Related papers: Data navigation on the ENCODE portal
DNA storage has matured from concept to practical stage, yet its integration with neural compression pipelines remains inefficient. Early DNA encoders applied redundancy-heavy constraint layers atop raw binary data - workable but primitive.…
This paper introduces ENFrame, a unified data processing platform for querying and mining probabilistic data. Using ENFrame, users can write programs in a fragment of Python with constructs such as bounded-range loops, list comprehension,…
Encoding and decoding models are widely used in systems, cognitive, and computational neuroscience to make sense of brain-activity data. However, the interpretation of their results requires care. Decoding models can help reveal whether…
Work in Computational Affective Science and Computational Social Science explores a wide variety of research questions about people, emotions, behavior, and health. Such work often relies on language data that is first labeled with relevant…
The National Institutes of Health's (NIH) Human Biomolecular Atlas Program (HuBMAP) aims to create a comprehensive high-resolution atlas of all the cells in the healthy human body. Multiple laboratories across the United States are…
Cancer is a complex disease driven by genomic alterations, and tumor sequencing is becoming a mainstay of clinical care for cancer patients. The emergence of multi-institution sequencing data presents a powerful resource for learning…
Foundation models are trained on massive amounts of data to distinguish complex patterns and can be adapted to a wide range of downstream tasks with minimal computational resources. Here, we develop a foundation model for prostate cancer…
Information is often encoded as an aperiodic chain of building blocks. Modern digital computers use bits as the building blocks, but in general the choice of building blocks depends on the nature of the information to be encoded. What are…
The comparative genomics revolution of the past decade has enabled the discovery of functional elements in the human genome via sequence comparison. While that is so, an important class of elements, those specific to humans, is entirely…
A quest to determine the complete sequence of a human DNA from telomere to telomere started three decades ago and was finally completed in 2021. This accomplishment was a result of a tremendous effort of numerous experts who engineered…
Disordered proteins play essential roles in myriad cellular processes, yet their structural characterization remains a major challenge due to their dynamic and heterogeneous nature. We here present a community-driven initiative to address…
The birth of new genes is an important motor of evolutionary innovation. Whereas many new genes arise by gene duplication, others originate at genomic regions that do not contain any gene or gene copy. Some of these newly expressed genes…
Common Data Elements (CDEs) standardize data collection and sharing across studies, enhancing data interoperability and improving research reproducibility. However, implementing CDEs presents challenges due to the broad range and variety of…
It has been shown that genome spatial structures largely affect both genome activity and DNA function. Knowing this, many researchers are currently attempting to accurately model genome structures. Despite these increased efforts there…
Nuclei instance segmentation in histopathological images is of great importance for biological analysis and cancer diagnosis but remains challenging for two reasons. (1) Similar visual presentation of intranuclear and extranuclear regions…
Methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly and to correctly interpret the results of subsequent analyses. BUSCO estimates the completeness and redundancy of processed genomic data…
A powerful approach to detecting erroneous data is to check which potentially dirty data records are incompatible with a user's domain knowledge. Previous approaches allow the user to specify domain knowledge in the form of logical…
The vast parallelism, exceptional energy efficiency and extraordinary information inherent in DNA molecules are being explored for computing, data storage and cryptography. DNA cryptography is a emerging field of cryptography. In this paper…
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…
Extracellular matrix (ECM) remodeling is central to a wide variety of healthy and diseased tissue processes. Unfortunately, predicting ECM remodeling under various chemical and mechanical conditions has proven to be excessively challenging,…