Results 151 to 160 of about 10,955,529 (276)

k-mer matrix compression

The analysis of k-mers matrices, essential in agronomy, health and ecology, poses significant challenges regarding Big Data storage and processing. Recently, the tool kmtricks [1] was proposed for creating such matrices and was later used in the kmindex tool [2], designed for indexing large datasets.
Regnier, Alix, Peterlongo, Pierre
openaire   +1 more source

Large language models for bioinformatics

Quantitative Biology, Volume 14, Issue 1, March 2026.
Abstract With the rapid advancements in large language model technology and the emergence of bioinformatics‐specific language models (BioLMs), there is a growing need for a comprehensive analysis of the current landscape, computational characteristics, and diverse applications.
Wei Ruan, Yanjun Lyu, Jing Zhang, Jiazhang Cai, Peng Shu, Yang Ge, Yao Lu, Shang Gao, Yue Wang, Peilong Wang, Lin Zhao, Tao Wang, Yufang Liu, Luyang Fang, Ziyu Liu, Zhengliang Liu, Yiwei Li, Zihao Wu, Junhao Chen, Hanqi Jiang, Yi Pan, Zhenyuan Yang, Jingyuan Chen, Shizhe Liang, Wei Zhang, Terry Ma, Yuan Dou, Jianli Zhang, Xinyu Gong, Qi Gan, Yusong Zou, Zebang Chen, Yuanxin Qian, Shuo Yu, Jin Lu, Kenan Song, Xianqiao Wang, Andrea Sikora, Gang Li, Xiang Li, Quanzheng Li, Yingfeng Wang, Lu Zhang, Yohannes Abate, Lifang He, Wenxuan Zhong, Rongjie Liu, Chao Huang, Wei Liu, Ye Shen, Ping Ma, Hongtu Zhu, Yajun Yan, Dajiang Zhu, Tianming Liu   +54 more
wiley   +1 more source

Genomic architecture of the resistance to Phytophthora cactorum 2 (RPc2) locus in strawberry (Fragaria × ananassa)

The Plant Genome, Volume 19, Issue 1, March 2026.
Abstract Phytophthora crown rot, caused by Phytophthora cactorum, is a soilborne disease with broad impacts on cultivated strawberry (Fragaria × ananassa). A resistance locus, RPc2, was previously identified in octoploid strawberries, but the underlying genomic architecture and causal genes remained uncharacterized.
Hyeondae Han, Youngjae Oh, Yoon Jeong Jang, Saket Chandra, Upinder Gill, Sujeet Verma, Young‐Hee Noh, Sachiko Isobe, Dominique D. A. Pincot, Glenn S. Cole, Randi A. Famula, Mitchell J. Feldmann, Steven J. Knapp, Vance M. Whitaker, Seonghee Lee   +14 more
wiley   +1 more source

Optimizing k-mer size using a variant grid search to enhance de novo genome assembly [PDF]

, 2016
Soyeon Cha, David McKBird
openalex   +1 more source

Extensive phenotyping and genome‐wide analysis of grain number‐related traits in a diverse wheat core collection

The Plant Genome, Volume 19, Issue 1, March 2026.
Abstract Bread wheat (Triticum aestivum L.) is one of the most important staple crops globally. Grain number per spikelet (GPS) is an important yield component in wheat. It is influenced by floret number per spikelet (FPS) and floret fertility. Through three consecutive years of observation of FPS, GPS, and floret fertility per spikelet (FFPS) in a ...
Zhuo Su, Shun Sakuma, Miyuki Nitta, Yasir S. A. Gorafi, Shuhei Nasuda   +4 more
wiley   +1 more source

Integrative chromosome‐scale genome analysis of cupuassu provides insights into witches' broom disease resistance and expands genomic resources for Theobroma

The Plant Genome, Volume 19, Issue 1, March 2026.
Abstract Cupuassu (Theobroma grandiflorum) is a fruit tree native to the Brazilian Amazon and increasingly relevant to regional bioeconomies. Its cultivation is severely affected by witches’ broom disease (WBD), caused by Moniliophthora perniciosa. While a chromosome‐scale genome of the susceptible genotype C1074 is available, the lack of a resistant ...
Vinicius A. C. de Abreu, Rafael Moysés Alves, Mauro de Medeiros Oliveira, Vitor Trinca, Loeni Ludke Falcão, Lucilia Helena Marcellino, Antonio Figueira, Douglas S. Domingues, Alessandro M. Varani   +8 more
wiley   +1 more source

Transipedia.org: k-mer-based exploration of large RNA sequencing datasets and application to cancer data

Genome Biology
Indexing techniques relying on k-mers have proven effective in searching for RNA sequences across thousands of RNA-seq libraries, but without enabling direct RNA quantification.
Chloé Bessière, Haoliang Xue, Benoit Guibert, Anthony Boureux, Florence Rufflé, Julien Viot, Rayan Chikhi, Mikaël Salson, Camille Marchet, Thérèse Commes, Daniel Gautheret   +10 more
doaj   +1 more source

Converting Time Series Data to Numeric Representations Using Alphabetic Mapping and k-mer strategy [PDF]

Sarwan Ali, Tamkanat E. Ali, Imdadullah Khan, Murray Patterson   +3 more
openalex   +1 more source

aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets

, 2023
Camila Duitama González, Samarth Rangavittal, Riccardo Vicedomini, Rayan Chikhi, Hugues Richard   +4 more
openalex   +1 more source

deltaHED predicts survival and immune evasion in PD‐1 blockade therapy: A multi‐cohort study across three cancer types

Clinical and Translational Medicine, Volume 16, Issue 2, February 2026.
deltaHED predicts survival and immune evasion in PD‐1 blockade therapy: a multi‐cohort study across three cancer types. deltaHED quantifies germlinesomatic HLA‐I divergence and predicts survival and immune evasion in PD‐1 blockade therapy. Across nasopharyngeal carcinoma, melanoma, and esophageal squamous cell carcinoma, high deltaHED is associated ...
Jianying Xu, Xiaoli Wei, Jicheng Yao, Ujjwal Mukund Mahajan, Ulf Dietrich Kahlert, Run Shi, Kaiying Zhang, Ahmed Alnatsha, Zhengyi Qian, Fei Han, Fenghua Wang   +10 more
wiley   +1 more source