List of works - Scott E. Baker

A comparative genomics study of 23 Aspergillus species from section Flavi

scientific article published on 27 February 2020

A molecular genetic toolbox for Yarrowia lipolytica

scientific article published on 03 January 2017

A parts list for fungal cellulosomes revealed by comparative genomics

scientific article published on 30 May 2017

Activation of an AP1-like transcription factor of the maize pathogen Cochliobolus heterostrophus in response to oxidative stress and plant signals.

scientific article published on February 2005

Anaerobic fungi: Neocallimastigomycota

scientific article (publication date: December 2010)

Analytical and computational approaches to define the Aspergillus niger secretome

scientific article published on 01 March 2009

Biomarker candidate identification in Yersinia pestis using organism-wide semiquantitative proteomics

scientific article

Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in Aspergillus nidulans.

scientific article published on 22 March 2018

Characterization of a polyketide synthase in Aspergillus niger whose product is a precursor for both dihydroxynaphthalene (DHN) melanin and naphtho-γ-pyrone ⬇️

scientific article

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

scientific article

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

scientific article

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

scientific article

Compartmentalized microchannel array for high-throughput analysis of single cell polarized growth and dynamics.

scientific article

Comprehensive Metabolomic, Lipidomic and Microscopic Profiling of Yarrowia lipolytica during Lipid Accumulation Identifies Targets for Increased Lipogenesis

scientific article

Dichomitus squalens partially tailors its molecular responses to the composition of solid wood

scientific article published on 18 October 2018

Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era

scientific article published on 17 February 2017

Draft Genome Sequence of Neurospora crassa Strain FGSC 73.

scientific article

Draft Genome Sequence of the Dimorphic Yeast Yarrowia lipolytica Strain W29.

scientific article

Erratum to: Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype.

scientific article published on 22 September 2015

Erratum: Corrigendum: Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

scholarly article published in Nature Biotechnology

Essential pathway identification: from in silico analysis to potential antifungal targets in Aspergillus fumigatus

scientific article published on 27 February 2009

Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication

scientific article

Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger

scientific article

Expression of naturally ionic liquid-tolerant thermophilic cellulases in Aspergillus niger

scientific article published on 27 December 2017

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

scientific article

Forward genetics screen coupled with whole-genome resequencing identifies novel gene targets for improving heterologous enzyme production in Aspergillus niger

scientific article published on 6 January 2018

Fungal Ligninolytic Enzymes and Their Applications.

scientific article published on December 2016

Genetic and genomic dissection of the Cochliobolus heterostrophus Tox1 locus controlling biosynthesis of the polyketide virulence factor T-toxin.

scientific article published on January 2007

Genome Sequence and Annotation of Trichoderma parareesei, the Ancestor of the Cellulase Producer Trichoderma reesei.

scientific article

Genome Sequence of the Mucoromycotina Fungus Umbelopsis isabellina, an Effective Producer of Lipids.

scientific article published on 27 February 2014

Genome sequence of the model mushroom Schizophyllum commune

scientific article

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

scientific article

Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction.

scientific article published on 7 September 2017

Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype

scientific article

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

scholarly article

Harnessing glycosylation to improve cellulase activity

scientific article published on 18 December 2011

High resolution visualization and exo-proteomics reveal the physiological role of XlnR and AraR in plant biomass colonization and degradation by Aspergillus niger

scientific article published on 13 October 2017

Identification and characterization of the polyketide synthase involved in ochratoxin A biosynthesis in Aspergillus carbonarius.

scientific article

Identification of a Classical Mutant in the Industrial Host Aspergillus niger by Systems Genetics: LaeA Is Required for Citric Acid Production and Regulates the Formation of Some Secondary Metabolites

scientific article

Impact of alg3 gene deletion on growth, development, pigment production, protein secretion, and functions of recombinant Trichoderma reesei cellobiohydrolases in Aspergillus niger

scientific article published on 25 September 2013

Increased production of fatty acids and triglycerides in Aspergillus oryzae by enhancing expressions of fatty acid synthesis-related genes.

scientific article published on 26 June 2012

Increased production of free fatty acids in Aspergillus oryzae by disruption of a predicted acyl-CoA synthetase gene.

scientific article published on 8 January 2015

Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri

article

Laminin-5 and modulation of keratin cytoskeleton arrangement in FG pancreatic carcinoma cells: involvement of IFAP300 and evidence that laminin-5/cell interactions correlate with a dephosphorylation of alpha 6A integrin

scientific article published on 01 January 1997

Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica

scientific article

Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species ⬇️

scientific article published on 9 January 2018

Mapping N-linked glycosylation sites in the secretome and whole cells of Aspergillus niger using hydrazide chemistry and mass spectrometry.

scientific article

Mixed-Effects Statistical Model for Comparative LC−MS Proteomics Studies†

article

Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica

scientific article

Multimodal microchannel and nanowell-based microfluidic platforms for bioimaging

Multimodal microfluidic platform for controlled culture and analysis of unicellular organisms

scientific article published on 19 September 2017

Mycotoxins: A Fungal Genomics Perspective

scientific article published on January 2017

Non-steady state mass action dynamics without rate constants: dynamics of coupled reactions using chemical potentials

scientific article published on 4 July 2017

Novel hydrophobins from Trichoderma define a new hydrophobin subclass: protein properties, evolution, regulation and processing.

scientific article

Ochratoxin A production by Penicillium thymicola

scientific article published on 12 April 2016

Omics Analyses of Trichoderma reesei CBS999.97 and QM6a Indicate the Relevance of Female Fertility to Carbohydrate-Active Enzyme and Transporter Levels

scientific article published on 15 September 2017

One fungus, one name: defining the genus Fusarium in a scientifically robust way that preserves longstanding use.

scientific article published in May 2013

Phylogenomic and functional domain analysis of polyketide synthases in Fusarium.

scientific article published on 19 December 2011

Post-genomic approaches to understanding interactions between fungi and their environment.

scientific article

Prediction of Metabolite Concentrations, Rate Constants and Post-Translational Regulation Using Maximum Entropy-Based Simulations with Application to Central Metabolism of Neurospora crassa

Protein hyperproduction in fungi by design

scientific article published in 2018

Proteome studies of filamentous fungi.

scientific article

Proteomics for Validation of Automated Gene Model Predictions

article

Purifying selection and birth-and-death evolution in the class II hydrophobin gene families of the ascomycete Trichoderma/Hypocrea

scientific article

Re-routing of Sugar Catabolism Provides a Better Insight Into Fungal Flexibility in Using Plant Biomass-Derived Monomers as Substrates

scientific article published on 08 March 2021

Rediscovery by Whole Genome Sequencing: Classical Mutations and Genome Polymorphisms in Neurospora crassa.

scientific article published on September 2011

Regulation of Nitrogen Metabolism by GATA Zinc Finger Transcription Factors in Yarrowia lipolytica

scientific article published on January 2017

Regulation of Yeast-to-Hyphae Transition in Yarrowia lipolytica

scientific article published in 2018

Resin-assisted enrichment of N-terminal peptides for characterizing proteolytic processing.

scientific article published on 27 June 2013

Sequencing the fungal tree of life

scientific article published on 14 March 2011

Structural analysis of N- and O-glycans using ZIC-HILIC/dialysis coupled to NMR detection

scientific article published on 10 August 2014

Structural reorganization of the fungal endoplasmic reticulum upon induction of mycotoxin biosynthesis

scientific article

The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization

scientific article

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

scientific article published on 10 February 2016

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

scientific article

The mitochondrial genome of the ethanol-metabolizing, wine cellar mold Zasmidium cellare is the smallest for a filamentous ascomycete.

scientific article

The polyketide synthase gene pks4 of Trichoderma reesei provides pigmentation and stress resistance.

scientific article published on 13 September 2013

The production of multiple small peptaibol families by single 14-module Peptide synthetases in Trichoderma/Hypocrea.

scientific article published in March 2012

The putative protein methyltransferase LAE1 controls cellulase gene expression in Trichoderma reesei.

scientific article

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

scientific article

Two Polyketide Synthase-Encoding Genes Are Required for Biosynthesis of the Polyketide Virulence Factor, T-toxin, byCochliobolus heterostrophus

article

period-1 encodes an ATP-dependent RNA helicase that influences nutritional compensation of the Neurospora circadian clock

scientific article

List of works by Scott E. Baker

A comparative genomics study of 23 Aspergillus species from section Flavi

A molecular genetic toolbox for Yarrowia lipolytica

A parts list for fungal cellulosomes revealed by comparative genomics

Activation of an AP1-like transcription factor of the maize pathogen Cochliobolus heterostrophus in response to oxidative stress and plant signals.

Anaerobic fungi: Neocallimastigomycota

Analytical and computational approaches to define the Aspergillus niger secretome

Biomarker candidate identification in Yersinia pestis using organism-wide semiquantitative proteomics

Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in Aspergillus nidulans.

Characterization of a polyketide synthase in Aspergillus niger whose product is a precursor for both dihydroxynaphthalene (DHN) melanin and naphtho-γ-pyrone ⬇️

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

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

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

Compartmentalized microchannel array for high-throughput analysis of single cell polarized growth and dynamics.

Comprehensive Metabolomic, Lipidomic and Microscopic Profiling of Yarrowia lipolytica during Lipid Accumulation Identifies Targets for Increased Lipogenesis

Dichomitus squalens partially tailors its molecular responses to the composition of solid wood

Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era

Draft Genome Sequence of Neurospora crassa Strain FGSC 73.

Draft Genome Sequence of the Dimorphic Yeast Yarrowia lipolytica Strain W29.

Erratum to: Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype.

Erratum: Corrigendum: Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

Essential pathway identification: from in silico analysis to potential antifungal targets in Aspergillus fumigatus

Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication

Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger

Expression of naturally ionic liquid-tolerant thermophilic cellulases in Aspergillus niger

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

Forward genetics screen coupled with whole-genome resequencing identifies novel gene targets for improving heterologous enzyme production in Aspergillus niger

Fungal Ligninolytic Enzymes and Their Applications.

Genetic and genomic dissection of the Cochliobolus heterostrophus Tox1 locus controlling biosynthesis of the polyketide virulence factor T-toxin.

Genome Sequence and Annotation of Trichoderma parareesei, the Ancestor of the Cellulase Producer Trichoderma reesei.

Genome Sequence of the Mucoromycotina Fungus Umbelopsis isabellina, an Effective Producer of Lipids.

Genome sequence of the model mushroom Schizophyllum commune

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

Genome sequencing and transcriptome analysis of Trichoderma reesei QM9978 strain reveals a distal chromosome translocation to be responsible for loss of vib1 expression and loss of cellulase induction.

Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype

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

Harnessing glycosylation to improve cellulase activity

High resolution visualization and exo-proteomics reveal the physiological role of XlnR and AraR in plant biomass colonization and degradation by Aspergillus niger

Identification and characterization of the polyketide synthase involved in ochratoxin A biosynthesis in Aspergillus carbonarius.

Identification of a Classical Mutant in the Industrial Host Aspergillus niger by Systems Genetics: LaeA Is Required for Citric Acid Production and Regulates the Formation of Some Secondary Metabolites

Impact of alg3 gene deletion on growth, development, pigment production, protein secretion, and functions of recombinant Trichoderma reesei cellobiohydrolases in Aspergillus niger

Increased production of fatty acids and triglycerides in Aspergillus oryzae by enhancing expressions of fatty acid synthesis-related genes.

Increased production of free fatty acids in Aspergillus oryzae by disruption of a predicted acyl-CoA synthetase gene.

Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri

Laminin-5 and modulation of keratin cytoskeleton arrangement in FG pancreatic carcinoma cells: involvement of IFAP300 and evidence that laminin-5/cell interactions correlate with a dephosphorylation of alpha 6A integrin

Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica

Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species ⬇️

Mapping N-linked glycosylation sites in the secretome and whole cells of Aspergillus niger using hydrazide chemistry and mass spectrometry.

Mixed-Effects Statistical Model for Comparative LC−MS Proteomics Studies†

Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica

Multimodal microchannel and nanowell-based microfluidic platforms for bioimaging

Multimodal microfluidic platform for controlled culture and analysis of unicellular organisms

Mycotoxins: A Fungal Genomics Perspective

Non-steady state mass action dynamics without rate constants: dynamics of coupled reactions using chemical potentials

Novel hydrophobins from Trichoderma define a new hydrophobin subclass: protein properties, evolution, regulation and processing.

Ochratoxin A production by Penicillium thymicola

Omics Analyses of Trichoderma reesei CBS999.97 and QM6a Indicate the Relevance of Female Fertility to Carbohydrate-Active Enzyme and Transporter Levels

One fungus, one name: defining the genus Fusarium in a scientifically robust way that preserves longstanding use.

Phylogenomic and functional domain analysis of polyketide synthases in Fusarium.

Post-genomic approaches to understanding interactions between fungi and their environment.

Prediction of Metabolite Concentrations, Rate Constants and Post-Translational Regulation Using Maximum Entropy-Based Simulations with Application to Central Metabolism of Neurospora crassa

Protein hyperproduction in fungi by design

Proteome studies of filamentous fungi.

Proteomics for Validation of Automated Gene Model Predictions

Purifying selection and birth-and-death evolution in the class II hydrophobin gene families of the ascomycete Trichoderma/Hypocrea

Re-routing of Sugar Catabolism Provides a Better Insight Into Fungal Flexibility in Using Plant Biomass-Derived Monomers as Substrates

Rediscovery by Whole Genome Sequencing: Classical Mutations and Genome Polymorphisms in Neurospora crassa.

Regulation of Nitrogen Metabolism by GATA Zinc Finger Transcription Factors in Yarrowia lipolytica

Regulation of Yeast-to-Hyphae Transition in Yarrowia lipolytica

Resin-assisted enrichment of N-terminal peptides for characterizing proteolytic processing.

Sequencing the fungal tree of life

Structural analysis of N- and O-glycans using ZIC-HILIC/dialysis coupled to NMR detection

Structural reorganization of the fungal endoplasmic reticulum upon induction of mycotoxin biosynthesis

The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

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

The mitochondrial genome of the ethanol-metabolizing, wine cellar mold Zasmidium cellare is the smallest for a filamentous ascomycete.