Related papers: Power-law Signatures and Patchiness in Genechip Ol…
Oligonucleotide arrays are used in a wide range of genomic analyses, such as gene expression profiling, comparative genomic hybridization, chromatin immunoprecipitation, SNP detection, etc. During fabrication, the sites of an…
Background: The availability of high throughput methods for measurement of mRNA concentrations makes the reliability of conclusions drawn from the data and global quality control of samples and hybridization important issues. We address…
In a recent paper [Phys. Rev. E 68, 011906 (2003)], Naef and Magnasco suggested that the "bright" mismatches observed in Affymetrix microarray experiments are caused by the fluorescent molecules used to label RNA target sequences, which…
Genome sequence analysis has enabled significant advancements in medical and scientific areas such as personalized medicine, outbreak tracing, and the understanding of evolution. Unfortunately, it is currently bottlenecked by the…
Machine learning interatomic potentials (MLIPs) enable atomistic simulations with near first-principles accuracy at substantially reduced computational cost, making them powerful tools for large-scale materials modeling. The accuracy of…
Recent attacks show that behavioural unlearning of large language models leaves internal traces recoverable by adversarial probes. We characterise where this retention lives and show it can be surgically removed without measurable…
Mass-spectrometry technologies are widely used in the fields of ionomics and metabolomics to simultaneously profile at the genome scale intracellular concentrations of e.g. amino acids or elements. Short profiles of molecular or…
High-dimensional phenotypes hold promise for richer findings in association studies, but testing of several phenotype traits aggravates the grand challenge of association studies, that of multiple testing. Several methods have recently been…
Many biomedical experiments are carried out by pooling individual biological samples. However, pooling samples can potentially hide biological variance and give false confidence concerning the data significance. In the context of microarray…
Feature selection for predictive analytics is the problem of identifying a minimal-size subset of features that is maximally predictive of an outcome of interest. To apply to molecular data, feature selection algorithms need to be scalable…
Quantifying interactions in DNA microarrays is of central importance for a better understanding of their functioning. Hybridization thermodynamics for nucleic acid strands in aqueous solution can be described by the so-called…
MOTIVATION: The use of oligonucleotide microarray technology requires a very detailed attention to the design of specific probes spotted on the solid phase. These problems are far from being commonplace since they refer to complex…
Gravitational-wave (GW) astronomy has advanced our understanding of compact mergers through instruments like the Laser Interferometer Gravitational-Wave Observatory (LIGO). However, the extreme sensitivity required for these detections…
Multiple technologies that measure expression levels of protein mixtures in the human body offer a potential for detection and understanding the disease. The recent increase of these technologies prompts researchers to evaluate the…
A plasma impedance probe (PIP) is a type of in-situ, radio-frequency (RF) probe that is traditionally used to measure plasma properties (e.g. density) in low-density environments such as the Earth's ionosphere. We believe that PIPs are…
While designing oligonucleotide-based microarrays, cross-hybridization between surface-bound oligos and non-intended labeled targets is probably the most difficult parameter to predict. Although literature describes rules-of-thumb…
Genetic Algorithms (GAs) are explored as a tool for probing new physics with high dimensionality. We study the 19-dimensional pMSSM, including experimental constraints from all sources and assessing the consistency of potential signals of…
Boolean formulae compactly encode huge, constrained search spaces. Thus, variability-intensive systems are often encoded with Boolean formulae. The search space of a variability-intensive system is usually too large to explore without…
Metagenome, a mixture of different genomes (as a rule, bacterial), represents a pattern, and the analysis of its composition is, currently, one of the challenging problems of bioinformatics. In the present study, the possibility of…
Probe theories are only applicable in the regime where the probe's perturbation of the plasma can be neglected. However, it is not always possible to know, a priori, that a particular probe theory can be successfully applied, especially in…