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Related Concept Videos

Genetic Lingo01:11

Genetic Lingo

Overview
Nucleic Acids02:43

Nucleic Acids

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and carry instructions for its functioning.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. In prokaryotes, the...
Genome Copying Errors02:46

Genome Copying Errors

DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their  survival. Therefore, the copying errors are checked and repaired at three levels.
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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Human Genetics01:28

Human Genetics

Human genetics provides a profound framework for understanding the interplay between genetic predispositions and human psychology. At the heart of this discipline lies the study of how genes influence physical traits, behaviors, and susceptibility to diseases. Each person carries a unique genetic code that subtly or significantly shapes their psychological and behavioral landscape.
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Genetic Material01:20

Genetic Material

Within the human body, a complex and detailed system of trillions of cells works in unison to sustain life. Each cell houses a nucleus, which contains 46 chromosomes divided into 23 pairs. Chromosomes are highly coiled structures made of the genetic material DNA. These chromosomes are essential carriers of genetic information, with half inherited from the mother through her egg and the other half from the father's sperm, combining to create the unique genetic makeup of an individual.

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Competitive Genomic Screens of Barcoded Yeast Libraries
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Universal Baseline for in vitro Selection of Genetically Encoded Libraries.

Kejia Yan1, Guilherme M Lima1, Tara Bahadur2

  • 1Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada.

Biorxiv : the Preprint Server for Biology
|February 23, 2026
PubMed
Summary

A new baseline response method using DNA-barcoded peptides improves reproducibility in genetically encoded (GE) molecular discovery. This framework enables standardized analysis and reproducible hit discovery for therapeutic development.

Keywords:
BiochemistryBiological Sciencesbaselinediversityphage displayreproducibility

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Area of Science:

  • Biotechnology and Molecular Biology
  • Drug Discovery and Development
  • Bioinformatics and Computational Biology

Background:

  • Genetically encoded (GE) libraries are crucial for identifying high-affinity ligands for molecular targets via in vitro selection and next-generation sequencing (NGS).
  • Reproducibility in GE-molecular discoveries is challenging due to the lack of a systematic evaluation framework.
  • Existing in vitro discovery systems rarely evaluate reproducibility against a defined experimental baseline.

Purpose of the Study:

  • To introduce a systematic framework for evaluating reproducibility in GE-molecular discoveries.
  • To establish a universal baseline response for normalizing and standardizing in vitro selection data.
  • To enable rigorous normalization, confidence assessment, and cross-target comparison of molecular discovery outcomes.

Main Methods:

  • Introduction of the 'baseline response' concept, achieved by spiking a random DNA-barcoded population into selection libraries.
  • Calibration of the baseline concept using Bioconductor EdgeR differential enrichment (DE) analysis of NGS data from phage-displayed selections.
  • Application of baseline-stratified DE-analysis to 66 parallel selections across 22 extracellular targets, including HER1-3, EpCAM, CAIX, PD-L1, and integrin receptors.

Main Results:

  • Automated DE-analysis of hundreds of NGS files yielded validated hits and synthetic macrocyclic ligands with mid-nanomolar affinity.
  • Demonstrated baseline-calibrated NGS data for optimizing peptide macrocycles, yielding potent single-digit nanomolar ligands for PD-L1.
  • Mixing discovery campaigns (e.g., chitin-enriched peptides as baseline for NS3a* selection) proved effective for baseline establishment.

Conclusions:

  • The baseline response provides a reproducible method to partition active and inactive members in in vitro selection.
  • Baseline-based analyses of NGS data offer a scalable framework for reproducible hit discovery and standardized analysis across diverse GE selection campaigns.
  • This framework introduces practical standards for reproducibility and statistical benchmarking across genetically encoded display platforms.