Semyon Kruglyak

Cytos MPS: an automated multimodal pooled screening platform for protein, morphology and transcriptomics

Cytos MPS integrates CRISPR guide identity, morphology, transcriptomics, and protein data to reveal multimodal phenotypes from perturbations.

Complete genomes of a multi-generational pedigree to expand studies of genetic and epigenetic inheritance

The paper presents T2T reference genomes from a multi-generational pedigree to study genetic and epigenetic inheritance across the complete genome.

Direct In-Sample Sequencing of the 3' Transcriptome Expands the Capabilities of Optical Pooled Screens

The paper introduces a platform that directly sequences 3'UTRs and guide RNAs in fixed cells alongside protein abundance and morphology, enabling CRISPR screening in lung cancer cells.

A simplified hybrid capture approach retains high specificity and enables PCR-free workflow

This paper introduces a simplified hybrid capture method that eliminates PCR and bead-based steps while maintaining specificity and improving variant calling.

Accurate human genome analysis with Element Avidity sequencing

This study compares Element Avidity sequencing to Illumina sequencing, finding higher accuracy in mapping and variant calling, especially at lower coverages and in challenging genomic regions.

FLEXIBLE, PRODUCTION-SCALE, HUMAN WHOLE GENOME SEQUENCING ON A BENCHTOP SEQUENCER

This paper demonstrates high-quality, scalable human whole-genome sequencing on a benchtop sequencer, achieving 30x coverage with flexibility and cost-effectiveness.

Unraveling Tyrosine-Kinase Inhibitor Resistance in NSCLC Cells via Same-cell Measurement of RNA, Protein, and Morphological Responses

The paper measures RNA, protein, and morphology in NSCLC cells treated with TKIs to identify resistance mechanisms and show that CDK4/6 inhibition enhances TKI efficacy.

High-Throughput Multiomics Profiling of Model Systems Using the AVITI24 Platform

The paper introduces a multiomics platform for high-throughput analysis of cellular responses, demonstrating its ability to capture dynamic cellular processes and drug responses in cancer cells.

A robust benchmark for detecting low-frequency variants in the HG002 Genome In A Bottle NIST reference material.

The paper develops a benchmark for detecting low-frequency mosaic variants in the HG002 reference material using high-coverage sequencing data and validates its utility across multiple technologies.

Characterizing and addressing error modes to improve sequencing accuracy

The paper demonstrates achieving over 70% Q50 accuracy on the AVITI sequencer by improving sequencing quality and mitigating library preparation and analysis errors.

Low-pass sequencing plus imputation using avidity sequencing displays comparable imputation accuracy to sequencing by synthesis while reducing duplicates

This study compares imputation accuracy between avidity sequencing and sequencing by synthesis, finding comparable performance with lower duplication rates in avidity sequencing.

Sequencing by avidity enables high accuracy with low reagent consumption

This paper introduces avidity sequencing, a new chemistry that improves sequencing accuracy and reduces reagent use, enabling applications like single-cell RNA-seq and whole-genome sequencing.