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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
..., such as the Saccharomyces Genome Database (Cherry 2015), Arabidopsis Gene Regulatory Information Server (Yilmaz et al. 2011), WormBase (Sternberg et al. 2024), and FlyBase (Jenkins et al. 2022). Finally, sometimes little known publications contain gems of prepublished experimental data that should not be overlooked...
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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
...significance (GUS) that are difficult to interpret, even with the integration of the latest bioinformatic tools. In this Perspective, we review how studies using the fruit fly Drosophila melanogaster have facilitated rare disease diagnosis by uncovering the clinical relevance of GUS and classifying rare...
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Research: Cnidarian microRNAs frequently regulate targets by cleavage
- Yehu Moran,
- David Fredman,
- Daniela Praher,
- Xin Z. Li,
- Liang Meng Wee,
- Fabian Rentzsch,
- Phillip D. Zamore,
- Ulrich Technau,
- and Hervé Seitz
Genome Res. April 2014 24: 651-663; Published in Advance March 18, 2014, doi:10.1101/gr.162503.113
...to the N. vectensis using BLASTN (version 2.2.18) to identify homologs of (1) Drosophila melanogaster annotated rRNAs, tRNAs, snRNAs, and snoRNAs (downloaded from FlyBase: http://flybase. org/ and GenBank: http://www.ncbi.nlm.nih.gov/Genbank/ index.html), (2) the most abundant rRNA variants found...
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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
...Science and Artificial Intelligence Laboratory, Cambridge, Massachusetts 02139, USA Abstract The availability of sequenced genomes from 12 Drosophila species has enabled the use of comparative genomics for the systematic discovery of functional elements conserved within this genus. We have...
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Research: Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus
- Jaaved Mohammed,
- Alex S. Flynt,
- Alexandra M. Panzarino,
- Md Mosharrof Hossain Mondal,
- Matthew DeCruz,
- Adam Siepel,
- and Eric C. Lai
Genome Res. January 2018 28: 52-65; Published in Advance December 12, 2017, doi:10.1101/gr.226068.117
...reveal miRNA diversity among Drosophila species and principles underlying their emergence and evolution.MicroRNAs (miRNAs) are an extensive class of ∼22-nt RNAs that play important regulatory roles in diverse eukaryotic species (Flynt and Lai 2008; Axtell et al. 2011). In the canonical metazoan pathway...
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Resource: Early genome activation in Drosophila is extensive with an initial tendency for aborted transcripts and retained introns
- Jamie C. Kwasnieski,
- Terry L. Orr-Weaver,
- and David P. Bartel
Genome Res. July 2019 29: 1188-1197; Published in Advance June 24, 2019, doi:10.1101/gr.242164.118
...Early activation in Drosophila is extensive with an initial tendency for aborted transcripts and retained introns Jamie C. Kwasnieski1,2,3, Terry L. Orr-Weaver2,3 and David P. Bartel1,2,3 1Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142...
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Research: Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence
- Eugene Berezikov,
- Nicolas Robine,
- Anastasia Samsonova,
- Jakub O. Westholm,
- Ammar Naqvi,
- Jui-Hung Hung,
- Katsutomo Okamura,
- Qi Dai,
- Diane Bortolamiol-Becet,
- Raquel Martin,
- Yongjun Zhao,
- Phillip D. Zamore,
- Gregory J. Hannon,
- Marco A. Marra,
- Zhiping Weng,
- Norbert Perrimon,
- and Eric C. Lai
Genome Res. February 2011 21: 203-215; Published in Advance December 22, 2010, doi:10.1101/gr.116657.110
...-Becet Samsonova, A Nicolas Gregory J Hannon Martin, R Jakub O Westholm Dai, Q Perrimon Norbert 1088-9051 10.1101/gr.116657.110 genome;gr.116657.110 Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence Research Deep annotation of Drosophila...
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Letter: Abundant primary piRNAs, endo-siRNAs, and microRNAs in a Drosophila ovary cell line
- Nelson C. Lau,
- Nicolas Robine,
- Raquel Martin,
- Wei-Jen Chung,
- Yuzo Niki,
- Eugene Berezikov,
- and Eric C. Lai
Genome Res. October 2009 19: 1776-1785; Published in Advance June 18, 2009, doi:10.1101/gr.094896.109
...Lau Raquel N.C. Lau N Robine E Lai WeiJen Chung Nelson C, Lau Lai, EC Lai, Eric C Nicolas Nelson C Lau W Chung Martin, R Lau Nelson C. genome;gr.094896.109 1088-9051 10.1101/gr.094896.109 Abundant primary piRNAs, endo-siRNAs, and microRNAs in a Drosophila ovary cell line Letter Abundant primary pi...
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12 Drosophila Genomes/Letter: Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs
- J. Graham Ruby,
- Alexander Stark,
- Wendy K. Johnston,
- Manolis Kellis,
- David P. Bartel,
- and Eric C. Lai
Genome Res. December 2007 17: 1850-1864; Published in Advance November 7, 2007, doi:10.1101/gr.6597907
...Johnston, Wendy K Manolis Kellis Bartel WK Johnston Lai, EC Lai, Eric C A Stark David P David P, Bartel DavidP Bartel Wendy K W.K. Johnston 10.1101/gr.6597907 1088-9051 genome;gr.6597907 Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs...
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12 Drosophila Genomes/Methods: Reliable prediction of regulator targets using 12 Drosophila genomes
- Pouya Kheradpour,
- Alexander Stark,
- Sushmita Roy,
- and Manolis Kellis
Genome Res. December 2007 17: 1919-1931; Published in Advance November 7, 2007, doi:10.1101/gr.7090407
...into a confidence measure for each motif instance, correcting for varying motif length, composition, and background conservation of the target regions. We predict targets of fly transcription factors and miRNAs in alignments of 12 recently sequenced Drosophila species. When compared to extensive genome...
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