CXCL14 in Epithelial-to-Mesenchymal Transition and Metastasis of Breast Cancer Open
Supplementary Figure Legends
View article: Supplementary Data from A Novel ACKR2-Dependent Role of Fibroblast-Derived CXCL14 in Epithelial-to-Mesenchymal Transition and Metastasis of Breast Cancer
Supplementary Data from A Novel ACKR2-Dependent Role of Fibroblast-Derived CXCL14 in Epithelial-to-Mesenchymal Transition and Metastasis of Breast Cancer Open
FIGURES. Fig S1, Bioinformatics reveal potential CXCL14-receptor candidates; Fig. S2, Expression of CXCL14 correlates with EMT in breast cancer patients; Fig. S3, Expression of CXCL14 correlates with EMT in breast, prostate and ovarian can…
View article: Supplementary Figure Legends from A Novel ACKR2-Dependent Role of Fibroblast-Derived CXCL14 in Epithelial-to-Mesenchymal Transition and Metastasis of Breast Cancer
Supplementary Figure Legends from A Novel ACKR2-Dependent Role of Fibroblast-Derived CXCL14 in Epithelial-to-Mesenchymal Transition and Metastasis of Breast Cancer Open
Supplementary Figure Legends
View article: Supplementary Data from A Novel ACKR2-Dependent Role of Fibroblast-Derived CXCL14 in Epithelial-to-Mesenchymal Transition and Metastasis of Breast Cancer
Supplementary Data from A Novel ACKR2-Dependent Role of Fibroblast-Derived CXCL14 in Epithelial-to-Mesenchymal Transition and Metastasis of Breast Cancer Open
FIGURES. Fig S1, Bioinformatics reveal potential CXCL14-receptor candidates; Fig. S2, Expression of CXCL14 correlates with EMT in breast cancer patients; Fig. S3, Expression of CXCL14 correlates with EMT in breast, prostate and ovarian can…
View article: Data from A Novel ACKR2-Dependent Role of Fibroblast-Derived CXCL14 in Epithelial-to-Mesenchymal Transition and Metastasis of Breast Cancer
Data from A Novel ACKR2-Dependent Role of Fibroblast-Derived CXCL14 in Epithelial-to-Mesenchymal Transition and Metastasis of Breast Cancer Open
Purpose:Fibroblasts expressing the orphan chemokine CXCL14 have been previously shown to associate with poor breast cancer prognosis and promote cancer growth. This study explores the mechanism underlying the poor survival associations of …
View article: Spatio-temporal analysis of prostate tumors in situ suggests pre-existence of treatment-resistant clones
Spatio-temporal analysis of prostate tumors in situ suggests pre-existence of treatment-resistant clones Open
View article: Optimal Sparsity Selection Based on an Information Criterion for Accurate Gene Regulatory Network Inference
Optimal Sparsity Selection Based on an Information Criterion for Accurate Gene Regulatory Network Inference Open
Accurate inference of gene regulatory networks (GRNs) is important to unravel unknown regulatory mechanisms and processes, which can lead to the identification of treatment targets for genetic diseases. A variety of GRN inference methods h…
View article: GRNbenchmark - a web server for benchmarking directed gene regulatory network inference methods
GRNbenchmark - a web server for benchmarking directed gene regulatory network inference methods Open
Accurate inference of gene regulatory networks (GRN) is an essential component of systems biology, and there is a constant development of new inference methods. The most common approach to assess accuracy for publications is to benchmark t…
View article: Corrigendum: Network Crosstalk as a Basis for Drug Repurposing
Corrigendum: Network Crosstalk as a Basis for Drug Repurposing Open
[This corrects the article DOI: 10.3389/fgene.2022.792090.].
View article: Benefits and Challenges of Pre-clustered Network-Based Pathway Analysis
Benefits and Challenges of Pre-clustered Network-Based Pathway Analysis Open
Functional analysis of gene sets derived from experiments is typically done by pathway annotation. Although many algorithms exist for analyzing the association between a gene set and a pathway, an issue which is generally ignored is that g…
View article: PathwAX II: network-based pathway analysis with interactive visualization of network crosstalk
PathwAX II: network-based pathway analysis with interactive visualization of network crosstalk Open
Motivation Pathway annotation tools are indispensable for the interpretation of a wide range of experiments in life sciences. Network-based algorithms have recently been developed which are more sensitive than traditional overlap-based alg…
View article: Network Crosstalk as a Basis for Drug Repurposing
Network Crosstalk as a Basis for Drug Repurposing Open
The need for systematic drug repurposing has seen a steady increase over the past decade and may be particularly valuable to quickly remedy unexpected pandemics. The abundance of functional interaction data has allowed mapping of substanti…
View article: Fast and accurate gene regulatory network inference by normalized least squares regression
Fast and accurate gene regulatory network inference by normalized least squares regression Open
Motivation Inferring an accurate gene regulatory network (GRN) has long been a key goal in the field of systems biology. To do this, it is important to find a suitable balance between the maximum number of true positive and the minimum num…
View article: Generation of Realistic Gene Regulatory Networks by Enriching for Feed-Forward Loops
Generation of Realistic Gene Regulatory Networks by Enriching for Feed-Forward Loops Open
The regulatory relationships between genes and proteins in a cell form a gene regulatory network (GRN) that controls the cellular response to changes in the environment. A number of inference methods to reverse engineer the original GRN fr…
View article: Drug repurposing improves disease targeting 11-fold and can be augmented by network module targeting, applied to COVID-19
Drug repurposing improves disease targeting 11-fold and can be augmented by network module targeting, applied to COVID-19 Open
View article: Inferring the experimental design for accurate gene regulatory network inference
Inferring the experimental design for accurate gene regulatory network inference Open
Motivation Accurate inference of gene regulatory interactions is of importance for understanding the mechanisms of underlying biological processes. For gene expression data gathered from targeted perturbations, gene regulatory network (GRN…
View article: FunCoup 5: Functional Association Networks in All Domains of Life, Supporting Directed Links and Tissue-Specificity
FunCoup 5: Functional Association Networks in All Domains of Life, Supporting Directed Links and Tissue-Specificity Open
FunCoup (https://funcoup.sbc.su.se) is one of the most comprehensive functional association networks of genes/proteins available. Functional associations are inferred by integrating different types of evidence using a redundancy-weighted n…
View article: PathBIX—a web server for network-based pathway annotation with adaptive null models
PathBIX—a web server for network-based pathway annotation with adaptive null models Open
Motivation Pathway annotation is a vital tool for interpreting and giving meaning to experimental data in life sciences. Numerous tools exist for this task, where the most recent generation of pathway enrichment analysis tools, network-bas…
View article: Fusion transcript detection using spatial transcriptomics
Fusion transcript detection using spatial transcriptomics Open
Background Fusion transcripts are involved in tumourigenesis and play a crucial role in tumour heterogeneity, tumour evolution and cancer treatment resistance. However, fusion transcripts have not been studied at high spatial resolution in…
View article: MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data
MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data Open
View article: Additional file 9 of MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data
Additional file 9 of MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data Open
Additional file 9. CNVcalling SKBR3–3 cells CNV calling results for SKBR3–3 cells.