Related papers: Massively Parallel RNA Chemical Mapping with a Red…
Large-scale proteomic analysis is emerging as a powerful technique in biology and relies heavily on data acquired by state-of-the-art mass spectrometers. As with any other field in Systems Biology, computational tools are required to deal…
Summary: We describe a tool for quantifying the uniformity of mapped reads in high-throughput sequencing experiments. Our statistic directly measures the uniformity of both read position and fragment length, and we explain how to compute a…
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…
Single-cell RNA sequencing (scRNA-seq) reveals cell heterogeneity, with cell clustering playing a key role in identifying cell types and marker genes. Recent advances, especially graph neural networks (GNNs)-based methods, have…
Rapid advancements in high-throughput single-cell RNA-seq (scRNA-seq) technologies and experimental protocols have led to the generation of vast amounts of genomic data that populates several online databases and repositories. Here, we…
Background: Connectivity mapping is a process to recognize novel pharmacological and toxicological properties in small molecules by comparing their gene expression signatures with others in a database. A simple and robust method for…
Structural variants compose the majority of human genetic variation, but are difficult to assess using current genomic sequencing technologies. Optical mapping technologies, which measure the size of chromosomal fragments between labeled…
We present a unique, multitask dataset comprising 143 drug and drug candidate molecules, each evaluated on in vitro, parallel artificial-membrane permeability assays (PAMPA) using six different model membranes. Using this resource, we…
High-throughput mRNA sequencing (RNA-Seq) is widely used for transcript quantification of gene isoforms. Since RNA-Seq data alone is often not sufficient to accurately identify the read origins from the isoforms for quantification, we…
Air-based molecular communication (MC) has the potential to be one of the first MC systems to be deployed in real-world applications, enabled by existing sensor technologies such as metal-oxide semi-conductor (MOS) sensors. However,…
Markov chain Monte Carlo (MCMC) methods are foundational algorithms for Bayesian inference and probabilistic modeling. However, most MCMC algorithms are inherently sequential and their time complexity scales linearly with the sequence…
RockIt is a maximum a-posteriori (MAP) query engine for statistical relational models. MAP inference in graphical models is an optimization problem which can be compiled to integer linear programs (ILPs). We describe several advances in…
In biological research machine learning algorithms are part of nearly every analytical process. They are used to identify new insights into biological phenomena, interpret data, provide molecular diagnosis for diseases and develop…
Single-cell RNA sequencing (scRNA-seq) is powerful technology that allows researchers to understand gene expression patterns at the single-cell level. However, analysing scRNA-seq data is challenging due to issues and biases in data…
Linearized string representations serve as the foundation of scalable autoregressive molecular generation; however, they introduce a fundamental modality mismatch where a single molecular graph maps to multiple distinct sequences. This…
Single-nucleotide-resolution chemical mapping for structured RNA is being rapidly advanced by new chemistries, faster readouts, and coupling to computational algorithms. Recent tests have shown that selective 2'-hydroxyl acylation by primer…
The determination of chemical mixture components is vital to a multitude of scientific fields. Oftentimes spectroscopic methods are employed to decipher the composition of these mixtures. However, the sheer density of spectral features…
The detection and flux estimation of point sources in cosmic microwave background (CMB) maps is a very important task in order to clean the maps and also to obtain relevant astrophysical information. In this paper we propose a maximum a…
Designing RNA molecules has garnered recent interest in medicine, synthetic biology, biotechnology and bioinformatics since many functional RNA molecules were shown to be involved in regulatory processes for transcription, epigenetics and…
Network inference has been attracting increasing attention in several fields, notably systems biology, control engineering and biomedicine. To develop a therapy, it is essential to understand the connectivity of biochemical units and the…