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View article: Inferring binding specificities of human transcription factors with the wisdom of crowds
Inferring binding specificities of human transcription factors with the wisdom of crowds Open
DNA motif discovery and, particularly, computational modeling of transcription factor binding motifs, has been a mecca of algorithmic bioinformatics for several decades. Here, we report the results of the largest open community challenge i…
View article: Cross-platform motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors
Cross-platform motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors Open
A sequence motif representing the DNA-binding specificity of a transcription factor (TF) is commonly modelled with a positional weight matrix (PWM). Focusing on understudied human TFs, we processed results of 4,237 experiments for 394 TFs,…
View article: Codebook Motif Explorer Supplementary Dataset
Codebook Motif Explorer Supplementary Dataset Open
This is the supplementary dataset of the GRECO-BIT/Codebook Motif Explorer (MEX),which is a detailed online catalog of DNA motifs built using a huge collection of experimental data produced by the Codebook Consortium to annotate the bindin…
View article: Fast barcode calling based on <i>k</i> -mer distances
Fast barcode calling based on <i>k</i> -mer distances Open
DNA barcodes, which are short DNA strings, are regularly used as tags in pooled sequencing experiments to enable the identification of reads originating from the same sample. A crucial task in the subsequent analysis of pooled sequences is…
View article: Advancing Anticancer Drug Discovery: Leveraging Metabolomics and Machine Learning for Mode of Action Prediction by Pattern Recognition (Adv. Sci. 47/2024)
Advancing Anticancer Drug Discovery: Leveraging Metabolomics and Machine Learning for Mode of Action Prediction by Pattern Recognition (Adv. Sci. 47/2024) Open
Advancing Anticancer Drug Discovery In article number 2404085, Ludger A. Wessjohann, Gerd U. Balcke, and co‐workers address the challenge of identifying the mode of action (MoA) of anti‐cancer drugs by integrating metabolomics and machine …
View article: Perspectives on Codebook: sequence specificity of uncharacterized human transcription factors
Perspectives on Codebook: sequence specificity of uncharacterized human transcription factors Open
SUMMARY We describe an effort (“Codebook”) to determine the sequence specificity of 332 putative and largely uncharacterized human transcription factors (TFs), as well as 61 control TFs. Nearly 5,000 independent experiments across multiple…
View article: Cross-platform DNA motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors
Cross-platform DNA motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors Open
A DNA sequence pattern, or “motif”, is an essential representation of DNA-binding specificity of a transcription factor (TF). Any particular motif model has potential flaws due to shortcomings of the underlying experimental data and comput…
View article: Zinc Influences the Efficacy of Betulinic Acid Treatment and Radiotherapy in Breast Cancer Cells
Zinc Influences the Efficacy of Betulinic Acid Treatment and Radiotherapy in Breast Cancer Cells Open
The trace element zinc influences a number of biological reactions, including cell growth, apoptosis, and DNA damage, which affect tumor therapy. The natural compound betulinic acid (BA) and its derivatives are known for their antiviral, a…
View article: Advancing Anticancer Drug Discovery: Leveraging Metabolomics and Machine Learning for Mode of Action Prediction by Pattern Recognition
Advancing Anticancer Drug Discovery: Leveraging Metabolomics and Machine Learning for Mode of Action Prediction by Pattern Recognition Open
A bottleneck in the development of new anti‐cancer drugs is the recognition of their mode of action (MoA). Metabolomics combined with machine learning allowed to predict MoAs of novel anti‐proliferative drug candidates, focusing on human p…
View article: Comprehensive annotations of alternative splicing, lncRNAs, and circRNAs in seven species of flowering plants
Comprehensive annotations of alternative splicing, lncRNAs, and circRNAs in seven species of flowering plants Open
The successful occupation of terrestrial habitats by early plants was catalyzed by the adaptive evolution of new organs able to supply water and compensate for the gravitational impact under changing land conditions. Because plants are ses…
View article: Rapid evolution of gene expression patterns in flowering plants
Rapid evolution of gene expression patterns in flowering plants Open
Phenotypic differences between species are largely driven by changes in both protein-coding sequence and gene expression 1 . The evolutionary history of angiosperms (flowering plants) is characterised by a highly accelerated rate of divers…
View article: Machine Learning-Based Metabolic Pattern Recognition Predicts Mode of Action for Anti-Cancer Drug Candidates
Machine Learning-Based Metabolic Pattern Recognition Predicts Mode of Action for Anti-Cancer Drug Candidates Open
A bottleneck in the development of new anti-cancer drugs is the recognition of their mode of action (MoA). We combined metabolomics and machine learning to predict MoAs of novel anti-proliferative drug candidates, focusing on human prostat…
View article: Codebook Motif Explorer Supplementary Dataset
Codebook Motif Explorer Supplementary Dataset Open
This is the supplementary dataset of the GRECO-BIT/Codebook Motif Explorer (MEX),which is a detailed online catalog of DNA motifs built using a huge collection of experimental data produced by the Codebook Consortium to annotate the bindin…
View article: Codebook Motif Explorer Supplementary Dataset
Codebook Motif Explorer Supplementary Dataset Open
This is the supplementary dataset of the GRECO-BIT/Codebook Motif Explorer (MEX), which is a detailed online catalog of DNA motifs built using a huge collection of experimental data produced by the Codebook Consortium to annotate the bindi…
View article: SESN2 Knockdown Increases Betulinic Acid-Induced Radiosensitivity of Hypoxic Breast Cancer Cells
SESN2 Knockdown Increases Betulinic Acid-Induced Radiosensitivity of Hypoxic Breast Cancer Cells Open
Betulinic acid (BA) is a natural compound well known for its anti-inflammatory, anti-viral, anti-bacterial, anti-malarial effects and anti-tumor properties. Its enhanced cytotoxicity in tumor cells and induction of cell death in various ca…
View article: Relationship of micro-RNA, mRNA and eIF Expression in Tamoxifen-Adapted MCF-7 Breast Cancer Cells: Impact of miR-1972 on Gene Expression, Proliferation and Migration
Relationship of micro-RNA, mRNA and eIF Expression in Tamoxifen-Adapted MCF-7 Breast Cancer Cells: Impact of miR-1972 on Gene Expression, Proliferation and Migration Open
Background: Tamoxifen-adapted MCF-7-Tam cells represent an in-vitro model for acquired tamoxifen resistance, which is still a problem in clinics. We here investigated the correlation of microRNA-, mRNA- and eukaryotic initiation factors (e…
View article: Genetic and Epigenetic Differentiation Across Intertidal Gradients in the Foundation Plant Spartina alterniflora
Genetic and Epigenetic Differentiation Across Intertidal Gradients in the Foundation Plant Spartina alterniflora Open
Ecological genomics approaches have informed us about the structure of genetic diversity in natural populations that might underlie patterns in trait variation. However, we still know surprisingly little about the mechanisms that permit or…
View article: Genetic and epigenetic differentiation across intertidal gradients in the foundation plant Spartina alterniflora
Genetic and epigenetic differentiation across intertidal gradients in the foundation plant Spartina alterniflora Open
This record contains supplementary information for the article "Genetic and epigenetic differentiation across intertidal gradients in the foundation plant Spartina alterniflora". It contains the barcodes (barcodes.txt), the reference conti…
View article: Genetic and epigenetic differentiation across intertidal gradients in the foundation plant Spartina alterniflora
Genetic and epigenetic differentiation across intertidal gradients in the foundation plant Spartina alterniflora Open
This record contains supplementary information for the article "Genetic and epigenetic differentiation across intertidal gradients in the foundation plant Spartina alterniflora". It contains the barcodes (barcodes.txt), the reference conti…
View article: Importance of RpoD- and Non-RpoD-Dependent Expression of Horizontally Acquired Genes in Cupriavidus metallidurans
Importance of RpoD- and Non-RpoD-Dependent Expression of Horizontally Acquired Genes in Cupriavidus metallidurans Open
In their natural environment, bacteria are constantly acquiring genes by horizontal gene transfer. To be of any benefit, these genes should be expressed.
View article: Transcriptional Analysis of Total CD8+ T Cells and CD8+CD45RA- Memory T Cells From Young and Old Healthy Blood Donors
Transcriptional Analysis of Total CD8+ T Cells and CD8+CD45RA- Memory T Cells From Young and Old Healthy Blood Donors Open
Memory CD8 + T cells accumulate with aging, while the naïve T cell compartment decreases, leading to an increased susceptibility to infections and a decreased vaccine efficiency. To get deeper insights into the underlying mechanisms, this …
View article: Test data for epiGBS
Test data for epiGBS Open
Test data for use with the epiGBS2 pipeline. Includes R1 and R2 reads and a barcode file. Can be used to see if the installation has worked correctly and output will be created as expected.
View article: Test data for epiGBS
Test data for epiGBS Open
Test data for use with the epiGBS2 pipeline. Includes R1 and R2 reads and a barcode file. Can be used to see if the installation has worked correctly and output will be created as expected.
View article: epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing
epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing Open
We present epiGBS2, a laboratory protocol based on epiGBS (Gurp et al., 2016) with a revised and user-friendly bioinformatics pipeline for a wide range of species with or without reference genome. Performance of several critical steps in e…
View article: epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing
epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing Open
We present epiGBS2, a laboratory protocol based on epiGBS (Gurp et al., 2016) with a revised and user-friendly bioinformatics pipeline for a wide range of species with or without reference genome. Performance of several critical steps in e…
View article: epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing
epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing Open
We present epiGBS2, a laboratory protocol based on epiGBS (Gurp et al., 2016) with a revised and user-friendly bioinformatics pipeline for a wide range of species with or without reference genome. Performance of several critical steps in e…
View article: Acute Effects of an Inorganic Phosphorus Additive on Mineral Metabolism and Cardiometabolic Risk Factors in Healthy Subjects
Acute Effects of an Inorganic Phosphorus Additive on Mineral Metabolism and Cardiometabolic Risk Factors in Healthy Subjects Open
Context Hyperphosphatemia and high levels of fibroblast growth factor 23 (FGF23) are risk factors for cardiovascular events in patients with chronic kidney diseases. However, the impact of an inorganic phosphorus additive in healthy people…
View article: Detection of SARS-CoV-2 Derived Small RNAs and Changes in Circulating Small RNAs Associated with COVID-19
Detection of SARS-CoV-2 Derived Small RNAs and Changes in Circulating Small RNAs Associated with COVID-19 Open
Cleavage of double-stranded RNA is described as an evolutionary conserved host defense mechanism against viral infection. Small RNAs are the product and triggers of post transcriptional gene silencing events. Up until now, the relevance of…
View article: tSFM 1.0: tRNA Structure–Function Mapper
tSFM 1.0: tRNA Structure–Function Mapper Open
Motivation Structure-conditioned information statistics have proven useful to predict and visualize tRNA Class-Informative Features (CIFs) and their evolutionary divergences. Although permutation P-values can quantify the significance of C…
View article: Taxonomic analysis of metagenomic data with kASA
Taxonomic analysis of metagenomic data with kASA Open
The taxonomic analysis of sequencing data has become important in many areas of life sciences. However, currently available tools for that purpose either consume large amounts of RAM or yield insufficient quality and robustness. Here, we p…