pypi: funannotate | Projects | Ecosyste.ms: Papers

10.1128/mBio.02275-17

A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity
Cited by: 99
Author(s): Benjamin Schwessinger, Jana Sperschneider, William S. Cuddy, Diana Garnica, Marisa E. Miller, Jennifer Taylor, Peter N. Dodds, Melania Figueroa, Robert Park, John P. Rathjen
Software Mentions: 13
Published: over 6 years ago

10.1038/s42003-021-02335-3

A de novo transcriptional atlas in Danaus plexippus reveals variability in dosage compensation across tissues
Cited by: 9
Author(s): José M. Ranz, Pablo M. González, Bryan D. Clifton, Nestor O. Nazario-Yepiz, Pablo Luis Hernández-Cervantes, María J. Palma-Martínez, Dulce I. Valdivia, Andrés Jiménez-Kaufman, Megan Lu, Therese A. Markow, Cei Abreu‐Goodger
Software Mentions: 13
Published: over 3 years ago

10.1038/s42003-020-01637-2

Horseshoe crab genomes reveal the evolution of genes and microRNAs after three rounds of whole genome duplication
Cited by: 23
Author(s): Wenyan Nong, Zhe Qu, Yiqian Li, Tom Barton-Owen, Hon Kit Wong, Ho Yin Yip, Hoi Ting Lee, Satya Narayana, Tobias Baril, Thomas Swale, Jianquan Cao, Ting‐Fung Chan, Hoi Shan Kwan, Sai Ming Ngai, Gianni Panagiotou, Pei‐Yuan Qian, Jian Qiu, Kevin Yuk‐Lap Yip, Normaz Wana Ismail, Siddhartha Pati, Akbar John, Stephen S. Tobe, William G. Bendena, Siu Gin Cheung, Alexander Hayward, Jerome H.L. Hui
Software Mentions: 8
Published: almost 4 years ago

10.1186/s12864-021-07489-2

Datura genome reveals duplications of psychoactive alkaloid biosynthetic genes and high mutation rate following tissue culture
Cited by: 5
Author(s): Alex Rajewski, Derreck Carter-House, Jason E. Stajich, Amy Litt
Software Mentions: 7
Published: over 3 years ago

10.1534/g3.120.401579

High-Quality Assemblies for Three Invasive Social Wasps from the Vespula Genus
Cited by: 19
Author(s): Thomas W. R. Harrop, Joseph Guhlin, Gemma M. McLaughlin, Elizabeth Permina, Peter A. Stockwell, Josh Gilligan, Marissa F. Le Lec, Monica A. M. Gruber, Oliver Quinn, Mackenzie Lovegrove, Elizabeth J. Duncan, Emily J. Remnant, Jens Van Eeckhoven, Brittany Graham, Rosemary A Knapp, Kyle W. Langford, Zev Kronenberg, Maximilian O. Press, Stephen Eacker, Erin E. Wilson Rankin, Jessica Purcell, Philip J. Lester, Peter K. Dearden
Software Mentions: 7
Published: about 4 years ago

10.1093/g3journal/jkab255

Improved draft reference genome for the Glassy-winged Sharpshooter (Homalodisca vitripennis), a vector for Pierce’s disease
Cited by: 8
Author(s): Cassandra L. Ettinger, Frank J. Byrne, Matthew A. Collin, Derreck Carter-House, Linda L. Walling, Peter W. Atkinson, Rick A Redak, Jason E. Stajich
Software Mentions: 7
Published: over 3 years ago

10.1128/mBio.01714-20

Repetitive Elements Contribute to the Diversity and Evolution of Centromeres in the Fungal Genus Verticillium
Cited by: 20
Author(s): Michael Seidl, Holger Kramer, David E. Cook, Gabriel Lorencini Fiorin, Grardy C. M. van den Berg, Luigi Faino, B.P.H.J. Thomma
Software Mentions: 6
Published: about 4 years ago

10.1186/s12864-021-07636-9

Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation
Cited by: 8
Author(s): Werner Pieter Veldsman, Ke Yan, Jerome H.L. Hui, Ting‐Fung Chan, Juán Antonio Baeza, Jing Qin, Ka Hou Chu
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-020-07027-6

Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster (Magallana hongkongensis) genome
Cited by: 21
Author(s): Yiqian Li, Wenyan Nong, Tobias Baril, Ho Yin Yip, Thomas Swale, Alexander Hayward, David Ferrier, Jerome H. L. Hui
Software Mentions: 5
Published: about 4 years ago

10.1038/s41597-021-01017-3

Chromosome-scale genome sequencing, assembly and annotation of six genomes from subfamily Leishmaniinae
Cited by: 5
Author(s): Hatim Almutairi, Michael D. Urbaniak, Michelle Bates, Narissara Jariyapan, Godwin Kwakye-Nuako, Vanete Thomaz Soccol, Waleed S. Al-Salem, Rod J. Dillon, Paul A. Bates, Derek Gatherer
Software Mentions: 4
Published: about 3 years ago

10.1186/s12862-017-1103-z

De novo assembling and primary analysis of genome and transcriptome of gray whale Eschrichtius robustus
Cited by: 11
Author(s): Alexey Moskalev, Anna V. Kudryavtseva, Alexander S. Graphodatsky, Violetta R. Beklemisheva, Natalia A. Serdyukova, Konstantin V. Krutovsky, Vadim V. Sharov, Ivan V. Kulakovskiy, Andrey S. Lando, Artem S. Kasianov, Dmitry A. Kuzmin, Yuliya A. Putintseva, Sergey Feranchuk, Mikhail Shaposhnikov, Vadim E. Fraifeld, Dmitri Toren, А. В. Снежкина, Vasily Sitnik
Software Mentions: 4
Published: almost 7 years ago

10.1111/1755-0998.13154

Chromosomal‐level reference genome of the incense tree Aquilaria sinensis
Cited by: 22
Author(s): Wenyan Nong, Sean T.S. Law, Hon Kit Wong, Tobias Baril, Thomas Swale, L.M. Chu, Alexander Hayward, David Tai-Wai Lau, Jerome H. L. Hui
Software Mentions: 3
Published: over 4 years ago

10.12688/f1000research.51613.2

A draft reference assembly of the Psilocybe cubensis genome
Cited by: 0
Author(s): Kevin McKernan, Liam T. Kane, Seth Crawford, Chen-Shan Chin, Aaron Trippe, Stephen McLaughlin
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-020-6657-2

An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data
Cited by: 8
Author(s): Vasanthan Jayakumar, Hiromi Ishii, Misato Seki, Wakako Kumita, Takashi Inoue, Sumitaka Hase, Kengo Sato, Hideyuki Okano, Erika Sasaki, Yasubumi Sakakibara
Software Mentions: 2
Published: over 4 years ago

10.1128/MRA.01444-18

Draft Genome Sequence of Azole-Resistant Aspergillus thermomutatus (Neosartorya pseudofischeri) Strain HMR-AF-39, Isolated from a Human Nasal Septum Abscess Aspirate
Cited by: 4
Author(s): Maxime Parent-Michaud, Philippe J. Dufresne, Éric Fournier, Christine Martineau, Sandrine Moreira, Vincent Perkins, Louis de Repentigny, Simon F. Dufresne
Software Mentions: 2
Published: almost 6 years ago

10.3390/microorganisms9081581

Genome and Secretome Analysis of Staphylotrichum longicolleum DSM105789 Cultured on Agro-Residual and Chitinous Biomass
Cited by: 2
Author(s): Asghar Ali, Bernhard Ellinger, Sophie Brandt, Christian Betzel, Martin Rühl, Carsten Wrenger, Hartmut Schlüter, Wilhelm Schäfer, H. Brognaro, Martin Gand
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0238611

A haplotype-phased genome of wheat stripe rust pathogen Puccinia striiformis f. sp. tritici, race PST-130 from the Western USA
Cited by: 8
Author(s): Hans Vasquez-Gross, Sukhwinder Kaur, Lynn Epstein, Jorge Dubcovsky
Software Mentions: 2
Published: about 4 years ago

10.1016/j.dib.2020.106674

Illumina short-read sequencing data, de novo assembly and annotations of the Drosophila nasuta nasuta genome
Cited by: 0
Author(s): Stafny DSouza, Koushik Ponnanna, C. Amruthavalli, Nallur B. Ramachandra
Software Mentions: 2
Published: almost 4 years ago

10.3389/fgene.2020.00959

High-Quality Genome Assembly of Fusarium oxysporum f. sp. lini
Cited by: 16
Author(s): George S. Krasnov, Elena N. Pushkova, Roman O. Novakovskiy, Ludmila P. Kudryavtseva, Tatiana A. Rozhmina, Ekaterina M. Dvorianinova, Liubov V. Povkhova, Anna V. Kudryavtseva, Alexey A. Dmitriev, Nataliya V. Melnikova
Software Mentions: 2
Published: about 4 years ago

10.1093/g3journal/jkaa007

Genomic analyses of two Italian oyster mushroom Pleurotus pulmonarius strains
Cited by: 6
Author(s): Guillermo Vidal-Diez de Ulzurrun, Yi-Yun Lee, Jason E. Stajich, Erich M. Schwarz, Yu-Ting Hsueh
Software Mentions: 2
Published: almost 4 years ago

10.3390/genes12040568

Deciphering the Monilinia fructicola Genome to Discover Effector Genes Possibly Involved in Virulence
Cited by: 19
Author(s): Laura Vilanova, Claudio A. Valero-Jiménez, Jan A.L. van Kan
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-020-79358-z

An ultra-high density SNP-based linkage map for enhancing the pikeperch (Sander lucioperca) genome assembly to chromosome-scale
Cited by: 5
Author(s): Lidia de los Ríos-Pérez, Julien Alban Nguinkal, Marieke Verleih, Alexander Rebl, Ronald M. Brunner, Jan Klosa, Nadine Schäfer, Marcus Stüeken, Tom Goldammer, Dörte Wittenburg
Software Mentions: 2
Published: almost 4 years ago

10.1128/MRA.00195-21

Draft Genome Sequences of Five Fungal Strains Isolated from Kefir
Cited by: 0
Author(s): Simonas Marcišauskas, Yong-Kyu Kim, Sonja Blasche, Kiran R. Patil, Boyang Ji, Jens Nielsen
Software Mentions: 1
Published: over 3 years ago

10.3390/md18120655

Proteomic Analysis of the Venom of Jellyfishes Rhopilema esculentum and Sanderia malayensis
Cited by: 6
Author(s): Thomas Leung, Zhe Qu, Wenyan Nong, Jerome H. L. Hui, Sai Ming Ngai
Software Mentions: 1
Published: almost 4 years ago

10.1128/genomeA.00557-17

Genome Sequence of the Saprophytic Ascomycete Epicoccum nigrum Strain ICMP 19927, Isolated from New Zealand
Cited by: 10
Author(s): Mikhaïl Fokín, Damien J. Fleetwood, Bevan S. Weir, Silas G. Villas‐Bôas
Software Mentions: 1
Published: over 7 years ago

10.1093/gbe/evab047

Predicted Input of Uncultured Fungal Symbionts to a Lichen Symbiosis from Metagenome-Assembled Genomes
Cited by: 18
Author(s): Gulnara Tagirdzhanova, Paul Saary, Jeffrey P. Tingley, David Díaz-Escandón, D. Wade Abbott, Alex Bateman, Toby Spribille
Software Mentions: 1
Published: over 3 years ago

10.1128/MRA.00149-19

Improved Reference Genome Sequence of Coccidioides immitis Strain WA_211, Isolated in Washington State
Cited by: 8
Author(s): Marcus de Melo Teixeira, Bridget M. Barker, Jason E. Stajich
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-018-26331-6

Raphidocelis subcapitata (=Pseudokirchneriella subcapitata) provides an insight into genome evolution and environmental adaptations in the Sphaeropleales
Cited by: 43
Author(s): Shigekatsu Suzuki, Haruyo Yamaguchi, Nobuyoshi Nakajima, Masanobu Kawachi
Software Mentions: 1
Published: over 6 years ago

10.1128/mSystems.00112-18

Characterization of Aspergillus niger Isolated from the International Space Station
Cited by: 35
Author(s): Jillian Romsdahl, Adriana Blachowicz, Abby J. Chiang, Nitin Kumar Singh, Jason E. Stajich, Markus Kalkum, Kasthuri Venkateswaran, Clay C. C. Wang
Software Mentions: 1
Published: about 6 years ago

10.3389/fgene.2021.638708

Effects of Simulated Microgravity on the Proteome and Secretome of the Polyextremotolerant Black Fungus Knufia chersonesos
Cited by: 10
Author(s): Donatella Tesei, Abby J. Chiang, Markus Kalkum, Jason E. Stajich, Ganesh Babu Malli Mohan, Katja Sterflinger, Kasthuri Venkateswaran
Software Mentions: 1
Published: over 3 years ago

10.3389/fgene.2020.590282

Genome Sequencing of Fiber Flax Cultivar Atlant Using Oxford Nanopore and Illumina Platforms
Cited by: 23
Author(s): Alexey A. Dmitriev, Elena N. Pushkova, Roman O. Novakovskiy, А. Д. Бениаминов, Tatiana A. Rozhmina, А. А. Жученко, Nadezhda L. Bolsheva, О. В. Муравенко, Liubov V. Povkhova, Ekaterina M. Dvorianinova, Parfait Kezimana, Anastasiya V. Snezhkina, Anna V. Kudryavtseva, George S. Krasnov, Nataliya V. Melnikova
Software Mentions: 1
Published: almost 4 years ago

10.1128/MRA.01619-18

Genome Sequence of a Lethal Vascular Wilt Fungus, Verticillium nonalfalfae, a Biological Control Used Against the Invasive Ailanthus altissima
Cited by: 6
Author(s): Matt T. Kasson, Lindsay R. Kasson, Kristen L. Wickert, Donald D. Davis, Jason E. Stajich
Software Mentions: 1
Published: almost 6 years ago

Ecosyste.ms: Papers

Projects: pypi: funannotate

Papers Mentioning funannotate 32