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Research Staff

Eve Byington

Bionformatics Analyst

Bioinformatics Analyst

HTS
Research scientist Hai Li holds up a 384-well plate, pictured in front of Columbia Genome Center's Hamilton Star automation system for HTS; Image credit: Systems Biology

Drug screening and analysis is critical in advancing research and discovery of cancer therapeutics. To this end, a Systems Biology-led team of investigators has recently developed PLATE-Seq, a new technique for low-cost, bulk mRNA sequencing. Coupled with genome-wide regulatory network analysis, the novel PLATE-Seq method advances the goal of providing cancer patients with personalized treatment.

Developed by the labs of Peter Sims and Andrea Califano , PLATE-Seq stands for “pooled library amplification for transcriptome expression” sequencing, and enables genome-wide mRNA profiling specifically designed to complement high-throughput screening assays. High-throughput screening, or HTS, represents a key component of drug discovery and technology used widely in biomedical research. Due to cost or complexity, most screens are still performed using low-complexity reporters, such as cell viability, protein-protein interactions and cell growth, for example, but there is a growing need to couple this screening protocol with genome-wide reporters, to measure the activity of many proteins across the genome.

“Our PLATE-Seq method helps us generate a more comprehensive portrait of drug activity,” said Dr. Sims, assistant professor of systems biology, known for his innovative work in single-cell RNA sequencing. “We’ve been able to show that our technique cuts the cost for gene expression profiling considerably, by incorporating a method we devised for ‘barcoding’ cDNA samples and combining this with computational methods from the Califano Lab that are highly effective on low-coverage sequencing data. This method allows us to sequence 96 samples per plate and 768 samples per sequencing run.”

On average, PLATE-Seq reduces the cost of genome-wide screening from around $400 per sample down to approximately $25 per sample. Genome-wide sequencing is important in advancing our understanding and prediction of disease and in identifying potential treatments.

Faculty

Hynek Wichterle

Associate Director, Columbia Genome Center
Co-director, Columbia Stem Cell Initiative
Vice-Chief, Division of Regenerative Medicine
Associate Professor, Departments of Pathology & Cell Biology, and Neuroscience (in Neurology)

Associate Director

Faculty

Donald Landry

Samuel Bard Professor of Medicine
Director, Organic Chemistry Collaborative Center

Faculty

Harris Wang

Associate Professor, Department of Systems Biology

Associate Professor, Department of Systems Biology

Faculty

Brent Stockwell

Professor, Departments of Biological Sciences and Chemistry
Co-director, High-Throughput Screening

Faculty

Peter Sims

Associate Professor, Department of Systems Biology

Associate Director for Novel Technologies

Faculty

Yufeng Shen

Associate Professor, Department of Systems Biology
Associate Director, Columbia Genome Center
Associate Professor, Department of Systems Biology
Associate Director, Columbia Genome Center

Faculty

Raul Rabadan

Gerald and Janet Carrus Professor
Professor, Department of Systems Biology

Co-director, Next-Generation Sequencing

Faculty

Andrea Califano

Chair, Department of Systems Biology Clyde and Helen Wu Professor of Chemical and Systems Biology
Chair, Department of Systems Biology Clyde and Helen Wu Professor of Chemical and Systems Biology