相关论文: Controlling uncertainty in aptamer selection
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…
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…
SELEX (Systematic Evolution of Ligands by Exponential Enrichment) is an experimental procedure that allows extracting, from an initially random pool of DNA, those oligomers with high affinity for a given DNA-binding protein. We address what…
Aptamers, short synthetic RNA/DNA molecules binding specific targets with high affinity and specificity, are utilized in an increasing spectrum of bio-medical applications. Aptamers are identified in vitro via the Systematic Evolution of…
Evolutionary dynamics and patterns of molecular evolution are strongly influenced by selection on linked regions of the genome, but our quantitative understanding of these effects remains incomplete. Recent work has focused on predicting…
The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through…
Aptamers are single stranded DNA, RNA or peptide sequences having the ability to bind a variety of specific targets (proteins, molecules as well as ions). Therefore, aptamer production and selection for therapeutic and diagnostic…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
The unwelcome evolution of malignancy during cancer progression emerges through a selection process in a complex heterogeneous population structure. In the present work, we investigate evolutionary dynamics in a phenotypically heterogeneous…
Multilevel selection occurs when short-term individual-level reproductive interests conflict with longer-term group-level fitness effects. Detecting and quantifying this phenomenon is key to understanding evolution of traits ranging from…
Single molecule and NMR measurements of protein dynamics increasingly uncover the complexity of binding scenarios. Here we describe an extended conformational selection model which embraces a repertoire of selection and adjustment…
Pervasive natural selection can strongly influence observed patterns of genetic variation, but these effects remain poorly understood when multiple selected variants segregate in nearby regions of the genome. Classical population genetics…
In this work, we consider the problem of identifying an unknown linear dynamical system given a finite hypothesis class. In particular, we analyze the effect of the excitation input on the sample complexity of identifying the true system…
Selective prediction aims to learn a reliable model that abstains from making predictions when uncertain. These predictions can then be deferred to humans for further evaluation. As an everlasting challenge for machine learning, in many…
Inverse design of short single-stranded RNA and DNA sequences (aptamers) is the task of finding sequences that satisfy a set of desired criteria. Relevant criteria may be, for example, the presence of specific folding motifs, binding to…
Different evolutionary models are known to make disparate predictions for the success of an invading mutant in some situations. For example, some evolutionary mechanics lead to amplification of selection in structured populations, while…
When a population inhabits an inhomogeneous environment, the fitness value of traits can vary with the position in the environment. Gene flow caused by random mating can nevertheless prevent that a sexually reproducing population splits…
The rate of biological evolution depends on the fixation probability and on the fixation time of new mutants. Intensive research has focused on identifying population structures that augment the fixation probability of advantageous mutants.…
Inspired by natural evolution, evolutionary search algorithms have proven remarkably capable due to their dual abilities to radiantly explore through diverse populations and to converge to adaptive pressures. A large part of this behavior…
Several mating restriction techniques have been implemented in Evolutionary Algorithms to promote diversity. From similarity-based selection to niche preservation, the general goal is to avoid premature convergence by not having fitness…