Matthew E. Hudson

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Assessed papers (1)

• Design considerations for workflow management systems use in production genomics research and the clinic.
  2021 L1 57/100

1 assessed by us (0 reproduced) · 139 not yet assessed — every PubMed paper on record, linked below.

• A sorghum pangenome reference improves global crop trait discovery ↗

  Nature · 2026 · PMID 41813899
  not yet assessed
• Retroelement expansions underlie genome evolution in stingless bees ↗

  BMC Genomics · 2026 · PMID 41501624
  not yet assessed
• Pangenome analysis of nine soybean cyst nematode genomes reveals hidden variation contributing to diversity and adaptation ↗

  BMC Genomics · 2026 · PMID 41535767
  not yet assessed
• Genetic diversity analysis of North Dakota public soybean breeding program cultivars ↗

  Scientific Reports · 2026 · PMID 41565852
  not yet assessed
• The silicon citizen naturalist ↗

  Cell · 2026 · PMID 42492492
  not yet assessed
• Enhancing lipid production in plant cells through automated high-throughput genome engineering and phenotyping ↗

  The Plant Cell · 2025 · PMID 39899469
  not yet assessed
• Genomic analysis and predictive modeling in the Northern Uniform Soybean Tests ↗

  Crop Science · 2025
  not yet assessed
• Assessment of the midgut microbiota in foragers of the stingless bee Melipona scutellaris following short-term sublethal exposure to imidacloprid ↗

  PLoS ONE · 2025 · PMID 41460865
  not yet assessed
• Retroelement expansions underlie genome evolution in stingless bees ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2025
  not yet assessed
• Developing future resilience from signatures of adaptation across the sorghum pangenome ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2025
  not yet assessed
• Synthetic feed-forward loop circuit boosts transgene expression in sugarcane ↗

  Plant Cell Reports · 2025 · PMID 40627042
  not yet assessed
• Vascular Trainees’ Peripheral Operative Experience in the Endovascular Era ↗

  Journal of Vascular Surgery · 2025
  not yet assessed
• Pangenome analysis of nine Soybean Cyst Nematode genomes reveal hidden variation contributing to diversity and adaptation ↗

  Research Square · 2025
  not yet assessed
• Intracellular aggregation of the transthyretin protein is limited by Hsp70 chaperones ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2025 · PMID 41446103
  not yet assessed
• Genome scans for selection signatures identify candidate virulence genes for adaptation of the soybean cyst nematode to host resistance ↗

  Molecular Ecology · 2024 · PMID 39135406
  not yet assessed
• The genomic case against genetic determinism ↗

  PLoS Biology · 2024 · PMID 38412239
  not yet assessed
• Soybean genomics research community strategic plan: A vision for 2024–2028 ↗

  The Plant Genome · 2024 · PMID 39572930
  not yet assessed
• Common signatures of selection reveal target loci for breeding across soybean populations ↗

  The Plant Genome · 2024 · PMID 38263616
  not yet assessed
• Impact of Rhg1 copy number variation on a soybean cyst nematode resistance transcriptional network ↗

  G3 Genes Genomes Genetics · 2024 · PMID 39295536
  not yet assessed
• Major impacts of widespread structural variation on sorghum ↗

  Genome Research · 2024 · PMID 38479835
  not yet assessed
• Enhancing lipid production in plant cells through high-throughput genome editing and phenotyping via a scalable automated pipeline ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2024
  not yet assessed
• Correction: The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes ↗

  BMC Genomics · 2024 · PMID 38822236
  not yet assessed
• An efficient virus‐induced gene silencing ( VIGS ) system for gene functional studies in Miscanthus ↗

  GCB Bioenergy · 2023
  not yet assessed
• Promoter deletion in the soybean Compact mutant leads to overexpression of a gene with homology to the C20-gibberellin 2-oxidase family ↗

  Journal of Experimental Botany · 2023 · PMID 37551820
  not yet assessed
• Fine mapping and cloning of the major seed protein quantitative trait loci on soybean chromosome 20 ↗

  The Plant Journal · 2022 · PMID 34978122
  not yet assessed
• CROPSR: an automated platform for complex genome-wide CRISPR gRNA design and validation ↗

  BMC Bioinformatics · 2022 · PMID 35172714
  not yet assessed
• An NBS‐LRR protein in the Rpp1 locus negates the dominance of Rpp1‐mediated resistance against Phakopsora pachyrhizi in soybean ↗

  The Plant Journal · 2022 · PMID 36424366
  not yet assessed
• Impact of multiple selective breeding programs on genetic diversity in soybean germplasm ↗

  Theoretical and Applied Genetics · 2022 · PMID 35220446
  not yet assessed
• Leveraging orthology within maize and Arabidopsis QTL to identify genes affecting natural variation in gravitropism ↗

  Proceedings of the National Academy of Sciences · 2022 · PMID 36161933
  not yet assessed
• Differential Effects of Chronic Methamphetamine Treatment on High-Frequency Oscillations and Responses to Acute Methamphetamine and NMDA Receptor Blockade in Conscious Mice ↗

  Preprints.org · 2022
  not yet assessed
• WI12Rhg1 interacts with DELLAs and mediates soybean cyst nematode resistance through hormone pathways ↗

  Plant Biotechnology Journal · 2021 · PMID 34532941
  not yet assessed
• Design considerations for workflow management systems use in production genomics research and the clinic

  Scientific Reports · 2021 · PMID 34737383
  L1 57/100
• A chromosomal assembly of the soybean cyst nematode genome ↗

  Molecular Ecology Resources · 2021 · PMID 34036752
  not yet assessed
• Genetic Variation for Seed Oil Biosynthesis in Soybean ↗

  Plant Molecular Biology Reporter · 2021
  not yet assessed
• Impact of variant-level batch effects on identification of genetic risk factors in large sequencing studies ↗

  PLoS ONE · 2021 · PMID 33861770
  not yet assessed
• Design considerations for workflow management systems use in production genomics research and the clinic ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2021
  not yet assessed
• A chromosomal assembly of the soybean cyst nematode genome ↗

  2021
  not yet assessed
• CROPSR: An Automated Platform for Complex Genome-Wide CRISPR gRNA Design and Validation ↗

  Research Square · 2021
  not yet assessed
• Genome biology of the paleotetraploid perennial biomass crop Miscanthus ↗

  Nature Communications · 2020 · PMID 33116128
  not yet assessed
• Genomic regions influencing aggressive behavior in honey bees are defined by colony allele frequencies ↗

  Proceedings of the National Academy of Sciences · 2020 · PMID 32631983
  not yet assessed
• t‐SNAREs bind the Rhg1 α‐SNAP and mediate soybean cyst nematode resistance ↗

  The Plant Journal · 2020 · PMID 32645235
  not yet assessed
• Comparative analysis of workflow management systems in production genomics research and the clinic ↗

  2020
  not yet assessed
• Impact of Variant-level Batch Effects on Identification of Genetic Risk Factors in Large Sequencing Studies ↗

  2020
  not yet assessed
• Sentieon DNASeq Variant Calling Workflow Demonstrates Strong Computational Performance and Accuracy ↗

  Frontiers in Genetics · 2019 · PMID 31481971
  not yet assessed
• Recommendations for performance optimizations when using GATK3.8 and GATK4 ↗

  BMC Bioinformatics · 2019 · PMID 31703611
  not yet assessed
• Bacterial steroid-17,20-desmolase is a taxonomically rare enzymatic pathway that converts prednisone to 1,4-androstanediene-3,11,17-trione, a metabolite that causes proliferation of prostate cancer cells ↗

  The Journal of Steroid Biochemistry and Molecular Biology · 2019 · PMID 31870912
  not yet assessed
• The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes ↗

  BMC Genomics · 2019 · PMID 30732586
  not yet assessed
• Early transcriptional responses to soybean cyst nematode HG Type 0 show genetic differences among resistant and susceptible soybeans ↗

  Theoretical and Applied Genetics · 2019 · PMID 31570969
  not yet assessed
• Correction to: Recommendations for performance optimizations when using GATK3.8 and GATK4 ↗

  BMC Bioinformatics · 2019 · PMID 31847808
  not yet assessed
• Additional file 5: of The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes ↗

  Figshare · 2019
  not yet assessed
• Additional file 6: of The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes ↗

  Figshare · 2019
  not yet assessed
• Additional file 3: of The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes ↗

  Figshare · 2019
  not yet assessed
• Additional file 4: of The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes ↗

  Figshare · 2019
  not yet assessed
• Additional file 2: of The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes ↗

  Figshare · 2019
  not yet assessed
• Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. ↗

  Nature Genetics · 2018 · PMID 30297971
  not yet assessed
• Identification of missing variants by combining multiple analytic pipelines ↗

  BMC Bioinformatics · 2018 · PMID 29661148
  not yet assessed
• Mapping of new quantitative trait loci for sudden death syndrome and soybean cyst nematode resistance in two soybean populations ↗

  Theoretical and Applied Genetics · 2018 · PMID 29582113
  not yet assessed
• Genetic Introgression from Glycine tomentella to Soybean to Increase Seed Yield ↗

  Crop Science · 2018
  not yet assessed
• Genome Sequence of the Soybean Cyst Nematode (Heterodera glycines) Endosymbiont “Candidatus Cardinium hertigii” Strain cHgTN10 ↗

  Genome Announcements · 2018 · PMID 29954916
  not yet assessed
• Publisher Correction: Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L ↗

  Nature Genetics · 2018 · PMID 30425353
  not yet assessed
• Performance benchmarking of GATK3.8 and GATK4 ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2018
  not yet assessed
• The genome of the soybean cyst nematode ( Heterodera glycines ) reveals complex patterns of duplications involved in the evolution of parasitism genes ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2018
  not yet assessed
• Computational performance and accuracy of Sentieon DNASeq variant calling workflow ↗

  bioRxiv (Cold Spring Harbor Laboratory) · 2018
  not yet assessed
• Additional file 7: of Identification of missing variants by combining multiple analytic pipelines ↗

  Figshare · 2018
  not yet assessed
• A comparison of genotyping-by-sequencing analysis methods on low-coverage crop datasets shows advantages of a new workflow, GB-eaSy ↗

  BMC Bioinformatics · 2017 · PMID 29281959
  not yet assessed
• Genome-wide association mapping of resistance to a Brazilian isolate of Sclerotinia sclerotiorum in soybean genotypes mostly from Brazil ↗

  BMC Genomics · 2017 · PMID 29115920
  not yet assessed
• A soft selective sweep during rapid evolution of gentle behaviour in an Africanized honeybee ↗

  Nature Communications · 2017 · PMID 29142254
  not yet assessed
• Genetically Diverse Soybean Cyst Nematode–Resistant Full‐Sib Soybean Germplasm Lines AR4SCN, AR5SCN, AR6SCN, AR7SCN, and AR8SCN ↗

  Journal of Plant Registrations · 2017
  not yet assessed
• Variant calling by assembly for detection of transposable elements in Glycine max ↗

  2017
  not yet assessed
• Reference-guided variant calling for novel non-repetitive sequences in Glycine max ↗

  2017
  not yet assessed
• Photoreceptor Biotechnology ↗

  Annual Plant Reviews online · 2017
  not yet assessed
• Additional file 4: Table S1. of Genome-wide association mapping of resistance to a Brazilian isolate of Sclerotinia sclerotiorum in soybean genotypes mostly from Brazil ↗

  Figshare · 2017
  not yet assessed
• Additional file 7: Table S4. of Genome-wide association mapping of resistance to a Brazilian isolate of Sclerotinia sclerotiorum in soybean genotypes mostly from Brazil ↗

  Figshare · 2017
  not yet assessed
• Simulating Next-Generation Sequencing Datasets from Empirical Mutation and Sequencing Models ↗

  PLoS ONE · 2016 · PMID 27893777
  not yet assessed
• An efficient method for measuring copy number variation applied to improvement of nematode resistance in soybean ↗

  The Plant Journal · 2016 · PMID 27310152
  not yet assessed
• Impact of Rhg1 copy number, type, and interaction with Rhg4 on resistance to Heterodera glycines in soybean ↗

  Theoretical and Applied Genetics · 2016 · PMID 27581541
  not yet assessed
• Evolutionary divergence of phytochrome protein function inZea maysPIF3 signaling ↗

  Journal of Experimental Botany · 2016 · PMID 27262126
  not yet assessed
• Genomic signatures of evolutionary transitions from solitary to group living ↗

  Science · 2015 · PMID 25977371
  not yet assessed
• The genomes of two key bumblebee species with primitive eusocial organization ↗

  Genome biology · 2015 · PMID 25908251
  not yet assessed
• From association to prediction: statistical methods for the dissection and selection of complex traits in plants ↗

  Current Opinion in Plant Biology · 2015 · PMID 25795170
  not yet assessed
• Evolution and selection of R hg1, a copy‐number variant nematode‐resistance locus ↗

  Molecular Ecology · 2015 · PMID 25735447
  not yet assessed
• A Classification of Basic Helix-Loop-Helix Transcription Factors of Soybean ↗

  International Journal of Genomics · 2015 · PMID 25763382
  not yet assessed
• Identification of Multiple Phytotoxins Produced by Fusarium virguliforme Including a Phytotoxic Effector (FvNIS1) Associated With Sudden Death Syndrome Foliar Symptoms ↗

  Molecular Plant-Microbe Interactions · 2015 · PMID 26646532
  not yet assessed
• Transposable elements, mRNA expression level and strand-specificity of small RNAs are associated with non-additive inheritance of gene expression in hybrid plants ↗

  BMC Plant Biology · 2015 · PMID 26139102
  not yet assessed
• Identification of genes that regulate phosphate acquisition and plant performance during arbuscular my corrhizal symbiosis in medicago truncatula and brachypodium distachyon ↗

  2015
  not yet assessed
• The Role of Small RNA in Biomass Deposition (Final Report for ER65039) ↗

  2015
  not yet assessed
• Data from: The genomes of two key bumblebee species with primitive eusocial organisation ↗

  ePrints Soton (University of Southampton) · 2015
  not yet assessed
• Additional files-1

  2015
  not yet assessed
• Addtional files-2

  2015
  not yet assessed
• RAD tag (SgrAI) derived SNPs from Bombus impatiens ↗

  DRYAD · 2015
  not yet assessed
• Sadd et al 2015 GenomeBiol

  2015
  not yet assessed
• Finding the missing honey bee genes: lessons learned from a genome upgrade ↗

  BMC Genomics · 2014 · PMID 24479613
  not yet assessed
• A survey of the small RNA population during far-red light-induced apical hook opening ↗

  Frontiers in Plant Science · 2014 · PMID 24808898
  not yet assessed
• The Basic Helix-Loop-Helix Transcription Factor Family in the Sacred Lotus, Nelumbo Nucifera ↗

  Tropical Plant Biology · 2014
  not yet assessed
• Effects of Selective Genetic Introgression from Wild Soybean to Soybean ↗

  Crop Science · 2014
  not yet assessed
• Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.) ↗

  Genome biology · 2013 · PMID 23663246
  not yet assessed
• Nelumbo nucifera [data set]

  Research Online (University of Wollongong) · 2013
  not yet assessed
• Intronic Non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees ↗

  BMC Genomics · 2013 · PMID 24079845
  not yet assessed
• A detailed gene expression study of the Miscanthusgenus reveals changes in the transcriptome associated with the rejuvenation of spring rhizomes ↗

  BMC Genomics · 2013 · PMID 24320546
  not yet assessed
• mBLAST: Keeping up with the Sequencing Explosion for (Meta) Genome

  2013
  not yet assessed
• Copy Number Variation of Multiple Genes at Rhg1 Mediates Nematode Resistance in Soybean ↗

  Science · 2012 · PMID 23065905
  not yet assessed
• Repeat associated small RNAs vary among parents and following hybridization in maize ↗

  Proceedings of the National Academy of Sciences · 2012 · PMID 22689990
  not yet assessed
• A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy ↗

  BMC Genomics · 2012 · PMID 22524439
  not yet assessed
• The Inheritance Pattern of 24 nt siRNA Clusters in Arabidopsis Hybrids Is Influenced by Proximity to Transposable Elements ↗

  PLoS ONE · 2012 · PMID 23118865
  not yet assessed
• Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max ↗

  BMC Plant Biology · 2012 · PMID 23031057
  not yet assessed
• Rapid Genotyping of Soybean Cultivars Using High Throughput Sequencing ↗

  PLoS ONE · 2011 · PMID 21949759
  not yet assessed
• Development of microsatellite markers in autopolyploid sugarcane and comparative analysis of conserved microsatellites in sorghum and sugarcane ↗

  Molecular Breeding · 2011
  not yet assessed
• Rapid, Organ-Specific Transcriptional Responses to Light Regulate Photomorphogenic Development in Dicot Seedlings ↗

  PLANT PHYSIOLOGY · 2011 · PMID 21653191
  not yet assessed
• Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes ↗

  BMC Genomics · 2010 · PMID 20416060
  not yet assessed
• Brain transcriptomic analysis in paper wasps identifies genes associated with behaviour across social insect lineages ↗

  Proceedings of the Royal Society B Biological Sciences · 2010 · PMID 20236980
  not yet assessed
• Genomic and small RNA sequencing of Miscanthus × giganteusshows the utility of sorghum as a reference genome sequence for Andropogoneae grasses ↗

  Genome biology · 2010 · PMID 20128909
  not yet assessed
• Fine mapping of the soybean aphid-resistance gene Rag2 in soybean PI 200538 ↗

  Theoretical and Applied Genetics · 2010 · PMID 20454773
  not yet assessed
• A Fluorescence in Situ Hybridization System for Karyotyping Soybean ↗

  Genetics · 2010 · PMID 20421607
  not yet assessed
• Endogenous, Tissue-Specific Short Interfering RNAs Silence the Chalcone Synthase Gene Family in Glycine max Seed Coats ↗

  The Plant Cell · 2009 · PMID 19820189
  not yet assessed
• Sympatric ecological speciation meets pyrosequencing: sampling the transcriptome of the apple maggot Rhagoletis pomonella ↗

  BMC Genomics · 2009 · PMID 20035631
  not yet assessed
• Cytochrome P450 Monooxygenases as Reporters for Circadian-Regulated Pathways ↗

  PLANT PHYSIOLOGY · 2009 · PMID 19386812
  not yet assessed
• Fine mapping the soybean aphid resistance gene Rag1 in soybean ↗

  Theoretical and Applied Genetics · 2009 · PMID 20035316
  not yet assessed
• Residues Clustered in the Light-Sensing Knot of Phytochrome B are Necessary for Conformer-Specific Binding to Signaling Partner PIF3 ↗

  PLoS Genetics · 2009 · PMID 19165330
  not yet assessed
• Human cell toxicogenomic analysis of bromoacetic acid: A regulated drinking water disinfection by‐product ↗

  Environmental and Molecular Mutagenesis · 2009 · PMID 19753638
  not yet assessed
• Plant genomes do a balancing act ↗

  Molecular Ecology · 2009 · PMID 19457202
  not yet assessed
• A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans ↗

  Genome biology · 2008 · PMID 19000309
  not yet assessed
• Microarray‐Based Genetic Mapping Using Soybean Near‐Isogenic Lines and Generation of SNP Markers in the Rag1 Aphid‐Resistance Interval ↗

  The Plant Genome · 2008
  not yet assessed
• Genomic DNA sequence comparison between two inbred soybean cyst nematode biotypes facilitated by massively parallel 454 micro-bead sequencing ↗

  Molecular Genetics and Genomics · 2008 · PMID 18324416
  not yet assessed
• Sequencing breakthroughs for genomic ecology and evolutionary biology ↗

  Molecular Ecology Resources · 2007 · PMID 21585713
  not yet assessed
• Wasp Gene Expression Supports an Evolutionary Link Between Maternal Behavior and Eusociality ↗

  Science · 2007 · PMID 17901299
  not yet assessed
• Mechanical Stress Induces Biotic and Abiotic Stress Responses via a Novel cis-Element ↗

  PLoS Genetics · 2007 · PMID 17953483
  not yet assessed
• Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey ↗

  BMC Genomics · 2007 · PMID 17524145
  not yet assessed
• Analysis of Gene Expression during Brassica Seed Germination Using a Cross‐Species Microarray Platform ↗

  Crop Science · 2007
  not yet assessed
• Contribution of transcriptional regulation to natural variations in Arabidopsis ↗

  Genome biology · 2005 · PMID 15833119
  not yet assessed
• Mechanical stress induces biotic and abiotic stress responses via a novel cis-element ↗

  PLoS Genetics · 2005
  not yet assessed
• PHYTOCHROME-INTERACTING FACTOR 1 Is a Critical bHLH Regulator of Chlorophyll Biosynthesis ↗

  Science · 2004 · PMID 15448264
  not yet assessed
• Expression profiling of phyB mutant demonstrates substantial contribution of other phytochromes to red‐light‐regulated gene expression during seedling de‐etiolation ↗

  The Plant Journal · 2004 · PMID 15144375
  not yet assessed
• Identification of Promoter Motifs Involved in the Network of Phytochrome A-Regulated Gene Expression by Combined Analysis of Genomic Sequence and Microarray Data ↗

  PLANT PHYSIOLOGY · 2003 · PMID 14681527
  not yet assessed
• The FHY3 and FAR1 genes encode transposase‐related proteins involved in regulation of gene expression by the phytochrome A‐signaling pathway ↗

  The Plant Journal · 2003 · PMID 12753585
  not yet assessed
• Identification of nutrient partitioning genes participating in rice grain filling by singular value decomposition (SVD) of genome expression data ↗

  BMC Genomics · 2003 · PMID 12854976
  not yet assessed
• The genetics of phytochrome signalling in Arabidopsis ↗

  Seminars in Cell and Developmental Biology · 2000 · PMID 11145877
  not yet assessed
• poc1 : An Arabidopsis mutant perturbed in phytochrome signaling because of a T DNA insertion in the promoter of PIF3 , a gene encoding a phytochrome-interacting bHLH protein ↗

  Proceedings of the National Academy of Sciences · 1999 · PMID 10318970
  not yet assessed
• The phytochrome B encoded by the HLG locus of Nicotiana plumbaginifolia is required for detection of photoperiod: hlg mutants show altered regulation of flowering and circadian movement ↗

  The Plant Journal · 1998
  not yet assessed
• Nicotiana plumbaginifolia hlg mutants have a mutation in a PHYB‐type phytochrome gene: they have elongated hypocotyls in red light, but are not elongated as adult plants ↗

  The Plant Journal · 1997 · PMID 9418050
  not yet assessed
• Analysis of phytochrome function in the genus Nicotiana using mutant and transgenic plants

  Figshare · 1997
  not yet assessed