Related papers: Counting unique molecular identifiers in sequencin…
Inherent stochasticity in gene expression leads to distributions of mRNA copy numbers in a population of identical cells. These distributions are determined primarily by the multitude of states of a gene promoter, each driving transcription…
The emergence of telomere-to-telomere (T2T) genome assemblies has opened new avenues for comparative genomics, yet effective tokenization strategies for genomic sequences remain underexplored. In this pilot study, we apply Byte Pair…
We introduce the Hawkes process with renewal immigration and make its statistical estimation possible with two Expectation Maximization (EM) algorithms. The standard Hawkes process introduces immigrant points via a Poisson process, and each…
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…
We study the amount of reliable information that can be stored in a DNA-based storage system with noisy sequencing, where each codeword is composed of short DNA molecules. We analyze a concatenated coding scheme, where the outer code is…
Due to their sequential nature, traditional DNA synthesis methods are expensive in terms of time and resources. They also fabricate multiple copies of the same strand, introducing redundancy. This redundancy can be leveraged to enhance the…
Motivation: A branching processes model yields an unevenly stochastically distributed dataset that consists of sparse and dense regions. This work addresses the problem of precisely evaluating parameters for such a model. Applying a…
In this paper, we consider certain linear-fractional branching processes with immigration in varying environments. For $n\ge0,$ let $Z_n$ counts the number of individuals of the $n$-th generation, which excludes the immigrant which enters…
Real time, or quantitative, PCR typically starts from a very low concentration of initial DNA strands. During iterations the numbers increase, first essentially by doubling, later predominantly in a linear way. Observation of the number of…
Brain tumor classification using MRI images is critical in medical diagnostics, where early and accurate detection significantly impacts patient outcomes. While recent advancements in deep learning (DL), particularly CNNs, have shown…
A machine learning approach is presented to accelerate the computation of block polymer morphology evolution for large domains over long timescales. The strategy exploits the separation of characteristic times between coarse-grained…
Epigenetic alterations have an important role in the development of several types of cancer. Epigenetic studies generate a large amount of data, which makes it essential to develop novel models capable of dealing with large-scale data. In…
Batched network coding (BNC) is a low-complexity solution to network transmission in multi-hop packet networks with packet loss. BNC encodes the source data into batches of packets. As a network coding scheme, the intermediate nodes perform…
DNA microarray technology enables the simultaneous measurement of expression levels of thousands of genes, thereby facilitating the understanding of the molecular mechanisms underlying complex diseases such as brain tumors and the…
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…
Sequencing by tunneling is a next-generation approach to read single-base information using electronic tunneling transverse to the single-stranded DNA (ssDNA) backbone while the latter is translocated through a narrow channel. The original…
Batch effects, artificial sources of variation due to experimental design, are a widespread phenomenon in high throughput data. Therefore, mechanisms for detection of batch effects are needed requiring comparison of multiple samples. We…
In this paper, we investigate a stochastic model describing the time evolution of a polymerization process. A polymer is a macro-molecule resulting from the aggregation of several elementary sub-units called monomers. Polymers can grow by…
Single-cell RNA-seq provides detailed molecular snapshots of individual cells but is notoriously noisy. Variability stems from biological differences and technical factors, such as amplification bias and limited RNA capture efficiency,…
Motivation: Cellular Electron CryoTomography (CECT) enables 3D visualization of cellular organization at near-native state and in sub-molecular resolution, making it a powerful tool for analyzing structures of macromolecular complexes and…