Related papers: Network-based Isoform Quantification with RNA-Seq …

We propose a new multi-network-based strategy to integrate different layers of genomic information and use them in a coordinate way to identify driving cancer genes. The multi-networks that we consider combine transcription factor…

CLIP-seq methods are valuable techniques to experimentally determine transcriptome-wide binding sites of RNA-binding proteins. Despite the constant improvement of such techniques (e.g. eCLIP), the results are affected by various types of…

The number of studies dealing with RNA-Seq data analysis has experienced a fast increase in the past years making this type of gene expression a strong competitor to the DNA microarrays. This paper proposes a Bayesian model to detect down…

Although RNA-Seq data provide unprecedented isoform-level expression information, detection of alternative isoform regulation (AIR) remains difficult, particularly when working with an incomplete transcript annotation. We introduce…

Most cellular phenotypes are genetically complex. Identifying the set of genes that are most closely associated with a specific cellular state is still an open question in many cases. Here we study the transcriptional profile of cellular…

High-throughput RNA sequencing (RNA-seq) has emerged as a revolutionary and powerful technology for expression profiling. Most proposed methods for detecting differentially expressed (DE) genes from RNA-seq are based on statistics that…

Isoforms are mRNAs produced from the same gene site in the phenomenon called Alternative Splicing. Studies have shown that more than 95% of human multi-exon genes have undergone alternative splicing. Although there are few changes in mRNA…

Single cell combinatorial indexing RNA sequencing (sci-RNA-seq) is a powerful method for recovering gene expression data from an exponentially scalable number of individual cells or nuclei. However, sci-RNA-seq is a complex protocol that…

Nuclei instance segmentation in pathological images is crucial for downstream tasks such as tumor microenvironment analysis. However, the high cost and scarcity of annotated data limit the applicability of fully supervised methods, while…

Histopathology whole-slide images (WSIs) are routinely acquired in clinical practice and contain rich tissue morphology but lack direct molecular architecture and functional programs defining pathological states, whereas RNA sequencing…

Use of next-generation sequencing technologies to transcriptomics (RNA-seq) for gene expression profiling has found widespread application in studying different biological conditions including cancers. However, RNA-seq experiments are still…

This paper presents incremental network quantization (INQ), a novel method, targeting to efficiently convert any pre-trained full-precision convolutional neural network (CNN) model into a low-precision version whose weights are constrained…

Direct cDNA preamplification protocols developed for single-cell RNA-seq have enabled transcriptome profiling of precious clinical samples and rare cells without sample pooling or RNA extraction. Currently, there is no algorithm optimized…

The NuCLS dataset contains over 220.000 annotations of cell nuclei in breast cancers. We show how to use these data to create a multi-rater model with the MIScnn Framework to automate the analysis of cell nuclei. For the model creation, we…

Systematic characterization of biological effects to genetic perturbation is essential to the application of molecular biology and biomedicine. However, the experimental exhaustion of genetic perturbations on the genome-wide scale is…

Predicting drug responses using genetic and transcriptomic features is crucial for enhancing personalized medicine. In this study, we implemented an ensemble of machine learning algorithms to analyze the correlation between genetic and…

With the increased affordability and availability of whole-genome sequencing, large-scale and high-throughput gene expression is widely used to characterize diseases, including cancers. However, establishing specificity in cancer diagnosis…

Deciphering complex gene-gene interactions remains challenging in transcriptomics as traditional methods often miss higher-order and nonlinear dependencies. This study introduces a quantum-inspired framework leveraging tensor networks (TNs)…

Defining and separating cancer subtypes is essential for facilitating personalized therapy modality and prognosis of patients. The definition of subtypes has been constantly recalibrated as a result of our deepened understanding. During…

Studies into the statistical properties of biological networks have led to important biological insights, such as the presence of hubs and hierarchical modularity. There is also a growing interest in studying the statistical properties of…