Related papers: TranspoGene and microTranspoGene: transposed eleme…
The evolutionary pressures that underlie the large-scale functional organization of the genome are not well understood in eukaryotes. Recent evidence suggests that functionally similar genes may colocalize (cluster) in the eukaryotic…
Evolution of the amino acid sequences of transthyretin (TTR) can provide additional information about its dynamics that both complements and extends the already extensive static structural data. Protein dynamics is largely driven by…
Currently, many studies view DNA sequences as a special type of language and utilize Transformers to model them. These studies use fixed-length k-mer segmentation and BPE subword tokenization but lack a systematic evaluation to determine…
Central to the functioning of a living cell is its ability to control the readout or expression of information encoded in the genome. In many cases, a single transcription factor protein activates or represses the expression of many genes.…
A new model for evolving Evolutionary Algorithms (EAs) is proposed in this paper. The model is based on the Multi Expression Programming (MEP) technique. Each MEP chromosome encodes an evolutionary pattern that is repeatedly used for…
During the continuous evolution of one organism's ancestry, its genes accumulate extensive experiences and knowledge, enabling newborn descendants to rapidly adapt to their specific environments. Motivated by this observation, we propose a…
The Semantic Theory of Evolution (STE) takes the existence of a number of arbitrary communication codes as a fundamental feature of life, from the genetic code to human cultural communication codes. Their arbitrariness enables, at each…
The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is…
Individual expression profiles from EBV transformed cell lines are an emerging resource for genomic investigation. In this study we characterize the effects of age, sex, and genetic variation on gene expression by surveying public datasets…
Background: Spatial transcriptomics have emerged as a powerful tool in biomedical research because of its ability to capture both the spatial contexts and abundance of the complete RNA transcript profile in organs of interest. However,…
Interaction between proteins is a fundamental mechanism that underlies virtually all biological processes. Many important interactions are conserved across a large variety of species. The need to maintain interaction leads to a high degree…
In plants, a subset of genes exhibit imprinting in endosperm tissue such that expression is primarily from the maternal or paternal allele. Imprinting may arise as a consequence of mechanisms for silencing of transposons during…
The continuity of life and its evolution, we proposed, emerge from an interactive group process manifested in networks of interaction. We term this process \textit{survival-of-the-fitted}. Here, we reason that survival of the fitted results…
Today's densely instrumented world offers tremendous opportunities for continuous acquisition and analysis of multimodal sensor data providing temporal characterization of an individual's behaviors. Is it possible to efficiently couple such…
Transcriptional repressor CTCF is an important regulator of chromatin 3D structure, facilitating the formation of topologically associating domains (TADs). However, its direct effects on gene regulation is less well understood. Here, we…
We investigate the knowledge graph entity typing task which aims at inferring plausible entity types. In this paper, we propose a novel Transformer-based Entity Typing (TET) approach, effectively encoding the content of neighbors of an…
The protein-protein interaction (PPI) network provides an overview of the complex biological reactions vital to an organism's metabolism and survival. Even though in the past PPI network were compared across organisms in detail, there has…
Recent genome-wide measurements of binding preferences of ~200 transcription regulators in the vicinity of transcription start sites in yeast, have provided a unique insight into the cis- regulatory code of a eukaryotic genome (Venters et…
Site-specific transcription factors (TFs) bind to their target sites on the DNA, where they regulate the rate at which genes are transcribed. Bacterial TFs undergo facilitated diffusion (a combination of 3D diffusion around and 1D random…
Computationally predicting protein-protein interactions (PPIs) is challenging due to the lack of integrated, multimodal protein representations. DPEB is a curated collection of 22,043 human proteins that integrates four embedding types:…