bioconductor: karyoploteR | Projects

10.1016/j.cell.2019.07.038

A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana
Cited by: 237
Author(s): Anna-Lena Van de Weyer, Freddy Monteiro, Oliver J. Furzer, Marc T. Nishimura, Volkan Çevik, Kamil Witek, Jonathan D. G. Jones, Jeffery L. Dangl, Detlef Weigel, Felix Bemm
Software Mentions: 23
Published: over 5 years ago

10.1111/jcmm.15705

Collagen Type III Alpha 1 chain regulated by GATA‐Binding Protein 6 affects Type II IFN response and propanoate metabolism in the recurrence of lower grade glioma
Cited by: 18
Author(s): Runzhi Huang, Zhenyu Li, Xiaolong Zhu, Penghui Yan, Dianwen Song, Huabin Yin, Peng Hu, Ruoyi Lin, Shengyu Wu, Tong Meng, Jie Zhang, Zongqiang Huang
Software Mentions: 14
Published: over 4 years ago

10.1186/s12885-021-07788-7

Comprehensive analysis of genomic mutation signature and tumor mutation burden for prognosis of intrahepatic cholangiocarcinoma
Cited by: 14
Author(s): Rui Zhang, Qi Li, Jiao Fu, Z C Jin, Jingbo Su, Jian Zhang, Chen Chen, Zhimin Geng, Dong Zhang
Software Mentions: 12
Published: almost 4 years ago

10.1534/g3.120.401612

A Reference Genome Sequence for Giant Sequoia
Cited by: 53
Author(s): Alison Dawn Scott, Aleksey V. Zimin, Daniela Puiu, Rachael E. Workman, Monica Britton, Sumaira Zaman, Madison Caballero, Andrew C. Read, Adam J. Bogdanove, Emily E. Burns, Jill L. Wegrzyn, Winston Timp, Steven L. Salzberg, David B. Neale
Software Mentions: 11
Published: about 4 years ago

10.7554/eLife.64846

NF1 regulates mesenchymal glioblastoma plasticity and aggressiveness through the AP-1 transcription factor FOSL1
Cited by: 36
Author(s): Carolina Marques, Thomas Unterkircher, Paula Kroon, Barbara Oldrini, Annalisa Izzo, Yuliia Dramaretska, Roberto Ferrarese, Eva Kling, Oliver Schnell, Sven Nelander, Erwin F. Wagner, Latifa Bakiri, Gaetano Gargiulo, Maria Stella Carro, Massimo Squatrito
Software Mentions: 11
Published: about 3 years ago

10.3390/jof6030182

ATAC-Seq Identifies Chromatin Landscapes Linked to the Regulation of Oxidative Stress in the Human Fungal Pathogen Candida albicans
Cited by: 14
Author(s): Sabrina Jenull, Michael Tscherner, Theresia Mair, Karl Kuchler
Software Mentions: 9
Published: about 4 years ago

10.7717/peerj-cs.251

RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms
Cited by: 221
Author(s): Zhaodong Hao, Dekang Lv, Ying Ge, Jisen Shi, Dolf Weijers, Guangchuang Yu, Jinhui Chen
Software Mentions: 8
Published: almost 5 years ago

10.1371/journal.pgen.1009386

Genomic rearrangements generate hypervariable mini-chromosomes in host-specific isolates of the blast fungus
Cited by: 39
Author(s): Thorsten Langner, Adeline Harant, Luis B. Gómez-Luciano, Ram-Krishna Shrestha, Angus Malmgren, Sergio M. Latorre, Hernán A. Burbano, Joe Win, Sophien Kamoun
Software Mentions: 8
Published: over 3 years ago

10.3390/pathogens10080988

Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021
Cited by: 11
Author(s): Vinícius Bonetti Franceschi, Gabriel Dickin Caldana, Christiano Perin, Alexandre Horn, Camila Peter, Gabriela Bettella Cybis, Patrícia Aline Gröhs Ferrareze, Liane Nanci Rotta, Flavio Cadegiani, Ricardo Ariel Zimerman, Claudia Elizabeth Thompson
Software Mentions: 8
Published: over 3 years ago

10.1093/bioinformatics/btx346

karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data
Cited by: 451
Author(s): Bernat Gel, Eduard Serra
Software Mentions: 7
Published: over 7 years ago

10.1534/g3.119.0011

Chromosome-Wide Evolution and Sex Determination in the Three-Sexed Nematode Auanema rhodensis
Cited by: 31
Author(s): Sophie Tandonnet, Georgios Koutsovoulos, Sally Adams, Delphine Cloarec, Manish Parihar, Mark Blaxter, André Pires-daSilva
Software Mentions: 7
Published: over 5 years ago

10.7554/eLife.56689

Genome streamlining in a minute herbivore that manipulates its host plant
Cited by: 30
Author(s): Robert Greenhalgh, Wannes Dermauw, Joris J. Glas, Stéphane Rombauts, Nicky Wybouw, Jainy Thomas, Juan M. Alba, Ellen J. Pritham, Saioa Legarrea, René Feyereisen, Yves Van de Peer, Thomas Van Leeuwen, Richard M. Clark, Merijn R. Kant
Software Mentions: 7
Published: about 4 years ago

10.3390/v12070695

Ross River Virus Provokes Differentially Expressed MicroRNA and RNA Interference Responses in Aedes aegypti Mosquitoes
Cited by: 10
Author(s): J. B. Sinclair, Sassan Asgari
Software Mentions: 6
Published: over 4 years ago

10.3390/ijms20164037

Consistent Biomarkers and Related Pathogenesis Underlying Asthma Revealed by Systems Biology Approach
Cited by: 18
Author(s): Xiner Nie, Jinyi Wei, Youjin Hao, Jingxin Tao, Yinghong Li, Mingwei Liu, Bo-Ying Xu, Bo Li
Software Mentions: 6
Published: about 5 years ago

10.3389/fcell.2021.662707

PLXNC1: A Novel Potential Immune-Related Target for Stomach Adenocarcinoma
Cited by: 12
Author(s): Zhizhan Ni, Chenshen Huang, Hongmei Zhao, Jinzhe Zhou, Muren Hu, Qing Chen, Bujun Ge, Qi Huang
Software Mentions: 5
Published: over 3 years ago

10.7717/peerj.10818

Cytochrome P450 monooxygenase genes in the wild silkworm, Bombyx mandarina
Cited by: 5
Author(s): Linrong Wan, Zhou Anlian, Wen‐Fu Xiao, Bangxing Zou, Yaming Jiang, Jing Xiao, Cao Deng, Youhong Zhang, Mengjia Liu
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41598-019-56386-y

Investigating a Plasmodium falciparum erythrocyte invasion phenotype switch at the whole transcriptome level
Cited by: 11
Author(s): Prince B. Nyarko, Sarah J. Tarr, Yaw Aniweh, Lindsay B. Stewart, David J. Conway, Gordon A. Awandare
Software Mentions: 5
Published: almost 5 years ago

10.1155/2020/8162524

High-Throughput Sequencing and Exploration of the lncRNA-circRNA-miRNA-mRNA Network in Type 2 Diabetes Mellitus
Cited by: 39
Author(s): Fang Yang, Chen Yang, Zhiqiang Xue, Yaogai Lv, Ли Шен, Kexin Li, Pingping Zheng, Pan Pan, Tianyu Feng, Lina Jin, Yan Yao
Software Mentions: 4
Published: over 4 years ago

10.1530/REP-19-0293

Blastocyst transfer in mice alters the placental transcriptome and growth
Cited by: 4
Author(s): Katerina Menelaou, Malwina Prater, Simon James Tunster, Georgina E T Blake, Colleen Geary Joo, James C. Cross, Russell S. Hamilton, Erica D. Watson
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12864-021-07417-4

Identification of novel genes involved in neutral lipid storage by quantitative trait loci analysis of Saccharomyces cerevisiae
Cited by: 3
Author(s): Klavdija Pačnik, Mojca Ogrizović, Matthias Diepold, Tobias Eisenberg, Mia Žganjar, Gašper Žun, Beti Kužnik, Cene Gostinčar, Tomaž Curk, Uroš Petrovič, Klaus Natter
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-020-77063-5

Machine learning approaches reveal genomic regions associated with sugarcane brown rust resistance
Cited by: 18
Author(s): Alexandre Hild Aono, Everardo Andrade da Costa, Hugo Vianna Silva Rody, James Shiniti Nagai, Ricardo José Gonzaga Pimenta, Melina Cristina Mancini, Fernanda Raquel Camilo dos Santos, Luciana Rossini Pinto, Marcos Guimarães de Andrade Landell, Anete Pereira de Souza, Reginaldo Massanobu Kuroshu
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13229-020-00407-5

Analysis of common genetic variation and rare CNVs in the Australian Autism Biobank
Cited by: 9
Author(s): Chloe X. Yap, Gail A. Alvares, Anjali K. Henders, Lin Tian, Leanne Wallace, Alaina Farrelly, Tiana McLaren, Jolene Berry, Anna A. E. Vinkhuyzen, Maciej Trzaskowski, Jian Zeng, Yuanhao Yang, Dominique Cleary, Rachel Grove, Claire Hafekost, Alexis Harun, Helen Holdsworth, Rachel Jellett, Feroza Khan, Lauren P. Lawson, Jodie Leslie, Mira Levis Frenk, Anne Masi, Nisha E. Mathew, Melanie Muniandy, Michaela Nothard, Peter M. Visscher, Paul A. Dawson, Cheryl Dissanayake, Valsamma Eapen, Helen Heussler, Andrew J. O. Whitehouse, Naomi R. Wray, Jacob Gratten
Software Mentions: 3
Published: over 3 years ago

10.1038/s41375-018-0103-3

Whole-genome sequencing of multiple myeloma reveals oncogenic pathways are targeted somatically through multiple mechanisms
Cited by: 62
Author(s): Phuc H. Hoang, Sara E. Dobbins, Alex J. Cornish, Daniel Chubb, Philip Law, Martin Kaiser, Richard S. Houlston
Software Mentions: 3
Published: over 6 years ago

10.1093/database/bay141

EnhancerDB: a resource of transcriptional regulation in the context of enhancers
Cited by: 24
Author(s): Ran Kang, Yiming Zhang, Qingqing Huang, Meng Ji, Ruofan Ding, Yunjian Chang, Lili Xiong, Zhiyun Guo
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2021.682501

Genome-Wide Association Study Using Whole-Genome Sequencing Identifies a Genomic Region on Chromosome 6 Associated With Comb Traits in Nandan-Yao Chicken
Cited by: 3
Author(s): Zhuliang Yang, Leqin Zou, Tiantian Sun, Wenwen Xu, Lei Zeng, Yinhai Jia, Jianping Jiang, Jixian Deng, Xiurong Yang
Software Mentions: 3
Published: over 3 years ago

10.1186/s12859-020-03772-3

Generating realistic null hypothesis of cancer mutational landscapes using SigProfilerSimulator
Cited by: 24
Author(s): Erik N. Bergstrom, Mark Barnes, Iñigo Martincorena, Ludmil B. Alexandrov
Software Mentions: 3
Published: about 4 years ago

10.1186/s13072-021-00396-6

Three putative DNA methyltransferases of Verticillium dahliae differentially contribute to DNA methylation that is dispensable for growth, development and virulence
Cited by: 6
Author(s): Holger Kramer, David E. Cook, Grardy C. M. van den Berg, Michael Seidl, Bart P.H.J. Thomma
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-021-07708-w

Genomic epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil
Cited by: 23
Author(s): Vinícius Bonetti Franceschi, Gabriel Dickin Caldana, Amanda de Menezes Mayer, Gabriela Bettella Cybis, Carla Andretta Moreira Neves, Patrícia Aline Gröhs Ferrareze, Meriane Demoliner, Paula Rodrigues de Almeida, Juliana Schons Gularte, Alana Witt Hansen, Matheus Nunes Weber, Juliane Deise Fleck, Ricardo Ariel Zimerman, Lívia Kmetzsch, Fernando Rosado Spilki, Claudia Elizabeth Thompson
Software Mentions: 2
Published: over 3 years ago

10.14202/vetworld.2020.1113-1125

Differential DNA methylation analysis across the promoter regions using methylated DNA immunoprecipitation sequencing profiling of porcine loin muscle
Cited by: 2
Author(s): Kaj Chokeshaiusaha, Denis Puthier, Thanida Sananmuang, Em-on Olanratmanee, Catherine Nguyen, Roongtham Kedkovid
Software Mentions: 2
Published: almost 5 years ago

10.3390/v12121414

Multiple Introductions Followed by Ongoing Community Spread of SARS-CoV-2 at One of the Largest Metropolitan Areas of Northeast Brazil
Cited by: 45
Author(s): Marcelo Henrique Santos Paiva, Duschinka Ribeiro Duarte Guedes, Cássia Docena, Matheus Filgueira Bezerra, Filipe Zimmer Dezordi, Laís Ceschini Machado, Larissa Krokovsky, Elisama Helvécio, Alexandre Freitas da Silva, Luydson Richardson Silva Vasconcelos, Antônio Mauro Rezende, Severino Jefferson Ribeiro da Silva, Kamila Gaudêncio da Silva Sales, Bruna Santos Lima Figueiredo de Sá, Derciliano Lopes da Cruz, Claudio Eduardo Cavalcanti, Armando de Menezes-Neto, Caroline Targino Alves da Silva, Renata Pessôa Germano Mendes, Maria Almerice Lopes da Silva, Tiago Gräf, Paola Cristina Resende, Gonzalo Bello, Michelle da Silva Barros, Wheverton Ricardo Correia do Nascimento, Rodrigo Moraes Loyo, Luciane Caroline Albuquerque Bezerra, Sinval Pinto Brandão-Filho, Constância Flávia Junqueira Ayres, Gabriel Luz Wallau
Software Mentions: 2
Published: almost 4 years ago

10.1111/pbi.13262

Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation
Cited by: 74
Author(s): Aria Dolatabadian, Philipp E. Bayer, Soodeh Tirnaz, Bhavna Hurgobin, David Edwards, Jacqueline Batley
Software Mentions: 2
Published: about 5 years ago

10.1016/j.cell.2020.05.024

Population Structure, Stratification, and Introgression of Human Structural Variation
Cited by: 56
Author(s): Mohamed A. Almarri, Anders Bergström, Javier Prado-Martinez, Fengtang Yang, Beiyuan Fu, Alistair S. Dunham, Yuan Chen, Matthew E. Hurles, Chris Tyler‐Smith, Yali Xue
Software Mentions: 2
Published: over 4 years ago

10.1128/AEM.02434-20

Industrially Applicable De Novo Lager Yeast Hybrids with a Unique Genomic Architecture: Creation and Characterization
Cited by: 10
Author(s): Zachari Turgeon, Thomas Sierocinski, Cedric A. Brimacombe, Yiqiong Jin, Brittany Goldhawke, Jessica M. J. Swanson, John I. Husnik, Matthew S. Dahabieh
Software Mentions: 2
Published: almost 4 years ago

10.3389/fpls.2020.01230

Big Genes, Small Effectors: Pea Aphid Cassette Effector Families Composed From Miniature Exons
Cited by: 6
Author(s): Matthew Dommel, Jong‐Nam Oh, José C. Huguet‐Tapia, Endrick Guy, Hélène Boulain, Akiko Sugio, M. Murugan, Fabrice Legeai, Michelle Heck, Charlotte M. Smith, Frank F. White
Software Mentions: 2
Published: about 4 years ago

10.3389/fpls.2021.630175

Comparing a Mixed Model Approach to Traditional Stability Estimators for Mapping Genotype by Environment Interactions and Yield Stability in Soybean [Glycine max (L.) Merr.]
Cited by: 4
Author(s): Mary Happ, George L. Graef, Haichuan Wang, Réka Howard, Luis Posadas, David L. Hyten
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-018-30335-7

Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae
Cited by: 61
Author(s): Andrew D. Armitage, Andrew Taylor, Maria K. Sobczyk, Laura Baxter, Bethany P. J. Greenfield, Helen Bates, Frank J. Wilson, Alison C. Jackson, Sascha Ott, Richard J. Harrison, John P. Clarkson
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-021-89091-w

Haplotype-resolved genome assembly enables gene discovery in the red palm weevil Rhynchophorus ferrugineus
Cited by: 16
Author(s): Guilherme Borges Dias, Musaad A. Altammami, Hamadttu A. F. El-Shafie, Fahad M. Alhoshani, Mohamed B. Al-Fageeh, Casey M. Bergman, Manee M. Manee
Software Mentions: 2
Published: over 3 years ago

10.1038/s41416-019-0682-4

Accelerating development of high-risk neuroblastoma patient-derived xenograft models for preclinical testing and personalised therapy
Cited by: 28
Author(s): Alvin Kamili, Andrew J. Gifford, Nancy Li, Chelsea Mayoh, Shu Oi Chow, Timothy W. Failes, Georgina Eden, Roxanne Cadiz, Jinhan Xie, Robyn Lukeis, Murray D. Norris, Michelle Haber, Geoffrey McCowage, Greg M. Arndt, Toby N. Trahair, Jamie I. Fletcher
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-019-53262-7

Functional and topographic effects on DNA methylation in IDH1/2 mutant cancers
Cited by: 26
Author(s): Ramona Bledea, Varshini Vasudevaraja, Seema Patel, James M. Stafford, Jonathan Serrano, Gianna Esposito, Lilian M. Tredwin, Nina Goodman, Andreas Kloetgen, John G. Golfinos, David Zagzag, Britta Weigelt, A. John Iafrate, Erik P. Sulman, S. Andrew, Snjezana Doğan, Jorge S. Reis‐Filho, Sarah Chiang, Dimitris G. Placantonakis, Aristotelis Tsirigos, Matija Snuderl
Software Mentions: 1
Published: almost 5 years ago

10.1534/g3.119.400486

Phased Diploid Genome Assemblies for Three Strains of Candida albicans from Oak Trees
Cited by: 6
Author(s): Jennafer A. P. Hamlin, Guilherme Borges Dias, Casey M. Bergman, Douda Bensasson
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-020-74375-4

Parental contribution to trisomy in heterozygous androgenetic complete moles
Cited by: 3
Author(s): Hirokazu Usui, Asuka Sato, Makio Shozu
Software Mentions: 1
Published: about 4 years ago

10.1111/1462-2920.15288

Comparative genomics reveals the in planta‐secreted Verticillium dahliae Av2 effector protein recognized in tomato plants that carry the <scp>V2</scp> resistance locus
Cited by: 26
Author(s): Edgar A Chavarro-Carrero, Jasper P. Vermeulen, David E Torres, Toshiyuki Usami, Henk J. Schouten, Yuling Bai, Michael Seidl, Bart P.H.J. Thomma
Software Mentions: 1
Published: about 4 years ago

10.3390/ijms22126257

Comparative Genomics of Eight Fusarium graminearum Strains with Contrasting Aggressiveness Reveals an Expanded Open Pangenome and Extended Effector Content Signatures
Cited by: 10
Author(s): Tarek Alouane, Hélène Rimbert, Jörg Bormann, Gisela A. González‐Montiel, Sandra Loesgen, Wilhelm Schäfer, Michael Freitag, Thierry Langin, Ludovic Bonhomme
Software Mentions: 1
Published: over 3 years ago

10.1016/j.theriogenology.2020.11.021

Analysis of bovine blastocysts indicates ovarian stimulation does not induce chromosome errors, nor discordance between inner-cell mass and trophectoderm lineages
Cited by: 14
Author(s): D.A.R. Tutt, Graciela Silvestri, María Serrano-Albal, R.J. Simmons, Wing Yee Kwong, Gizem Guven-Ates, Carla Canedo-Ribeiro, Rémi Labrecque, Patrick Blondin, Alan H. Handyside, Darren K. Griffin, Kevin D. Sinclair
Software Mentions: 1
Published: almost 4 years ago

10.1002/ccr3.2884

Novel homozygous variant in WISP3 in a family with unrecognized progressive pseudorheumatoid dysplasia
Cited by: 0
Author(s): Chandreshkumar Patel, Anas M. Khanshour, David Wilkes, Jonathan J. Rios, Kelly Sheff, Lorien Nassi, Carol A. Wise
Software Mentions: 1
Published: over 4 years ago

10.3390/cells10092284

Preimplantation Genetic Testing for Aneuploidy Improves Live Birth Rates with In Vitro Produced Bovine Embryos: A Blind Retrospective Study
Cited by: 13
Author(s): Graciela Silvestri, Carla Canedo-Ribeiro, María Serrano-Albal, Rémi Labrecque, Patrick Blondin, Steven Larmer, Gabriele Marras, Desmond Tutt, Alan H. Handyside, Marta Farré, Kevin D. Sinclair, Darren K. Griffin
Software Mentions: 1
Published: about 3 years ago

10.7554/eLife.70339

Loss of heterozygosity results in rapid but variable genome homogenization across yeast genetic backgrounds
Cited by: 21
Author(s): Abhishek Dutta, Fabien Dutreux, Joseph Schacherer
Software Mentions: 1
Published: over 3 years ago

10.1093/braincomms/fcab197

Levodopa-responsive dystonia caused by biallelic PRKN exon inversion invisible to exome sequencing
Cited by: 4
Author(s): Hagar Mor‐Shaked, Emuna Paz-Ebstein, Adily Basal, Simona Ben‐Haim, Hanna Grobe, Sami Heymann, Zvi Israel, Montaser Namnah, Anat Nitzan, Chaggai Rosenbluh, Ann Saada, Tomer Tzur, Shira Yanovsky‐Dagan, Ronen Zaidel-Bar, Tamar Harel, David Arkadir
Software Mentions: 1
Published: almost 4 years ago

10.1083/jcb.202007005

Drosophila USP22/nonstop polarizes the actin cytoskeleton during collective border cell migration
Cited by: 4
Author(s): Hammed A Badmos, Neville Cobbe, Amy E. Campbell, Richard Jackson, Daimark Bennett
Software Mentions: 1
Published: over 3 years ago

10.1534/g3.119.400922

Chromosome-Level Assembly of Drosophila bifasciata Reveals Important Karyotypic Transition of the X Chromosome
Cited by: 8
Author(s): Ryan Bracewell, Anita Tran, Kamalakar Chatla, Doris Bachtrog
Software Mentions: 1
Published: over 4 years ago

Projects: bioconductor: karyoploteR

Papers Mentioning karyoploteR 50