The protein recombinase can change the knot type of circular DNA. The action of a recombinase converting one knot into another knot is normally mathematically modeled by band surgery. Band surgeries on a 2-bridge knot N((4mn-1)/(2m)) yielding a (2,2k)-torus link are characterized. We apply this and other rational tangl…
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48 results for “DNA recombination”
We categorise coherent band (aka nullification) pathways between knots and 2-component links. Additionally, we characterise the minimal coherent band pathways (with intermediates) between any two knots or 2-component links with small crossing number. We demonstrate these band surgeries for knots and links with small cr…
Site-specific recombination on supercoiled circular DNA molecules can yield a variety of knots and catenanes. Twist knots are some of the most common conformations of these products and they can act as substrates for further rounds of site-specific recombination. They are also one of the simplest families of knots and …
Betti Numbers of Prodsimplicial Complexes for Directed Graphs with Applications to Word Reductionsmath.CO
Study of Betti numbers in prodsimplicial complexes for directed graphs, focusing on DNA recombination.
problem Analyzing Betti numbers in directed graphs for DNA recombination.
method Custom prodsimplicial complexes for acyclic directed graphs, investigating Betti numbers.
result Investigated Betti numbers and cycles in prodsimplicial complexes for DNA recombination.
From tangle fractions to DNAmath.GT
This paper is an introduction to rational tangles, rational knots and links and their applications to DNA. The paper can be read as an introduction to our more technical papers on rational tangles (math.GT/0311499) and on rational knots (math.GT/0212011). The present paper includes a self-contained account of the tangl…
This paper gives new and elementary combinatorial topological proofs of the classification of unoriented and oriented rational knots and links. These proofs are based on the known classification of alternating knots through flyping, and the calculus of continued fractions. We characterize the class of strongly invertib…
In this paper, we study a geometric/topological measure of knots and links called the nullification number. The nullification of knots/links is believed to be biologically relevant. For example, in DNA topology, one can intuitively regard it as a way to measure how easily a knotted circular DNA can unknot itself throug…
We prove that if the lens space is obtained by a surgery along a knot in the lens space that is distance one from the meridional slope, then is in . This result yields a classification of the coherent and non-coherent band surgeries from the trefoil to tor…
Site-specific recombination is an enzymatic process where two sites of precise sequence and orientation along a circle come together, are cleaved, and the ends are recombined. Site-specific recombination on a knotted substrate produces another knot or a two-component link depending on the relative orientation of the si…
Topological surgery is a mathematical technique used for creating new manifolds out of known ones. We observe that it occurs in natural phenomena where a sphere of dimension 0 or 1 is selected, forces are applied and the manifold in which they occur changes type. For example, 1-dimensional surgery happens during chromo…
DNA rearrangement processes recombine gene segments that are organized on the chromosome in a variety of ways. The segments can overlap, interleave or one may be a subsegment of another. We use directed graphs to represent segment organizations on a given locus where contigs containing rearranged segments represent ver…
A New Trinomial Recombination Tree Algorithm and Its Applications
A high-order recombination algorithm for weak approximation of stochastic differential equationsmath.PR
Paper develops a high-order recombination algorithm for financial modeling.
problem Creating accurate approximations of stochastic differential equations in finance.
method High-order recombination method applied to practical financial problems.
result Algorithm effectively avoids explosive growth in support cardinality for high-order approximations.
DNA Methylation has been the most extensively studied epigenetic mark. Usually a change in the genotype, DNA sequence, leads to a change in the phenotype, observable characteristics of the individual. But DNA methylation, which happens in the context of CpG (cytosine and guanine bases linked by phosphate backbone) dinu…
We introduce a notion of genus range as a set of values of genera over all surfaces into which a graph is embedded cellularly, and we study the genus ranges of a special family of four-regular graphs with rigid vertices that has been used in modeling homologous DNA recombination. We show that the genus ranges are sets …
An evolutionary algorithm separates mixed DNA profiles in forensic genetics.
problem Deconvolving mixed DNA profiles from crime samples.
method Multiple population evolutionary algorithm (MEA) with guided mutation.
result The MEA successfully deconvoluted DNA profiles from crime samples.
We introduce an evolutionary algorithm called recombinator--means for optimizing the highly non-convex kmeans problem. Its defining feature is that its crossover step involves all the members of the current generation, stochastically recombining them with a repurposed variant of the -means++ seeding algorithm. Th…
The theme in this paper is the recombining binomial tree to price American put option when the underlying stock follows constant elasticity of variance(CEV) process. Recombining nodes of binomial tree are decided from finite difference scheme to emulate CEV process and the tree has a linear complexity. Also it is deriv…
In Divide & Recombine (D&R), big data are divided into subsets, each analytic method is applied to subsets, and the outputs are recombined. This enables deep analysis and practical computational performance. An innovate D\&R procedure is proposed to compute likelihood functions of data-model (DM) parameters for big dat…
We develop a topological model of site-specific recombination that applies to substrates which are the connected sum of two torus links of the form . Then we use our model to prove that all knots and links that can be produced by site-specific recombination on such substrates are contained in one of two…
The folding structure of the DNA molecule combined with helper molecules, also referred to as the chromatin, is highly relevant for the functional properties of DNA. The chromatin structure is largely determined by the underlying primary DNA sequence, though the interaction is not yet fully understood. In this paper we…
Many researches demonstrated that the DNA methylation, which occurs in the context of a CpG, has strong correlation with diseases, including cancer. There is a strong interest in analyzing the DNA methylation data to find how to distinguish different subtypes of the tumor. However, the conventional statistical methods …
This paper gives infinitely many examples of unknot diagrams that are hard, in the sense that the diagrams need to be made more complicated by Reidemeister moves before they can be simplified. In order to construct these diagrams, we prove theorems characterizing when the numerator of the sum of two rational tangles is…
A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networkscs.LG
An explosion of high-throughput DNA sequencing in the past decade has led to a surge of interest in population-scale inference with whole-genome data. Recent work in population genetics has centered on designing inference methods for relatively simple model classes, and few scalable general-purpose inference techniques…
New RL approach builds short ancestral recombination graphs.
problem Building short ancestral recombination graphs (ARGs).
method Reinforcement Learning applied to genetic sequences.
result RL can build ARGs as short as heuristic algorithms.
Paper develops a new method for game options in local volatility models.
problem Optimal stopping in one-dimensional diffusion with general coefficients.
method Skorokhod embedding to construct recombining tree approximations.
result Construct nearly optimal stopping times with convergence rates.
This research adapts superpixels for Shapley value computation in DNA profile classification.
problem Efficiently computing Shapley values for large, multidimensional time-series data.
method Adapting the concept of superpixels to streamline Shapley value computation for time-series-like data.
result Realistic, accurate, and fast computation of Shapley values for DNA profile classification.
We extend the tangle model, originally developed by Ernst and Sumners, to include composite knots. We show that, for any prime tangle, there are no rational tangle attachments of distance greater than one that first yield a 4-plat and then a connected sum of 4-plats. This is done by building on results on exceptional D…
We develop topological methods for analyzing difference topology experiments involving 3-string tangles. Difference topology is a novel technique used to unveil the structure of stable protein-DNA complexes involving two or more DNA segments. We analyze such experiments for the Mu protein-DNA complex. We characterize t…
We propose generative neural network methods to generate DNA sequences and tune them to have desired properties. We present three approaches: creating synthetic DNA sequences using a generative adversarial network; a DNA-based variant of the activation maximization ("deep dream") design method; and a joint procedure wh…
New model improves DNA methylation data analysis.
problem Analyzing DNA methylation data with complex distributions.
method Doubly non-central beta (DNCB) distribution for non-negative matrix factorization.
result Improves predictive performance and yields meaningful latent representations.
DNAS disentangles neural architecture search for better interpretability and performance.
problem Lack of interpretability in existing neural architecture search methods.
method DNAS disentangles the hidden representation of the controller into semantically meaningful concepts.
result DNAS achieves state-of-the-art performance and competitive architectures.
Market portfolio decomposed into body and tail legs
problem Separation of market portfolio into body and tail legs
method Dynamic value-weighted body and tail legs
result Recombination identity holds for all models
Study decomposes market portfolio into body and tail legs, revealing systematic differences.
problem Understanding the relationship between body and tail components in market portfolios.
method Decomposes CRSP market portfolio into body and tail legs, analyzes their recombination identity.
result Recombination identity holds for all models but not for all, indicating systematic differences.
Genomic models learn DNA sequences to predict functions.
problem Understanding complex genetic interactions.
method Training LLMs on DNA sequences to predict functions.
result gLMs can predict functions of DNA elements.
In this paper, we consider recommender systems with side information in the form of graphs. Existing collaborative filtering algorithms mainly utilize only immediate neighborhood information and have a hard time taking advantage of deeper neighborhoods beyond 1-2 hops. The main caveat of exploiting deeper graph informa…
DNA Methylation Data to Predict Suicidal and Non-Suicidal Deaths: A Machine Learning Approachq-bio.GN
Study uses DNA methylation data to predict suicidal and non-suicidal deaths.
problem Predicting suicidal and non-suicidal deaths from DNA methylation data.
method Support Vector Machines (SVM) with dimensionality reduction using PCA and t-SNE.
result t-SNE outperforms PCA in reducing data dimensionality.
Gaussian Recombining Split Treeq-fin.CP
A new tree model, GRST, improves option pricing without log-normality assumptions.
problem Limitations of CRR binomial trees in valuing securities with early exercise characteristics.
method Gaussian Recombining Split Tree (GRST) that generates a discrete probability mass function approximating a Gaussian distribution.
result Option prices from GRST align closely with market prices.
We study two systems of tangle equations that arise when modeling the action of the Integrase family of proteins on DNA. These two systems--direct and inverted repeats--correspond to two different possibilities for the initial DNA sequence. We present one new class of solutions to the tangle equations. In the case of i…
A faster method for optimizing DNA and protein sequences using machine learning.
problem Designing DNA and protein sequences with improved function.
method Activation maximization with a straight-through approximation and adaptive entropy variable.
result Fast SeqProp achieves up to 100-fold faster convergence and improved fitness optima.
A deep probabilistic model analyzes DNA-encoded library data for efficient screening.
problem Complex data from DNA-encoded library experiments mask underlying signals.
method Compositional deep probabilistic model of DEL data, modeling latent reactions between synthons.
result DEL-Compose model demonstrates strong performance and valuable insights.
In this paper we propose network methodology to infer prognostic cancer biomarkers based on the epigenetic pattern DNA methylation. Epigenetic processes such as DNA methylation reflect environmental risk factors, and are increasingly recognised for their fundamental role in diseases such as cancer. DNA methylation is a…
Measures DNA quality degradation effects.
problem Identifying degraded DNA sequence data.
method Novel quality quantification based on intentional degradation effects.
result Quantified measures of degradation can be used for multiple purposes.
When analyzing the genome, researchers have discovered that proteins bind to DNA based on certain patterns of the DNA sequence known as "motifs". However, it is difficult to manually construct motifs due to their complexity. Recently, externally learned memory models have proven to be effective methods for reasoning ov…
A new data-level recombination strategy improves RGB-D salient object detection.
problem RGB-D salient object detection struggles with depth information.
method Proposes a novel data-level recombination strategy to fuse RGB and depth data before feature extraction.
result Achieves a new state-of-the-art performance in RGB-D salient object detection.
Parallelized Bayesian quadrature improves sample efficiency and inference.
problem Efficient Bayesian inference and model evidence calculation.
method Batch Bayesian quadrature with kernel recombination for parallel sampling.
result Empirically, outperforms state-of-the-art methods in various datasets.
Paper uses transfer learning and Bayesian optimization to reduce DNA sequence design experiments.
problem Designing many similar DNA sequences for specific applications is expensive and time-consuming.
method Combines transfer learning with Bayesian optimization to reduce experiment count.
result Total number of experiments can be significantly reduced by sharing information between tasks.
We consider the task of detecting regulatory elements in the human genome directly from raw DNA. Past work has focused on small snippets of DNA, making it difficult to model long-distance dependencies that arise from DNA's 3-dimensional conformation. In order to study long-distance dependencies, we develop and release …