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View article: Comparison on Sensor Fault Detection Techniques for SHM Systems
Comparison on Sensor Fault Detection Techniques for SHM Systems Open
Engineering systems are designed to serve society for decades and are exposed to multiple environmental and load conditions. This circumstance leads to the degradation of the system, causing different structural behaviours. In this regard,…
View article: Investigation of Robustness in Detecting and Localizing Sensor Malfunctions in Deteriorating Structural Health Monitoring Systems
Investigation of Robustness in Detecting and Localizing Sensor Malfunctions in Deteriorating Structural Health Monitoring Systems Open
Structural Health Monitoring (SHM) systems are essential for damage detection and maintenance planning in aging infrastructure. However, sensor degradation increases epistemic uncertainty and leads to incorrect SHM assessments, making it n…
View article: Investigating Robustness in Detection, Localization and Compensation of Sensor Malfunctions in Degrading Structural Health Monitoring Systems
Investigating Robustness in Detection, Localization and Compensation of Sensor Malfunctions in Degrading Structural Health Monitoring Systems Open
Structural Health Monitoring (SHM) systems are essential for damage detection and maintenance planning in aging infrastructure. However, sensor degradation increases epistemic uncertainty and leads to incorrect SHM assessments, making it n…
View article: Perturb-seq reveals distinct responses to pluripotency regulator dosages underlying the control of self-renewal and differentiation
Perturb-seq reveals distinct responses to pluripotency regulator dosages underlying the control of self-renewal and differentiation Open
Precise regulation of transcription factor (TF) expression is critical for maintaining cell identity, but studies on how graded expression levels affect cellular phenotypes are limited. To address this gap, we employed human embryonic stem…
View article: Regulation of translation elongation and integrated stress response in heat-shocked neurons
Regulation of translation elongation and integrated stress response in heat-shocked neurons Open
View article: FLT1 and other candidate fetal haemoglobin modifying loci in sickle cell disease in African ancestries
FLT1 and other candidate fetal haemoglobin modifying loci in sickle cell disease in African ancestries Open
Known fetal haemoglobin (HbF)-modulating loci explain 10-24% variation of HbF level in Africans with Sickle Cell Disease (SCD), compared to 50% among Europeans. Here, we report fourteen candidate loci from a genome-wide association study (…
View article: Theory and application of possibility and evidence in reliability analysis and design optimization
Theory and application of possibility and evidence in reliability analysis and design optimization Open
Numerous design optimization methodologies and reliability analysis techniques have been developed to address aleatory and epistemic uncertainties in engineering system design. Aleatory uncertainty is modeled by statistical distributions, …
View article: UncertaintyQuantification.jl: Efficient Reliability Analysis Powered by Julia
UncertaintyQuantification.jl: Efficient Reliability Analysis Powered by Julia Open
View article: Bayesian Updating for Reliability with Imprecise Probabilities: Julia Implementation and Application to the NASA Langley UQ Challenge 2019
Bayesian Updating for Reliability with Imprecise Probabilities: Julia Implementation and Application to the NASA Langley UQ Challenge 2019 Open
View article: An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation
An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation Open
Mammalian genomes contain millions of regulatory elements that control the complex patterns of gene expression. Previously, The ENCODE consortium mapped biochemical signals across many cell types and tissues and integrated these data to de…
View article: RNA-seq protocol v1
RNA-seq protocol v1 Open
RNA-seq protocol for ESC-DE differentiation timecourse
View article: ATAC-seq protocol v1
ATAC-seq protocol v1 Open
ATAC-seq protocol for ESC-DE differentiation
View article: Hi-C protocol v1
Hi-C protocol v1 Open
Hi-C protocol for ESC DE differentiation time course.
View article: scRNA-seq protocol v1
scRNA-seq protocol v1 Open
scRNA-seq protocol for ESC DE differentiation time course
View article: Flow-cytometry CRISPRi screen v1
Flow-cytometry CRISPRi screen v1 Open
Flow-cytometry CRISPRi screen
View article: ChIP-seq protocol v1
ChIP-seq protocol v1 Open
ChIP-seq protocol for ESC-DE differentiation
View article: Parallel genome-scale CRISPR-Cas9 screens uncouple human pluripotent stem cell identity versus fitness
Parallel genome-scale CRISPR-Cas9 screens uncouple human pluripotent stem cell identity versus fitness Open
View article: MicroRNAs provide negative feedback and stability in gene regulatory network models of cell-state transitions
MicroRNAs provide negative feedback and stability in gene regulatory network models of cell-state transitions Open
The development of multicellular organisms occurs through a series of cell state transitions controlled by gene regulatory networks. Central to these networks are transcription factors (TFs) which bind enhancers and activate the expression…
View article: Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals
Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals Open
View article: How to Be Certain: Using Known Relations and Trust Discount to Determine Confidence About the Degree of Uncertainty
How to Be Certain: Using Known Relations and Trust Discount to Determine Confidence About the Degree of Uncertainty Open
Ensuring certainty in the rapidly evolving digital twin environments amidst inherent uncertainty is paramount in decision-making for critical engineering systems. This paper presents a novel approach for quantifying and tracking confidence…
View article: Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer
Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer Open
Gastric cancer (GC) is the fifth most common cancer worldwide and is a heterogeneous disease. Among GC subtypes, the mesenchymal phenotype (Mes-like) is more invasive than the epithelial phenotype (Epi-like). Although gene expression of th…
View article: Multicenter integrated analysis of noncoding CRISPRi screens
Multicenter integrated analysis of noncoding CRISPRi screens Open
View article: CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods
CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods Open
View article: An encyclopedia of enhancer-gene regulatory interactions in the human genome
An encyclopedia of enhancer-gene regulatory interactions in the human genome Open
Identifying transcriptional enhancers and their target genes is essential for understanding gene regulation and the impact of human genetic variation on disease 1–6 . Here we create and evaluate a resource of >13 million enhancer-gene regu…
View article: Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals
Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals Open
Gene regulatory elements drive many complex biological phenomena such as fetal development, and their mutations are linked to a multitude of common human diseases. The phenotypic impacts of regulatory variants are often tested using their …
View article: Growth media affects susceptibility of air-lifted human nasal epithelial cell cultures to SARS-CoV2, but not Influenza A, virus infection
Growth media affects susceptibility of air-lifted human nasal epithelial cell cultures to SARS-CoV2, but not Influenza A, virus infection Open
Primary differentiated human epithelial cell cultures have been widely used by researchers to study viral fitness and virus-host interactions, especially during the COVID19 pandemic. These cultures recapitulate important characteristics of…
View article: Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions
Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions Open
View article: The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity
The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity Open
The majority of mammalian genes encode multiple transcript isoforms that result from differential promoter use, changes in exonic splicing, and alternative 3’ end choice. Detecting and quantifying transcript isoforms across tissues, cell t…
View article: Parallel genome-scale CRISPR-Cas9 screens uncouple human pluripotent stem cell identity versus fitness
Parallel genome-scale CRISPR-Cas9 screens uncouple human pluripotent stem cell identity versus fitness Open
Pluripotent stem cells are defined by their self-renewal capacity, which is the ability of the stem cells to proliferate indefinitely while maintaining the pluripotent identity essential for their ability to differentiate into any somatic …
View article: Early Transcriptional Responses of Human Nasal Epithelial Cells to Infection with Influenza A and SARS-CoV-2 Virus Differ and Are Influenced by Physiological Temperature
Early Transcriptional Responses of Human Nasal Epithelial Cells to Infection with Influenza A and SARS-CoV-2 Virus Differ and Are Influenced by Physiological Temperature Open
Influenza A (IAV) and SARS-CoV-2 (SCV2) viruses represent an ongoing threat to public health. Both viruses target the respiratory tract, which consists of a gradient of cell types, receptor expression, and temperature. Environmental temper…