Related papers: Systematic transcriptome wide analysis of lncRNA-m…
Linear thresholding systems have been used as a model of neural activation and more recently proposed as a model of gene regulation. Here we exhibit linear thresholding systems whose dynamics produce surprisingly long cycles.
Reconstructing transcriptional regulatory networks is an important task in functional genomics. Data obtained from experiments that perturb genes by knockouts or RNA interference contain useful information for addressing this reconstruction…
A transversal topic of my research has been the development and application of computational methods for DNA sequence analysis. The methods I have been developing aim at improving our understanding of the regulation processes happening in…
In many applications of shape analysis, lengths between some landmarks are constrained. For instance, biomolecules often have some bond lengths and some bond angles constrained, and variation occurs only along unconstrained bonds and…
Biological sequences encode fundamental instructions for the building blocks of life, in the form of DNA, RNA, and proteins. Modeling these sequences is key to understand disease mechanisms and is an active research area in computational…
Genes are fundamental for analyzing biological systems and many recent works proposed to utilize gene expression for various biological tasks by deep learning models. Despite their promising performance, it is hard for deep neural networks…
Industrial large-scale recommendation models (LRMs) face the challenge of jointly modeling long-range user behavior sequences and heterogeneous non-sequential features under strict efficiency constraints. However, most existing…
The intrinsic stochasticity of gene expression is usually mitigated in higher eukaryotes by post-transcriptional regulation channels that stabilise the output layer, most notably protein levels. The discovery of small non-coding RNAs…
Growing evidence from recent studies implies that microRNA or miRNA could serve as biomarkers in various complex human diseases. Since wet-lab experiments are expensive and time-consuming, computational techniques for miRNA-disease…
The connectome, a map of the structural and/or functional connections in the brain, provides a complex representation of the neurobiological phenotypes on which it supervenes. This information-rich data modality has the potential to…
Large Language Models (LLMs) possess vast amounts of knowledge within their parameters, prompting research into methods for locating and editing this knowledge. Previous work has largely focused on locating entity-related (often…
A novel information-theoretic method for reconstruction of interaction networks is introduced. We prove that the method is exact for some class of networks. Performance tests on large synthetic transcriptional regulatory networks produce…
In post-transcriptional regulation, an mRNA molecule is bound by many proteins and/or miRNAs to modulate its function. To enable combinatorial gene regulation, these binding partners of an RNA must communicate with each other, exhibiting…
Identification of genes that initiate cell anomalies and cause cancer in humans is among the important fields in the oncology researches. The mutation and development of anomalies in these genes are then transferred to other genes in the…
Small non-coding RNAs can exert significant regulatory activity on gene expression in bacteria. In recent years, substantial progress has been made in understanding bacterial gene expression by sRNAs. However, recent findings that…
Genetic interaction measures how different genes collectively contribute to a phenotype, and can reveal functional compensation and buffering between pathways under genetic perturbations. Recently, genome-wide screening for genetic…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
A non-linear Penner type interaction is introduced and studied in the random matrix model of homo-RNA. The asymptotics in length of the partition function is discussed for small and large $N$ (size of matrix). The interaction doubles the…
Regulatory networks describe the interactions between molecular or cellular regulators, like transcription factors and genes in gene regulatory networks, kinases and their receptors in signalling networks, or neurons in neural networks. A…
DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…