Related papers: Data navigation on the ENCODE portal
We investigate the possibility of encoding multiple solutions of a problem in a single chromosome. The best solution encoded in an individual will represent (will provide the fitness of) that individual. In order to obtain some benefits the…
This paper presents the Ensemble Nucleotide Byte-level Encoder-Decoder (ENBED) foundation model, analyzing DNA sequences at byte-level precision with an encoder-decoder Transformer architecture. ENBED uses a sub-quadratic implementation of…
Analyzing a functional genomics experiment, such as ATAC-, ChIP- or RNA-sequencing, requires reference data including a genome assembly and gene annotation. These resources can generally be retrieved from different organizations and in…
With the boom in modern software development, open-source software has become an integral part of various industries, driving progress in computer science. However, the immense complexity and diversity of the open-source ecosystem also pose…
Long-term user behavior sequences are a goldmine for businesses to explore users' interests to improve Click-Through Rate. However, it is very challenging to accurately capture users' long-term interests from their long-term behavior…
With the rapid increase of available digital data, DNA storage is identified as a storage media with high density and capability of long-term preservation, especially for archival storage systems. However, the encoding density (i.e., how…
The building sector plays a crucial role in the worldwide decarbonization effort, accounting for significant portions of energy consumption and environmental effects. However, the scarcity of open data sources is a continuous challenge for…
Considering vast amounts of genomic sequences of mostly unknown functionality, in-silico prediction of functional regions is an important enterprise. Many genomic browsers employ GC content, which was observed to be elevated in gene-rich…
DNA constructs and their annotated sequence maps have been rapidly accumulating with the advancement of DNA cloning, synthesis, and assembly methods. Such a resource has the potential to be optimally utilized in an autonomous DNA building…
Reliable identification of encrypted file fragments is a requirement for several security applications, including ransomware detection, digital forensics, and traffic analysis. A popular approach consists of estimating high entropy as a…
Several cybersecurity domains, such as ransomware detection, forensics and data analysis, require methods to reliably identify encrypted data fragments. Typically, current approaches employ statistics derived from byte-level distribution,…
RNAnet provides a bridge between two widely used Human gene databases. Ensembl describes DNA sequences and transcripts but not experimental gene expression. Whilst NCBI's GEO contains actual expression levels from Human samples. RNAnet…
Since the completion of the human genome sequencing project in 2001, significant progress has been made in areas such as gene regulation editing and protein structure prediction. However, given the vast amount of genomic data, the segments…
While there has been a plethora of approaches for detecting disjoint communities from real-world complex networks, some methods for detecting overlapping community structures have also been recently proposed. In this work, we argue that,…
How to artificially encode observer in universal information coding structure like DNA ? It requires naturally creating information Bits and natural encoding triplet code enables recognizing other encoded information. These Bits become…
Extracting meaningful drug-related information chunks, such as adverse drug events (ADE), is crucial for preventing morbidity and saving many lives. Most ADEs are reported via an unstructured conversation with the medical context, so…
The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to…
Reading emotions precisely from segments of neural activity is crucial for the development of emotional brain-computer interfaces. Among all neural decoding algorithms, deep learning (DL) holds the potential to become the most promising…
BOLD, the Barcode of Life Data System, supports the acquisition, storage, validation, analysis, and publication of DNA barcodes, activities requiring the integration of molecular, morphological, and distributional data. Its pivotal role in…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…