Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: bioconductor: karyoploteR
https://packages.ecosyste.ms/registries/bioconductor.org/packages/karyoploteR
Plot customizable linear genomes displaying arbitrary data
1 version
Latest release: about 1 year ago
7 dependent packages
68,807 downloads total
Papers Mentioning karyoploteR 50
10.1016/j.cell.2019.07.038
A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thalianaCited 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 gliomaCited 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 cholangiocarcinomaCited 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 SequoiaCited 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 FOSL1Cited 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: over 3 years ago
10.3390/jof6030182
ATAC-Seq Identifies Chromatin Landscapes Linked to the Regulation of Oxidative Stress in the Human Fungal Pathogen Candida albicansCited 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
<i>RIdeogram</i>: drawing SVG graphics to visualize and map genome-wide data on the idiogramsCited 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 fungusCited 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: almost 4 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 2021Cited 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 dataCited 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 <i>Auanema rhodensis</i>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 plantCited 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 MosquitoesCited 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 ApproachCited 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: over 5 years ago
10.3389/fcell.2021.662707
PLXNC1: A Novel Potential Immune-Related Target for Stomach AdenocarcinomaCited 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, <i>Bombyx mandarina</i>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 levelCited 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 MellitusCited 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 growthCited 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 cerevisiaeCited 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: almost 4 years ago
10.1038/s41598-020-77063-5
Machine learning approaches reveal genomic regions associated with sugarcane brown rust resistanceCited 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: about 4 years ago
10.1186/s13229-020-00407-5
Analysis of common genetic variation and rare CNVs in the Australian Autism BiobankCited 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: almost 4 years ago
10.1038/s41375-018-0103-3
Whole-genome sequencing of multiple myeloma reveals oncogenic pathways are targeted somatically through multiple mechanismsCited 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 enhancersCited 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 ChickenCited 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 SigProfilerSimulatorCited 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 virulenceCited 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, BrazilCited 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 muscleCited 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 BrazilCited 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 <i>Brassica napus</i> pangenome reveals significant structural variationCited 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 VariationCited 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 <i>De Novo</i> Lager Yeast Hybrids with a Unique Genomic Architecture: Creation and CharacterizationCited 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 ExonsCited 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. cepaeCited 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 ferrugineusCited 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 therapyCited 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 cancersCited 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: about 5 years ago
10.1534/g3.119.400486
Phased Diploid Genome Assemblies for Three Strains of <i>Candida albicans</i> from Oak TreesCited 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 molesCited 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 <i>in planta‐</i>secreted <i>Verticillium dahliae</i> Av2 effector protein recognized in tomato plants that carry the <scp><i>V2</i></scp> resistance locusCited 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 SignaturesCited 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 lineagesCited 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 dysplasiaCited 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 StudyCited 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 backgroundsCited 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 <i>PRKN</i> exon inversion invisible to exome sequencingCited 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
<i>Drosophila</i> USP22/nonstop polarizes the actin cytoskeleton during collective border cell migrationCited 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 <i>Drosophila bifasciata</i> Reveals Important Karyotypic Transition of the X ChromosomeCited by: 8
Author(s): Ryan Bracewell, Anita Tran, Kamalakar Chatla, Doris Bachtrog
Software Mentions: 1
Published: over 4 years ago