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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...on mutational processes shaping two functionally important tandem arrays in the Drosophila .ResultsGenome assembliesThe strains selected include the Drosophila community's reference strain (iso-1) (Adams et al. 2000) and two strains from the Drosophila Synthetic Population Resource (A3 and A4) (King et al. 2012...
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Research: The mode of expression divergence in Drosophila fat body is infection-specific
- Bryan A. Ramirez-Corona,
- Stephanie Fruth,
- Oluchi Ofoegbu,
- and Zeba Wunderlich
Genome Res. June 2021 31: 1024-1034; Published in Advance April 15, 2021, doi:10.1101/gr.269597.120
...- and trans-acting effects in the innate immune response, we needed two inbred, sequenced strains of D. melanogaster with abundant genetic variation and phenotypic differences in the immune response. The founder lines of the Drosophila Synthetic Population Resource fit these requirements, making them ideal...
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Review: Population genetic inference from genomic sequence variation
- John E. Pool,
- Ines Hellmann,
- Jeffrey D. Jensen,
- and Rasmus Nielsen
Genome Res. March 2010 20: 291-300; Published in Advance January 12, 2010, doi:10.1101/gr.079509.108
...mapping (Cheung and Nelson 1998; Albrechtsen et al. 2009), and related techniques, population genetics has found its way into medical genetics as a core analytical discipline. Currently, large-scale next-generation sequencingprojects are moving forward in a number of organisms including humans, Drosophila...
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Method: Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort
- Christopher M. Vockley,
- Cong Guo,
- William H. Majoros,
- Michael Nodzenski,
- Denise M. Scholtens,
- M. Geoffrey Hayes,
- William L. Lowe, Jr.,
- and Timothy E. Reddy
Genome Res. August 2015 25: 1206-1214; Published in Advance June 17, 2015, doi:10.1101/gr.190090.115
.... ↵Gisselbrecht SS, Barrera LA, Porsch M, Aboukhalil A, Estep PW III., Vedenko A, Palagi A, Kim Y, Zhu X, Busser BW, et al. 2013. Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos. Nat Methods 10: 774–780. ↵Guo C, Ludvik AE, Arlotto ME, Hayes MG, Armstrong LL, Scholtens DM, Brown CD...
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Resource: ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
- Stephen G. Landt,
- Georgi K. Marinov,
- Anshul Kundaje,
- Pouya Kheradpour,
- Florencia Pauli,
- Serafim Batzoglou,
- Bradley E. Bernstein,
- Peter Bickel,
- James B. Brown,
- Philip Cayting,
- Yiwen Chen,
- Gilberto DeSalvo,
- Charles Epstein,
- Katherine I. Fisher-Aylor,
- Ghia Euskirchen,
- Mark Gerstein,
- Jason Gertz,
- Alexander J. Hartemink,
- Michael M. Hoffman,
- Vishwanath R. Iyer,
- Youngsook L. Jung,
- Subhradip Karmakar,
- Manolis Kellis,
- Peter V. Kharchenko,
- Qunhua Li,
- Tao Liu,
- X. Shirley Liu,
- Lijia Ma,
- Aleksandar Milosavljevic,
- Richard M. Myers,
- Peter J. Park,
- Michael J. Pazin,
- Marc D. Perry,
- Debasish Raha,
- Timothy E. Reddy,
- Joel Rozowsky,
- Noam Shoresh,
- Arend Sidow,
- Matthew Slattery,
- John A. Stamatoyannopoulos,
- Michael Y. Tolstorukov,
- Kevin P. White,
- Simon Xi,
- Peggy J. Farnham,
- Jason D. Lieb,
- Barbara J. Wold,
- and Michael Snyder
Genome Res. September 2012 22: 1813-1831; doi:10.1101/gr.136184.111
.../modENCODE ChIP experiments in human cells and in Drosophila embryos were performed with antibodies directed against individual factors and histone modifications. A total of 145 polyclonal and 43 monoclonal antibodies had been used to successfully generate ChIP-seq data as of October 2011. Antibody deficiencies...
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Method: Predicting genetic modifier loci using functional gene networks
- Insuk Lee,
- Ben Lehner,
- Tanya Vavouri,
- Junha Shin,
- Andrew G. Fraser,
- and Edward M. Marcotte
Genome Res. August 2010 20: 1143-1153; Published in Advance June 9, 2010, doi:10.1101/gr.102749.109
...-YY code, in which XX represents origin species of data—CE, C. elegans; DM, Drosophila melanogaster, HS, Homo sapiens, SC, Saccharomyces cerevisiae—and YY represents data type—CC, cocitation; CX, coexpression; GN, gene neighbors; GT, genetic interaction; LC, literature curated protein–protein interaction...
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Research: Genetic analysis of complex traits in the emerging Collaborative Cross
- David L. Aylor,
- William Valdar,
- Wendy Foulds-Mathes,
- Ryan J. Buus,
- Ricardo A. Verdugo,
- Ralph S. Baric,
- Martin T. Ferris,
- Jeff A. Frelinger,
- Mark Heise,
- Matt B. Frieman,
- Lisa E. Gralinski,
- Timothy A. Bell,
- John D. Didion,
- Kunjie Hua,
- Derrick L. Nehrenberg,
- Christine L. Powell,
- Jill Steigerwalt,
- Yuying Xie,
- Samir N.P. Kelada,
- Francis S. Collins,
- Ivana V. Yang,
- David A. Schwartz,
- Lisa A. Branstetter,
- Elissa J. Chesler,
- Darla R. Miller,
- Jason Spence,
- Eric Yi Liu,
- Leonard McMillan,
- Abhishek Sarkar,
- Jeremy Wang,
- Wei Wang,
- Qi Zhang,
- Karl W. Broman,
- Ron Korstanje,
- Caroline Durrant,
- Richard Mott,
- Fuad A. Iraqi,
- Daniel Pomp,
- David Threadgill,
- Fernando Pardo-Manuel de Villena,
- and Gary A. Churchill
Genome Res. August 2011 21: 1213-1222; Published in Advance March 15, 2011, doi:10.1101/gr.111310.110
...-wide analysis of the incipient strains reveals high genetic diversity, balanced allele frequencies, and dense, evenly distributed recombination sites—all ideal qualities for a systems genetics resource. We map discrete, complex, and biomolecular traits and contrast two quantitative trait locus (QTL) mapping...
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Research: Genetic architecture of regulatory variation in Arabidopsis thaliana
- Xu Zhang,
- Andrew J. Cal,
- and Justin O. Borevitz
Genome Res. May 2011 21: 725-733; Published in Advance April 5, 2011, doi:10.1101/gr.115337.110
...regulatory region is interesting (Fig. 4B), as they could be local polymorphisms acting in trans through genetic feedback (Gjuvsland et al. 2010) or transvection as discovered in Drosophila (Lewis 1954). Probe binding, however, could be Table 2. Summary of local scan for gene expression, intron splicing...
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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
...sequences and their association with expression quantitative trait loci (eQTLs) to form the most comprehensive resource of this type, accessible through the UCSC Genome Browser. If your GOI and/or candidate TF are known to be expressed in human cancer, two useful tools that are relevant are DepMap, which...
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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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