Oren Avram

Integrated ambient modeling and genetic demultiplexing of single-cell RNA+ATAC multiome experiments with Ambimux

The paper introduces ambimux, a method to estimate and demultiplex ambient molecule contamination in single-cell RNA+ATAC multiome data, improving the detection of biologically meaningful signals.

Single-cell DNA methylome and 3D genome atlas of the human subcutaneous adipose tissue

The paper characterizes the epigenomic and 3D genomic landscape of human subcutaneous adipose tissue at the cell-type level and links epigenomic variation to abdominal obesity risk.

BetaAlign: a deep learning approach for multiple sequence alignment

BetaAlign uses deep learning to align biological sequences, achieving accuracy comparable to or better than existing tools.

Identification of selective sweeps in bacteria

The paper introduces SINCOPA, a phylogeny-based method for detecting locus-specific selective sweeps in bacterial strains, and applies it to over 500 microbial genomes to identify sweeps in genes related to biofilm formation and environmental adaptation.

A probabilistic model for indel evolution: differentiating insertions from deletions

This paper introduces a probabilistic model for indel evolution that distinguishes insertions from deletions, showing higher deletion rates and negative correlation with population size in empirical data.