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Leveraging Transcriptomics Data for Genomic Prediction Models in Cassava

https://doi.org/10.1101/208181

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/0471250953.bi1112s47openalex-snapshot

BEDTools: The Swiss‐Army Tool for Genome Feature Analysis

inferredcites →https://doi.org/10.1007/s00122-017-2943-zopenalex-snapshot

QTL associated with resistance to cassava brown streak and cassava mosaic diseases in a bi-parental cross of two Tanzanian farmer varieties, Namikonga and Albert

inferredcites →https://doi.org/10.1007/s00705-009-0581-8openalex-snapshot

The complete genome sequence of the Tanzanian strain of Cassava brown streak virus and comparison with the Ugandan strain sequence

inferredcites →https://doi.org/10.1007/s10681-010-0301-1openalex-snapshot

Genomic selection for durable stem rust resistance in wheat

inferredcites →https://doi.org/10.1016/j.ajhg.2015.11.020openalex-snapshot

Genotype Imputation with Millions of Reference Samples

inferredcites →https://doi.org/10.1016/j.livsci.2014.05.036openalex-snapshot

Machine learning methods and predictive ability metrics for genome-wide prediction of complex traits

inferredcites →https://doi.org/10.1016/j.neurobiolaging.2013.05.001openalex-snapshot

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inferredcites →https://doi.org/10.1016/j.tplants.2014.05.006openalex-snapshot

Genomic selection: genome-wide prediction in plant improvement

inferredcites →https://doi.org/10.1038/ejhg.2012.129openalex-snapshot

RNA-Seq and human complex diseases: recent accomplishments and future perspectives

inferredcites →https://doi.org/10.1038/hdy.2013.13openalex-snapshot

Toward genomic prediction from whole-genome sequence data: impact of sequencing design on genotype imputation and accuracy of predictions

inferredcites →https://doi.org/10.1038/hdy.2015.113openalex-snapshot

Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement

inferredcites →https://doi.org/10.1038/hdy.2017.4openalex-snapshot

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inferredcites →https://doi.org/10.1038/nature15393openalex-snapshot

A global reference for human genetic variation

inferredcites →https://doi.org/10.1038/nbt.1621openalex-snapshot

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

inferredcites →https://doi.org/10.1038/nbt.2450openalex-snapshot

Differential analysis of gene regulation at transcript resolution with RNA-seq

inferredcites →https://doi.org/10.1038/nbt.3535openalex-snapshot

Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity

inferredcites →https://doi.org/10.1038/ng.3211openalex-snapshot

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

inferredcites →https://doi.org/10.1038/ng.3845openalex-snapshot

Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nprot.2013.084openalex-snapshot

De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity

inferredcites →https://doi.org/10.1038/s41598-017-00729-0openalex-snapshot

Imputation-Based Whole-Genome Sequence Association Study Rediscovered the Missing QTL for Lumbar Number in Sutai Pigs

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A time series transcriptome analysis of cassava (Manihot esculenta Crantz) varieties challenged with Ugandan cassava brown streak virus

inferredcites →https://doi.org/10.1038/s41598-018-19696-1openalex-snapshot

Genome-wide association mapping and genomic prediction for CBSD resistance in Manihot esculenta

inferredcites →https://doi.org/10.1046/j.1365-313x.1999.00606.xopenalex-snapshot

Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily

inferredcites →https://doi.org/10.1073/pnas.1002044107openalex-snapshot

Association weight matrix for the genetic dissection of puberty in beef cattle

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Genomic selection in plant breeding: from theory to practice

inferredcites →https://doi.org/10.1093/bioinformatics/btp120openalex-snapshot

TopHat: discovering splice junctions with RNA-Seq

inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot

BEDTools: a flexible suite of utilities for comparing genomic features

inferredcites →https://doi.org/10.1093/bioinformatics/btr330openalex-snapshot

The variant call format and VCFtools

inferredcites →https://doi.org/10.1093/bioinformatics/btv118openalex-snapshot

Guidance for RNA-seq co-expression network construction and analysis: safety in numbers

inferredcites →https://doi.org/10.1093/genetics/157.4.1819openalex-snapshot

Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps

inferredcites →https://doi.org/10.1093/nar/gkv1344openalex-snapshot

The Pfam protein families database: towards a more sustainable future

inferredcites →https://doi.org/10.1094/pd-74-0404openalex-snapshot

African Cassava Mosaic Virus: Etiology, Epidemiology, and Control

inferredcites →https://doi.org/10.1101/gr.169375.113openalex-snapshot

MultiBLUP: improved SNP-based prediction for complex traits

inferredcites →https://doi.org/10.1111/j.1439-0388.2007.00694.xopenalex-snapshot

Machine learning classification procedure for selecting SNPs in genomic selection: application to early mortality in broilers

inferredcites →https://doi.org/10.1111/j.1439-0388.2007.00698.xopenalex-snapshot

Estimation of genome‐wide haplotype effects in half‐sib designs

inferredcites →https://doi.org/10.1111/j.1439-0434.2005.00974.xopenalex-snapshot

Transmission of Cassava brown streak virus by Bemisia tabaci (Gennadius)

inferredcites →https://doi.org/10.1111/jbg.12199openalex-snapshot

Accuracy of genomic prediction using imputed whole‐genome sequence data in white layers

inferredcites →https://doi.org/10.1111/mpp.12565openalex-snapshot

Molecular insights into Cassava brown streak virus susceptibility and resistance by profiling of the early host response

inferredcites →https://doi.org/10.1111/ppa.12343openalex-snapshot

Distribution and accumulation of cassava brown streak viruses within infected cassava ( Manihot esculenta ) plants

inferredcites →https://doi.org/10.1159/000317279openalex-snapshot

Machine Learning Classification Procedure for Selecting SNPs in Genomic Selection: Application to Early Mortality in Broilers

inferredcites →https://doi.org/10.1186/1297-9686-41-55openalex-snapshot

Deregressing estimated breeding values and weighting information for genomic regression analyses

inferredcites →https://doi.org/10.1186/1297-9686-43-18openalex-snapshot

Different models of genetic variation and their effect on genomic evaluation

inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot

BLAST+: architecture and applications

inferredcites →https://doi.org/10.1186/1471-2105-9-559openalex-snapshot

WGCNA: an R package for weighted correlation network analysis

inferredcites →https://doi.org/10.1186/1752-0509-1-54openalex-snapshot

Eigengene networks for studying the relationships between co-expression modules

inferredcites →https://doi.org/10.1186/gb-2013-14-4-r36openalex-snapshot

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

inferredcites →https://doi.org/10.1186/s12711-014-0074-4openalex-snapshot

Improved precision of QTL mapping using a nonlinear Bayesian method in a multi-breed population leads to greater accuracy of across-breed genomic predictions

inferredcites →https://doi.org/10.1186/s12711-015-0149-xopenalex-snapshot

Genomic prediction using imputed whole-genome sequence data in Holstein Friesian cattle

inferredcites →https://doi.org/10.1186/s12711-016-0225-xopenalex-snapshot

Efficient genomic prediction based on whole-genome sequence data using split-and-merge Bayesian variable selection

inferredcites →https://doi.org/10.1186/s12711-016-0274-1openalex-snapshot

Genomic prediction using preselected DNA variants from a GWAS with whole-genome sequence data in Holstein–Friesian cattle

inferredcites →https://doi.org/10.1186/s12711-016-0277-yopenalex-snapshot

Whole-genome sequence-based genomic prediction in laying chickens with different genomic relationship matrices to account for genetic architecture

inferredcites →https://doi.org/10.1186/s12711-016-0279-9openalex-snapshot

Comparison of alternative approaches to single-trait genomic prediction using genotyped and non-genotyped Hanwoo beef cattle

inferredcites →https://doi.org/10.1186/s12711-017-0319-0openalex-snapshot

Exploring the genetic architecture and improving genomic prediction accuracy for mastitis and milk production traits in dairy cattle by mapping variants to hepatic transcriptomic regions responsive to intra-mammary infection

inferredcites →https://doi.org/10.1186/s12711-017-0335-0openalex-snapshot

Incorporation of causative quantitative trait nucleotides in single-step GBLUP

inferredcites →https://doi.org/10.1186/s12864-015-1397-4openalex-snapshot

A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes

inferredcites →https://doi.org/10.1186/s12864-015-1554-9openalex-snapshot

Identification and distribution of the NBS-LRR gene family in the Cassava genome

inferredcites →https://doi.org/10.1186/s12864-016-2443-6openalex-snapshot

Exploiting biological priors and sequence variants enhances QTL discovery and genomic prediction of complex traits

inferredcites →https://doi.org/10.1186/s12918-017-0420-6openalex-snapshot

An additional k-means clustering step improves the biological features of WGCNA gene co-expression networks

inferredcites →https://doi.org/10.1186/s12985-014-0216-xopenalex-snapshot

Field evaluation of selected cassava genotypes for cassava brown streak disease based on symptom expression and virus load

inferredcites →https://doi.org/10.1371/journal.pcbi.1005457openalex-snapshot

Transcriptomics technologies

inferredcites →https://doi.org/10.1371/journal.pgen.1000529openalex-snapshot

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

inferredcites →https://doi.org/10.1371/journal.pgen.1003608openalex-snapshot

Prediction of Complex Human Traits Using the Genomic Best Linear Unbiased Predictor

inferredcites →https://doi.org/10.1371/journal.pgen.1004982openalex-snapshot

Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice Breeding Lines

inferredcites →https://doi.org/10.1371/journal.pone.0019379openalex-snapshot

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

inferredcites →https://doi.org/10.1371/journal.pone.0022196openalex-snapshot

Gene Coexpression Network Analysis as a Source of Functional Annotation for Rice Genes

inferredcites →https://doi.org/10.1371/journal.pone.0026801openalex-snapshot

The Transcriptome of the Reference Potato Genome Solanum tuberosum Group Phureja Clone DM1-3 516R44

inferredcites →https://doi.org/10.1371/journal.pone.0090346openalex-snapshot

TASSEL-GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline

inferredcites →https://doi.org/10.1371/journal.pone.0139321openalex-snapshot

Analyses of Twelve New Whole Genome Sequences of Cassava Brown Streak Viruses and Ugandan Cassava Brown Streak Viruses from East Africa: Diversity, Supercomputing and Evidence for Further Speciation

inferredcites →https://doi.org/10.1534/g3.111.001198openalex-snapshot

Genotype Imputation with Thousands of Genomes

inferredcites →https://doi.org/10.1534/g3.114.015008/-/dc1openalex-snapshot

High-resolution linkage map and chromosome-scale genome assembly for cassava (Manihot esculenta Crantz) from 10 populations

inferredcites →https://doi.org/10.1534/genetics.109.101501openalex-snapshot

Predicting Quantitative Traits With Regression Models for Dense Molecular Markers and Pedigree

inferredcites →https://doi.org/10.1534/genetics.110.116590openalex-snapshot

Accurate Prediction of Genetic Values for Complex Traits by Whole-Genome Resequencing

inferredcites →https://doi.org/10.1534/genetics.112.143313openalex-snapshot

Whole-Genome Regression and Prediction Methods Applied to Plant and Animal Breeding

inferredcites →https://doi.org/10.1534/genetics.116.187161openalex-snapshot

Genomic Prediction for Quantitative Traits Is Improved by Mapping Variants to Gene Ontology Categories in Drosophila melanogaster

inferredcites →https://doi.org/10.18637/jss.v040.i01openalex-snapshot

The Split-Apply-Combine Strategy for Data Analysis

inferredcites →https://doi.org/10.18637/jss.v040.i08openalex-snapshot

Rcpp : Seamless R and C++ Integration

inferredcites →https://doi.org/10.18637/jss.v067.i01openalex-snapshot

Fitting Linear Mixed-Effects Models Using lme4

inferredcites →https://doi.org/10.2135/cropsci2011.06.0297openalex-snapshot

Genomic Selection in Plant Breeding: A Comparison of Models

inferredcites →https://doi.org/10.2135/cropsci2014.02.0160openalex-snapshot

The Effects of Restriction‐Enzyme Choice on Properties of Genotyping‐by‐Sequencing Libraries: A Study in Cassava ( Manihot esculenta )

inferredcites →https://doi.org/10.2202/1544-6115.1128openalex-snapshot

A General Framework for Weighted Gene Co-Expression Network Analysis

inferredcites →https://doi.org/10.2307/1271436openalex-snapshot

Ridge Regression: Biased Estimation for Nonorthogonal Problems

inferredcites →https://doi.org/10.2527/jas.2012-5784openalex-snapshot

BREEDING AND GENETICS SYMPOSIUM: Networks and pathways to guide genomic selection1–3

inferredcites →https://doi.org/10.3168/jds.2012-6316openalex-snapshot

Comparison of different methods for imputing genome-wide marker genotypes in Swedish and Finnish Red Cattle

inferredcites →https://doi.org/10.3168/jds.2014-8210openalex-snapshot

Comparison of genomic predictions using genomic relationship matrices built with different weighting factors to account for locus-specific variances

inferredcites →https://doi.org/10.3389/fpls.2017.01168openalex-snapshot

QTL Mapping for Pest and Disease Resistance in Cassava and Coincidence of Some QTL with Introgression Regions Derived from Manihot glaziovii

inferredcites →https://doi.org/10.3835/plantgenome2011.08.0024openalex-snapshot

Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP

inferredcites →https://doi.org/10.3835/plantgenome2012.07.0017openalex-snapshot

Genomic Prediction of Genetic Values for Resistance to Wheat Rusts

inferredcites →https://doi.org/10.3835/plantgenome2015.07.0062openalex-snapshot

The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly

inferredcites →https://doi.org/10.3835/plantgenome2015.11.0118openalex-snapshot

Genome‐Wide Association and Prediction Reveals Genetic Architecture of Cassava Mosaic Disease Resistance and Prospects for Rapid Genetic Improvement

inferredcites →https://doi.org/10.3835/plantgenome2017.03.0015openalex-snapshot

Prospects for Genomic Selection in Cassava Breeding

inferredcites →https://doi.org/10.5897/jgmvopenalex-snapshot

Journal of General and Molecular Virology

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Role of multi-omics in aquaculture genetics and breeding: current status and future perspective

inferred← citeshttps://doi.org/10.1007/s42976-026-00789-xopenalex-snapshot

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RNA polymerase mapping in plants identifies enhancers enriched in causal variants

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inferred← citeshttps://doi.org/10.1534/g3.118.200710openalex-snapshot

Training Population Optimization for Prediction of Cassava Brown Streak Disease Resistance in West African Clones

inferred← citeshttps://doi.org/10.1534/g3.120.401240openalex-snapshot

Genomic Prediction Informed by Biological Processes Expands Our Understanding of the Genetic Architecture Underlying Free Amino Acid Traits in Dry Arabidopsis Seeds

inferred← citeshttps://doi.org/10.1534/genetics.119.302757openalex-snapshot

Historical Introgressions from a Wild Relative of Modern Cassava Improved Important Traits and May Be Under Balancing Selection

inferred← citeshttps://doi.org/10.18174/634641openalex-snapshot

Knowledge-driven approaches to improve genomic prediction in plants

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