25 papers · ranked by Valyu relevance
Russell L Marsden, Tony A Lewis, Christine A Orengo
Background Structural genomics initiatives were established with the aim of solving protein structures on a large-scale. For many initiatives, such as the Protein Structure Initiative (PSI), the primary aim of target selection is focussed towards structurally characterising protein families which, so far, lack a…
Daron M. Standley, Tokuichiro Nakanishi, Zichang Xu, Soichiro Haruna + 3 more
'Songling Li' 'Sedat Aybars Nazlica' 'Kazutaka Katoh'] Structural genomics began as a global effort in the 1990s to determine the tertiary structures of all protein families as a response to large-scale genome sequencing projects. The immediate outcome was an influx of tens of thousands of protein structures, many of…
Karolina Michalska, Andrzej Joachimiak
The field of Structural Genomics arose over the last 3 decades to address a large and rapidly growing divergence between microbial genomic, functional, and structural data. Several international programs took advantage of the vast genomic sequence information and evaluated the feasibility of structure determination for…
Marc-André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley + 3 more
'John Wooley' 'Kurt Wüthrich' 'Ian A. Wilson'] The Joint Center for Structural Genomics high-throughput structural biology pipeline has delivered more than 1000 structures to the community over the past ten years and has made a significant contribution to the overall goal of the NIH Protein Structure Initiative (PSI)…
Gabriel Dorado, Sergio Gálvez, Teresa E. Rosales, Víctor F. Vásquez + 1 more
'Pilar Hernández'] Recent developments have revolutionized the study of biomolecules. Among them are molecular markers, amplification and sequencing of nucleic acids. The latter is classified into three generations. The first allows to sequence small DNA fragments. The second one increases throughput, reducing…
Lei Xie, Philip E Bourne, Janet Thornton
The bias in protein structure and function space resulting from experimental limitations and targeting of particular functional classes of proteins by structural biologists has long been recognized, but never continuously quantified. Using the Enzyme Commission and the Gene Ontology classifications as a reference…
Ashwini V. Mohan, Anjali Goswami, Jeffrey W. Streicher
Chromosomal architecture has played a key role in the evolution of biodiversity. Detecting structural variants (SVs) on chromosomes has informed the study of speciation, sex determination, adaptation, and some of the earliest divergences in the tree of life. Here we present a computationally non-intensive approach…
Le Li, Tsz-Piu Kwok, Alden King-Yung Leung, Yvonne Y. Y. Lai + 17 more
Human genomes contain structural variations (SVs) that are associated with various phenotypic variations and diseases. SV detection by sequencing is incomplete due to limited read length. Nanochannel-based optical mapping (OM) allows direct observation of SVs up to hundreds of kilo-bases in size on individual DNA…
David Kouřil, Trevor Manz, Tereza Clarence, Nils Gehlenborg
Summary: Uchimata is a toolkit for visualization of 3D structures of genomes. It consists of two packages: a Javascript library facilitating the rendering of 3D models of genomes, and a Python widget for visualization in Jupyter Notebooks. Main features include an expressive way to specify visual encodings, and…
Jackson Nowotny, Avery Wells, Oluwatosin Oluwadare, Lingfei Xu + 4 more
'Renzhi Cao' 'Tuan Trieu' 'Chenfeng He' 'Jianlin Cheng'] 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 still exists a shortage of…
Kang-Jian Hua, Bin-Guang Ma
More and more 3C/Hi-C experiments on prokaryotes have been published. However, most of the published modeling tools for chromosome 3D structures are targeting at eukaryotes. How to transform prokaryotic experimental chromosome interaction data into spatial structures is an important task and in great need. We have…
Zilong Li, Ran Sun, Thomas C. Bishop
Genomics is a sequence-based informatics science and a 3D structure-based material science. Here we describe a framework for developing genome dashboards specifically designed to unify informatics with studies of chromatin structure and dynamics. The framework is based on the mathematical representation of…
Heng Yang, Ke Li
Foundation Models Authors: ['Heng Yang' 'Ke Li'] Abstract: The alignment between RNA sequences and structures in foundation models (FMs) has yet to be thoroughly investigated. Existing FMs have struggled to establish sequence-structure alignment, hindering the free flow of genomic information between RNA sequences and…
Carl Barton, Sandro Morganella, Øyvind Ødegård-Fougner, Stephanie Alexander + 4 more
The 3D structure of chromatin plays a key role in genome function, including gene expression, DNA replication, chromosome segregation, and DNA repair. Furthermore the location of genomic loci within the nucleus, especially relative to each other and nuclear structures such as the nuclear envelope and nuclear bodies…
M. Johnsson
This paper will argue that one of the biggest challenges for livestock genomics is to make whole-genome sequencing and functional genomics applicable to breeding practice. It discusses potential explanations for why it is so difficult to consistently improve the accuracy of genomic prediction by means of wholegenome…
Chen-Shan Chin, Sairam Behera, Asif Khalak, Fritz J Sedlazeck + 2 more
The advancement in sequencing technologies and assembly methods enable the regular production of high-quality genome assemblies characterizing complex regions. However, challenges remain in efficiently interpreting variations at various scales, from smaller tandem repeats to megabase re-arrangements, across many human…
Authors not listed
The Protein Data Bank (PDB) is one of the richest open‑source repositories in biology, housing over 277,000 macromolecular structural models alongside much of the experimental data that underpins these models. By systematically collecting, validating, and indexing these models, the PDB has accelerated structural…
Ashar J. Malik, Chandra S. Verma, Anthony M. Poole, Jane R. Allison
Protein structures carry signal of common ancestry and can therefore aid in reconstructing their evolutionary histories. To expedite the structure-informed inference process, a web server, Structome, has been developed, that allows users to rapidly identify protein structures similar to a query protein and to assemble…
Dariia Yehorova, Rory Crean, Peter Kasson, Shina Caroline Lynn Kamerlin
Protein structure (and thus function) is dictated by non-covalent interaction networks. These can be highly evolutionarily conserved across protein families, the members of which can diverge in sequence and evolutionary history. Here we present KIN, a tool to identify and analyze conserved non-covalent interaction…
Fathima Nuzla Ismail, Abira Sengupta
A significant advancement in bioinformatics is using genome graph techniques to improve variation discovery across organisms. Traditional approaches, such as bwa mem, rely on linear reference genomes for genomic analyses but may introduce biases when applied to highly diverse bacterial genomes of the same species.…
Victor Daniel Aldas-Bulos, Fabien Plisson
Machine learning models provide an informed and efficient strategy to create novel peptide and protein sequences with the desired profiles. Nevertheless, they are primarily trained on sequences where the tridimensional structures of peptides and proteins are often overlooked. We need a fast and reliable approach to…
Authors not listed
RNA molecules fold into complex three-dimensional structures that determine their function. A wide range of mathematical frameworks, such as chord diagrams, fatgraphs, and context-free grammars, have been used to represent these structures; however, these models have largely been developed from mathematical motivations…
Yuncan Ai, Hannan Ai, Fanmei Meng, Lei Zhao
How to compare whole genome sequences at large scale has not been achieved via conventional methods based on pair-wisely base-to-base comparison; nevertheless, no attention was paid to handle in-one-sitting a number of genomes crossing genetic category (chromosome, plasmid, and phage) with farther divergences (much…
Jürgen Behr, Timm Michel, Maya Giridhar, Santra Santhosh + 11 more
Large- to ultra-large-scale synthesis of nucleic acids is becoming an increasingly important tool for understanding and manipulating biological systems, as well as for developing new technologies based on engineered biological materials, including DNA-based nanofabrication, aptamers and writing digital data at the…
Jonas Schaub, Julian Zander, Achim Zielesny, Christoph Steinbeck
The concept of molecular scaffolds as defining core structures of organic molecules is utilised in many areas of chemistry and cheminformatics, e.g. drug design, chemical classification, or the analysis of high-throughput screening data. Here, we present Scaffold Generator, a comprehensive open library for the…