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Resource: The Drosophila brain on cocaine at single-cell resolution
- Brandon M. Baker,
- Sneha S. Mokashi,
- Vijay Shankar,
- Jeffrey S. Hatfield,
- Rachel C. Hannah,
- Trudy F.C. Mackay,
- and Robert R.H. Anholt
Genome Res. October 2021 31: 1927-1937; Published in Advance May 25, 2021, doi:10.1101/gr.268037.120
...were visualized using Cytoscape version 3.7.2. The MCODE algorithm (Bader and Hogue 2003) was utilized to identify highly interconnected modules within the larger cluster network. Genetic interaction networks were constructed by converting the gene IDs to gene names/symbols using the FlyBase Consortium...
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Resource: Gene expression networks in the Drosophila Genetic Reference Panel
- Logan J. Everett,
- Wen Huang,
- Shanshan Zhou,
- Mary Anna Carbone,
- Richard F. Lyman,
- Gunjan H. Arya,
- Matthew S. Geisz,
- Junwu Ma,
- Fabio Morgante,
- Genevieve St. Armour,
- Lavanya Turlapati,
- Robert R.H. Anholt,
- and Trudy F.C. Mackay
Genome Res. March 2020 30: 485-496; Published in Advance March 6, 2020, doi:10.1101/gr.257592.119
...was computed as the mean degree across all features in the module. Modules were sorted by average degree, such that module 1 has the highest average degree in each analysis.Gene set enrichment analysesLists of known gene IDs (FlyBase FBgn accessions) were uploaded to FlyMine (Lyne et al. 2007) or Panther (Mi...
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Research: Dynamic A-to-I RNA editing in response to gut microbiome in honeybees
- Yuange Duan,
- Min Huang,
- Lin Ye,
- Ling Ma,
- Yashuai Wu,
- Yating Du,
- Jiyao Liu,
- Fan Song,
- Li Tian,
- Wanzhi Cai,
- Hu Li,
- Xin Zhou,
- and Shiqi Luo
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
...-specific primers for 5′ RACE (5′ GSP, 5′ nested GSP) and 3′ RACE (3′ GSP, 3′ nested GSP) were designed (Supplemental Table S3) based on the known sequences of Adar (gene ID: 408529) in NCBI. The detailed experimental procedures are described in the Supplemental Methods. Duan et al. 10 Genome Research www...
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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
...Genome Annotation Assessment in Drosophila melanogaster Martin G. Reese 1 , 4 , George Hartzell 1 , Nomi L. Harris 1 , Uwe Ohler 1 , 2 , Josep F. Abril 3 , and Suzanna E. Lewis 1 1Berkeley Drosophila Genome...
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12 Drosophila Genomes/Letter: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes
- Michael F. Lin,
- Joseph W. Carlson,
- Madeline A. Crosby,
- Beverley B. Matthews,
- Charles Yu,
- Soo Park,
- Kenneth H. Wan,
- Andrew J. Schroeder,
- L. Sian Gramates,
- Susan E. St. Pierre,
- Margaret Roark,
- Kenneth L. Wiley, Jr.,
- Rob J. Kulathinal,
- Peili Zhang,
- Kyl V. Myrick,
- Jerry V. Antone,
- Susan E. Celniker,
- William M. Gelbart,
- and Manolis Kellis
Genome Res. December 2007 17: 1823-1836; Published in Advance November 7, 2007, doi:10.1101/gr.6679507
...Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes Michael F. Lin 1 , Joseph W. Carlson 2 , Madeline A. Crosby 3 , Beverley B. Matthews 3 , Charles Yu 2 , Soo Park 2 , Kenneth H. Wan 2...
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Method: GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes
- Tomáš Brůna,
- Alexandre Lomsadze,
- and Mark Borodovsky
Genome Res. May 2024 34: 757-768; Published in Advance June 12, 2024, doi:10.1101/gr.278373.123
..., probabilistic models of functional sites controlling translation and splicing, intron/exon length distributions, etc. All these probabilistic models served as elements of a generalized HMM (GHMM), for example, Genie (Kulp et al. 1996), GENSCAN (Burge and Karlin 1997), and GeneID (Parra et al. 2000...
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LETTER: Gene Discovery Using Computational and Microarray Analysis of Transcription in the Drosophila melanogaster Testis
- Justen Andrews,
- Gerard G. Bouffard,
- Chris Cheadle,
- Jining Lü,
- Kevin G. Becker,
- and Brian Oliver
Genome Res. December 1, 2000 10: 2030-2043; doi:10.1101/gr.159800
...Gene Discovery Using Computational and Microarray Analysis of Transcription in the Drosophila melanogaster Testis Justen Andrews 1 , Gerard G. Bouffard 2 , Chris Cheadle 3 , Jining Lü 1 , Kevin G. Becker 3 , and Brian Oliver 1 , 4...
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Research: Genome-wide chromatin interaction profiling reveals a vital role of super-enhancers and rearrangements in host enhancer contacts during BmNPV infection
- Shudi Zhao,
- Yuedong Li,
- Guanping Chen,
- Xingyang Wang,
- Nan Chen,
- and Xiaofeng Wu
Genome Res. November 2023 33: 1958-1974; Published in Advance October 23, 2023, doi:10.1101/gr.277931.123
...of HA-tagged BmBRD4 (gene ID 101735474) (Supplemental Fig. S3A), the plasmids for enhancer activity analysis (Supplemental Fig. S9B), the plasmid serving as the internal reference of the luciferase assays (Supplemental Fig. S9A), and the plasmid PB-luc-Zeo (Supplemental Fig. S9C) were generated from p...
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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
...into exons or introns of protein-coding genes; a fourth instance may be termination of mRNAs from adjacent genes. The possibility remains that TRs are specifically transcribed into ncRNAs (Subirana and Messeguer 2021), as is known to occur for some loci in the Drosophila melanogaster (Biswas et al. 2024...
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Research: Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon
- Koichi Kitao,
- Kenji Ichiyanagi,
- and So Nakagawa
Genome Res. June 2025 35: 1287-1300; Published in Advance May 8, 2025, doi:10.1101/gr.280007.124
...merged using StringTie2 with the “‐‐merge” option. Reads mapped to features in the merged GTF file were counted using featureCounts v2.0.1 (Liao et al. 2014) with the “-T 8 -s 2 -t exon -g gene_id -J” options. The transcripts of MYL4 and Lyosin were identified by the sequence similarity search...

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