Related papers: Modelling background intensity in Affymetrix Genec…
This paper presents a robust regression approach for image binarization under significant background variations and observation noises. The work is motivated by the need of identifying foreground regions in noisy microscopic image or…
High-throughput and quantitative experimental technologies are experiencing rapid advances in the biological sciences. One important recent technique is multiplexed fluorescence in situ hybridization (mFISH), which enables the…
The development of cancer is largely driven by the gain or loss of subsets of the genome, promoting uncontrolled growth or disabling defenses against it. Identifying genomic regions whose DNA copy number deviates from the normal is…
Analysis of DNA samples is an important step in forensics, and the speed of analysis can impact investigations. Comparison of DNA sequences is based on the analysis of short tandem repeats (STRs), which are short DNA sequences of 2-5 base…
Intensity mapping observations measure galaxy clustering fluctuations from spectral-spatial maps, requiring stable noise properties on large angular scales. We have developed specialized readouts and analysis methods for achieving…
The ability to detect and discriminate DNA bases by reading it directly using simple and cost-effective methods is an important problem whose solution can produce significant value for areas such as cancer and human genetic disorders.…
A major task in particle physics is the measurement of rare signal processes. Even modest improvements in background rejection, at a fixed signal efficiency, can significantly enhance the measurement sensitivity. Building on prior research…
Mid-infrared photothermal (MIP) microscopy has been a promising label-free chemical imaging technique for functional characterization of specimens owing to its enhanced spatial resolution and high specificity. Recently developed wide-field…
The Wide Field Imager (WFI) flying on Athena will usher in the next era of studying the hot and energetic Universe. WFI observations of faint, diffuse sources will be limited by uncertainty in the background produced by high-energy…
DNA microarray experiments, a well-established experimental technique, aim at understanding the function of genes in some biological processes. One of the most common experiments in functional genomics research is to compare two groups of…
Intensity mapping experiments survey the spectrum of diffuse line radiation rather than detect individual objects at high signal-to-noise. Spectral maps of unresolved atomic and molecular line radiation contain three-dimensional information…
The values of the signal-to-noise ratio are determined, at which the method of processing X-ray diffraction data reveals reflections with intensity less than the noise component of the background. The possibilities of the method are…
Foundation models (FMs) pretrained on large datasets have become fundamental for various downstream machine learning tasks, in particular in scenarios where obtaining perfectly labeled data is prohibitively expensive. In this paper, we…
We consider the problem of coding for the substring channel, in which information strings are observed only through their (multisets of) substrings. Due to existing DNA sequencing techniques and applications in DNA-based storage systems,…
We study mathematically a method for discovering which gene is related to a cell phenotype of interest. The method is based on RNA interference -- a molecular process for gene deactivation -- and on coupling the phenotype with fluorescence…
Recent advances in the fingerprinting of deep neural networks detect instances of models, placed in a black-box interaction scheme. Inputs used by the fingerprinting protocols are specifically crafted for each precise model to be checked…
Microarray is a technology to quantitatively monitor the expression of large number of genes in parallel. It has become one of the main tools for global gene expression analysis in molecular biology research in recent years. The large…
The problem of foreground material signature extraction in an intimate (nonlinear) mixing setting is considered. It is possible for a foreground material signature to appear in combination with multiple background material signatures. We…
We aim to automatize the identification of collective variables to simplify and speed up enhanced sampling simulations of conformational dynamics in biomolecules. We focus on anharmonic low-frequency vibrations that exhibit fluctuations on…
Modern radio interferometric arrays offer high sensitivity, wide fields of view, and broad frequency coverage, but also pose significant data calibration challenges. Standard direction-independent calibration is insufficient to correct…