Searching journal content for articles similar to Varshney et al. 23 (4): 727.

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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
...explain the transcriptional regulation of your GOI, this does not mean that you have to do all of the “wet-laboratory” experiments yourself: Data mining is a crucial step in developing your hypotheses. Proliferation of easily accessible, large-scale, high-throughput studies provides fertile ground...
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Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
- Prashanthi Ravichandran,
- Princy Parsana,
- Rebecca Keener,
- Kasper D. Hansen,
- and Alexis Battle
Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
...inference by significantly increasing the number of samples used in network inference, leveraging large-scale publicly available and uniformly processed RNA-seq data from recount3 (Wilks et al. 2021) which includes human RNA-seq samples from GTEx (The GTEx Consortium 2020), TCGA (Tomczak et al. 2015...
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Resource: Genome-wide dynamics of alternative polyadenylation in rice
- Haihui Fu,
- Dewei Yang,
- Wenyue Su,
- Liuyin Ma,
- Yingjia Shen,
- Guoli Ji,
- Xinfu Ye,
- Xiaohui Wu,
- and Qingshun Q. Li
Genome Res. December 2016 26: 1753-1760; Published in Advance October 12, 2016, doi:10.1101/gr.210757.116
...and one 3′ UTR shortening gene using primers that amplify a common region (PA1 + PA2) and the longer 3′ UTR (PA2). The qRT-PCR results match what were tallied from the PAT-seq large-scale data (Supplemental Fig. S7). Intriguingly, with the development of rice, more genes used longer 3′ UTRs than shorter 3...
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Resource: Large-scale analysis of branchpoint usage across species and cell lines
- Allison J. Taggart,
- Chien-Ling Lin,
- Barsha Shrestha,
- Claire Heintzelman,
- Seongwon Kim,
- and William G. Fairbrother
Genome Res. April 2017 27: 639-649; Published in Advance January 24, 2017, doi:10.1101/gr.202820.115
...of branch site are imprecise as reverse transcriptase skips several nucleotides while traversing a 2–5 linkage. Here, we report large-scale mapping of the branchpoints from deep sequencing data in three different species and in the SF3B1 K700E oncogenic mutant background.We have developed a novel method...
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Method: Large-scale identification of chemically induced mutations in Drosophila melanogaster
- Nele A. Haelterman,
- Lichun Jiang,
- Yumei Li,
- Vafa Bayat,
- Hector Sandoval,
- Berrak Ugur,
- Kai Li Tan,
- Ke Zhang,
- Danqing Bei,
- Bo Xiong,
- Wu-Lin Charng,
- Theodore Busby,
- Adeel Jawaid,
- Gabriela David,
- Manish Jaiswal,
- Koen J.T. Venken,
- Shinya Yamamoto,
- Rui Chen,
- and Hugo J. Bellen
Genome Res. October 2014 24: 1707-1718; Published in Advance September 25, 2014, doi:10.1101/gr.174615.114
...on a large scale, permitting forward genetic screens to annotate the function of numerous genes at a much greater pace than currently available methodologies. Results 303 sequence coverage identifies the majority of SNVs We generated a collection of EMS-induced lethal mutations on the Drosophila X chromosome...
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Method: Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations
- Jonathan S. Brammeld,
- Mia Petljak,
- Inigo Martincorena,
- Steven P. Williams,
- Luz Garcia Alonso,
- Alba Dalmases,
- Beatriz Bellosillo,
- Carla Daniela Robles-Espinoza,
- Stacey Price,
- Syd Barthorpe,
- Patrick Tarpey,
- Constantine Alifrangis,
- Graham Bignell,
- Joana Vidal,
- Jamie Young,
- Lucy Stebbings,
- Kathryn Beal,
- Michael R. Stratton,
- Julio Saez-Rodriguez,
- Mathew Garnett,
- Clara Montagut,
- Francesco Iorio,
- and Ultan McDermott
Genome Res. April 2017 27: 613-625; Published in Advance February 8, 2017, doi:10.1101/gr.213546.116
...Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer and identification of drug resistance mutations Jonathan S. Brammeld,1 Mia Petljak,1 Inigo Martincorena,1 Steven P. Williams,1 Luz Garcia Alonso,2 Alba Dalmases,3 Beatriz Bellosillo,3 Carla Daniela Robles-Espinoza,4...
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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
...transposons, including the rarer types, can be found within the zebrafish , which harbors a much greater diversity of TEs than is typically observed in mammalian s (Furano et al. 2004; Howe et al. 2013; Chalopin et al. 2015).Genome-wide studies have revealed that TEs are expressed in a tightly regulated...
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Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
- Junling Shi,
- Jiaqi Xu,
- Jun Ma,
- and Feng He
Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
...respond to environmental fluctuations by rewiring gene regulatory networks. In particular, suppression on protein synthesis usually provides cells with a resource allocating solution within a few minutes of exposure to stress (López-Maury et al. 2008). As a class of key informational molecules...
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Resource: Systematic genome editing of the genes on zebrafish Chromosome 1 by CRISPR/Cas9
- Yonghua Sun,
- Bo Zhang,
- Lingfei Luo,
- De-Li Shi,
- Han Wang,
- Zongbin Cui,
- Honghui Huang,
- Ying Cao,
- Xiaodong Shu,
- Wenqing Zhang,
- Jianfeng Zhou,
- Yun Li,
- Jiulin Du,
- Qingshun Zhao,
- Jun Chen,
- Hanbing Zhong,
- Tao P. Zhong,
- Li Li,
- Jing-Wei Xiong,
- Jinrong Peng,
- Wuhan Xiao,
- Jian Zhang,
- Jihua Yao,
- Zhan Yin,
- Xianming Mo,
- Gang Peng,
- Jun Zhu,
- Yan Chen,
- Yong Zhou,
- Dong Liu,
- Weijun Pan,
- Yiyue Zhang,
- Hua Ruan,
- Feng Liu,
- Zuoyan Zhu,
- Anming Meng,
- and The ZAKOC Consortium
Genome Res. January 2020 30: 118-126; Published in Advance December 12, 2019, doi:10.1101/gr.248559.119
...lineages. (B) Quantitative real-time PCR showing the expression of Klf members klf1, klf3, klf4b, klf6a, and klf8 in klf3 mutants.DiscussionIn this study, we performed large-scale knockout of 1333 genes on zebrafish Chromosome 1 and successfully mutated 1029 of them. Among them, 962 are coding genes and 67...
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Method: High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9
- Gaurav K. Varshney,
- Wuhong Pei,
- Matthew C. LaFave,
- Jennifer Idol,
- Lisha Xu,
- Viviana Gallardo,
- Blake Carrington,
- Kevin Bishop,
- MaryPat Jones,
- Mingyu Li,
- Ursula Harper,
- Sunny C. Huang,
- Anupam Prakash,
- Wenbiao Chen,
- Raman Sood,
- Johan Ledin,
- and Shawn M. Burgess
Genome Res. July 2015 25: 1030-1042; Published in Advance June 5, 2015, doi:10.1101/gr.186379.114
...reported for the same gene. This is a significant setback to researchers interested in rapidly testing candidate gene validity in a vertebrate model system. Recently, many large-scale reverse genetics projects have generated thousands of mutants in zebrafish, which will have a major impact...
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