Searching journal content for articles similar to Ashburner 10 (4): 391.

Displaying results 1-10 of 92

For checked items

view abstracts
download to citation manager

Select this article
Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
.... elegans, along with repetitive DNA elements and pseudogenes, have been identified by manual curation of its N2 reference over the past 25 years (Sternberg et al. 2024). For the new CGC1 reference to be useful to biologists, it must be annotated in a way that preserves as much of the older N2 annotation...
OPEN ACCESS ARTICLE
Select this article
Perspective: Functional assays in Drosophila facilitate classification of variants of uncertain significance associated with rare diseases
- Jung-Wan Mok,
- Shelley B. Gibson,
- Haley A. Dostalik,
- and Shinya Yamamoto
Genome Res. July 2025 35: 1473-1484; Published in Advance June 4, 2025, doi:10.1101/gr.278291.123
...and characterization of novel clinical conditions. In the Supplemental Text, we provide additional practical tips and technical insights to help support Drosophila scientists to begin to engage in these types of research projects. Such information can be further leveraged to design effective MAVEs to decipher the vast...
Select this article
Resource: Building better genome annotations across the tree of life
- Adam H. Freedman and
- Timothy B. Sackton
Genome Res. May 2025 35: 1261-1276; Published in Advance April 15, 2025, doi:10.1101/gr.280377.124
...Sequencing and Analysis Consortium et al. 2007)—and had been previously published for smaller s such as Drosophila melanogaster (Adams et al. 2000)—the high cost of generating assemblies at the time made it prohibitive to research groups working on nonmodel organisms. Absent assemblies and annotations...
Select this article
Research: Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species
- Charles Plessy,
- Michael J. Mansfield,
- Aleksandra Bliznina,
- Aki Masunaga,
- Charlotte West,
- Yongkai Tan,
- Andrew W. Liu,
- Jan Grašič,
- María Sara del Río Pisula,
- Gaspar Sánchez-Serna,
- Marc Fabrega-Torrus,
- Alfonso Ferrández-Roldán,
- Vittoria Roncalli,
- Pavla Navratilova,
- Eric M. Thompson,
- Takeshi Onuma,
- Hiroki Nishida,
- Cristian Cañestro,
- and Nicholas M. Luscombe
Genome Res. March 2024 34: 426-440; Published in Advance April 15, 2024, doi:10.1101/gr.278295.123
...that challenges our previous vision of speciation in which similar animals always share similar structures.The concept of “reference ” for each species comes from the notion that genomic structural variations and chromosomal rearrangements within species are rare, which is a fundamental aspect sustaining projects...
OPEN ACCESS ARTICLE
Select this article
Method: AIDE: annotation-assisted isoform discovery with high precision
- Wei Vivian Li,
- Shan Li,
- Xin Tong,
- Ling Deng,
- Hubing Shi,
- and Jingyi Jessica Li
Genome Res. December 2019 29: 2056-2072; Published in Advance November 6, 2019, doi:10.1101/gr.251108.119
...assessment has shown that methods achieving good accuracy in identifying isoforms in Drosophila melanogaster (34,776 annotated isoforms) and Caenorhabditis elegans (61,109 annotated isoforms) fail to maintain good performance in Homo sapiens (200,310 annotated isoforms) (Steijger et al. 2013; Zerbino et al...
Select this article
Method: Ultrafast and scalable variant annotation and prioritization with big functional genomics data
- Dandan Huang,
- Xianfu Yi,
- Yao Zhou,
- Hongcheng Yao,
- Hang Xu,
- Jianhua Wang,
- Shijie Zhang,
- Wenyan Nong,
- Panwen Wang,
- Lei Shi,
- Chenghao Xuan,
- Miaoxin Li,
- Junwen Wang,
- Weidong Li,
- Hoi Shan Kwan,
- Pak Chung Sham,
- Kai Wang,
- and Mulin Jun Li
Genome Res. December 2020 30: 1789-1801; Published in Advance October 15, 2020, doi:10.1101/gr.267997.120
...(IHEC) project (Bujold et al. 2016), efficient interpretation of variants is profoundly affected by the unprecedented scale of genomic features and the resources used for their annotation. For example, a widely used metric for mutation deleteriousness, Combined Annotation Dependent Depletion (CADD...
Select this article
Resource: The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals
- Christine E. Schnitzler,
- E. Sally Chang,
- Justin Waletich,
- Gonzalo Quiroga-Artigas,
- Wai Yee Wong,
- Anh-Dao Nguyen,
- Sofia N. Barreira,
- Liam B. Doonan,
- Paul Gonzalez,
- Sergey Koren,
- James M. Gahan,
- Steven M. Sanders,
- Brian Bradshaw,
- Timothy Q. DuBuc,
- Febrimarsa,
- Danielle de Jong,
- Eric P. Nawrocki,
- Alexandra Larson,
- Samantha Klasfeld,
- Sebastian G. Gornik,
- R. Travis Moreland,
- Tyra G. Wolfsberg,
- Adam M. Phillippy,
- James C. Mullikin,
- Oleg Simakov,
- Paulyn Cartwright,
- Matthew Nicotra,
- Uri Frank,
- and Andreas D. Baxevanis
Genome Res. March 2024 34: 498-513; Published in Advance March 20, 2024, doi:10.1101/gr.278382.123
...and tentaculozooids). The colonies lend themselves to experimental study as they are easily cultured on glass microscope slides (Fig. 1A). Marine hydroids, including Hydractinia, have fascinated biologists since the late 1800s (Weismann 1883) owing to their population of pluripotent stem cells, called “i-cells” given...
OPEN ACCESS ARTICLE
Select this article
Resource: The western redcedar genome reveals low genetic diversity in a self-compatible conifer
- Tal J. Shalev,
- Omnia Gamal El-Dien,
- Macaire M.S. Yuen,
- Shu Shengqiang,
- Shaun D. Jackman,
- René L. Warren,
- Lauren Coombe,
- Lise van der Merwe,
- Ada Stewart,
- Lori B. Boston,
- Christopher Plott,
- Jerry Jenkins,
- Guifen He,
- Juying Yan,
- Mi Yan,
- Jie Guo,
- Jesse W. Breinholt,
- Leandro G. Neves,
- Jane Grimwood,
- Loren H. Rieseberg,
- Jeremy Schmutz,
- Inanc Birol,
- Matias Kirst,
- Alvin D. Yanchuk,
- Carol Ritland,
- John H. Russell,
- and Joerg Bohlmann
Genome Res. October 2022 32: 1952-1964; Published in Advance September 15, 2022, doi:10.1101/gr.276358.121
...complement, outcrossing (1 – s), are of interest to evolutionary biologists owing to their implications for genetic diversity and fitness and have been investigated extensively over the past century (Stebbins 1957; Lande and Schemske 1985; Barrett and Eckert 1990; Barrett et al. 2003; Wright et al. 2013...
OPEN ACCESS ARTICLE
Select this article
Resource: Alignathon: a competitive assessment of whole-genome alignment methods
- Dent Earl,
- Ngan Nguyen,
- Glenn Hickey,
- Robert S. Harris,
- Stephen Fitzgerald,
- Kathryn Beal,
- Igor Seledtsov,
- Vladimir Molodtsov,
- Brian J. Raney,
- Hiram Clawson,
- Jaebum Kim,
- Carsten Kemena,
- Jia-Ming Chang,
- Ionas Erb,
- Alexander Poliakov,
- Minmei Hou,
- Javier Herrero,
- William James Kent,
- Victor Solovyev,
- Aaron E. Darling,
- Jian Ma,
- Cedric Notredame,
- Michael Brudno,
- Inna Dubchak,
- David Haussler,
- and Benedict Paten
Genome Res. December 2014 24: 2077-2089; Published in Advance October 1, 2014, doi:10.1101/gr.174920.114
...(Drosophila 12 Genomes Consortium 2007; Lindblad-Toh et al. 2011), including cis-regulatory elements (Kellis et al. 2003), enhancers, and noncoding RNAs. The lack of accepted gold standard reference alignments has made it hard to objectively assess the relative merits of WGA methods. Previous evaluations...
OPEN ACCESS ARTICLE
Select this article
LETTER: Genome Annotation Assessment in Drosophila melanogaster
- Martin G. Reese,
- George Hartzell,
- Nomi L. Harris,
- Uwe Ohler,
- Josep F. Abril,
- and Suzanna E. Lewis
Genome Res. April 1, 2000 10: 483-501; doi:10.1101/gr.10.4.483
...in the genomes of higher organisms, we evaluated their performance on a large, well-characterized sequence contig from the Adh region of Drosophila melanogaster . This experiment, known as the Genome Annotation Assessment Project (GASP), was launched in May 1999. Twelve groups, applying state-of-the-art tools...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Ashburner 10 (4): 391.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: