Trends in biological data integration for the selection of enzymes and transcription factors related to cellulose and hemicellulose degradation in fungi

Distribution of a novel enzyme of sialidase family among native filamentous fungi

(2021) Radoslav Abrashev et al.   Fungal Biology

High Quality Aspergillus aculeatus Genomes and Transcriptomes: A Platform for Cellulase Activity Optimization Toward Industrial Applications

(2021) Wuttichai Mhuantong et al.   Frontiers in Bioengineering and Biotechnology

Assessing genome assembly quality prior to downstream analysis: N50 versus BUSCO

(2021) April A. Jauhal et al.   Molecular Ecology Resources

New Method for Identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences

(2021) Lene Lange et al.   Journal of Fungi

Comparative transcriptome profiling and co-expression network analysis uncover the key genes associated withearly-stage resistance to Aspergillus flavus in maize

(2021) Huanhuan Liu et al.   BMC PLANT BIOLOGY

Aspergillus terreus as an industrial filamentous fungus for pharmaceutical biotechnology

(2021) Xuenian Huang et al.   CURRENT OPINION IN BIOTECHNOLOGY

The synergistic actions of hydrolytic genes reveal the mechanism of Trichoderma harzianum for cellulose degradation

(2021) Déborah Aires Almeida et al.   JOURNAL OF BIOTECHNOLOGY

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Closing the loop of cereal waste and residues with sustainable technologies: An overview of enzyme production via fungal solid-state fermentation

(2021) Dominika Alexa Teigiserova et al.   Sustainable Production and Consumption

A review on catalytic-enzyme degradation of toxic environmental pollutants: Microbial enzymes

(2021) A. Saravanan et al.   JOURNAL OF HAZARDOUS MATERIALS

Decoupled diversity patterns in bacteria and fungi across continental forest ecosystems

(2020) Shengen Liu et al.   SOIL BIOLOGY & BIOCHEMISTRY

Re-epithelialization and immune cell behaviour in an ex vivo human skin model

(2020) Ana Rakita et al.   Scientific Reports

Studies of Cellulose and Starch Utilization and the Regulatory Mechanisms of Related Enzymes in Fungi

(2020) Bao-Teng Wang et al.   Polymers

Bioinformatics and Computational Tools for Next-Generation Sequencing Analysis in Clinical Genetics

(2020) Rute Pereira et al.   Journal of Clinical Medicine

A Guide to Conquer the Biological Network Era Using Graph Theory

(2020) Mikaela Koutrouli et al.   Frontiers in Bioengineering and Biotechnology

Weighted Gene Co-expression Network Analysis Identifies Critical Genes for the Production of Cellulase and Xylanase in Penicillium oxalicum

(2020) Cheng-Xi Li et al.   Frontiers in Microbiology

Genome sequence of Acremonium strictum AAJ6 strain isolated from the Cerrado biome in Brazil and CAZymes expression in thermotolerant industrial yeast for ethanol production

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Diversity of Cellulase-Producing Filamentous Fungi From Tibet and Transcriptomic Analysis of a Superior Cellulase Producer Trichoderma harzianum LZ117

(2020) Jia-Xiang Li et al.   Frontiers in Microbiology

Comparative genomics of rice false smut fungi Ustilaginoidea virens Uv-Gvt strain from India reveals genetic diversity and phylogenetic divergence

(2020) Devanna Pramesh et al.   3 Biotech

Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases

(2020) Qingyu Chen et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Whole-genome sequencing of the endemic Antarctic fungus Antarctomyces pellizariae reveals an ice-binding protein, a scarce set of secondary metabolites gene clusters and provides insights on Thelebolales phylogeny

(2020) Thiago Mafra Batista et al.   GENOMICS

Biotransformation of lignocellulosic biomass into industrially relevant products with the aid of fungi-derived lignocellulolytic enzymes

(2020) Sara Saldarriaga-Hernández et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Inferring directional relationships in microbial communities using signed Bayesian networks

(2020) Musfiqur Sazal et al.   BMC GENOMICS

Recent developments of tools for genome and metabolome studies in basidiomycete fungi and their application to natural product research

(2020) Fabrizio Alberti et al.   Biology Open

Large-scale production of enzymes for biotechnology uses

(2020) Aneesa Fasim et al.   CURRENT OPINION IN BIOTECHNOLOGY

Occurrence of the potent mutagens 2- nitrobenzanthrone and 3-nitrobenzanthrone in fine airborne particles

(2019) Aldenor G. Santos et al.   Scientific Reports

SignalP 5.0 improves signal peptide predictions using deep neural networks

(2019) José Juan Almagro Armenteros et al.   NATURE BIOTECHNOLOGY

De novo genome sequencing and secretome analysis of Tilletia indica inciting Karnal bunt of wheat provides pathogenesis-related genes

(2019) Malkhan Singh Gurjar et al.   3 Biotech

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

Machine-learning-guided directed evolution for protein engineering

(2019) Kevin K. Yang et al.   NATURE METHODS

A Novel Cys2His2 Zinc Finger Homolog of AZF1 Modulates Holocellulase Expression in Trichoderma reesei

(2019) Amanda Cristina Campos Antonieto et al.   mSystems

Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community

(2019) Farhana R. Pinu et al.   Metabolites

Machine learning for discovering missing or wrong protein function annotations

(2019) Felipe Kenji Nakano et al.   BMC BIOINFORMATICS

Sequence and Structural Analysis of AA9 and AA10 LPMOs: An Insight into the Basis of Substrate Specificity and Regioselectivity

(2019) Xiaoli Zhou et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Optimization of Protease and Amylase Production by Rhizopus oryzae Cultivated on Bread Waste Using Solid-State Fermentation

(2019) Olfa Benabda et al.   Journal of Chemistry

Correction to: Comparative transcriptomics reveals PrrABmediated control of metabolic, respiration, energy-generating, and dormancy pathways in Mycobacterium smegmatis

(2019) Jason D. Maarsingh et al.   BMC GENOMICS

Engineering strategies for enhanced production of protein and bio-products in Pichia pastoris : A review

(2018) Zhiliang Yang et al.   BIOTECHNOLOGY ADVANCES

Transcriptome and secretome analysis of Aspergillus fumigatus in the presence of sugarcane bagasse

(2018) Paula Fagundes de Gouvêa et al.   BMC GENOMICS

Fungal glucuronoyl esterases: Genome mining based enzyme discovery and biochemical characterization

(2018) Adiphol Dilokpimol et al.   New Biotechnology

Structural insights into β-glucosidase transglycosylation based on biochemical, structural and computational analysis of two GH1 enzymes from Trichoderma harzianum

(2018) Renata N. Florindo et al.   New Biotechnology

Double blind microarray-based polysaccharide profiling enables parallel identification of uncharacterized polysaccharides and carbohydrate-binding proteins with unknown specificities

(2018) Armando A. Salmeán et al.   Scientific Reports

Draft genome sequence of Penicillium chrysogenum strain HKF2, a fungus with potential for production of prebiotic synthesizing enzymes

(2018) Vaibhav V. Gujar et al.   3 Biotech

Paenibacillus polymyxa ND25: candidate genome for lignocellulosic biomass utilization

(2018) Varsha Bohra et al.   3 Biotech

Draft genome sequence of Penicillium chrysogenum strain HKF2, a fungus with potential for production of prebiotic synthesizing enzymes

(2018) Vaibhav V. Gujar et al.   3 Biotech

Paenibacillus polymyxa ND25: candidate genome for lignocellulosic biomass utilization

(2018) Varsha Bohra et al.   3 Biotech

Computational Genomics of Specialized Metabolism: from Natural Product Discovery to Microbiome Ecology

(2018) Marnix H. Medema   mSystems

Genome evolution across 1,011 Saccharomyces cerevisiae isolates

(2018) Jackson Peter et al.   NATURE

New Genomic Approaches to Enhance Biomass Degradation by the Industrial Fungus Trichoderma reesei

(2018) Renato Graciano de Paula et al.   International Journal of Genomics

In-Silico Bioprospecting: Finding Better Enzymes

(2018) Asmita Kamble et al.   MOLECULAR BIOTECHNOLOGY

Strategies for Engineering Natural Product Biosynthesis in Fungi

(2018) Elizabeth Skellam   TRENDS IN BIOTECHNOLOGY

Whole-Genome Alignment and Comparative Annotation

(2018) Joel Armstrong et al.   Annual Review of Animal Biosciences

Engineering of the Filamentous Fungus Penicillium chrysogenum as Cell Factory for Natural Products

(2018) Fernando Guzmán-Chávez et al.   Frontiers in Microbiology

REVIEW-ARTICLE Bioinformatics: an overview and its applications

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Co-expression networks reveal the tissue-specific regulation of transcription and splicing

(2017) Ashis Saha et al.   GENOME RESEARCH

Production of a recombinant swollenin from Trichoderma harzianum in Escherichia coli and its potential synergistic role in biomass degradation

(2017) Clelton A. Santos et al.   Microbial Cell Factories

Rce1, a novel transcriptional repressor, regulates cellulase gene expression by antagonizing the transactivator Xyr1 in Trichoderma reesei

(2017) Yanli Cao et al.   MOLECULAR MICROBIOLOGY

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation

(2017) Le Huang et al.   NUCLEIC ACIDS RESEARCH

Optimization of acetyl xylan esterase gene expression in Trichoderma reesei and its application to improve the saccharification efficiency on different biomasses

(2017) Tamilvendan Manavalan et al.   PROCESS BIOCHEMISTRY

Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study

(2017) Qingyu Chen et al.   Database-The Journal of Biological Databases and Curation

Genetic engineering of Trichoderma reesei cellulases and their production

(2017) Irina S. Druzhinina et al.   Microbial Biotechnology

RNA-Seq differential expression analysis: An extended review and a software tool

(2017) Juliana Costa-Silva et al.   PLoS One

Crystal structure and biochemical characterization of the recombinant ThBgl, a GH1 β-glucosidase overexpressed in Trichoderma harzianum under biomass degradation conditions

(2016) Clelton A. Santos et al.   Biotechnology for Biofuels

High Throughput Sequencing: An Overview of Sequencing Chemistry

(2016) Sheetal Ambardar et al.   INDIAN JOURNAL OF MICROBIOLOGY

Bioinformatics tools and databases for whole genome sequence analysis of Mycobacterium tuberculosis

(2016) Kiatichai Faksri et al.   INFECTION GENETICS AND EVOLUTION

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace

(2016) Kun Qu et al.   NATURE METHODS

Identification and Network-Enabled Characterization of Auxin Response Factor Genes in Medicago truncatula

(2016) David J. Burks et al.   Frontiers in Plant Science

Xpp1 regulates the expression of xylanases, but not of cellulases in Trichoderma reesei

(2015) Christian Derntl et al.   Biotechnology for Biofuels

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

Analysis of Genomic Regions of Trichoderma harzianum IOC-3844 Related to Biomass Degradation

(2015) Aline Crucello et al.   PLoS One

Estimating the success of enzyme bioprospecting through metagenomics: current status and future trends

(2015) Manuel Ferrer et al.   Microbial Biotechnology

Helically agitated mixing in dry dilute acid pretreatment enhances the bioconversion of corn stover into ethanol

(2014) Yanqing He et al.   Biotechnology for Biofuels

Fungal enzyme production and biodegradation of polychlorinated dibenzo-p-dioxins and dibenzofurans in contaminated sawmill soil

(2014) Festus Anasonye et al.   CHEMOSPHERE

Transcriptome Profile of Trichoderma harzianum IOC-3844 Induced by Sugarcane Bagasse

(2014) Maria Augusta Crivelente Horta et al.   PLoS One

Deciphering the Cis-Regulatory Elements for XYR1 and CRE1 Regulators in Trichoderma reesei

(2014) Rafael Silva-Rocha et al.   PLoS One

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

The Fusarium graminearum Genome Reveals More Secondary Metabolite Gene Clusters and Hints of Horizontal Gene Transfer

(2014) Christian M. K. Sieber et al.   PLoS One

The VELVET A Orthologue VEL1 of Trichoderma reesei Regulates Fungal Development and Is Essential for Cellulase Gene Expression

(2014) Razieh Karimi Aghcheh et al.   PLoS One

Transcription factors: specific DNA binding and specific gene regulation

(2014) Anne-Laure Todeschini et al.   TRENDS IN GENETICS

Discovering Functions of Unannotated Genes from a Transcriptome Survey of Wild Fungal Isolates

(2014) C. E. Ellison et al.   mBio

Genome-Wide Characterization of Light-Regulated Genes in Neurospora crassa

(2014) C. Wu et al.   G3-Genes Genomes Genetics

Plant Cell Wall Deconstruction by Ascomycete Fungi

(2013) N. Louise Glass et al.   Annual Review of Microbiology

Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes

(2013) Anthony Levasseur et al.   Biotechnology for Biofuels

The complex transcriptional landscape of the anucleate human platelet

(2013) Paul F Bray et al.   BMC GENOMICS

Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum

(2013) Katherine Lawler et al.   BMC Systems Biology

Transcriptomics in the RNA-seq era

(2013) Paul A McGettigan   CURRENT OPINION IN CHEMICAL BIOLOGY

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

When Is Hub Gene Selection Better than Standard Meta-Analysis?

(2013) Peter Langfelder et al.   PLoS One

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Trichoderma harzianum expressed sequence tags for identification of genes with putative roles in mycoparasitism against Fusarium solani

(2012) Andrei Stecca Steindorff et al.   BIOLOGICAL CONTROL

GuiTope: an application for mapping random-sequence peptides to protein sequences

(2012) Rebecca F Halperin et al.   BMC BIOINFORMATICS

A new Zn(II)2Cys6-type transcription factor BglR regulates β-glucosidase expression in Trichoderma reesei

(2012) Mikiko Nitta et al.   FUNGAL GENETICS AND BIOLOGY

Systems biological approaches towards understanding cellulase production by Trichoderma reesei

(2012) Christian P. Kubicek   JOURNAL OF BIOTECHNOLOGY

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

(2012) Bernhard Seiboth et al.   MOLECULAR MICROBIOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Transcriptome analysis of Aspergillus niger grown on sugarcane bagasse

(2011) Wagner R de Souza et al.   Biotechnology for Biofuels

The CRE1 carbon catabolite repressor of the fungus Trichoderma reesei: a master regulator of carbon assimilation

(2011) Thomas Portnoy et al.   BMC GENOMICS

Gene network inference and visualization tools for biologists: application to new human transcriptome datasets

(2011) Daniel Hurley et al.   NUCLEIC ACIDS RESEARCH

Translational Research onTrichoderma: From 'Omics to the Field

(2010) Matteo Lorito et al.   Annual Review of Phytopathology

Identification of modules in Aspergillus niger by gene co-expression network analysis

(2010) Robert A. van den Berg et al.   FUNGAL GENETICS AND BIOLOGY

Weighted Gene Coexpression Network Analysis: State of the Art

(2010) Wei Zhao et al.   Journal of Biopharmaceutical Statistics

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Rank of Correlation Coefficient as a Comparable Measure for Biological Significance of Gene Coexpression

(2009) T. Obayashi et al.   DNA RESEARCH

Identification of specific binding sites for XYR1, a transcriptional activator of cellulolytic and xylanolytic genes in Trichoderma reesei

(2009) Takanori Furukawa et al.   FUNGAL GENETICS AND BIOLOGY

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

(2009) BJ��RN USADEL et al.   PLANT CELL AND ENVIRONMENT

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

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

(2008) Diego Martinez et al.   NATURE BIOTECHNOLOGY

Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum

(2008) Marco A van den Berg et al.   NATURE BIOTECHNOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH

Bioinformatics challenges of new sequencing technology

(2008) Mihai Pop et al.   TRENDS IN GENETICS

Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus

(2008) Natalie D. Fedorova et al.   PLoS Genetics