Related papers: Quantitative modeling and data analysis of SELEX e…
A Systematic Evolution of Ligands by EXponential enrichment (SELEX) experiment begins in round one with a random pool of oligonucleotides in equilibrium solution with a target. Over a few rounds, oligonucleotides having a high affinity for…
The search for high-affinity aptamers for targets such as proteins, small molecules, or cancer cells remains a formidable endeavor. Systematic Evolution of Ligands by EXponential Enrichment (SELEX) offers an iterative process to discover…
Model-based reinforcement learning is a powerful tool, but collecting data to fit an accurate model of the system can be costly. Exploring an unknown environment in a sample-efficient manner is hence of great importance. However, the…
Often a screening or selection experiment targets a cell or tissue, which presents many possible molecular targets and identifies a correspondingly large number of ligands. We describe a statistical method to extract an estimate of the…
Transcriptomic analysis are characterized by being not directly quantitative and only providing relative measurements of expression levels up to an unknown individual scaling factor. This difficulty is enhanced for differential expression…
We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic…
Gene-gene interactions play a crucial role in the manifestation of complex human diseases. Uncovering significant gene-gene interactions is a challenging task. Here, we present an innovative approach utilizing data-driven computational…
In human cells, estrogenic signals induce cyclical association and dissociation of specific proteins with the DNA in order to activate transcription of estrogen-responsive genes. These oscillations can be modeled by assuming a large number…
In this review we focus on the idea of establishing connections between the mechanical properties of DNAligand complexes and the physical chemistry of DNA-ligand interactions. This type of connection is interesting because it opens the…
Modern genomics experiments measure functional behaviors for many thousands of DNA sequences. We suggest that, especially when these sequences are chosen at random, it is natural to compute correlation functions between sequences and…
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…
This study presents the approach to analyzing the evolution of an arbitrary complex system whose behavior is characterized by a set of different time-dependent factors. The key requirement for these factors is only that they must contain an…
Molecular ecology uses molecular genetic data to answer traditional ecological questions in biogeography and biodiversity among others. Several ecological principles, such as the niche hypothesis and the competitive exclusions, are based on…
Tethered particle motion experiments are versatile single-molecule techniques enabling one to address in vitro the molecular properties of DNA and its interactions with various partners involved in genetic regulations. These techniques…
We introduce a test for the overall effect of interaction between DNA methylation and a set of single nucleotide polymorphisms (SNPs) on a quantitative phenotype. The developed inference procedure is based on a functional approach that…
We combine replica exchange (parallel tempering) with normalizing flows, a class of deep generative models. These two sampling strategies complement each other, resulting in an efficient strategy for sampling molecular systems characterized…
We study theoretical ``design principles'' for transcription factor-DNA interaction in bacteria, focusing particularly on the statistical interaction of the transcription factors (TF's) with the genomic background (i.e., the genome without…
Most protocols for the high-throughput directed evolution of enzymes rely on random encapsulation to link phenotype and genotype. In order to optimize these approaches, or compare one to another, one needs a measure of their performance at…
Feature interaction selection is a fundamental problem in commercial recommender systems. Most approaches equally enumerate all features and interactions by the same pre-defined operation under expert guidance. Their recommendation is…
We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with…