相关论文: Genetic transfer in Staphylococcus: a case study o…
Transcription factors (TFs) exert their regulatory action by binding to DNA with specific sequence preferences. However, different TFs can partially share their binding sequences due to their common evolutionary origin. This `redundancy' of…
Theoretical works on supervised transfer learning (STL) -- where the learner has access to labeled samples from both source and target distributions -- have for the most part focused on statistical aspects of the problem, while efficient…
Dominance is usually considered a constant value that describes the relative difference in fitness or phenotype between heterozygotes and the average of homozygotes at a focal polymorphic locus. However, the observed dominance can vary with…
Heritable differences in gene expression between individuals are an important source of phenotypic variation. The question of how closely the effects of genetic variation on protein levels mirror those on mRNA levels remains open. Here, we…
Unsupervised and unpaired domain translation using generative adversarial neural networks, and more precisely CycleGAN, is state of the art for the stain translation of histopathology images. It often, however, suffers from the presence of…
Sequence differences between the strains of bacteria comprising host-associated and environmental microbiota may play a role in community assembly and influence the resilience of microbial communities to disturbances. Tools for…
Stochastic models of sequential mutation acquisition are widely used to quantify cancer and bacterial evolution. Across manifold scenarios, recurrent research questions are: how many cells are there with $n$ alterations, and how long will…
Gene gains and losses have shaped the gene repertoire of species since the universal last common ancestor to species today. Genes in extant species were gained at different historical times via de novo creation of new genes, duplication of…
Genetic alterations initiate tumors and enable the evolution of drug resistance. The pro-cancer view of mutations is however incomplete, and several studies show that mutational load can reduce tumor fitness. Given its negative effect,…
Studies of the genetic loci that contribute to variation in gene expression frequently identify loci with broad effect on gene expression: expression quantitative trait locus (eQTL) hotspots. We describe a set of exploratory graphical…
This paper presents and compares alternative transfer learning methods that can increase the power of conditional testing via knockoffs by leveraging prior information in external data sets collected from different populations or measuring…
The stylistic properties of text have intrigued computational linguistics researchers in recent years. Specifically, researchers have investigated the Text Style Transfer (TST) task, which aims to change the stylistic properties of the text…
The phage $\lambda$ infection of an \textit{E. coli} cell has become a paradigm for understanding the molecular processes involved in gene expression and cell signaling. This system provides an example of a genetic switch, as cells with…
Gene transcription is a highly stochastic and dynamic process. As a result, the mRNA copy number of a given gene is heterogeneous both between cells and across time. We present a framework to model gene transcription in populations of cells…
Genes are not located randomly along genomes. Synteny, the conservation of their relative positions in genomes of different species, reflects fundamental constraints on natural evolution. We present approaches to infer pairs of co-localized…
Gene expression levels are important molecular quantitative traits that link genotypes to molecular functions and fitness. In Drosophila, population-genetic studies in recent years have revealed substantial adaptive evolution at the genomic…
Segmental duplications (SDs), or low-copy repeats (LCR), are segments of DNA greater than 1 Kbp with high sequence identity that are copied to other regions of the genome. SDs are among the most important sources of evolution, a common…
Hybrid evolution and horizontal gene transfer (HGT) are processes where evolutionary relationships may more accurately be described by a reticulated network than by a tree. In such a network, there will often be several paths between any…
Glioblastoma is a highly aggressive form of brain cancer characterized by rapid progression and poor prognosis. Despite advances in treatment, the underlying genetic mechanisms driving this aggressiveness remain poorly understood. In this…
Splicing sites provide unique statistics in human genome due to their large number and reasonably complete annotation. Analyses of the cumulative SNPs distribution in splicing sites reveal a few interesting observations. While a degree of…