Telescope: an interactive tool for managing large-scale analysis from mobile devices

Brito, Jaqueline J.; Mosqueiro, Thiago; Rotman, Jeremy; Xue, Victor; Chapski, Douglas J.; Hoz, Juan De la; Matias, Paulo; Martin, Lana S.; Zelikovsky, Alexander; Pellegrini, Matteo; Mangul, Serghei

doi:10.1093/gigascience/giz163

Cited by 3 publications

(3 citation statements)

References 20 publications

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“…First, it can hide the complexity and details of the underlying hardware from users who are not necessarily fluent in handling complex hardware 245 . Second, it helps to reduce the total analysis time 245,246 , by starting read alignment while still sequencing.…”

Section: Discussionmentioning

confidence: 99%

Technology dictates algorithms: recent developments in read alignment

et al. 2021

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Aligning sequencing reads onto a reference is an essential step of the majority of genomic analysis pipelines. Computational algorithms for read alignment have evolved in accordance with technological advances, leading to today’s diverse array of alignment methods. We provide a systematic survey of algorithmic foundations and methodologies across 107 alignment methods, for both short and long reads. We provide a rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read alignment. We discuss how general alignment algorithms have been tailored to the specific needs of various domains in biology.

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Section: Discussionmentioning

confidence: 99%

Technology dictates algorithms: recent developments in read alignment

et al. 2021

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“…The Quantitative RT-PCR was conducted using TransStart top green qPCR SuperMix. (4) The selection of the reference gene, PbEF1α, was done (Yang et al 2019) (5). The preparation of the RT-qPCR Reaction Mixture involved mixing 10 µL of SYBR Premix Ex TaqTM II, 1 µL of cDNA, 7 µL of ddH2O, and 2 µL of speci c primers.…”

Section: Rna Extraction and Qrt-pcr Analysismentioning

confidence: 99%

“…The subfamily, group K, has only two motifs (motif 7 and motif 8). In plants, introns regulate gene expressions (Yang et al 2019;Brito et al 2020). Therefore, elucidating gene function through the analysis of the intron-exon structure is important.…”

Section: Motif Analysis Of Pbbzip Gene and Exon-intron Structure Of T...mentioning

confidence: 99%

Identification and Expression Profiling of the bZIP Gene Family Throughout the Genome in Phoebe bournei under Abiotic Stress

Bakari,

Guan,

Liu

et al. 2024

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The bZIPgene family plays a crucial role in supporting plant life as one of the most important transcription factors. Its involvement in various processes such as light signaling, seed maturation, flower development, and cell elongation has been established, but limited to perennial and agricultural crops. This study focused on the classification of 71 bZIP genes across 12 chromosomes based on their evolutionary relationships. Each group exhibited distinct gene structures and variations in the number of conserved motifs. The presence of multiple cis-acting elements suggested that the PbbZIP gene family played a vital role in hormonal and regulatory signaling, which were essential for plant growth, development, and resilience against abiotic stress. RNA and qPCR analysis revealed expression levels of PbbZIP32, PbbZIP14, PbbZIP26, PbbZIP67, and PbbZIP69 under salt, drought, and temperature stress conditions. This research contributed to a deeper understanding of the underlying mechanisms governing stress resistance, growth, and development processes mediated by the bZIP gene family. It also can serve as a foundation for future investigations on the bZIPgene family in forestry species.

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Telescope: an interactive tool for managing large-scale analysis from mobile devices

et al. 2020

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In today's world of big data, computational analysis has become a key driver of biomedical research. High-performance computational facilities are capable of processing considerable volumes of data, yet often lack an easy-to-use interface to guide the user in supervising and adjusting bioinformatics analysis via a tablet or smartphone. Telescope is a novel tool that interfaces with high-performance computational clusters to deliver an intuitive user interface for controlling and monitoring bioinformatics analyses in real-time. Telescope provides a user-friendly method for integrating computational analyses with experimental biomedical research. Telescope is freely available at https://github.com/Mangul-Lab-USC/telescope . 2

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Telescope: an interactive tool for managing large-scale analysis from mobile devices

Cited by 3 publications

References 20 publications

Technology dictates algorithms: recent developments in read alignment

Technology dictates algorithms: recent developments in read alignment

Identification and Expression Profiling of the bZIP Gene Family Throughout the Genome in Phoebe bournei under Abiotic Stress

Telescope: an interactive tool for managing large-scale analysis from mobile devices

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