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: pypi: jellyfish
https://packages.ecosyste.ms/registries/pypi.org/packages/jellyfish
Approximate and phonetic matching of strings.
40 versions
Latest release: about 1 year ago
57 dependent packages
2,323,429 downloads last month
Papers Mentioning jellyfish 33
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
10.1093/gbe/evaa071
Distinct Life Histories Impact Dikaryotic Genome Evolution in the Rust Fungus Puccinia striiformis Causing Stripe Rust in WheatCited by: 30
Author(s): Benjamin Schwessinger, Yan Jun Chen, Richard Tien, Josef Korbinian Vogt, Jana Sperschneider, Ramawatar Nagar, Mark McMullan, Thomas Sicheritz-Pontén, Chris K. Sørensen, Mogens S. Hovmøller, John P. Rathjen, Annemarie Fejer Justesen
Software Mentions: 6
Published: over 4 years ago
10.3390/plants8090354
Population Genomic Approaches for Weed ScienceCited by: 14
Author(s): Sara L. Martin, Jean-Sébastien Parent, Martin Laforest, Eric R. Page, Julia M. Kreiner, Tracey James
Software Mentions: 6
Published: about 5 years ago
10.3389/frai.2020.536086
Attitudes Toward Multilingualism in Luxembourg. A Comparative Analysis of Online News Comments and Crowdsourced Questionnaire DataCited by: 5
Author(s): Christoph Purschke
Software Mentions: 5
Published: about 4 years ago
10.1093/dnares/dsaa029
<i>De novo</i> genome assembly of two tomato ancestors, <i>Solanum pimpinellifolium</i> and <i>Solanum</i> <i> lycopersicum</i> var. <i>cerasiforme</i>, by long-read sequencingCited by: 19
Author(s): Hitomi Takei, Kenta Shirasawa, Kosuke Kuwabara, Atsushi Toyoda, Yuma Matsuzawa, Shinji Iioka, Tohru Ariizumi
Software Mentions: 5
Published: almost 4 years ago
10.1371/journal.pone.0081760
When Whole-Genome Alignments Just Won't Work: kSNP v2 Software for Alignment-Free SNP Discovery and Phylogenetics of Hundreds of Microbial GenomesCited by: 205
Author(s): Shea N. Gardner, Barry G. Hall
Software Mentions: 4
Published: almost 11 years ago
10.1186/s12915-020-00797-1
The roles of hybridization and habitat fragmentation in the evolution of Brazil’s enigmatic longwing butterflies, Heliconius nattereri and H. hermathenaCited by: 14
Author(s): Darli Massardo, Nicholas W. VanKuren, Sumitha Nallu, Renato Rogner Ramos, Pedro G. Ribeiro, Karina Lucas Silva‐Brandão, Marcelo Mendes Brandão, Marília Bruzzi Lion, André Victor Lucci Freitas, Márcio Zikán Cardoso, Marcus R. Kronforst
Software Mentions: 4
Published: over 4 years ago
10.1093/gigascience/giaa036
Chromosome-level reference genome of the jellyfish Rhopilema esculentumCited by: 16
Author(s): Yunfeng Li, Lei Gao, Yongjia Pan, Meilin Tian, Yulong Li, Chongbo He, Ying Dong, Yamin Sun, Zunchun Zhou
Software Mentions: 4
Published: over 4 years ago
10.1186/s12864-018-4783-x
The genomic features of parasitism, Polyembryony and immune evasion in the endoparasitic wasp Macrocentrus cingulumCited by: 27
Author(s): Chuanlin Yin, Meizhen Li, Jian Hu, Kun Lang, Qiming Chen, Jinding Liu, Dan Guo, Kang He, Yipei Dong, Jiapeng Luo, Zhenkun Song, James R. Walters, Wenqing Zhang, Fĕi Li, Xue-Xin Chen
Software Mentions: 4
Published: over 6 years ago
10.1371/journal.pgen.1009448
Recent loss of the Dim2 DNA methyltransferase decreases mutation rate in repeats and changes evolutionary trajectory in a fungal pathogenCited by: 27
Author(s): Mareike Möller, Michael Habig, Cécile Lorrain, Alice Feurtey, Janine Haueisen, Wagner C. Fagundes, A. Alizadeh, Michael Freitag, Eva H. Stukenbrock
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pgen.1005954
Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered ScaffoldingCited by: 102
Author(s): Shubha Vij, Heiner Kuhl, Irina M. Kuznetsova, Aleksey Komissarov, Andrey A. Yurchenko, Peter van Heusden, Siddharth Singh, Natascha May Thevasagayam, Sai Rama Sridatta Prakki, K. Purushothaman, Jolly M. Saju, Junhui Jiang, Stanley Kimbung Mbandi, Mario Jonas, Amy Tong, Sarah Mwangi, Doreen Lau, Si Yan Ngoh, Woei Chang Liew, Xueyan Shen, Lawrence S. Hon, James Drake, Matthew Boitano, Richard J. Hall, Chen-Shan Chin, Ramkumar Lachumanan, Jonas Korlach, Vladimir A. Trifonov, Мarsel R. Kabilov, Alexey E. Tupikin, Darrell Green, Simon Moxon, Tyler Garvin, Fritz J. Sedlazeck, Gregory W. Vurture, G. Gopikrishna, Vinaya Kumar Katneni, Tansyn H. Noble, Vinod Scaria, Sridhar Sivasubbu, Dean R. Jerry, Stephen J. O’Brien, Michael C. Schatz, Tamás Dalmay, Stephen W. Turner, Si Lok, Alan Christoffels, László Orbán
Software Mentions: 4
Published: over 8 years ago
10.1534/g3.118.200030
Genomic Variation Among and Within Six<i>Juglans</i>SpeciesCited by: 40
Author(s): Kristian Stevens, Keith Woeste, Sandeep Chakraborty, Marc W. Crepeau, Charles A. Leslie, Pedro J. Martínez-García, Daniela Puiu, Jeanne Romero‐Severson, Mark V. Coggeshall, Abhaya M. Dandekar, Daniel A. Kluepfel, David B. Neale, Steven L. Salzberg, Charles H. Langley
Software Mentions: 3
Published: over 6 years ago
10.1186/s12864-020-06862-x
RNA-Seq of three free-living flatworm species suggests rapid evolution of reproduction-related genesCited by: 12
Author(s): Jeremias N. Brand, R. Axel W. Wiberg, Robert Pjeta, Philip Bertemes, Christian Beisel, Peter Ladurner, Lukas Schärer
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pone.0166162
Real-Time Pathogen Detection in the Era of Whole-Genome Sequencing and Big Data: Comparison of k-mer and Site-Based Methods for Inferring the Genetic Distances among Tens of Thousands of Salmonella SamplesCited by: 13
Author(s): James B. Pettengill, Arthur W. Pightling, Joseph D. Baugher, Hugh Rand, Errol Strain
Software Mentions: 3
Published: about 8 years ago
10.3390/ijerph17165958
ARDEP, a Rapid Degenerate Primer Design Pipeline Based on k-mers for Amplicon Microbiome StudiesCited by: 3
Author(s): Yueni Wu, Kai Feng, Ziyan Wei, Zhujun Wang, Ye Deng
Software Mentions: 2
Published: over 4 years ago
10.1186/s12864-015-2147-3
Combined metabolome and transcriptome profiling provides new insights into diterpene biosynthesis in S. pomifera glandular trichomesCited by: 38
Author(s): Fotini A. Trikka, Alexandros K. Nikolaidis, Codruţa Ignea, Aphrodite Tsaballa, Leto‐Aikaterini Tziveleka, Efstathia Iοannou, Vassilios Roussis, Eleni A. Stea, Dragana Božić, Anagnostis Argiriou, Angelos K. Kanellis, Sotirios C. Kampranis, Antonios M. Makris
Software Mentions: 2
Published: about 9 years ago
10.1093/molbev/msz182
NUQA: Estimating Cancer Spatial and Temporal Heterogeneity and Evolution through Alignment-Free MethodsCited by: 1
Author(s): Aideen C. Roddy, Anna Jurek-Loughrey, José Ivanildo de Souza, Alan Gilmore, Paul G. O’Reilly, Alexey Stupnikov, David González de Castro, Kevin M. Prise, Manuel Salto-Tellez, Darragh G. McArt
Software Mentions: 2
Published: over 5 years ago
10.1371/journal.pbio.3001309
Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomesCited by: 22
Author(s): Diamantis Sellis, Frédéric Guèrin, Olivier Arnaiz, Walker Pett, Emmanuelle Lerat, Nicole Boggetto, Sascha Krenek, Thomas U. Berendonk, Arnaud Couloux, Jean‐Marc Aury, Karine Labadie, Sophie Malinsky, Simran Bhullar, Éric Meyer, Linda Sperling, Laurent Duret, Sandra Duharcourt
Software Mentions: 2
Published: over 3 years ago
10.1093/dnares/dsab015
Exploring the evolutionary process of alkannin/shikonin <i>O</i>-acyltransferases by a reliable <i>Lithospermum erythrorhizon</i> genomeCited by: 4
Author(s): Cheng-Yi Tang
Software Mentions: 2
Published: about 3 years ago
10.3389/fgene.2019.01340
High-Quality Genome Assembly of Eriocheir japonica sinensis Reveals Its Unique Genome EvolutionCited by: 29
Author(s): Boping Tang, Zhongkai Wang, Qiu-Ning Liu, Huabin Zhang, Senhao Jiang, Xinzheng Li, Zhengfei Wang, Yue Sun, Zhongli Sha, Hui Jiang, Xugan Wu, Yandong Ren, Haorong Li, Fujun Xuan, Baoming Ge, Wei Jiang, Shusheng She, Hongying Sun, Qiang Qiu, Wen Wang, Qun Wang, Gao‐Feng Qiu, Dai-Zhen Zhang, Yongxin Li
Software Mentions: 2
Published: almost 5 years ago
10.1534/g3.116.030411
First Draft Assembly and Annotation of the Genome of a California Endemic Oak<i>Quercus lobata</i>Née (Fagaceae)Cited by: 83
Author(s): Victoria L. Sork, Sorel Fitz‐Gibbon, Daniela Puiu, Marc W. Crepeau, Paul F. Gugger, Rachel M. Sherman, Kristian Stevens, Charles H. Langley, Matteo Pellegrini, Steven L. Salzberg
Software Mentions: 2
Published: about 8 years ago
10.1038/sdata.2016.75
Genomic resources for wild populations of the house mouse, Mus musculus and its close relative Mus spretusCited by: 117
Author(s): Bettina Harr, Emre Karakoç, Rafik Neme, Meike Teschke, Christine Pfeifle, Željka Pezer, Hiba Babiker, Miriam Linnenbrink, Inka Montero, Rick J. Scavetta, Mohammad Reza Abai, Marta Puente Molins, Mathias Schlegel, Rainer G. Ulrich, Janine Altmüller, Marek Franitza, Anna Büntge, Sven Künzel, Diethard Tautz
Software Mentions: 2
Published: about 8 years ago
10.1038/s41598-021-87237-4
Genome survey and high-resolution genetic map provide valuable genetic resources for Fenneropenaeus chinensisCited by: 3
Author(s): Xianhong Meng, Qiang Fu, Sheng Luan, Kun Luo, Juan Sui, Jie Kong
Software Mentions: 2
Published: over 3 years ago
10.1007/s00122-019-03519-6
Structural genome analysis in cultivated potato taxaCited by: 31
Author(s): Maria Kyriakidou, Sai Reddy Achakkagari, José Héctor Gálvez López, Xinyi Zhu, Chen Yu Tang, Helen H. Tai, Noelle L. Anglin, David Ellis, Martina V. Strömvik
Software Mentions: 2
Published: almost 5 years ago
10.1186/s12859-021-03996-x
MQF and buffered MQF: quotient filters for efficient storage of k-mers with their counts and metadataCited by: 3
Author(s): Moustafa Shokrof, C. Titus Brown, Tamer Mansour
Software Mentions: 2
Published: almost 4 years ago
10.1093/gigascience/giz089
A chromosomal-level genome assembly for the insect vector for Chagas disease, Triatoma rubrofasciataCited by: 16
Author(s): Qin Liu, Yuhong Guo, Yi Zhang, Wei Hu, Yuanyuan Li, Dan Zhu, Zhengbin Zhou, Jia-Tong Wu, Nansheng Chen, Xiao‐Nong Zhou
Software Mentions: 1
Published: over 5 years ago
10.1186/1471-2164-15-467
Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondriaCited by: 51
Author(s): Robert Ekblom, Linnéa Smeds, Hans Ellegren
Software Mentions: 1
Published: almost 11 years ago
10.1038/s41598-019-46550-9
In Silico Identification of Novel Biomarkers and Development of New Rapid Diagnostic Tests for the Filarial Parasites Mansonella perstans and Mansonella ozzardiCited by: 19
Author(s): Catherine B. Poole, Amit Sinha, Laurence Ettwiller, Lynne Apone, K. A. McKay, Vaish Panchapakesa, Nathália F. Lima, Marcelo U. Ferreira, Samuel Wanji, Clotilde K. S. Carlow
Software Mentions: 1
Published: over 5 years ago
10.1038/s41597-020-0428-4
Genome assembly of six polyploid potato genomesCited by: 29
Author(s): Maria Kyriakidou, Noelle L. Anglin, David Ellis, Helen H. Tai, Martina V. Strömvik
Software Mentions: 1
Published: over 4 years ago
10.3389/fpls.2019.00599
Computational Analysis of AmpSeq Data for Targeted, High-Throughput Genotyping of AmpliconsCited by: 104
Author(s): Jonathan Fresnedo-Ramírez, Shanshan Yang, Qi Sun, Avinash Karn, Bruce I. Reisch, Lance Cadle‐Davidson
Software Mentions: 1
Published: over 5 years ago
10.3390/genes10090708
The First Highly Contiguous Genome Assembly of Pikeperch (Sander lucioperca), an Emerging Aquaculture Species in EuropeCited by: 30
Author(s): Julien Alban Nguinkal, Ronald M. Brunner, Marieke Verleih, Alexander Rebl, Lidia de los Ríos-Pérez, Nadine Schäfer, Frieder Hadlich, Marcus Stüeken, Dörte Wittenburg, Tom Goldammer
Software Mentions: 1
Published: about 5 years ago
10.1042/BSR20202709
Genome survey sequencing of<i>Atractylodes lancea</i>and identification of its SSR markersCited by: 3
Author(s): Tingyu Shan, Junxian Wu, Da-Qing Yu, Jin Xie, Qin Fang, Liangping Zha, Huasheng Peng
Software Mentions: 1
Published: about 4 years ago
10.1093/gigascience/gix014
Genome sequence of pacific abalone (Haliotis discus hannai): the first draft genome in family HaliotidaeCited by: 72
Author(s): Bo‐Hye Nam, Woori Kwak, Young‐Ok Kim, Dong-Gyun Kim, Hee Jeong Kong, Woo Jin Kim, Jeong-Ha Kang, Jung Youn Park, Cheul Min An, Ji‐Young Moon, Choul Ji Park, Jae‐Woong Yu, Joon Yoon, Minseok Seo, Kwondo Kim, Duk Kyung Kim, SaetByeol Lee, Samsun Sung, Chul Lee, Younhee Shin, Myunghee Jung, Byeong-Chul Kang, Ga-Hee Shin, Sojeong Ka, Kelsey Caetano-Anollés, Seoae Cho, Heebal Kim
Software Mentions: 1
Published: over 7 years ago