26 papers · ranked by Valyu relevance
Nancy F. Hansen, Nathan Dwarshuis, Hyun Joo Ji, Arang Rhie + 61 more
Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and structurally polymorphic regions of the genome unmapped. Consequently, existing variant benchmarks, generated by the…
DongAhn Yoo, Arang Rhie, Prajna Hebbar, Francesca Antonacci + 119 more
We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. We achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215…
Brock A. Peters, Jia Liu, Radoje Drmanac
Next generation sequencing (NGS) technologies, primarily based on massively parallel sequencing, have touched and radically changed almost all aspects of research worldwide. These technologies have allowed for the rapid analysis, to date, of the genomes of more than 2,000 different species. In humans, NGS has arguably…
Karen H. Miga, Sergey Koren, Arang Rhie, Mitchell R. Vollger + 48 more
After nearly two decades of improvements, the current human reference genome (GRCh38) is the most accurate and complete vertebrate genome ever produced. However, no one chromosome has been finished end to end, and hundreds of unresolved gaps persist ^1,2^. The remaining gaps include ribosomal rDNA arrays, large…
Justin M. Zook, Brad Chapman, Jason Wang, David Mittelman + 3 more
'Oliver Hofmann' 'Yoshihide Hayashizaki' 'Marc Salit'] Clinical adoption of human genome sequencing requires methods with known accuracy of genotype calls at millions or billions of positions across a genome. Previous work showing discordance amongst sequencing methods and algorithms has made clear the need for a…
Tobias Marschall, Manja Marz, Thomas Abeel, Louis Dijkstra + 54 more
Many disciplines, from human genetics and oncology to plant and animal breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling…
Khalid Raza, Sabahuddin Ahmad
Next Generation Sequencing (NGS), a recently evolved technology, have served a lot in the research and development sector of our society. This novel approach is a newbie and has critical advantages over the traditional Capillary Electrophoresis (CE) based Sanger Sequencing. The advancement of NGS has led to numerous…
Stephanie Clare Roth
Genomic medicine is rapidly changing the future of medicine. Medical librarians need to understand this field of research and keep current with its latest advancements. Even if they are not directly involved in genomic medicine, librarians can play an integral role by helping health care consumers and practitioners who…
Yulián A. Alvarez-Ballesteros, Mario A. Quiroz‐Juárez, José L. Del-Rio-Correa, A. M. Escobar-Ruiz
Graphical Representations and Cytogenetics Authors: ['Yulián A. Alvarez-Ballesteros' 'Mario A. Quiroz‐Juárez' 'José L. Del-Rio-Correa' 'A. M. Escobar-Ruiz'] In this work, we applied the Chaos Game Representation (CGR) to the complete human genomic sequence T2T-CHM13v2.0, analyzing the entire chromosome assembly and…
Sebastian Deorowicz, Agnieszka Danek, Marcin Niemiec
The fall of prices of the high-throughput genome sequencing changes the landscape of modern genomics. A number of large scale projects aimed at sequencing many human genomes are in progress. Genome sequencing also becomes an important aid in the personalized medicine. One of the significant side effects of this change…
Mary Jane C. Espina, John T. Lovell, Jerry Jenkins, Shengqiang Shu + 13 more
Cultivar ‘Williams 82’ has served as the reference genome for the soybean research community since 2008, but is known to have areas of genomic heterogeneity among different sub-lines. This work provides an updated assembly (version Wm82.a6) derived from a specific sub-line known as ‘Wm82-ISU-01’ (seeds available under…
Yuta Aoyagi Blue, Hideaki Iimura, Mitsuhiko P. Sato, Kenta Shirasawa
Advances in sequencing technologies have enabled the determination of genome sequences of multiple lines within a single species. Comparative analysis of multiple genome sequences reveals all genes present within a species, providing insight into the genetic mechanisms that lead to the establishment of species. Highly…
Yingyan Yu, Chaochun Wei
The pan-genome refers to the entire genome composition of a clade, which can be a species, and encompasses the gene pool of all individuals in that clade (species). The pan-genome of a species consists of three parts: core genes, distributed genes, and individual-specific genes. Core genes are those found in all…
Paolo Abondio, Elisabetta Cilli, Donata Luiselli, Fan Zhang + 1 more
'Zhiqiang Hu'] A pangenome is a collection of the common and unique genomes that are present in a given species. It combines the genetic information of all the genomes sampled, resulting in a large and diverse range of genetic material. Pangenomic analysis offers several advantages compared to traditional genomic…
Kerstin Lindblad-Toh
During the past 20 years, since I started as a postdoc, the world of genetics and genomics has changed dramatically. My main research goal throughout my career has been to understand human disease genetics, and I have developed comparative genomics and comparative genetics to generate resources and tools for…
Katharine M. Jenike, Lucía Campos, Marilou Boddé, José Cerca + 3 more
'Christina N. Hodson' 'Michael C. Schatz' 'Kamil S. Jaroň'] The wide array of currently available genomes display a wonderful diversity in size, composition and structure with many more to come thanks to several global biodiversity genomics initiatives starting in recent years. However, sequencing of genomes, even with…
Harpreet Kaur, Laura M. Shannon, Deborah A. Samac
Background The concept of pangenomics and the importance of structural variants is gaining recognition within the plant genomics community. Due to advancements in sequencing and computational technology, it has become feasible to sequence the entire genome of numerous individuals of a single species at a reasonable…
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…
Eef M. Jonkheer, Dick de Ridder, Theo A. J. van der Lee, Jorn R. de Haan + 2 more
'Jorn R. de Haan' 'Lidija Berke' 'Sandra Smit'] Title: Summary With advances in long-read sequencing and assembly techniques, haplotype-resolved (phased) genome assemblies are becoming more common, also in the field of plant genomics. Computational tools to effectively explore these phased genomes, particularly for…
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…
Miloje Rakočević
In some previous works (2018a,b; 2019, 2021a,b, 2022) we presented a new type of mirror symmetry, expressed in the set of protein amino acids; such a symmetry, that it simultaneously represents the semiotic essence of the genetic code. In this paper we provide new evidences that the genetic code represents the unity of…
Authors not listed
The rise of antibiotic resistance has necessitated the exploration of unconventional sources for novel antimicrobial agents. One emerging novel frontier is "de-extinct" molecules – bioactive peptides, antibiotics, and other bioactive agents reconstructed from ancient or extinct organisms – a groundbreaking convergence…
Authors not listed
Molecular mechanisms governing initiation steps of the assembly of thousands of endogenous multi-protein complexes (EMCs) remain incompletely understood. Here, multiple lines of observations are reported reflecting the biological functions-aligned initiation sequence of hybrid assembly pathways (HAPs) of EMCs. HAPs…
Authors not listed
One aim of the international Human Proteome Organization (HUPO) Human Proteome Project (HPP) is to obtain high-confidence translation evidence for every human protein-coding gene established in its target list of 19433 entries based on the protein-coding genes from Ensembl-GENCODE. However, 76 are annotated in…
Authors not listed
In this report, we examine the extensive research landscape of CRISPR with an emphasis on CRISPR therapeutics and showcase our results from an in-depth analysis of the most up-to-date scientific information consisting of more than 53,000 publications encompassing academic journal articles and patents, spanning nearly…
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…