4.7 Article

DeepBSA: A deep-learning algorithm improves bulked segregant analysis for dissecting complex traits

Related references

Note: Only part of the references are listed.
Article Genetics & Heredity

Predicting the genomic resolution of bulk segregant analysis

Runxi Shen et al.

Summary: Bulk segregant analysis is a technique for identifying genetic loci associated with phenotypic trait differences. This study uses coalescence theory to calculate the expected genomic resolution of bulk segregant analysis. The researchers developed a model that closely matches numerical simulations and is robust to contamination of the segregant pools. The framework allows researchers to predict the expected power of their mapping experiments and optimize mapping resolution.

G3-GENES GENOMES GENETICS (2022)

Article Astronomy & Astrophysics

RU-net: A Residual U-net for Automatic Interplanetary Coronal Mass Ejection Detection

Jun Chen et al.

Summary: This paper proposes a new method called RU-net, which uses the U-net architecture and residual elements for the automatic detection of interplanetary coronal mass ejections (ICMEs). Experimental results demonstrate that the proposed RU-net shows competitive accuracy and efficiency.

ASTROPHYSICAL JOURNAL SUPPLEMENT SERIES (2022)

Article Biochemistry & Molecular Biology

A Chromosome-Level Assembly of Blunt Snout Bream (Megalobrama amblycephala) Genome Reveals an Expansion of Olfactory Receptor Genes in Freshwater Fish

Han Liu et al.

Summary: This study reports a major OR expansion in a freshwater herbivorous fish, Megalobrama amblycephala, and evaluates the possible contribution of OR expansion to habitat and feeding specialization by comparing the OR repertoire in 28 phylogenetically and ecologically diverse teleosts. The research found a strong association between duplications of beta and epsilon ORs and freshwater habitat, with the expanded beta and epsilon ORs highly expressed in the olfactory epithelium of Megalobrama amblycephala.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

Article Agronomy

Genetic mapping of green curd gene Gr in cauliflower

Huaqiang Tan et al.

THEORETICAL AND APPLIED GENETICS (2020)

Article Genetics & Heredity

Mapping Gene Markers for Apple Fruit Ring Rot Disease Resistance Using a Multi-omics Approach

Fei Shen et al.

G3-GENES GENOMES GENETICS (2019)

Letter Biotechnology & Applied Microbiology

Identification of anthocyanin biosynthesis genes in rice pericarp using PCAMP

Xinghai Yang et al.

PLANT BIOTECHNOLOGY JOURNAL (2019)

Article Multidisciplinary Sciences

Dissecting a heterotic gene through GradedPool-Seq mapping informs a rice-improvement strategy

Changsheng Wang et al.

NATURE COMMUNICATIONS (2019)

Article Multidisciplinary Sciences

Improved maize reference genome with single-molecule technologies

Yinping Jiao et al.

NATURE (2017)

Article Multidisciplinary Sciences

Altered expression of maize PLASTOCHRON1 enhances biomass and seed yield by extending cell division duration

Xiaohuan Sun et al.

NATURE COMMUNICATIONS (2017)

Article Genetics & Heredity

Target Enrichment Improves Mapping of Complex Traits by Deep Sequencing

Jianjun Guo et al.

G3-GENES GENOMES GENETICS (2016)

Review Biotechnology & Applied Microbiology

Bulked sample analysis in genetics, genomics and crop improvement

Cheng Zou et al.

PLANT BIOTECHNOLOGY JOURNAL (2016)

Article Biotechnology & Applied Microbiology

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

Babak Alipanahi et al.

NATURE BIOTECHNOLOGY (2015)

Article Biochemistry & Molecular Biology

FASCIATED EAR4 Encodes a bZIP Transcription Factor That Regulates Shoot Meristem Size in Maize

Michael Pautler et al.

PLANT CELL (2015)

Article Multidisciplinary Sciences

Dissecting meiotic recombination based on tetrad analysis by single-microspore sequencing in maize

Xiang Li et al.

NATURE COMMUNICATIONS (2015)

Article Biochemistry & Molecular Biology

MMAPPR: Mutation Mapping Analysis Pipeline for Pooled RNA-seq

Jonathon T. Hill et al.

GENOME RESEARCH (2013)

Article Biotechnology & Applied Microbiology

Genome sequencing reveals agronomically important loci in rice using MutMap

Akira Abe et al.

NATURE BIOTECHNOLOGY (2012)

Article Biochemical Research Methods

The Statistics of Bulk Segregant Analysis Using Next Generation Sequencing

Paul M. Magwene et al.

PLOS COMPUTATIONAL BIOLOGY (2011)

Article Biochemistry & Molecular Biology

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

Aaron McKenna et al.

GENOME RESEARCH (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Letter Biochemical Research Methods

SHOREmap: simultaneous mapping and mutation identification by deep sequencing

Korbinian Schneeberger et al.

NATURE METHODS (2009)

Article Multidisciplinary Sciences

The map-based sequence of the rice genome

T Matsumoto et al.

NATURE (2005)