Vineet Bafna

This paper introduces ecEvol, a method to infer ecDNA emergence time and other parameters from bulk whole-genome sequencing data, finding that ecDNA typically emerges early and is associated with poorer survival.

DipSkmer improves population genomics by accurately estimating genetic diversity in diploid organisms using low-coverage genome skims, outperforming existing methods.

This study compares ecDNA prevalence, conservation, and clonal dynamics in PDX models and primary tumors of childhood cancers, finding high sequence conservation and selective growth advantage of ecDNA-positive clones.

Cycle-Extractor accurately reconstructs ecDNA structures from both short- and long-read sequencing data, outperforming existing methods in speed and completeness.

This study identifies subtype-specific mutational mechanisms and links them to host metabolic factors in endometrial cancer using genomic and transcriptomic data from 440 tumors.

SPrUCE estimates genetic diversity from UCE data by correcting underestimation bias using a Gompertz function model, providing accurate results comparable to whole-genome methods.

scAmp detects and analyzes ecDNA at single-cell resolution, showing its impact on chromatin accessibility in cancer cells.

The paper introduces ec3D, a method to reconstruct 3D structures of ecDNA from Hi-C data, revealing spherical configurations and unique long-range interactions in cancer.

OMKar generates virtual karyotypes from optical genome mapping data to identify constitutional abnormalities with high precision and recall.

The paper identifies enhancer-like elements on ecDNA in colorectal cancer that are derived from transposable elements and are functionally active in cancer cell fitness.

This study investigates the spatial-temporal evolution of extrachromosomal DNA (ecDNA) in glioblastoma, showing that EGFR ecDNA drives tumor evolution and identifies a potential therapeutic window for early intervention.

The paper introduces interSeg, a deep learning tool that accurately predicts oncogene amplification status from interphase FISH images, achieving high accuracy in detecting ecDNA and chromosomal amplifications.

This study shows that ecDNA mis-segregation leads to micronuclei formation, reduced oncogene transcription, and improved patient survival in neuroblastoma.

The paper shows that ecDNA-borne PVT1 fusions stabilize oncogenic mRNAs by interacting with SRSF1, enhancing RNA stability and supporting MYC dependency in cancer.

This paper identifies transcription-replication conflict as a vulnerability in ecDNA-containing cancers and demonstrates that CHK1 inhibition selectively kills these tumors.

AmpliconSuite identifies focal amplifications in cancer genomes, showing ecDNA has higher copy numbers and stronger oncogene enrichment compared to other amplification types.

CoRAL improves ecDNA structure reconstruction using long-read sequencing, outperforming short-read methods in simulations and cell-line datasets.

The paper creates a deep population reference panel of tandem repeat variation using whole genome sequencing and develops a method to genotype over 1.7 million TR loci, identifying novel eQTL signals and a phased haplotype panel for imputation.

The paper identifies pathogenic variants in tubulointerstitial kidney disease genes in 12.5% of a CKD cohort using targeted sequencing and clinical criteria.

The paper investigates the development and evolution of extrachromosomal DNA (ecDNA) in Barrett's esophagus patients progressing to esophageal adenocarcinoma, finding ecDNA is strongly associated with cancer progression and enriched for oncogenes and immunomodulatory genes.

RESPECT estimates genome length and repeat spectra from low-coverage genome skims with <1.5% error, outperforming previous methods.

CONSULT improves contamination detection in sequencing reads using locality-sensitive hashing, outperforming existing methods and enhancing mitochondrial assembly from genome skims.

The paper develops adVNTR-NN to genotype VNTRs efficiently and identifies eVNTR loci associated with gene expression in multiple tissues.

AmpliconReconstructor integrates optical mapping and NGS to resolve focal amplifications in cancer, revealing complex structures and origins of ecDNA and other rearrangements.

The paper evaluates how contaminant DNA affects genome skimming accuracy and proposes a filtering method using Kraken-II to improve sample identification.

The paper improves genome annotation for Chinese hamster by integrating RNA-Seq, proteomics, and Ribo-Seq, identifying new proteins and translational events, and addressing retroviral contamination in CHO cell lines.

The paper develops methods to compute statistical significance of interval overlaps and introduces a tool, iStat, to analyze simulated and real datasets.

adVNTR is a method for genotyping Variable Number Tandem Repeats using Hidden Markov Models, applicable to short-read and single molecule sequencing data.

AmpliconArchitect reconstructs focal amplifications in cancer genomes, revealing novel insights into extrachromosomal mechanisms and oncoviral pathogenesis.

This paper introduces a method for accurate single-cell genome sequencing and haplotyping with low error rates and long haplotype assembly.