Related papers: Data navigation on the ENCODE portal
The Encoder-Decoder architecture is a main stream deep learning model for biomedical image segmentation. The encoder fully compresses the input and generates encoded features, and the decoder then produces dense predictions using encoded…
As the amount of data on the World Wide Web continues to grow exponentially, access to semantically structured information remains limited. The Semantic Web has emerged as a solution to enhance the machine-readability of data, making it…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
DNA-Encoded Library (DEL) has proven to be a powerful tool that utilizes combinatorially constructed small molecules to facilitate highly-efficient screening assays. These selection experiments, involving multiple stages of washing,…
As artificial intelligence (AI) applications continue to expand in next-generation networks, there is a growing need for deep neural network (DNN) models. Although DNN models deployed at the edge are promising for providing AI as a service…
Understanding human behavior is a fundamental goal of social sciences, yet its analysis presents significant challenges. Conventional methodologies employed for the study of behavior, characterized by labor-intensive data collection…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (i.e. rarely accessed), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
Gene-regulatory enhancers have been identified by many lines of evidence, including evolutionary conservation, regulatory protein binding, chromatin modifications, and DNA sequence motifs. To integrate these different approaches, we…
The genetic blueprint for the essential functions of life is encoded in DNA, which is translated into proteins -- the engines driving most of our metabolic processes. Recent advancements in genome sequencing have unveiled a vast diversity…
Rapid advances in human genomics are enabling researchers to gain a better understanding of the role of the genome in our health and well-being, stimulating hope for more effective and cost efficient healthcare. However, this also prompts a…
Capturing the vast amount of meaningful information encoded in the human genome is a fascinating research problem. The outcome of these researches have significant influences in a number of health related fields --- personalized medicine,…
Over the last 20 years, there has been an explosion of genomic data collected for disease association, functional analyses, and other large-scale discoveries. At the same time, there have been revolutions in cloud computing that enable…
In this paper, we consider recommender systems with side information in the form of graphs. Existing collaborative filtering algorithms mainly utilize only immediate neighborhood information and have a hard time taking advantage of deeper…
Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…
The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4]…
Noncoding RNAs are integral to a wide range of biological processes, including translation, gene regulation, host-pathogen interactions and environmental sensing. While genomics is now a mature field, our capacity to identify noncoding RNA…
DNA has been considered a promising medium for storing digital information. As an essential step in the DNA-based data storage workflow, coding algorithms are responsible to implement functions including bit-to-base transcoding, error…
The NIAID Data Ecosystem Discovery Portal (https://data.niaid.nih.gov) provides a unified search interface for over 4 million datasets relevant to infectious and immune-mediated disease (IID) research. Integrating metadata from…
Identification of functional elements of a genome often requires dividing a sequence of measurements along a genome into segments differing from adjacent segments. In many applications, the mean of the measured values at multiple genomic…