Works matching DE "PAN-genome"

Results: 381

Pangenome Analysis of the Plant Pathogen Pseudomonas syringae Reveals Unique Natural Products for Niche Adaptation.

Published in:

Angewandte Chemie, 2025, v. 137, n. 25, p. 1, doi. 10.1002/ange.202503679

By:

Zhang, Shuaibing;
Huang, Ying;
Nachawati, Raed;
Huber, Philipp;
Walther, Grit;
Gregor, Lucas;
Vilotijević, Ivan;
Stallforth, Pierre

Publication type:

Article

Effectidor II: a pan-genomic AI-based algorithm for the prediction of type III secretion system effectors Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf272

By:

Wagner, Naama;
Baumer, Ella;
Lyubman, Iris;
Shimony, Yair;
Bracha, Noam;
Martins, Leonor;
Potnis, Neha;
Chang, Jeff H;
Teper, Doron;
Koebnik, Ralf;
Pupko, Tal

Publication type:

Article

Pitfalls of bacterial pan-genome analysis approaches: a case study of Mycobacterium tuberculosis and two less clonal bacterial species Open Access.

Published in:

Bioinformatics, 2025, v. 41, n. 5, p. 1, doi. 10.1093/bioinformatics/btaf219

By:

Marin, Maximillian G;
Quinones-Olvera, Natalia;
Wippel, Christoph;
Behruznia, Mahboobeh;
Jeffrey, Brendan M;
Harris, Michael;
Mann, Brendon C;
Rosenthal, Alex;
Jacobson, Karen R;
Warren, Robin M;
Li, Heng;
Meehan, Conor J;
Farhat, Maha R

Publication type:

Article

Pangenomic analysis of three putative hydrocarbon degrading genera Limnohabitans, Aquabacterium , and Novosphingobium collected from freshwater sources.

Published in:

Genome, 2025, v. 68, p. 1, doi. 10.1139/gen-2023-0099

By:

Kharey, Gurpreet S.;
Palace, Vince;
Whyte, Lyle;
Greer, Charles W.

Publication type:

Article

Pan-Genome-Wide Investigation and Expression Analysis of GATA Gene Family in Maize.

Published in:

Plants (2223-7747), 2025, v. 14, n. 11, p. 1693, doi. 10.3390/plants14111693

By:

Zhao, Fangfang;
Li, Xia;
Chen, Ziqi;
Guo, Changhong

Publication type:

Article

Graph-based pan-genome analysis reveals diversity of structural variations in native and commercial chicken.

Published in:

Frontiers of Agricultural Science & Engineering, 2025, v. 12, n. 2, p. 355, doi. 10.15302/J-FASE-2024591

By:

Yiming WANG;
Zijia NI;
Yinhua HUANG

Publication type:

Article

Pan-genome analysis of the R2R3-MYB genes family in Brassica napus unveils phylogenetic divergence and expression profiles under hormone and abiotic stress treatments.

Published in:

Frontiers in Plant Science, 2025, p. 1, doi. 10.3389/fpls.2025.1588362

By:

Fan, Haiyan;
Li, Jiawei;
Huang, Wencong;
Liang, Aoshuang;
Jing, Liqing;
Li, Jintao;
Yang, Qing-Yong;
Liu, Kede;
Yang, Zhiquan

Publication type:

Article

Mining sorghum pangenome enabled identification of new dw3 alleles for breeding stable-dwarfing hybrids Open Access.

Published in:

G3: Genes | Genomes | Genetics, 2025, v. 15, n. 5, p. 1, doi. 10.1093/g3journal/jkaf054

By:

Marla, Sandeep R;
Olatoye, Marcus;
Davis, Matthew;
Otchere, Vincent;
Sexton-Bowser, Sarah;
Morris, Geoffrey P;
Felderhoff, Terry

Publication type:

Article

Pan-Genome Analysis Reveals Local Adaptation to Climate Driven by Introgression in Oak Species Open Access.

Published in:

Molecular Biology & Evolution, 2025, v. 42, n. 5, p. 1, doi. 10.1093/molbev/msaf088

By:

Liang, Yi-Ye;
Liu, Hui;
Lin, Qiong-Qiong;
Shi, Yong;
Zhou, Biao-Feng;
Wang, Jing-Shu;
Chen, Xue-Yan;
Shen, Zhao;
Qiao, Liang-Jing;
Niu, Jing-Wei;
Ling, Shao-Jun;
Luo, Wen-Ji;
Zhao, Wei;
Liu, Jian-Feng;
Kuang, Yuan-Wen;
Ingvarsson, Pär K;
Guo, Ya-Long;
Wang, Baosheng

Publication type:

Article

Identification of Novel Gene-Specific Markers for Differentiating Various Pathogenic Campylobacter Species Using a Pangenome Analysis Approach.

Published in:

Pathogens, 2025, v. 14, n. 5, p. 477, doi. 10.3390/pathogens14050477

By:

Kuufire, Emmanuel;
Bentum, Kingsley E.;
Nyarku, Rejoice;
Osei, Viona;
Elrefaey, Asmaa;
James, Tyric;
Woube, Yilkal;
Folitse, Raphael;
Samuel, Temesgen;
Abebe, Woubit

Publication type:

Article

Whole-genome probe capture sequencing reveals genomic diversity and characteristics of Mycoplasma pneumoniae in Nanjing, China.

Published in:

Frontiers in Microbiology, 2025, p. 1, doi. 10.3389/fmicb.2025.1589971

By:

Zhou, Guilan;
Yu, Yan;
Ge, Teng;
Tang, Chenyu;
Zhang, Hongbo;
He, Min

Publication type:

Article

Nitrite-oxidizing bacteria adapted to low-oxygen conditions dominate nitrite oxidation in marine oxygen minimum zones.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2024, v. 18, n. 1, p. 1, doi. 10.1093/ismejo/wrae160

By:

Fortin, Samantha G;
Sun, Xin;
Jayakumar, Amal;
Ward, Bess B

Publication type:

Article

Molecular mechanisms and environmental adaptations of flagellar loss and biofilm growth of Rhodanobacter under environmental stress.

Published in:

ISME Journal: Multidisciplinary Journal of Microbial Ecology, 2024, v. 18, n. 1, p. 1, doi. 10.1093/ismejo/wrae151

By:

Chen, Mingfei;
Trotter, Valentine V;
Walian, Peter J;
Chen, Yan;
Lopez, Romario;
Lui, Lauren M;
Nielsen, Torben N;
Malana, Ria Gracielle;
Thorgersen, Michael P;
Hendrickson, Andrew J;
Carion, Héloïse;
Deutschbauer, Adam M;
Petzold, Christopher J;
Smith, Heidi J;
Arkin, Adam P;
Adams, Michael W W;
Fields, Matthew W;
Chakraborty, Romy

Publication type:

Article

A Genome-wide comparative analysis to characterise the phylogenetic relationship and the pathogenicity of Pseudomonas syringae pv. actinidiae strains.

Published in:

European Journal of Plant Pathology, 2024, v. 168, n. 1, p. 97, doi. 10.1007/s10658-023-02731-x

By:

Turco, Silvia;
Ferrucci, Andrea;
Drais, Mounira Inas;
Mazzaglia, Angelo

Publication type:

Article

解淀粉芽孢杆菌群体遗传特征分析.

Published in:

Food Research & Development, 2023, v. 44, n. 17, p. 160, doi. 10.12161/j.issn.1005-6521.2023.17.022

By:

王依婷;
李素珍;
毛志涛;
廖小平;
许慧敏;
邱艺华;
闫雪崧;
杨凤妍;
李贞景;
郭庆彬;
刘欢欢

Publication type:

Article

Pan-Genome Analysis Reveals Functional Divergences in Gut-Restricted Gilliamella and Snodgrassella.

Published in:

Bioengineering (Basel), 2022, v. 9, n. 10, p. N.PAG, doi. 10.3390/bioengineering9100544

By:

Zhang, Zhengyi;
Guo, Yulong;
Yang, Fan;
Li, Jilian

Publication type:

Article

Correction to: Female space use correlates with extra-pair mating in barn swallow replacement clutches.

Published in:

2025

By:

Kenny-Duddela, Heather V.;
Schield, Drew R.;
Keller, Kayleigh P.;
Safran, Rebecca J.

Publication type:

Correction Notice

The characterization of genome sequences diversity of Pseudomonas aeruginosa strains from international reference panel using wide range of in silico techniques.

Published in:

Acta Universitatis Lodziensis Folia Biologica et Oecologica, 2024, v. 18, p. 72, doi. 10.18778/1730-2366.18.11

By:

PETRUŃKO, LEON;
MUSIAŁ, KLAUDIA;
GMITER, DAWID

Publication type:

Article

Unraveling Allelic Impacts on Pre-Harvest Sprouting Resistance in TaVP1 -B of Chinese Wheat Accessions Using Pan-Genome.

Published in:

Plants (2223-7747), 2025, v. 14, n. 4, p. 504, doi. 10.3390/plants14040504

By:

Wang, Danfeng;
Xie, Jinjin;
Wang, Jingwen;
Mu, Mengdi;
Xiong, Haifeng;
Ma, Fengshuo;
Li, Peizhen;
Jia, Menghan;
Li, Shuangjing;
Li, Jiaxin;
Zhu, Mingyue;
Li, Peiwen;
Guan, Haiyan;
Zhang, Yi;
Li, Hao

Publication type:

Article

Comparative Analysis of Transposable Elements in the Genomes of Citrus and Citrus -Related Genera.

Published in:

Plants (2223-7747), 2024, v. 13, n. 17, p. 2462, doi. 10.3390/plants13172462

By:

Wu, Yilei;
Wang, Fusheng;
Lyu, Keliang;
Liu, Renyi

Publication type:

Article

Genome Assembly and Structural Variation Analysis of Luffa acutangula Provide Insights on Flowering Time and Ridge Development.

Published in:

Plants (2223-7747), 2024, v. 13, n. 13, p. 1828, doi. 10.3390/plants13131828

By:

Huang, Aizheng;
Feng, Shuo;
Ye, Zhuole;
Zhang, Ting;
Chen, Shenglong;
Chen, Changming;
Chen, Shijun

Publication type:

Article

A Quantitative Trait Locus with a Major Effect on Root-Lesion Nematode Resistance in Barley.

Published in:

Plants (2223-7747), 2024, v. 13, n. 12, p. 1663, doi. 10.3390/plants13121663

By:

Mather, Diane;
Vassos, Elysia;
Sheedy, Jason;
Guo, Wenbin;
McKay, Alan

Publication type:

Article

What makes a good reference? First steps toward a Chlamydomonas pangenome.

Published in:

Plant Cell, 2023, v. 35, n. 2, p. 628, doi. 10.1093/plcell/koac361

By:

Chan, Ching;
Salomé, Patrice A

Publication type:

Article

Insights into the Maize Pan-Genome and Pan-Transcriptome.

Published in:

Plant Cell, 2014, v. 26, n. 1, p. 121, doi. 10.1105/tpc.113.119982

By:

Hirsch, Candice N.;
Foerster, Jillian M.;
Johnson, James M.;
Sekhon, Rajandeep S.;
Muttoni, German;
Vaillancourt, Brieanne;
Peñagaricano, Francisco;
Lindquist, Erika;
Pedraza, Mary Ann;
Barry, Kerrie;
Leon, Natalia de;
Kaeppler, Shawn M.;
Buell, C. Robin

Publication type:

Article

Pangenome Data Analysis Reveals Characteristics of Resistance Gene Analogs Associated with Sclerotinia sclerotiorum Resistance in Sunflower.

Published in:

Life (2075-1729), 2024, v. 14, n. 10, p. 1322, doi. 10.3390/life14101322

By:

Lu, Yan;
Huang, Jiaying;
Liu, Dongqi;
Kong, Xiangjiu;
Song, Yang;
Jing, Lan

Publication type:

Article

Draft Genome Sequence Analyses of Two Novel Marinobacter suadae sp. nov. and Wenyingzhuangia gilva sp. nov. Isolated from the Root of Suaeda japonica Makino.

Published in:

Life (2075-1729), 2024, v. 14, n. 3, p. 296, doi. 10.3390/life14030296

By:

Park, Sunho;
Kim, Inhyup;
Chhetri, Geeta;
Jung, Yonghee;
Woo, Haejin;
Seo, Taegun

Publication type:

Article

Human Pangenomics: Promises and Challenges of a Distributed Genomic Reference.

Published in:

Life (2075-1729), 2023, v. 13, n. 6, p. 1360, doi. 10.3390/life13061360

By:

Abondio, Paolo;
Cilli, Elisabetta;
Luiselli, Donata

Publication type:

Article

Population genetic analysis of clinical Mycobacterium abscessus complex strains in China.

Published in:

Frontiers in Cellular & Infection Microbiology, 2025, p. 1, doi. 10.3389/fcimb.2024.1496896

By:

Li, Xiangchen;
Zhu, Yelei;
Lu, Yewei;
Wu, Kunyang;
Che, Yang;
Wang, Xiaomeng;
Wang, Weixin;
Gao, Junli;
Gao, Junshun;
Liu, Zhengwei;
Zhou, Zhuxian

Publication type:

Article

Whole genome sequencing distinguishes skin colonizing from infection-associated Cutibacterium acnes isolates.

Published in:

Frontiers in Cellular & Infection Microbiology, 2024, p. 1, doi. 10.3389/fcimb.2024.1433783

By:

Podbielski, Andreas;
Köller, Thomas;
Warnke, Philipp;
Barrantes, Israel;
Kreikemeyer, Bernd

Publication type:

Article

Campylobacter coli of porcine origin exhibits an open pan-genome within a single clonal complex: insights from comparative genomic analysis.

Published in:

Frontiers in Cellular & Infection Microbiology, 2024, p. 1, doi. 10.3389/fcimb.2024.1449856

By:

Ghatak, Sandeep;
Prince Milton, Arockiasamy Arun;
Das, Samir;
Momin, Kasanchi M.;
Srinivas, Kandhan;
Pyngrope, Daniel Aibor;
Priya, G. Bhuvana

Publication type:

Article

Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus.

Published in:

Journal of Animal Science & Biotechnology, 2025, v. 16, n. 1, p. 1, doi. 10.1186/s40104-024-01133-1

By:

Azam, Sarwar;
Sahu, Abhisek;
Pandey, Naveen Kumar;
Neupane, Mahesh;
Van Tassell, Curtis P;
Rosen, Benjamin D;
Gandham, Ravi Kumar;
Rath, Subha Narayan;
Majumdar, Subeer S

Publication type:

Article

Near telomere-to-telomere genome assemblies of Silkie Gallus gallus and Mallard Anas platyrhynchos restored the structure of chromosomes and "missing" genes in birds.

Published in:

Journal of Animal Science & Biotechnology, 2025, v. 16, n. 1, p. 1, doi. 10.1186/s40104-024-01141-1

By:

Zhao, Qiangsen;
Yin, Zhongtao;
Hou, Zhuocheng

Publication type:

Article

The goat pan-genome reveals patterns of gene loss during domestication.

Published in:

Journal of Animal Science & Biotechnology, 2024, v. 15, n. 1, p. 1, doi. 10.1186/s40104-024-01092-7

By:

Liu, Jiaxin;
Shi, Yilong;
Mo, Dongxin;
Luo, Lingyun;
Xu, Songsong;
Lv, Fenghua

Publication type:

Article

Pangenome and multi-tissue gene atlas provide new insights into the domestication and highland adaptation of yaks.

Published in:

Journal of Animal Science & Biotechnology, 2024, v. 15, n. 1, p. 1, doi. 10.1186/s40104-024-01027-2

By:

Lan, Daoliang;
Fu, Wei;
Ji, Wenhui;
Mipam, Tserang-Donko;
Xiong, Xianrong;
Ying, Shi;
Xiong, Yan;
Sheng, Peng;
Ni, Jiangping;
Bai, Lijun;
Shan, Tongling;
Kong, Xiangdong;
Li, Jian

Publication type:

Article

Pig pangenome graph reveals functional features of non-reference sequences.

Published in:

Journal of Animal Science & Biotechnology, 2024, v. 15, p. 1, doi. 10.1186/s40104-023-00984-4

By:

Miao, Jian;
Wei, Xingyu;
Cao, Caiyun;
Sun, Jiabao;
Xu, Yuejin;
Zhang, Zhe;
Wang, Qishan;
Pan, Yuchun;
Wang, Zhen

Publication type:

Article

Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis.

Published in:

Journal of Animal Science & Biotechnology, 2023, v. 14, n. 1, p. 1, doi. 10.1186/s40104-023-00944-y

By:

Gao, Guangliang;
Zhang, Hongmei;
Ni, Jiangping;
Zhao, Xianzhi;
Zhang, Keshan;
Wang, Jian;
Kong, Xiangdong;
Wang, Qigui

Publication type:

Article

A review of the pangenome: how it affects our understanding of genomic variation, selection and breeding in domestic animals?

Published in:

Journal of Animal Science & Biotechnology, 2023, v. 14, n. 1, p. 1, doi. 10.1186/s40104-023-00860-1

By:

Gong, Ying;
Li, Yefang;
Liu, Xuexue;
Ma, Yuehui;
Jiang, Lin

Publication type:

Article

An alignment- and reference-free strategy using k-mer present pattern for population genomic analyses.

Published in:

Mycology: An International Journal on Fungal Biology, 2025, v. 16, n. 1, p. 309, doi. 10.1080/21501203.2024.2358868

By:

Shi, Guohui;
Dai, Yi;
Zhou, Da;
Chen, Mengmeng;
Zhang, Jiaqi;
Bi, Yilong;
Liu, Shuai;
Wu, Qi

Publication type:

Article

Comprehensive Analysis of Ghd7 Variations Using Pan-Genomics and Prime Editing in Rice.

Published in:

Genes, 2025, v. 16, n. 4, p. 462, doi. 10.3390/genes16040462

By:

Wang, Jiarui;
Liu, Shihang;
Pu, Jisong;
Li, Jun;
He, Changcai;
Zhang, Lanjing;
Zhou, Xu;
Xu, Dongyu;
Zhou, Luyao;
Guo, Yuting;
Zhang, Yuxiu;
Wang, Yang;
Yang, Bin;
Wang, Pingrong;
Deng, Xiaojian;
Sun, Changhui

Publication type:

Article

Worldwide Population Dynamics of Salmonella Saintpaul: Outbreaks, Epidemiology, and Genome Structure.

Published in:

Genes, 2025, v. 16, n. 3, p. 254, doi. 10.3390/genes16030254

By:

Panzenhagen, Pedro;
Shah, Devendra H.;
Rodrigues, Dalia dos Prazeres;
Conte Junior, Carlos Adam

Publication type:

Article

Comparative Evolutionary Genomics Reveals Genetic Diversity and Differentiation in Bacteroides fragilis.

Published in:

Genes, 2024, v. 15, n. 12, p. 1519, doi. 10.3390/genes15121519

By:

Muto, Yoshinori;
Tanaka, Kaori

Publication type:

Article

A Case Report of SYNE1 Deficiency-Mimicking Mitochondrial Disease and the Value of Pangenomic Investigations.

Published in:

Genes, 2023, v. 14, n. 12, p. 2154, doi. 10.3390/genes14122154

By:

Serag, Mounir;
Plutino, Morgane;
Charles, Perrine;
Azulay, Jean-Philippe;
Chaussenot, Annabelle;
Paquis-Flucklinger, Véronique;
Ait-El-Mkadem Saadi, Samira;
Rouzier, Cécile

Publication type:

Article

How is the Human Pangenome Project Like a Whole Person Psychology.

Published in:

International Journal of Transpersonal Studies, 2023, v. 42, n. 1, p. III, doi. 10.24972/ijts.2023.42.1.iii

By:

Hartelius, Glenn

Publication type:

Article

In This Issue of IJTS.

Published in:

International Journal of Transpersonal Studies, 2023, v. 42, n. 1, p. vi

By:

Hartelius, Glenn

Publication type:

Article

Pan-genome Analysis Reveals Comparative Genomic Features of Central Metabolic Pathways in Methylorubrum extorquens.

Published in:

Biotechnology & Bioprocess Engineering, 2023, v. 28, n. 6, p. 990, doi. 10.1007/s12257-022-0154-1

By:

Lee, Gyu Min;
Scott-Nevros, Zoe K.;
Lee, Sang-Mok;
Kim, Donghyuk

Publication type:

Article

Identification of key drivers of antimicrobial resistance in Enterococcus using machine learning.

Published in:

Canadian Journal of Microbiology, 2024, v. 70, n. 10, p. 446, doi. 10.1139/cjm-2024-0049

By:

Kim, Jee In;
Manuele, Alexander;
Maguire, Finlay;
Zaheer, Rahat;
McAllister, Tim A.;
Beiko, Robert G.

Publication type:

Article

Comparison of Recombination Rate, Reference Bias, and Unique Pangenomic Haplotypes in Cannabis sativa Using Seven De Novo Genome Assemblies.

Published in:

International Journal of Molecular Sciences, 2025, v. 26, n. 3, p. 1165, doi. 10.3390/ijms26031165

By:

Stack, George M.;
Quade, Michael A.;
Wilkerson, Dustin G.;
Monserrate, Luis A.;
Bentz, Philip C.;
Carey, Sarah B.;
Grimwood, Jane;
Toth, Jacob A.;
Crawford, Seth;
Harkess, Alex;
Smart, Lawrence B.

Publication type:

Article

Pan-genome de Bruijn graph using the bidirectional FM-index.

Published in:

BMC Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s12859-023-05531-6

By:

Depuydt, Lore;
Renders, Luca;
Abeel, Thomas;
Fostier, Jan

Publication type:

Article

HLA‐OLI: A new MHC class I pseudogene and HLA‐Y are located on a 60 kb indel in the human MHC between HLA‐W and HLA‐J.

Published in:

HLA: Immune Response Genetics, 2023, v. 102, n. 5, p. 599, doi. 10.1111/tan.15180

By:

Alexandrov, Nickolai;
Wang, Ting;
Blair, Lindley;
Nadon, Brian;
Sayer, David

Publication type:

Article

Trio-binning Assemblies of the Duroc and Landrace swine breeds.

Published in:

2024

By:

Ackerson, Leland K.;
Kuhn, Kristen;
Gondro, Cedric;
Jicai Jiang;
Maltecca, Christian;
Rohrer, Gary A.;
Rosen, Benjamin D.;
Smith, Timothy;
Tuggle, Christopher K.;
Wen Huang

Publication type:

Abstract