Results 21 to 30 of about 1,162,644 (75)

Zimin patterns in genomes [PDF]

arXiv
Zimin words are words that have the same prefix and suffix. They are unavoidable patterns, with all sufficiently large strings encompassing them. Here, we examine for the first time the presence of k-mers not containing any Zimin patterns, defined hereafter as Zimin avoidmers, in the human genome. We report that in the reference human genome all k-mers
arxiv  

TwoPaCo: An efficient algorithm to build the compacted de Bruijn graph from many complete genomes [PDF]

arXiv, 2016
Motivation: De Bruijn graphs have been proposed as a data structure to facilitate the analysis of related whole genome sequences, in both a population and comparative genomic settings. However, current approaches do not scale well to many genomes of large size (such as mammalian genomes).
arxiv  

A Conceptual Framework for Human-AI Collaborative Genome Annotation [PDF]

arXiv
Genome annotation is essential for understanding the functional elements within genomes. While automated methods are indispensable for processing large-scale genomic data, they often face challenges in accurately predicting gene structures and functions.
arxiv  

OmniGenBench: Automating Large-scale in-silico Benchmarking for Genomic Foundation Models [PDF]

arXiv
The advancements in artificial intelligence in recent years, such as Large Language Models (LLMs), have fueled expectations for breakthroughs in genomic foundation models (GFMs). The code of nature, hidden in diverse genomes since the very beginning of life's evolution, holds immense potential for impacting humans and ecosystems through genome modeling.
arxiv  

A Misclassification Network-Based Method for Comparative Genomic Analysis [PDF]

arXiv
Classifying genome sequences based on metadata has been an active area of research in comparative genomics for decades with many important applications across the life sciences. Established methods for classifying genomes can be broadly grouped into sequence alignment-based and alignment-free models.
arxiv  

Expression of concern for global biomedical research by the human genome organization (HUGO). [PDF]

Hum Genomics
Hamosh A, Arzuaga F, B Avraham K, Bin Alwi Z, Bowcock A, Burn SJ, Carninci P, Dandara C, Lopes-Cendes I, Mutesa L, P Majumder P, K V Reichardt J, A Veltman J.   +12 more
europepmc   +1 more source

Three-dimensional genome structures of single mammalian sperm. [PDF]

Nat Commun
Xu H, Chi Y, Yin C, Li C, Chen Y, Liu Z, Liu X, Xie H, Chen ZJ, Zhao H, Wu K, Zhao S, Xing D.   +12 more
europepmc   +1 more source

A genome-wide One Health study of Klebsiella pneumoniae in Norway reveals overlapping populations but few recent transmission events across reservoirs. [PDF]

Genome Med
Hetland MAK, Winkler MA, Kaspersen HP, Håkonsholm F, Bakksjø RJ, Bernhoff E, Delgado-Blas JF, Brisse S, Correia A, Fostervold A, Lam MMC, Lunestad BT, Marathe NP, Raffelsberger N, Samuelsen Ø, Sunde M, Sundsfjord A, Urdahl AM, Wick RR, Löhr IH, Holt KE.   +20 more
europepmc   +1 more source

Predicting viral host codon fitness and path shifting through tree-based learning on codon usage biases and genomic characteristics. [PDF]

Sci Rep
Su S, Ni Z, Lan T, Ping P, Tang J, Yu Z, Hutvagner G, Li J.   +7 more
europepmc   +1 more source

Comparative genomic analysis of food-animal-derived and human-derived <i>Clostridium perfringens</i> isolates from markets in Shandong, China. [PDF]

Front Microbiol
Zhu X, Huang Y, Shi Y, Gao X, Chen D, Liu C, Cao S, Xue X, Li Y.   +8 more
europepmc   +1 more source