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View article: Flexynesis: A deep learning toolkit for bulk multi-omics data integration for precision oncology and beyond
Flexynesis: A deep learning toolkit for bulk multi-omics data integration for precision oncology and beyond Open
Accurate decision making in precision oncology depends on integration of multimodal molecular information, for which various deep learning methods have been developed. However, most deep learning-based bulk multi-omics integration methods …
View article: PocketVina Enables Scalable and Highly Accurate Physically Valid Docking through Multi-Pocket Conditioning
PocketVina Enables Scalable and Highly Accurate Physically Valid Docking through Multi-Pocket Conditioning Open
Sampling physically valid ligand-binding poses remains a major challenge in molecular docking, particularly for unseen or structurally diverse targets. We introduce PocketVina, a fast and memory-efficient, search-based docking framework th…
View article: Pro-inflammatory secretome from intestinal epithelium recruits regulatory T cells for barrier defence
Pro-inflammatory secretome from intestinal epithelium recruits regulatory T cells for barrier defence Open
Resolution of inflammation, including of colitis, requires carefully coordinated communication between different tissues. While the role of immune cells in colitis is well established, less is known about epithelial communication to its mi…
View article: Flexynesis: A deep learning framework for bulk multi-omics data integration for precision oncology and beyond
Flexynesis: A deep learning framework for bulk multi-omics data integration for precision oncology and beyond Open
Accurate decision making in precision oncology depends on integration of multimodal molecular information, such as the genetic data, gene expression, protein abundance, and epigenetic measurements. Deep learning methods facilitate integrat…
View article: Oncogene inactivation-induced senescence facilitates tumor relapse
Oncogene inactivation-induced senescence facilitates tumor relapse Open
SUMMARY Oncogene-targeted therapy has emerged as a promising avenue for delaying tumor progression. However, patients often develop drug resistance and early tumor recurrence. We analyzed the effects of oncogene inactivation in vitro , and…
View article: Pathogenic mutations of human phosphorylation sites affect protein–protein interactions
Pathogenic mutations of human phosphorylation sites affect protein–protein interactions Open
Despite their lack of a defined 3D structure, intrinsically disordered regions (IDRs) of proteins play important biological roles. Many IDRs contain short linear motifs (SLiMs) that mediate protein-protein interactions (PPIs), which can be…
View article: Pathogenic mutations of human phosphorylation sites affect protein-protein interactions
Pathogenic mutations of human phosphorylation sites affect protein-protein interactions Open
Despite their lack of a defined 3D structure, intrinsically disordered regions (IDRs) of proteins play important biological roles. Many IDRs contain short linear motifs (SLiMs) that mediate protein-protein interactions (PPIs), which can be…
View article: Multi-Omics Alleviates the Limitations of Panel Sequencing for Cancer Drug Response Prediction
Multi-Omics Alleviates the Limitations of Panel Sequencing for Cancer Drug Response Prediction Open
Comprehensive genomic profiling using cancer gene panels has been shown to improve treatment options for a variety of cancer types. However, genomic aberrations detected via such gene panels do not necessarily serve as strong predictors of…
View article: Multi-omics alleviates the limitations of panel-sequencing for cancer drug response prediction
Multi-omics alleviates the limitations of panel-sequencing for cancer drug response prediction Open
Comprehensive genomic profiling using cancer gene panels has been shown to improve treatment options for a variety of cancer types. However, genomic aberrations detected via such gene panels don’t necessarily serve as strong predictors of …
View article: Identifying tumor cells at the single-cell level using machine learning
Identifying tumor cells at the single-cell level using machine learning Open
Tumors are complex tissues of cancerous cells surrounded by a heterogeneous cellular microenvironment with which they interact. Single-cell sequencing enables molecular characterization of single cells within the tumor. However, cell annot…
View article: Additional file 2 of Identifying tumor cells at the single-cell level using machine learning
Additional file 2 of Identifying tumor cells at the single-cell level using machine learning Open
Additional file 2. Tables with data description and results.
View article: Additional file 3 of Identifying tumor cells at the single-cell level using machine learning
Additional file 3 of Identifying tumor cells at the single-cell level using machine learning Open
Additional file 3. Results of statistical analysis.
View article: SARS-CoV-2 infection dynamics revealed by wastewater sequencing analysis and deconvolution
SARS-CoV-2 infection dynamics revealed by wastewater sequencing analysis and deconvolution Open
The use of RNA sequencing from wastewater samples is a valuable way for estimating infection dynamics and circulating lineages of SARS-CoV-2. This approach is independent from testing individuals and can therefore become the key tool to mo…
View article: Identifying tumor cells at the single cell level
Identifying tumor cells at the single cell level Open
Tumors are highly complex tissues composed of cancerous cells, surrounded by a heterogeneous cellular microenvironment. Tumor response to treatments is governed by an interaction of cancer cell intrinsic factors with external influences of…
View article: Multi-omics and deep learning provide a multifaceted view of cancer
Multi-omics and deep learning provide a multifaceted view of cancer Open
Cancer is a complex disease with a large financial and healthcare burden on society. One hallmark of the disease is the uncontrolled growth and proliferation of malignant cells. Unlike Mendelian diseases which may be explained by a few gen…
View article: Parallel genetics of regulatory sequences using scalable genome editing in vivo
Parallel genetics of regulatory sequences using scalable genome editing in vivo Open
How regulatory sequences control gene expression is fundamental for explaining phenotypes in health and disease. Regulatory elements must ultimately be understood within their genomic environment and development- or tissue-specific context…
View article: Transcriptional repression of <i>NFKBIA</i> triggers constitutive IKK‐ and proteasome‐independent p65/RelA activation in senescence
Transcriptional repression of <i>NFKBIA</i> triggers constitutive IKK‐ and proteasome‐independent p65/RelA activation in senescence Open
The IκB kinase (IKK)-NF-κB pathway is activated as part of the DNA damage response and controls both inflammation and resistance to apoptosis. How these distinct functions are achieved remained unknown. We demonstrate here that DNA double-…
View article: Parallel genetics of regulatory sequences<i>in vivo</i>
Parallel genetics of regulatory sequences<i>in vivo</i> Open
Understanding how regulatory sequences control gene expression is fundamental to explain how phenotypes arise in health and disease. Traditional reporter assays inform about function of individual regulatory elements, typically in isolatio…
View article: A novel IKK- and proteasome-independent mechanism of RelA activation triggers senescence associated secretome via transcriptional repression of NFKBIA
A novel IKK- and proteasome-independent mechanism of RelA activation triggers senescence associated secretome via transcriptional repression of NFKBIA Open
The IκB kinase (IKK) - NF-κB pathway is activated as part of the DNA damage response and controls both resistance to apoptosis and inflammation. How these different functions are achieved remained unknown. We demonstrate here that DNA doub…
View article: The conserved histone chaperone LIN‐53 is required for normal lifespan and maintenance of muscle integrity in <i>Caenorhabditis elegans</i>
The conserved histone chaperone LIN‐53 is required for normal lifespan and maintenance of muscle integrity in <i>Caenorhabditis elegans</i> Open
Whether extension of lifespan provides an extended time without health deteriorations is an important issue for human aging. However, to which degree lifespan and aspects of healthspan regulation might be linked is not well understood. Chr…
View article: HOT or not: examining the basis of high-occupancy target regions
HOT or not: examining the basis of high-occupancy target regions Open
High-occupancy target (HOT) regions are segments of the genome with unusually high number of transcription factor binding sites. These regions are observed in multiple species and thought to have biological importance due to high transcrip…
View article: PiGx: reproducible genomics analysis pipelines with GNU Guix
PiGx: reproducible genomics analysis pipelines with GNU Guix Open
In bioinformatics, as well as other computationally intensive research fields, there is a need for workflows that can reliably produce consistent output, from known sources, independent of the software environment or configuration settings…
View article: Reproducible genomics analysis pipelines with GNU Guix
Reproducible genomics analysis pipelines with GNU Guix Open
In bioinformatics, as well as other computationally-intensive research fields, there is a need for workflows that can reliably produce consistent output, independent of the software environment or configuration settings of the machine on w…
View article: FACT sets a barrier for cell fate reprogramming in <i>C. elegans</i> and Human
FACT sets a barrier for cell fate reprogramming in <i>C. elegans</i> and Human Open
Summary Abstract Figure The chromatin regulator FACT (Facilitates Chromatin Transcription) is essential for ensuring stable gene expression by promoting transcription. In a genetic screen using C. elegans we identified that FACT maintains …