List of works by Jeremy Schmutz

A 5-Enolpyruvylshikimate 3-Phosphate Synthase Functions as a Transcriptional Repressor in Populus

scientific article published on 11 June 2018

A Variable Polyglutamine Repeat Affects Subcellular Localization and Regulatory Activity of a ANGUSTIFOLIA Protein

scientific article published on 31 July 2018

A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis

scientific article published on 10 April 2019

A generalist-specialist trade-off between switchgrass cytotypes impacts climate adaptation and geographic range

scientific article published on 04 April 2022

A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa

scientific article published on 06 October 2020

A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci

scientific article published on 05 October 2020

A genome-wide SNP genotyping array reveals patterns of global and repeated species-pair divergence in sticklebacks

scientific article

A genome-wide survey of switchgrass genome structure and organization

scientific article

A mosaic monoploid reference sequence for the highly complex genome of sugarcane.

scientific article published on 6 July 2018

A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism

article

A physical map of the highly heterozygous Populus genome: integration with the genome sequence and genetic map and analysis of haplotype variation

article

A physical map of the human genome

scientific article

A reference genome for common bean and genome-wide analysis of dual domestications

scientific article published on 8 June 2014

A role for a neo-sex chromosome in stickleback speciation

scientific article published on 27 September 2009

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

scientific article

A willow sex chromosome reveals convergent evolution of complex palindromic repeats

scientific article published on 14 February 2020

Adaptation to heavy-metal contaminated environments proceeds via selection on pre-existing genetic variation

Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer

scientific article

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs

scientific article

Amplification and adaptation of centromeric repeats in polyploid switchgrass species.

scientific article published on 25 March 2018

Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ).

scientific article

Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta

scientific article published on 21 June 2019

Annotation of the Corymbia terpene synthase gene family shows broad conservation but dynamic evolution of physical clusters relative to Eucalyptus

article

Assembly of DNA sequencing data

scientific article

Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes.

scientific article published on 28 March 2018

Assembly of the threespine stickleback Y chromosome reveals convergent signatures of sex chromosome evolution

scientific article published on 19 July 2020

Association mapping, transcriptomics, and transient expression identify candidate genes mediating plant-pathogen interactions in a tree

article published in the Proceedings of the National Academy of Sciences of the United States of America

Characterization of a large sex determination region in Salix purpurea L. (Salicaceae)

scientific article published on 18 July 2018

Coding potential of laboratory and clinical strains of human cytomegalovirus

scientific article

Coelacanth genome sequence reveals the evolutionary history of vertebrate genes

scientific article (publication date: December 2004)

Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens

scientific article

Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris

scientific article

Comparative genomics analysis of drought response between obligate CAM and C3 photosynthesis plants

scientific article published in 2022

Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum

scientific article

Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome

scientific article (publication date: 23 February 2010)

Complete genome sequence of Polynucleobacter necessarius subsp. asymbioticus type strain (QLW-P1DMWA-1(T)).

scientific article

Complete genome sequence of Rhodospirillum rubrum type strain (S1).

scientific article

Complete genome sequence of Tolumonas auensis type strain (TA 4)

scientific article published on 23 September 2011

Complete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114-95(T)).

scientific article

Complete genome sequence of the halophilic and highly halotolerant Chromohalobacter salexigens type strain (1H11(T)).

scientific article

Complete plastome sequences from Glycine syndetika and six additional perennial wild relatives of soybean

scientific article

Construction and comparison of three reference-quality genome assemblies for soybean

scientific article published on 28 October 2019

Correction to: Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta

scientific article published on 09 August 2019

Deeply conserved synteny resolves early events in vertebrate evolution

scientific article published on 20 April 2020

Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L.).

scientific article

Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs.

scientific article published on 20 January 2017

Divergent selection and climate adaptation fuel genomic differentiation between sister species of <i>Sphagnum</i> (peat moss)

scientific article published in 2023

Draft Nuclear Genome Sequence of the Liquid Hydrocarbon-Accumulating Green Microalga Botryococcus braunii Race B (Showa)

scientific article

Empty Niches after Extinctions Increase Population Sizes of Modern Corals

scientific article

Environmentally responsive QTL controlling surface wax load in switchgrass

scientific article published on 14 August 2020

Erratum: Genome sequence of the palaeopolyploid soybean

scientific article published in Nature

Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants

scientific article

Evolution of an expanded sex-determining locus in Volvox

scientific article

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.

scientific article published on 16 January 2017

Evolving New Skeletal Traits by cis-Regulatory Changes in Bone Morphogenetic Proteins

scientific journal article

Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication

scientific article

Exploring the loblolly pine (Pinus taeda L.) genome by BAC sequencing and Cot analysis.

scientific article published on 12 April 2018

Extensive linkage disequilibrium, a common 16.7-kilobase deletion, and evidence of balancing selection in the human protocadherin alpha cluster

scientific article

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

scientific article

Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence

scientific article published on 08 October 2019

Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing

scientific article

Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis

scientific article

GENESPACE tracks regions of interest and gene copy number variation across multiple genomes

scientific article published in 2022

Gene conversion and the evolution of protocadherin gene cluster diversity

scientific article published on March 2004

Generation and annotation of the DNA sequences of human chromosomes 2 and 4

scientific article

Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences

scientific article

Genetic Analysis of Physcomitrella patens Identifies ABSCISIC ACID NON-RESPONSIVE, a Regulator of ABA Responses Unique to Basal Land Plants and Required for Desiccation Tolerance. ⬇️

scientific article

Genetic architecture of variation in the lateral line sensory system of threespine sticklebacks.

scientific article

Genetic dissection of natural variation in oilseed traits of camelina by whole‐genome resequencing and QTL mapping

scientific article published in 2021

Genome Analysis of Planctomycetes Inhabiting Blades of the Red Alga Porphyra umbilicalis

scientific article

Genome Sequence of the ethene- and vinyl chloride-oxidizing actinomycete Nocardioides sp. strain JS614

scientific article

Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet

scientific article published in 2023

Genome biology of the paleotetraploid perennial biomass crop Miscanthus

scientific article published on 28 October 2020

Genome evolution in the allotetraploid frog Xenopus laevis

scientific article

Genome mapping of quantitative trait loci (QTL) controlling domestication traits of intermediate wheatgrass (Thinopyrum intermedium)

scientific article published on 06 June 2019

Genome organization of the vg1 and nodal3 gene clusters in the allotetraploid frog Xenopus laevis.

scientific article

Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche

scientific article published on 8 October 2012

Genome sequence of the chestnut blight fungus Cryphonectria parasitica EP155: A fundamental resource for an archetypical invasive plant pathogen

scientific article published on 24 March 2020

Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis

scientific article

Genome sequence of the model mushroom Schizophyllum commune

scientific article

Genome sequence of the model rice variety KitaakeX

scientific article published on 27 November 2019

Genome sequence of the palaeopolyploid soybean

scientific article

Genome sequence of the verrucomicrobium Opitutus terrae PB90-1, an abundant inhabitant of rice paddy soil ecosystems

scientific article

Genome sequencing and analysis of the model grass Brachypodium distachyon

scientific article

Genome-Wide Association Study Identifies Candidate Loci Underlying Agronomic Traits in a Middle American Diversity Panel of Common Bean

scientific article published on 01 November 2016

Genome-wide association studies and expression-based quantitative trait loci analyses reveal roles of HCT2 in caffeoylquinic acid biosynthesis and its regulation by defense-responsive transcription factors in Populus

scientific article published on 11 July 2018

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.

scientific article

Genomes: fowl sequence

scientific article published on 01 December 2004

Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri

scientific article

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

scientific article published on 20 April 2020

Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass

scientific article published on 27 January 2021

Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors

scientific article published on 29 July 2020

Habitat‐adapted microbial communities mediate <i>Sphagnum</i> peatmoss resilience to warming

scientific article published in 2022

Hardwood Tree Genomics: Unlocking Woody Plant Biology

article

Hemichordate genomes and deuterostome origins

scientific article

High Density Genetic Maps of Seashore Paspalum Using Genotyping-By-Sequencing and Their Relationship to The Sorghum Bicolor Genome

scientific article published on 21 August 2019

Hybridization History and Repetitive Element Content in the Genome of a Homoploid Hybrid, <i>Yucca gloriosa</i> (Asparagaceae)

scientific article published on 01 January 2020

Initial sequencing and analysis of the human genome

scientific article published on 15 February 2001

Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen

scientific article published on 28 March 2012

Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome.

scientific article

Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta)

scientific article

Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response

scientific article

Integrative genomics reveals paths to sex dimorphism in Salix purpurea L

scientific article published on 01 August 2021

Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoë fedtschenkoi, a plant with crassulacean acid metabolism

scientific article published on 01 March 2020

Long-read sequence assembly: a technical evaluation in barley

scientific article published on 01 July 2021

Marker-free carotenoid-enriched rice generated through targeted gene insertion using CRISPR-Cas9

scientific article published on 04 March 2020

Mediation of plant-mycorrhizal interaction by a lectin receptor-like kinase

scientific article published on 08 July 2019

Multi-Phenotype Association Decomposition: Unraveling Complex Gene-Phenotype Relationships

article

Newly identified sex chromosomes in the Sphagnum (peat moss) genome alter carbon sequestration and ecosystem dynamics

scientific article published in 2023

Novel metabolic interactions and environmental conditions mediate the boreal peatmoss-cyanobacteria mutualism

scientific article published on 29 November 2021

Obligate biotrophy features unraveled by the genomic analysis of rust fungi

scientific article

On the origin and evolutionary consequences of gene body DNA methylation

scientific article published on 25 July 2016

Optimizing genomic selection for blight resistance in American chestnut backcross populations: A trade-off with American chestnut ancestry implies resistance is polygenic

scientific article published on 29 December 2019

Overexpression of a Prefoldin β subunit gene reduces biomass recalcitrance in the bioenergy crop Populus

scientific article published on 27 September 2019

PEATmoss (Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens

scientific article published on 12 November 2019

Predicted structural proteome of <i>Sphagnum divinum</i> and proteome-scale annotation

scientific article published in 2023

Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization.

scientific article published on 28 March 2018

Publisher correction: Young inversion with multiple linked QTLs under selection in a hybrid zone

scientific article published on 01 October 2017

QTL × environment interactions underlie adaptive divergence in switchgrass across a large latitudinal gradient

scientific article published on 10 June 2019

Quality assessment of finished BAC sequences

scientific article published in January 2004

Quality assessment of the human genome sequence

scientific article

Reference genome sequence of the model plant Setaria

scientific article

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.

scientific article published in December 2012

Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment

scientific article published on 26 January 2024

Sequence finishing

scientific article published on 01 January 2004

Sequence-Based Introgression Mapping Identifies Candidate White Mold Tolerance Genes in Common Bean

scientific article published on July 2016

Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa

scientific article published on 24 July 2020

Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling

scientific article

Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome

scientific article published on 07 August 2015

Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

scientific article (publication date: July 2014)

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

scientific article published on 18 April 2016

Six is seventh

scientific article published in Nature

Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids.

scientific article

The Aquilegia genome: adaptive radiation and an extraordinarily polymorphic chromosome with a unique history

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

scientific article

The Capsella rubella genome and the genomic consequences of rapid mating system evolution

scientific article

The Chlamydomonas genome project: a decade on.

scientific article

The Chlamydomonas genome reveals the evolution of key animal and plant functions

scientific article

The DNA sequence and biology of human chromosome 19

scientific article

The DNA sequence and comparative analysis of human chromosome 5

scientific article

The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism

scientific article

The P. patens chromosome-scale assembly reveals moss genome structure and evolution. ⬇️

scientific article

The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes

scientific article

The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity

scientific article

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

scientific article

The Physcomitrella patens gene atlas project: large scale RNA-seq based expression data.

scientific article published on 22 April 2018

The Plant Cell Wall-Decomposing Machinery Underlies the Functional Diversity of Forest Fungi

scientific article

The Reference Genome of the Halophytic Plant Eutrema salsugineum

scientific article (publication date: 2013)

The Selaginella genome identifies genetic changes associated with the evolution of vascular plants

scientific article

The Sorghum bicolor genome and the diversification of grasses

scientific article

The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization

scientific article published on 21 November 2017

The Trichoplax genome and the nature of placozoans

scientific article

The a genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history

scientific article published on 16 October 2018

The amphioxus genome and the evolution of the chordate karyotype

scientific article

The barley pan-genome reveals the hidden legacy of mutation breeding

scientific article published on 25 November 2020

The completion of the Mammalian Gene Collection (MGC).

scientific article published on 18 September 2009

The genetics of divergence and reproductive isolation between ecotypes of Panicum hallii

scientific article

The genome of Eucalyptus grandis

scientific article

The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion

scientific article

The genome of the Western clawed frog Xenopus tropicalis

scientific article

The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation

scientific article

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea.

scientific article published on 27 January 2016

The genome sequence of segmental allotetraploid peanut Arachis hypogaea

scientific article published on 01 May 2019

The genomic basis of adaptive evolution in threespine sticklebacks

scientific article

The genomic landscape of molecular responses to natural drought stress in Panicum hallii

scientific article published in Nature Communications

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution

scientific article

The master sex-determination locus in threespine sticklebacks is on a nascent Y chromosome

scientific article

The reference genome and abiotic stress responses of the model perennial grass <i>Brachypodium sylvaticum</i>

scientific article published in 2023

The sequence and analysis of duplication-rich human chromosome 16

scientific article

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)

scientific article

The tepary bean genome provides insight into evolution and domestication under heat stress

scientific article published on 11 May 2021

The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation

scientific article

Theria-specific homeodomain and cis-regulatory element evolution of the Dlx3-4 bigene cluster in 12 different mammalian species

scientific article published on 5 September 2012

Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles

scientific article published on 13 June 2016

Wavelet-Based Genomic Signal Processing for Centromere Identification and Hypothesis Generation.

scientific article published on 31 May 2019

Widespread natural variation of DNA methylation within angiosperms

scientific article published on 27 September 2016

Young inversion with multiple linked QTLs under selection in a hybrid zone.

scientific article

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