Sebastian D. Mackowiak
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View article: Atopic Dermatitis ( <scp>AD</scp> ) Related Cord Blood <scp>DNA</scp> Methylation Patterns Are Linked to Maternal <scp>AD</scp>
Atopic Dermatitis ( <span>AD</span> ) Related Cord Blood <span>DNA</span> Methylation Patterns Are Linked to Maternal <span>AD</span> Open
View article: crossNN is an explainable framework for cross-platform DNA methylation-based classification of tumors
crossNN is an explainable framework for cross-platform DNA methylation-based classification of tumors Open
View article: DNA methylation changes during acute COVID-19 are associated with long-term transcriptional dysregulation in patients’ airway epithelial cells
DNA methylation changes during acute COVID-19 are associated with long-term transcriptional dysregulation in patients’ airway epithelial cells Open
Molecular changes underlying the persistent health effects after SARS-CoV-2 infection remain poorly understood. To discern the gene regulatory landscape in the upper respiratory tract of COVID-19 patients, we performed enzymatic DNA methyl…
View article: An activity-specificity trade-off encoded in human transcription factors
An activity-specificity trade-off encoded in human transcription factors Open
Transcription factors (TFs) control specificity and activity of gene transcription, but whether a relationship between these two features exists is unclear. Here we provide evidence for an evolutionary trade-off between the activity and sp…
View article: Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells
Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells Open
MicroRNAs are small RNA molecules that can repress the expression of protein coding genes post-transcriptionally. Previous studies have shown that microRNAs can also have alternative functions including target noise buffering and co-expres…
View article: crossNN: an explainable framework for cross-platform DNA methylation-based classification of cancer
crossNN: an explainable framework for cross-platform DNA methylation-based classification of cancer Open
DNA methylation-based classification of brain tumors has emerged as a powerful and indispensable diagnostic technique. Initial implementations have used methylation microarrays for data generation, but different sequencing approaches are i…
View article: Global hypomethylation in childhood asthma identified by genome‐wide DNA‐methylation sequencing preferentially affects enhancer regions
Global hypomethylation in childhood asthma identified by genome‐wide DNA‐methylation sequencing preferentially affects enhancer regions Open
Background Childhood asthma is a result of a complex interaction of genetic and environmental components causing epigenetic and immune dysregulation, airway inflammation and impaired lung function. Although different microarray based EWAS …
View article: T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation
T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation Open
Long non-coding RNAs (lncRNAs) have emerged as fundamental regulators in various biological processes, including embryonic development and cellular differentiation. Despite much progress over the past decade, the genome-wide annotation of …
View article: Author response: T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation
Author response: T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation Open
View article: Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells
Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells Open
View article: Selective Mediator dependence of cell-type-specifying transcription
Selective Mediator dependence of cell-type-specifying transcription Open
View article: Unblending of Transcriptional Condensates in Human Repeat Expansion Disease
Unblending of Transcriptional Condensates in Human Repeat Expansion Disease Open
View article: The SWI/SNF subunits BRG1 affects alternative splicing by changing RNA binding factor interactions with RNA
The SWI/SNF subunits BRG1 affects alternative splicing by changing RNA binding factor interactions with RNA Open
BRG1 and BRM are ATPase core subunits of the human SWI/SNF chromatin remodelling complexes. The function of the SWI/SNF complexes in transcriptional initiation has been well studied, while a function in alternative splicing has only been s…
View article: Extensive identification and analysis of conserved small ORFs in animals
Extensive identification and analysis of conserved small ORFs in animals Open
View article: Comprehensive identification and characterization of conserved small ORFs in animals
Comprehensive identification and characterization of conserved small ORFs in animals Open
There is increasing evidence that non-annotated short open reading frames (sORFs) can encode functional micropeptides, but computational identification remains challenging. We expand our published method and predict conserved sORFs in huma…
View article: Specific microRNAs Regulate Heat Stress Responses in Caenorhabditis elegans
Specific microRNAs Regulate Heat Stress Responses in Caenorhabditis elegans Open
The ability of animals to sense and respond to elevated temperature is essential for survival. Transcriptional control of the heat stress response has been much studied, whereas its posttranscriptional regulation by microRNAs (miRNAs) is n…
View article: Additional file 23: Table S12. of Extensive identification and analysis of conserved small ORFs in animals
Additional file 23: Table S12. of Extensive identification and analysis of conserved small ORFs in animals Open
Experimental evidence for zebrafish sORFs. (ODS 49 kb)
View article: Additional file 24: Table S13. of Extensive identification and analysis of conserved small ORFs in animals
Additional file 24: Table S13. of Extensive identification and analysis of conserved small ORFs in animals Open
Experimental evidence for fruit fly sORFs. (ODS 69 kb)
View article: Additional file 15: Table S9. of Extensive identification and analysis of conserved small ORFs in animals
Additional file 15: Table S9. of Extensive identification and analysis of conserved small ORFs in animals Open
Summary of datasets used in Fig. 6b (mass spectrometry). (ODS 13 kb)
View article: Additional file 22: Table S11. of Extensive identification and analysis of conserved small ORFs in animals
Additional file 22: Table S11. of Extensive identification and analysis of conserved small ORFs in animals Open
Experimental evidence for mouse sORFs. (ODS 91 kb)
View article: Additional file 4: Table S3. of Extensive identification and analysis of conserved small ORFs in animals
Additional file 4: Table S3. of Extensive identification and analysis of conserved small ORFs in animals Open
All sORF information for zebrafish. (TXT 734 kb)
View article: Additional file 8: Table S6. of Extensive identification and analysis of conserved small ORFs in animals
Additional file 8: Table S6. of Extensive identification and analysis of conserved small ORFs in animals Open
Summary of datasets used in Fig. 3 (other sORF predictions). (ODS 13 kb)
View article: Additional file 5: Table S4. of Extensive identification and analysis of conserved small ORFs in animals
Additional file 5: Table S4. of Extensive identification and analysis of conserved small ORFs in animals Open
All sORF information for fly. (TXT 535 kb)
View article: Additional file 3: Table S2. of Extensive identification and analysis of conserved small ORFs in animals
Additional file 3: Table S2. of Extensive identification and analysis of conserved small ORFs in animals Open
All sORF information for mouse. (TXT 3192 kb)
View article: Additional file 14: Table S8. of Extensive identification and analysis of conserved small ORFs in animals
Additional file 14: Table S8. of Extensive identification and analysis of conserved small ORFs in animals Open
Summary of datasets used in Fig. 6a (ribosome profiling). (ODS 14 kb)
View article: Additional file 2: Table S1. of Extensive identification and analysis of conserved small ORFs in animals
Additional file 2: Table S1. of Extensive identification and analysis of conserved small ORFs in animals Open
All sORF information for human. (TXT 6997 kb)
View article: Additional file 12: Table S7. of Extensive identification and analysis of conserved small ORFs in animals
Additional file 12: Table S7. of Extensive identification and analysis of conserved small ORFs in animals Open
Summary of datasets used in Additional file 13: Figure S6A and B (RNA-seq). (ODS 11 kb)
View article: Additional file 21: Table S10. of Extensive identification and analysis of conserved small ORFs in animals
Additional file 21: Table S10. of Extensive identification and analysis of conserved small ORFs in animals Open
Experimental evidence for human sORFs. (ODS 85 kb)
View article: Additional file 6: Table S5. of Extensive identification and analysis of conserved small ORFs in animals
Additional file 6: Table S5. of Extensive identification and analysis of conserved small ORFs in animals Open
All sORF information for worm. (TXT 1536 kb)
View article: Additional file 25: Table S14. of Extensive identification and analysis of conserved small ORFs in animals
Additional file 25: Table S14. of Extensive identification and analysis of conserved small ORFs in animals Open
Experimental evidence for C. elegans sORFs. (ODS 43 kb)