Latest updates for Qtl-Seq

Fresh curated links around QTL-seq are collected here so marketers can spot useful updates and turn timely ideas into posts faster.

Recent items include:

  • Direct microhaplotype genotyping for GT-seq (Genotyping-in-Thousands by Sequencing) using a diploid abundance model
  • DeCTCF: Decoding CTCF binding sequences by leveraging predicted epigenomic features
  • HiFIseek: Gene-specific enrichment of high-impact mutations in associated genomic regions

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Fresh articles and ideas

Recent curated links from global sources. Generate one free draft from any story, then use SocialBu to schedule and refine your content calendar.

journals.plos.org /1 month ago

Direct microhaplotype genotyping for GT-seq (Genotyping-in-Thousands by Sequencing) using a diploid abundance model

by Nathan R. Campbell, Amanda R. Campbell, Shannon K. Blair, Amanda J. Finger GT-seq (Genotyping-in-Thousands by Sequencing) is widely used for high-throughput amplicon genotyping...

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journals.plos.org /2 weeks ago

DeCTCF: Decoding CTCF binding sequences by leveraging predicted epigenomic features

by Lu Chai, Jie Gao, Tinghe Guo, Teer Ba, Zihan Li, Junjie Liu, Yong Wang, Lirong Zhang CTCF is a key architectural protein with diverse roles in genome organization and gene regu...

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journals.plos.org /2 weeks ago

HiFIseek: Gene-specific enrichment of high-impact mutations in associated genomic regions

by Rafael Riudavets Puig, Denise G. O’Mahony, Ina Skaara Brorson, Ksenia Sokolova, Vessela N. Kristensen, Anthony Mathelier Transcription is regulated through the sequence-specifi...

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rna-seqblog.com /4 weeks ago

Single-cell TimeLapse-seq reveals MTA is an essential retrotransposon

Very early in development, an embryo must begin using its own genome instead of relying only on RNA and proteins inherited from the egg. This transition is known as zygotic genome...

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journals.plos.org /1 month ago

FM-GPT: Bayesian fine mapping for phenome-wide transcriptome-wide association studies

by Travis Canida, Zhenyao Ye, Shao-Hsuan Wang, Hsin-Hsiung Huang, Yezhi Pan, Menglu Liang, Shuo Chen, Tianzhou Ma Transcriptome-wide association studies (TWAS) integrate genome wi...

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journals.plos.org /1 month ago

Pervasive context-dependent effects in the genetic architecture of complex and quantitative traits revealed by a powerfu...

by Gareth A. Cromie, Russell S. Lo, Lauren Ames, Trey S. Morgan, Katherine Owens, Anne E. Clark, Martin S. Timour, Julee Ashmead, Michelle Tang, J. Nathan Kutz, Joshua M. Akey, Aim...

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journals.plos.org /1 month ago

Assessing Hardy-Weinberg equilibrium in T2T-aligned 1000 genomes project

by Elika Garg, Jaffa Romain, Lei Sun, Andrew D. Paterson Quality control of markers in genome-wide association studies often includes testing for Hardy-Weinberg equilibrium (HWE)....

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journals.plos.org /1 month ago

Development of a low-coverage whole genome sequencing screen for apomixis using a diverse set of <i>Malus</i&gt...

by Charity Z. Goeckeritz, Václav Polcar, Benjamin Gutierrez, Tomáš Urfus, Alex Harkess In the past decade, plant biologists have made several major discoveries pertaining to the g...

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rna-seqblog.com /1 month ago

An end-to-end computational framework for “Record-seq” transcriptional recording data

A new framework adapts RNA sequencing analysis for Record-seq, improving spacer extraction, transcription-unit quantification, normalization, differential expression, and modeling...

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journals.plos.org /1 month ago

Not every gene is special: Modelling scale controls the false discovery rate when analysing high-throughput sequencing d...

by Scott J. Dos Santos, Andreea C. Murariu, Justin D. Silverman, Gregory B. Gloor Differential expression/abundance analyses are commonplace in studies employing high-throughput s...

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rna-seqblog.com /1 month ago

scLS – a computationally efficient differentially expressed gene detection algorithm

A new RNA sequencing analysis method uses the Lomb-Scargle periodogram to efficiently identify genes associated with pseudotime across complex single-cell trajectories...

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rna-seqblog.com /1 month ago

PotatoRTD and TomatoRTD: comprehensive reference transcript datasets for accurate transcriptome analysis and isoform dis...

RNA sequencing and Iso-Seq improve potato and tomato transcript annotations, revealing additional isoforms and enabling more accurate analysis of gene expression and alternative sp...

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bioengineer.org /2 weeks ago

Mystery Rice Gene With Propeller-Shaped Protein Emerges as Key to Iron-Deficiency Tolerance

Researchers in India combined QTL-seq, transcriptomics and structural modeling to identify OsFe2200, a little-known DUF1677 gene with a predicted Kelch β-propeller-like fold, as a...

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journals.plos.org /1 month ago

Multi-organ single-cell transcriptomic atlas identifies <i>QrIAA14</i> as a candidate negative regulator of...

by Wenkai Hui, Jiayue Li, Hao Li, Hongyi Wu, Yi He, Shuangying Yang, Xiong Huang, Hanbo Yang, Gang Chen, Peng Zhu, Xiaohong Chen, Xingcui Xiao, Yu Zhong, Zhenfeng Xu, Fang He Plan...

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journals.plos.org /3 weeks ago

Integrating zero-inflation correction and transcriptional kinetics for single-cell transcriptomic analysis

by Chengkai Yang, Yu Liao, Ying Sheng, Feng Jiao Single-cell transcriptomic data exhibit pervasive zero inflation, while traditional models either neglect this issue or fail to ca...

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rna-seqblog.com /1 month ago

A real-data approach to evaluating RNA transcript analysis methods

RNA sequencing data provide a real-world framework for comparing differential transcript usage methods across bulk, single-cell, spatial, long-read, and short-read transcriptomics....

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rna-seqblog.com /1 month ago

Benchmarking RNA sequencing for more accurate alternative splicing analysis

RNA sequencing benchmarking across 42 laboratories identifies data quality, sequencing depth, and bioinformatics choices that improve alternative splicing and isoform analysis...

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rna-seqblog.com /1 month ago

Ultrafast and reference-free sequence discovery in single-cell data

Malva enables ultrafast, reference-free searches across massive single-cell RNA sequencing datasets for mutations, splice junctions, pathogens, transcripts, and other sequence-leve...

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journals.plos.org /4 weeks ago

Univariate-guided sparse regression for Biobank-scale high-dimensional omics data

by Joshua Richland, Tuomo Kiiskinen, William Wang, Wenhui Sophia Lu, Balasubramanian Narasimhan, Trevor Hastie, Manuel Rivas, Robert Tibshirani We present a scalable framework for...

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bioengineer.org /1 month ago

New multi-omics study reveals wheat QTL TaFhb-6A conferring scab resistance

A devastating fungal disease that can wipe out wheat harvests and poison the grain we eat has met a formidable new opponent. Scientists in China have developed a novel wheat line,...

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journals.plos.org /2 weeks ago

A binding-activated CRISPR/dCas13X imaging system enables precise RNA tracking in plants

by Jiayu Zhang, Yiran Tao, Yun Zhao, Miaomiao Lei, Yucheng Shen, Qicong Li, Chenxu Liu, Jiuyuan Bai Visualizing the spatiotemporal dynamics of native RNA molecules with single-tra...

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rna-seqblog.com /3 weeks ago

ResolVI improves accuracy in spatial transcriptomics analysis

ResolVI improves spatial RNA sequencing analysis by correcting RNA assignment errors and technical variation, helping researchers distinguish cell states and detect subtle gene exp...

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bioengineer.org /1 week ago

Low-Coverage Genome Sequencing Uncovers Hidden Clonal Seed Formation in Apple Relatives

A low-coverage whole-genome sequencing screen of USDA apple germplasm identified 17 previously unknown apomictic genotypes, offering a cheaper, faster method for detecting clonal s...

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rna-seqblog.com /2 weeks ago

GP-DHT uses single-cell RNA sequencing to map gene regulatory networks

Single-cell RNA sequencing combined with GP-DHT helps predict transcription factor and target gene relationships, providing a...

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journals.plos.org

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rna-seqblog.com

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