List of works - Erika Lindquist

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

scientific article published on 11 June 2018

A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing.

scientific article published on 31 March 2014

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs

scientific article

Analyses of expressed sequence tags from the maize foliar pathogen Cercospora zeae-maydis identify novel genes expressed during vegetative, infectious, and reproductive growth.

scientific article

Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential.

scientific article

Analysis of the Phlebiopsis gigantea genome, transcriptome and secretome provides insight into its pioneer colonization strategies of wood

scientific article

Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics.

scientific article published on 29 November 2012

Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies

scientific article

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 four endophytic fungi as potential consolidated bioprocessing hosts for conversion of lignocellulose into advanced biofuels

scientific article published on 12 January 2017

Chimeric plastid proteome in the Florida "red tide" dinoflagellate Karenia brevis

scientific article published on 28 July 2006

Combating a Global Threat to a Clonal Crop: Banana Black Sigatoka Pathogen Pseudocercospora fijiensis (Synonym Mycosphaerella fijiensis) Genomes Reveal Clues for Disease Control

scientific article

Comparative Genomics in Switchgrass Using 61,585 High-Quality Expressed Sequence Tags

Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma

scientific article (publication date: 2011)

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 and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists

scientific article published on 7 January 2018

Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis

scientific article published on 20 March 2012

Comparative genomics of biotechnologically important yeasts

scientific article

Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88 ⬇️

scientific article

Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum

scientific article

Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize

scientific article

Comparative genomics of xylose-fermenting fungi for enhanced biofuel production

scientific article

Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus.

scientific article

Comparative genomics, proteomics and transcriptomics give new insight into the exoproteome of the basidiomycete Hebeloma cylindrosporum and its involvement in ectomycorrhizal symbiosis.

scientific article

Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists

scientific article

Correction: Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

scientific article

Correction: The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry

scientific article published on 22 December 2015

Degradation of Bunker C Fuel Oil by White-Rot Fungi in Sawdust Cultures Suggests Potential Applications in Bioremediation

scientific article published on 25 June 2015

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

scientific article

Discovery and annotation of small proteins using genomics, proteomics, and computational approaches

scientific article

Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi

scientific article published on 6 December 2012

Draft Genome Sequence of Tuber borchii Vittad., a Whitish Edible Truffle.

scientific article

Draft Nuclear Genome Sequence of the Halophilic and Beta-Carotene-Accumulating Green Alga Dunaliella salina Strain CCAP19/18.

scientific article published on 26 October 2017

Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum.

scientific article

Erratum: Genome sequence of the palaeopolyploid soybean

scientific article published in Nature

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.

scientific article published on 16 January 2017

Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication

scientific article

Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments

scientific article

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

scientific article

Feathermoss and epiphytic Nostoc cooperate differently: expanding the spectrum of plant-cyanobacteria symbiosis

scientific article published on 11 August 2017

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

scientific article

Fungal and plant gene expression in the Tulasnella calospora-Serapias vomeracea symbiosis provides clues about nitrogen pathways in orchid mycorrhizas

scientific article published on 11 November 2016

Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage

scientific article published on 3 March 2016

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 lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis

scientific article

Genome sequence of the model mushroom Schizophyllum commune

scientific article

Genome sequence of the palaeopolyploid soybean

scientific article

Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1.

scientific article published on 17 September 2015

Genome sequencing and analysis of the model grass Brachypodium distachyon

scientific article

Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici

scientific article published on October 2012

Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion

scholarly article

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

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

scientific article

Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus

scientific article (publication date: 7 August 2012)

Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas

scientific article

Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen

scientific article

Identification of a Novel Nematotoxic Protein by Challenging the Model Mushroom Coprinopsis cinerea with a Fungivorous Nematode

scientific article

Identification of functional single nucleotide polymorphism of Populus trichocarpa PtrEPSP-TF and determination of its transcriptional effect

scientific article published on 03 January 2020

Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations.

scientific article published on 14 October 2008

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 maize pan-genome and pan-transcriptome

scientific article published on 31 January 2014

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

scientific article

MAJOR DEVELOPMENTAL REGULATORS AND THEIR EXPRESSION IN TWO CLOSELY RELATED SPECIES OF PORPHYRA (RHODOPHYTA)(1).

scientific article

Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma

scientific article

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

scientific article published on 08 July 2019

Metatranscriptomic Analyses of Diel Metabolic Functions During a Microcystis Bloom in Western Lake Erie (United States)

scientific article published on 10 September 2019

Modulation of Plant and Fungal Gene Expression Upon Cd Exposure and Symbiosis in Ericoid Mycorrhizal Vaccinium myrtillus

scientific article published on 09 March 2020

Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics

scientific article

Obligate biotrophy features unraveled by the genomic analysis of rust fungi

scientific article

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

scientific article published on 27 September 2019

Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle

scientific article published on 12 November 2018

Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants

scientific article

Porphyra (Bangiophyceae) Transcriptomes Provide Insights Into Red Algal Development And Metabolism

scientific article

Rapid evolution of coral proteins responsible for interaction with the environment

scientific article

Reference genome sequence of the model plant Setaria

scientific article

Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization

scientific article

Succession of physiological stages hallmarks the transcriptomic response of the fungus Aspergillus niger to lignocellulose

scientific article published on 13 April 2020

Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals

scientific article

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

scientific article

The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex

scientific article

The Genome of Naegleria gruberi Illuminates Early Eukaryotic Versatility

scientific article

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

scientific article

The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants

scientific article

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

scientific article

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

scientific article

The amphioxus genome and the evolution of the chordate karyotype

scientific article

The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole

scientific article published in 2021

The ecoresponsive genome of Daphnia pulex

scientific article

The ectomycorrhizal fungus Paxillus involutus converts organic matter in plant litter using a trimmed brown-rot mechanism involving Fenton chemistry

scientific article published on 30 March 2012

The genome of Eucalyptus grandis

scientific article

The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

scientific article

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

scientific article

The genome of Tetranychus urticae reveals herbivorous pest adaptations

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 xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction

scientific article

The genome of wine yeast Dekkera bruxellensis provides a tool to explore its food-related properties

scientific article published on 14 May 2012

The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry

scientific article

The porcelain crab transcriptome and PCAD, the porcelain crab microarray and sequence database.

scientific article

The transcriptome of the arbuscular mycorrhizal fungus Glomus intraradices (DAOM 197198) reveals functional tradeoffs in an obligate symbiont

scientific article

Transcriptomic response of the mycoparasitic fungus Trichoderma atroviride to the presence of a fungal prey

scientific article

Validation of two ribosomal RNA removal methods for microbial metatranscriptomics

scientific article published on 19 September 2010

Widespread adenine N6-methylation of active genes in fungi.

scientific article

List of works by Erika Lindquist

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

A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing.

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs

Analyses of expressed sequence tags from the maize foliar pathogen Cercospora zeae-maydis identify novel genes expressed during vegetative, infectious, and reproductive growth.

Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential.

Analysis of the Phlebiopsis gigantea genome, transcriptome and secretome provides insight into its pioneer colonization strategies of wood

Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics.

Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies

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

Characterization of four endophytic fungi as potential consolidated bioprocessing hosts for conversion of lignocellulose into advanced biofuels

Chimeric plastid proteome in the Florida "red tide" dinoflagellate Karenia brevis

Combating a Global Threat to a Clonal Crop: Banana Black Sigatoka Pathogen Pseudocercospora fijiensis (Synonym Mycosphaerella fijiensis) Genomes Reveal Clues for Disease Control

Comparative Genomics in Switchgrass Using 61,585 High-Quality Expressed Sequence Tags

Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma

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

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

Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists

Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis

Comparative genomics of biotechnologically important yeasts

Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88 ⬇️

Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum

Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize

Comparative genomics of xylose-fermenting fungi for enhanced biofuel production

Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus.

Comparative genomics, proteomics and transcriptomics give new insight into the exoproteome of the basidiomycete Hebeloma cylindrosporum and its involvement in ectomycorrhizal symbiosis.

Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists

Correction: Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

Correction: The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry

Degradation of Bunker C Fuel Oil by White-Rot Fungi in Sawdust Cultures Suggests Potential Applications in Bioremediation

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

Discovery and annotation of small proteins using genomics, proteomics, and computational approaches

Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi

Draft Genome Sequence of Tuber borchii Vittad., a Whitish Edible Truffle.

Draft Nuclear Genome Sequence of the Halophilic and Beta-Carotene-Accumulating Green Alga Dunaliella salina Strain CCAP19/18.

Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum.

Erratum: Genome sequence of the palaeopolyploid soybean

Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.

Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication

Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments

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

Feathermoss and epiphytic Nostoc cooperate differently: expanding the spectrum of plant-cyanobacteria symbiosis

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

Fungal and plant gene expression in the Tulasnella calospora-Serapias vomeracea symbiosis provides clues about nitrogen pathways in orchid mycorrhizas

Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage

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

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

Genome sequence of the model mushroom Schizophyllum commune

Genome sequence of the palaeopolyploid soybean

Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1.

Genome sequencing and analysis of the model grass Brachypodium distachyon

Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici

Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion

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

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

Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus

Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas

Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen

Identification of a Novel Nematotoxic Protein by Challenging the Model Mushroom Coprinopsis cinerea with a Fungivorous Nematode

Identification of functional single nucleotide polymorphism of Populus trichocarpa PtrEPSP-TF and determination of its transcriptional effect

Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations.

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

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

Insights into the maize pan-genome and pan-transcriptome

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

MAJOR DEVELOPMENTAL REGULATORS AND THEIR EXPRESSION IN TWO CLOSELY RELATED SPECIES OF PORPHYRA (RHODOPHYTA)(1).

Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma

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

Metatranscriptomic Analyses of Diel Metabolic Functions During a Microcystis Bloom in Western Lake Erie (United States)

Modulation of Plant and Fungal Gene Expression Upon Cd Exposure and Symbiosis in Ericoid Mycorrhizal Vaccinium myrtillus

Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics

Obligate biotrophy features unraveled by the genomic analysis of rust fungi

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

Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle

Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants

Porphyra (Bangiophyceae) Transcriptomes Provide Insights Into Red Algal Development And Metabolism

Rapid evolution of coral proteins responsible for interaction with the environment

Reference genome sequence of the model plant Setaria

Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization

Succession of physiological stages hallmarks the transcriptomic response of the fungus Aspergillus niger to lignocellulose