Yeast Functional Genomics

Using RNA-seq for Analysis of Differential Gene Expression in Fungal Species.- Enhancing Structural Annotation of Yeast Genomes with RNA-Seq Data.- Pathogen Gene Expression Profiling During Infection Using a Nanostring Ncounter Platform.- Comparative Transcriptomics in Yeasts.- Mapping the Transcriptome-Wide Landscape of RBP Binding sites using gPAR-CLIP-seq: Experimental Procedures.- Mapping the Transcriptome-wide Landscape of RBP Binding Sites using gPAR-CLIP-seq: Bioinformatic Analysis.- Translation Analysis at the Genome Scale by Ribosome Profiling.- Biotin-Genomic Run-on (Bio-GRO): A High-Resolution Method for the Analysis of Nascent Transcription in Yeast.- Genome-wide Probing of RNA Structures in Vitro Using Nucleases and Deep Sequencing.- Genome-wide Chromatin Immunoprecipitation in Candida albicans and other Yeasts.- ChIPseq in Yeast Species: from Chromatin Immumoprecipitation to High-Throughput Sequencing and Bioinformatics Data Analyses.- Systematic Determination of Transcription factor DNA-binding Specificities in Yeast.- Generation and Analysis of Chromosomal Contact Maps of Yeast Species.- A Versatile Procedure to Generate Genome-Wide Spatio-Temporal Program of Replication in Yeast Species.- Single-Step Affinity Purification (ssAP) and Mass Spectrometry of Macromolecular Complexes in the Yeast S. cerevisiae.- Label-Free Quantitative Proteomics in Yeast.- Profiling of Yeast Lipids by Shotgun Lipidomics.- Identification of Links between Cellular Pathways by Genetic Interaction Mapping (GIM).- On The Mapping of Epistatic Genetic Interactions in Natural Isolates: Combining Classical Genetics and Genomics.- Experimental Evolution and Resequencing Analysis of Yeast.- Reconstruction and Analysis of the Evolution of Modular Transcriptional Regulatory Programs using Arboretum.- Predicting Gene and Genomic Regulation in Saccharomyces cerevisiae, using the YEASTRACT Database: A Step By Step Guided Analysis.