Related papers: The Stanford RNA Mapping Database for sharing and …
While RNA has recently been recognized as an interesting small-molecule drug target, many challenges remain to be addressed before we take full advantage of it. This emphasizes the necessity to improve our understanding of its structures…
Accurate prediction of RNA three-dimensional (3D) structure remains an unsolved challenge. Determining RNA 3D structures is crucial for understanding their functions and informing RNA-targeting drug development and synthetic biology design.…
Crunchbase is an online platform collecting information about startups and technology companies, including attributes and relations of companies, people, and investments. Data contained in Crunchbase is, to a large extent, not available…
The volume of biological data being generated by the scientific community is growing exponentially, reflecting technological advances and research activities. The National Institutes of Health's (NIH) Sequence Read Archive (SRA), which is…
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray…
DNA-based storage offers unprecedented density and durability, but its scalability is fundamentally limited by the efficiency of parallel strand synthesis. Existing methods either allow unconstrained nucleotide additions to individual…
Objective: The majority of detailed patient information in real-world data (RWD) is only consistently available in free-text clinical documents. Manual curation is expensive and time-consuming. Developing natural language processing (NLP)…
Information on the structure of molecules, retrieved via biochemical databases, plays a pivotal role in various disciplines, such as metabolomics, systems biology, and drug discovery. However, no such database can be complete, and the…
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…
The formation of secondary structures by a random RNA sequence is studied as a model system for the sequence-structure problem omnipresent in biopolymers. Several toy energy models are introduced to allow detailed analytical and numerical…
Combinatorial analysis of a certain abstract of RNA structures has been studied to investigate their statistics. Our approach regards the backbone of secondary structures as an alternate sequence of paired and unpaired sets of nucleotides,…
Over the last decades the Web has evolved from a human-human communication network to a network of complex human-machine interactions. An increasing amount of data is available as Linked Data which allows machines to "understand" the data,…
The newly developed deep-sequencing technologies make it possible to acquire both quantitative and qualitative information regarding transcript biology. By measuring messenger RNA levels for all genes in a sample, RNA-seq provides an…
RNA 3D motifs are recurrent substructures, modelled as networks of base pair interactions, which are crucial for understanding structure-function relationships. The task of automatically identifying such motifs is computationally hard, and…
The continually increasing number of complex datasets each year necessitates ever improving machine learning methods for robust and accurate categorization of these data. This paper introduces Random Multimodel Deep Learning (RMDL): a new…
Open and reproducible research in materials science relies on the availability of data, code, and common metadata standards. Journal research data policies (RDPs) remain a primary mechanism by which publication norms are defined and…
All-atom simulations have become increasingly popular to study conformational and dynamical properties of nucleic acids as they are accurate and provide high spatial and time resolutions. This high resolution however comes at a heavy…
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces research on their structure and functional interactions. We mine the evolutionary sequence record to derive precise information about function and…
The yearly global production of data is growing exponentially, outpacing the capacity of existing storage media, such as tape and disk, and surpassing our ability to store it. DNA storage - the representation of arbitrary information as…
DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…