Yeast Functional Genomics

Single-Cell RNA-Sequencing in Yeast using the 10x Genomics Chromium Device.- Genome-Wide Profiling of Transcription Initiation with STRIPE-seq.- A Modified Crosslinking Analysis of cDNAs (CRAC) Protocol for Detecting RNA-Protein Interactions and Transcription at Single Nucleotide Resolution.- High-Resolution Deep Sequencing of Nascent Transcription in Yeast with BioGRO-seq.- Direct Sequencing of RNA and RNA Modification Identification using Nanopore.- UNAGI: Yeast Transcriptome Reconstruction and Gene Discovery using Nanopore Sequencing.- Identification of Taxonomically Restricted Transcripts from Illumina RNA Sequencing Data.- FORK-seq: Single Molecule Profiling of DNA Replication.- CUT&RUN Profiling of the Budding Yeast Epigenome.- ChIP-SICAP: A New Tool to Explore Gene-Regulatory Networks in Candida albicans and Other Yeasts.- Purification of Ribosome-Nascent-Chain Complex for Ribosome Profiling and Selective Ribosome Profiling.- Single-Step Affinity Purification (ssAP) and Mass Spectrometry of Macromolecular Complexes in the Yeast S. cerevisiae.- Composition and Dynamics of Protein Complexes Measured by Quantitative Mass Spectrometry of Affinity Purified Samples.- Deep Mutational Scanning of Protein-Protein Interaction Stability between Partner Expressed from Their Endogenous Loci In Vivo.- Proteomic Mapping by APEX2-Catalyzed Proximity Labeling in Saccharomyces cerevisiae Semi-Permeabilized Cells.- Quantitative Proteomics in Yeast: From bSLIM and Proteome Discoverer Outputs to Graphical Assessment of the Significance of Protein Quantification Scores.- A Strong Cation Exchange Chromatography Protocol for Examining N-Terminal Proteoforms.- RNA Interference (RNAi) as a Tool for High-Resolution Phenotypic Screening of the Pathogenic Yeast Candida glabrata.- High Throughput Gene Mutagenesis Screening using Base Editing.- Saturated Transposon Analysis in Yeast (SATAY) for Deep Functional Mapping of Yeast Genomes.- High-Throughput, High-Precision Colony Phenotyping with Pyphe.- Bulk-Fitness Measurements using Barcode Sequencing Analysis in Yeast.- Prediction of Gene and Genomic Regulation in Candida Species, using the PathoYeastract Database: A Comparative Genomics Approach.- Enabling Studies of Genome-Scale Regulatory Network Evolution in Large Phylogenies with MRTLE.- Omics Analyses, How to Navigate through a Constant Data Deluge.