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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…
Functional annotation of microbial genomes is often biased toward protein-coding genes, leaving a vast, unexplored landscape of non-coding RNAs (ncRNAs) that are critical for regulating bacterial and archaeal physiology, stress response and…
RNA 3D architectures are stabilized by sophisticated networks of (non-canonical) base pair interactions, which can be conveniently encoded as multi-relational graphs and efficiently exploited by graph theoretical approaches and recent…
High-throughput mRNA sequencing (RNA-Seq) is widely used for transcript quantification of gene isoforms. Since RNA-Seq data alone is often not sufficient to accurately identify the read origins from the isoforms for quantification, we…
Summary: The AptaBlocks Web Interface is focused on providing graphical, intuitive, and platform independent access to AptaBlocks, an experimentally validated algorithmic approach for the in-silico design of oligonucleotide sticky bridges.…
Functionalization of nanoparticles or colloids is increasingly being used to develop customizable "atoms". Functionalization by attaching single strands of DNA allows for direct control of the binding between nanoparticles, since…
An important challenge in cancer systems biology is to uncover the complex network of interactions between genes (tumor suppressor genes and oncogenes) implicated in cancer. Next generation sequencing provides unparalleled ability to probe…
Cross-domain recommendation (CDR) aims to leverage the correlation of users' behaviors in both the source and target domains to improve the user preference modeling in the target domain. Conventional CDR methods typically explore the…
RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensional (3D) structures and stability play essential roles in a variety of biological functions. Therefore, to predict 3D structures and stability of…
Non-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With…
Protein-RNA interactions are of vital importance to a variety of cellular activities. Both experimental and computational techniques have been developed to study the interactions. Due to the limitation of the previous database, especially…
In this paper, we introduce data multiplexing (DataMUX), a technique that enables deep neural networks to process multiple inputs simultaneously using a single compact representation. DataMUX demonstrates that neural networks are capable of…
Gene essentiality refers to the degree to which a gene is necessary for the survival and reproductive efficacy of a living organism. Although the essentiality of non-coding genes has been documented, there are still aspects of non-coding…
Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication…
Click-through rate (CTR) prediction tasks play a pivotal role in real-world applications, particularly in recommendation systems and online advertising. A significant research branch in this domain focuses on user behavior modeling. Current…
The explosive growth of large language models (LLMs) has created a vast but opaque landscape: millions of models exist, yet their evolutionary relationships through fine-tuning, distillation, or adaptation are often undocumented or unclear,…
Leveraging Large Language Models (LLMs) to write policy code for controlling robots has gained significant attention. However, in long-horizon implicative tasks, this approach often results in API parameter, comments and sequencing errors,…
Molecular recognition between two double stranded (ds) DNA with homologous sequences may not seem compatible with the B-DNA structure because the sequence information is hidden when it is used for joining the two strands. Nevertheless, it…
The interaction between Ribonucleic Acids (RNAs) and proteins, also called RNA Protein Interaction (RPI), plays an important role in the life activities of organisms, including in various regulatory processes, such as gene splicing, gene…
Multi-task dense prediction aims to perform multiple pixel-level tasks simultaneously. However, capturing global cross-task interactions remains non-trivial due to the quadratic complexity of standard self-attention on high-resolution…