Meta-analysis of incomplete microarray studies

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Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify al ...

A key challenge across many disciplines is to extract meaningful information from data which is often obscured by noise. These datasets are typically represented as large matrices. Given the current trend of ever-increasing data volumes, with datasets grow ...

Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint ...

Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data st ...

Context. We present a novel approach to the construction of mock galaxy catalogues for large-scale structure analysis based on the distribution of dark matter halos obtained with effective bias models at the field level. Aims. We aim to produce mock galaxy ...

DNA methylation (DNAm) is one of the most frequently studied epigenetic mechanisms facilitating the interplay of genomic and environmental factors, which can contribute to externalizing behaviours and related psychiatric disorders. Previous epigenome-wide ...

Zebrafish have the capacity to fully regenerate the heart after an injury, which lies in sharp contrast to the irreversible loss of cardiomyocytes after a myocardial infarction in humans. Transcriptomics analysis has contributed to dissect underlying signa ...

Background: Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryo- genesis to innate ...

In certain cases of astronomical data analysis, the meaningful physical quantity to extract is the ratio R between two data sets. Examples include the lensing ratio, the interloper rate in spectroscopic redshift samples, and the decay rate of gravitational ...

BackgroundIt is generally accepted that most evolutionary transformations at the phenotype level are associated either with rearrangements of genomic regulatory elements, which control the activity of gene networks, or with changes in the amino acid conten ...

Information collected through sensor measurements has the potential to improve knowledge of complex-system behavior, leading to better decisions related to system management. In this situation, and particularly when using digital twins, the quality of sens ...

To build biophysically detailed models of brain cells, circuits, and regions, a data-driven approach is increasingly being adopted. This helps to obtain a simulated activity that reproduces the experimentally recorded neural dynamics as faithfully as possi ...

Learning-based outlier (mismatched correspondence) rejection for robust 3D registration generally formulates the outlier removal as an inlier/outlier classification problem. The core for this to be successful is to learn the discriminative inlier/outlier f ...

Investigating the dynamic activities of protein expression and signaling in living organisms is a crucial focus of intense research aimed at elucidating the processes that underlie disease progression and improving treatments and drug development. Resolvin ...

Automating experimental procedures has resulted in an unprecedented increase in the volume of generated data, which, in turn, has caused an accumulation of unprocessed data. As a result, the need to develop tools to analyze data systematically has been ris ...

Galaxy redshift surveys are subject to incompleteness and inhomogeneous sampling due to the various constraints inherent to spectroscopic observations. This can introduce systematic errors on the summary statistics of interest, which need to be mitigated i ...

Cancer is the second leading cause of death worldwide. Cancer develops through multiple hallmark functions including apoptosis evasion, unlimited replicative potential, metastasis, and immune avoidance. Over the past few decades, researchers have reported ...

We present the La Mobiliere insurance customers dataset: a 12-year-long longitudinal collection of data on policies of customers of the Swiss insurance company La Mobiliere. To preserve the privacy of La Mobiliere customers, we propose the data aggregated ...

Pancreatic cancer cells with limited access to free amino acids can grow by scavenging extracellular protein. In a murine model of pancreatic cancer, we performed a genome-wide CRISPR screen for genes required for scavenging-dependent growth. The screen id ...

There are 377 Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) in the human genome, making them the largest family of transcription factors. KZFPs are defined by a N-terminal KRAB domain and several zinc-finger domains arranged ...

Meta-analysis of incomplete microarray studies

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The dynamic genetic determinants of increased transcriptional divergence in spermatids

Spectral Estimators for High-Dimensional Matrix Inference

Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN

Orchestrating chromosome conformation capture analysis with Bioconductor

DESI mock challenge Halo and galaxy catalogues with the bias assignment method

Epigenome-wide DNA methylation in externalizing behaviours: A review and combined analysis

Transcriptomic data meta-analysis reveals common and injury model specific gene expression changes in the regenerating zebrafish heart

Statistical learning quantifies transposable element-mediated cis-regulation

An Unbiased Method of Measuring the Ratio of Two Data Sets

Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

Methodology for selecting measurement points that optimize information gain for model updating

Online interoperable resources for building hippocampal neuron models via the Hippocampus Hub

Robust Outlier Rejection for 3D Registration with Variational Bayes

Label-free plasmonic microarray for multiplexed analysis of cells and tumor organoids

Modeling, analysis, and design of complex biological networks

Angular systematics-free cosmological analysis of galaxy clustering in configuration space

Integrative transcriptome analyses of Transposable Elements (TEs) and genes contribute to a better understanding of colorectal cancer

High spatial resolution dataset of La Mobiliere insurance customers

GCN2 adapts protein synthesis to scavenging-dependent growth

KRAB zinc-finger proteins and their transposable element targets: between antagonism and cooperation