Related papers: Data navigation on the ENCODE portal
Gene studies are crucial for fields such as protein structure prediction, drug discovery, and cancer genomics, yet they face challenges in fully utilizing the vast and diverse information available. Gene studies require clean, factual…
Background: Transitioning from an old medical coding system to a new one can be challenging, especially when the two coding systems are significantly different. The US experienced such a transition in 2015. Objective: This research aims to…
The problem of differentiating the informational content of coding (exons) and non-coding (introns) regions of a DNA sequence is one of the central problems of genomics. The introns are estimated to be nearly 95% of the DNA and since they…
In social networks, the discovery of community structures has received considerable attention as a fundamental problem in various network analysis tasks. However, due to privacy concerns or access restrictions, the network structure is…
A full-fledged data exploration system must combine different access modalities with a powerful concept of guiding the user in the exploration process, by being reactive and anticipative both for data discovery and for data linking. Such…
The Genome Warehouse (GWH), accessible at https://ngdc.cncb.ac.cn/gwh, is an extensively utilized public repository dedicated to the deposition, management and sharing of genome assembly sequences, annotations, and metadata. This paper…
Cell imaging and analysis are fundamental to biomedical research because cells are the basic functional units of life. Among different cell-related analysis, cell counting and detection are widely used. In this paper, we focus on one common…
Scientists, governments, and companies increasingly publish datasets on the Web. Google's Dataset Search extracts dataset metadata -- expressed using schema.org and similar vocabularies -- from Web pages in order to make datasets…
Network embedding aims to find a way to encode network by learning an embedding vector for each node in the network. The network often has property information which is highly informative with respect to the node's position and role in the…
Sharing genome data in a privacy-preserving way stands as a major bottleneck in front of the scientific progress promised by the big data era in genomics. A community-driven protocol named genomic data-sharing beacon protocol has been…
Deep learning empowers the mainstream medical image segmentation methods. Nevertheless current deep segmentation approaches are not capable of efficiently and effectively adapting and updating the trained models when new incremental…
Just as physicists strive to develop a TOE (theory of everything), which explains and unifies the physical laws of the universe, the life-scientist wishes to uncover the TOE as it relates to cellular systems. This can only be achieved with…
Image-to-fMRI encoding is important for both neuroscience research and practical applications. However, such "Brain-Encoders" have been typically trained per-subject and per fMRI-dataset, thus restricted to very limited training data. In…
The nucleotide sequence representation of DNA can be inadequate for resolving protein-DNA binding sites and regulatory substrates, such as those involved in gene expression and horizontal gene transfer. Considering that sequence-like…
Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highly-detailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including…
Recent work pairs LLMs with evolutionary search to iteratively generate, modify, and select code using task-specific feedback. These systems have produced strong results in mathematical discovery and algorithm design, yet a fundamental…
The data revolution holds significant promise for the health sector. Vast amounts of data collected from individuals will be transformed into knowledge, AI models, predictive systems, and best practices. One area of health that stands to…
We present the Open Supernova Catalog, an online collection of observations and metadata for presently 36,000+ supernovae and related candidates. The catalog is freely available on the web (https://sne.space), with its main interface having…
When translating UI design prototypes to code in industry, automatically generating code from design prototypes can expedite the development of applications and GUI iterations. However, in design prototypes without strict design…
Objective. Epidemiological studies require data that are in alignment with the classifications established for occupations or economic activities. The classifications usually include hundreds of codes and titles. Manual coding of raw data…