ChiNet uncovers rewired transcription subnetworks in tolerant yeast for advanced biofuels conversion

Transcription factor Rpn4 promotes a complex antistress response in Saccharomyces cerevisiae cells exposed to methyl methanesulfonate

(2014) D. S. Spasskaya et al.   MOLECULAR BIOLOGY

Proteogenomic characterization of human colon and rectal cancer

(2014) Bing Zhang et al.   NATURE

Hunting complex differential gene interaction patterns across molecular contexts

(2014) Mingzhou Song et al.   NUCLEIC ACIDS RESEARCH

EDDY: a novel statistical gene set test method to detect differential genetic dependencies

(2014) Sungwon Jung et al.   NUCLEIC ACIDS RESEARCH

Regulation of transcription factor activity by interconnected post-translational modifications

(2014) Theresa M. Filtz et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Roles of the Yap1 Transcription Factor and Antioxidants in Saccharomyces cerevisiae's Tolerance to Furfural and 5-Hydroxymethylfurfural, Which Function as Thiol-Reactive Electrophiles Generating Oxidative Stress

(2013) D. Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Engineering redox cofactor utilization for detoxification of glycolaldehyde, a key inhibitor of bioethanol production, in yeast Saccharomyces cerevisiae

(2013) Lahiru N. Jayakody et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Gene Sets Net Correlations Analysis (GSNCA): a multivariate differential coexpression test for gene sets

(2013) Yasir Rahmatallah et al.   BIOINFORMATICS

Differential network analysis for the identification of condition-specific pathway activity and regulation

(2013) Gennaro Gambardella et al.   BIOINFORMATICS

Comparative proteomic analysis of a new adaptive Pichia Stipitis strain to furfural, a lignocellulosic inhibitory compound

(2013) Xue-Cai Hao et al.   Biotechnology for Biofuels

Genome-scale analyses of butanol tolerance in Saccharomyces cerevisiae reveal an essential role of protein degradation

(2013) Daniel González-Ramos et al.   Biotechnology for Biofuels

Integrative approaches for finding modular structure in biological networks

(2013) Koyel Mitra et al.   NATURE REVIEWS GENETICS

The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation inSaccharomyces cerevisiae

(2013) Miguel Cacho Teixeira et al.   NUCLEIC ACIDS RESEARCH

Pentose Phosphate Pathway Function Affects Tolerance to the G-Quadruplex Binder TMPyP4

(2013) Elizabeth J. Andrew et al.   PLoS One

Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics

(2013) Ekta Khurana et al.   SCIENCE

Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells

(2012) Samuel Marguerat et al.   CELL

Pathway-directed weighted testing procedures for the integrative analysis of gene expression and metabolomic data

(2012) Laila M. Poisson et al.   GENOMICS

SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets

(2012) Sara J. C. Gosline et al.   Integrative Biology

Differential network biology

(2012) Trey Ideker et al.   Molecular Systems Biology

Proteomic Research Reveals the Stress Response and Detoxification of Yeast to Combined Inhibitors

(2012) Ming-Zhu Ding et al.   PLoS One

Network Evolution: Rewiring and Signatures of Conservation in Signaling

(2012) Mark G. F. Sun et al.   PLoS Computational Biology

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

Molecular mechanisms of yeast tolerance and in situ detoxification of lignocellulose hydrolysates

(2011) Z. Lewis Liu   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Kinetic mechanism of an aldehyde reductase of Saccharomyces cerevisiae that relieves toxicity of furfural and 5-hydroxymethylfurfural

(2011) Douglas B. Jordan et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

COSINE: COndition-SpecIfic sub-NEtwork identification using a global optimization method

(2011) Haisu Ma et al.   BIOINFORMATICS

Conserved and differential gene interactions in dynamical biological systems

(2011) Zhengyu Ouyang et al.   BIOINFORMATICS

Engineered NADH-dependent GRE2 from Saccharomyces cerevisiae by directed enzyme evolution enhances HMF reduction using additional cofactor NADPH

(2011) Jaewoong Moon et al.   ENZYME AND MICROBIAL TECHNOLOGY

Differential Oxidant Tolerance Determined by the Key Transcription Factor Yap1 Is Controlled by Levels of the Yap1-binding Protein, Ybp1

(2011) Kailash Gulshan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Enhancement of xylose uptake in 2-deoxyglucose tolerant mutant of Saccharomyces cerevisiae

(2011) Prihardi Kahar et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Approximated distributions of the weighted sum of correlated chi-squared random variables

(2011) Li-Ling Chuang et al.   JOURNAL OF STATISTICAL PLANNING AND INFERENCE

Metabolic pathway engineering based on metabolomics confers acetic and formic acid tolerance to a recombinant xylose-fermenting strain of Saccharomyces cerevisiae

(2011) Tomohisa Hasunuma et al.   Microbial Cell Factories

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Furfural induces reactive oxygen species accumulation and cellular damage in Saccharomyces cerevisiae

(2010) Sandra A Allen et al.   Biotechnology for Biofuels

Testing for mean and correlation changes in microarray experiments: an application for pathway analysis

(2010) Mayer Alvo et al.   BMC BIOINFORMATICS

Comparative transcriptome profiling analyses during the lag phase uncover YAP1, PDR1, PDR3, RPN4, and HSF1 as key regulatory genes in genomic adaptation to the lignocellulose derived inhibitor HMF for Saccharomyces cerevisiae

(2010) Menggen Ma et al.   BMC GENOMICS

Network Enrichment Analysis in Complex Experiments

(2010) Ali Shojaie et al.   Statistical Applications in Genetics and Molecular Biology

Gene set enrichment analysis made simple

(2010) Rafael A Irizarry et al.   STATISTICAL METHODS IN MEDICAL RESEARCH

Transcriptomic Profiling of the Saccharomyces cerevisiae Response to Quinine Reveals a Glucose Limitation Response Attributable to Drug-Induced Inhibition of Glucose Uptake

(2009) S. C. dos Santos et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Comparative Proteomic Analysis of Tolerance and Adaptation of Ethanologenic Saccharomyces cerevisiae to Furfural, a Lignocellulosic Inhibitory Compound

(2009) F.-M. Lin et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Statistical methods for gene set co-expression analysis

(2009) YounJeong Choi et al.   BIOINFORMATICS

ConceptGen: a gene set enrichment and gene set relation mapping tool

(2009) Maureen A. Sartor et al.   BIOINFORMATICS

Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative analysis

(2009) Ming Yi et al.   BMC BIOINFORMATICS

Identification of differentially expressed sub-networks based on multivariate ANOVA scoring method

(2009) Taeyoung Hwang et al.   BMC BIOINFORMATICS

Proteasomal Degradation of Rpn4 in Saccharomyces cerevisiae Is Critical for Cell Viability Under Stressed Conditions

(2009) X. Wang et al.   GENETICS

Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast

(2009) M. Song et al.   IET Systems Biology

Evolutionarily engineered ethanologenic yeast detoxifies lignocellulosic biomass conversion inhibitors by reprogrammed pathways

(2009) Z. Lewis Liu et al.   MOLECULAR GENETICS AND GENOMICS

Multiple gene-mediated NAD(P)H-dependent aldehyde reduction is a mechanism of in situ detoxification of furfural and 5-hydroxymethylfurfural by Saccharomyces cerevisiae

(2008) Z. Lewis Liu et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Proline as a stress protectant in yeast: physiological functions, metabolic regulations, and biotechnological applications

(2008) Hiroshi Takagi   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

A novel signaling pathway impact analysis

(2008) Adi Laurentiu Tarca et al.   BIOINFORMATICS

SLEPR: A Sample-Level Enrichment-Based Pathway Ranking Method — Seeking Biological Themes through Pathway-Level Consistency

(2008) Ming Yi et al.   PLoS One