Mohammed El-Kebir

DecoDiPhy deconvolves phylogenetic distance mixtures to improve interpretability and downstream analysis in metagenomics.

The paper introduces a framework to summarize RNA structural ensembles by identifying shared motifs and clustering structures, showing it can find conserved scaffolds and motifs across species and transcripts.

Sapling infers and summarizes tumor phylogenies from bulk data using backbone trees, demonstrating high-quality results on simulated and real data.

The paper introduces fastppm, a fast tool for solving the regression problem in tumor phylogeny reconstruction, achieving significant speedups and accuracy improvements.

This paper improves genomic prediction accuracy by using synthetic traits derived from hyperspectral data, showing higher accuracy than single-trait models for leaf traits in sorghum.

DeepCopy improves haplotype-specific copy number calling in single-cell DNA sequencing by incorporating evolutionary constraints, leading to more accurate and biologically plausible CNA phylogenies.

The paper introduces MACH2, a method to systematically enumerate all plausible migration histories of metastatic cancers, outperforming existing methods and detecting extensive uncertainty in real cancer data.

This paper introduces a method to jointly reconstruct the evolutionary history of SNVs and CNAs from low-coverage single-cell DNA sequencing data, demonstrating improved accuracy over single-modality approaches.

This paper introduces a method to infer clonal trees from ultra-low coverage single-cell DNA sequencing data of tumors, showing improved accuracy in uncovering clonal structure and genotypes.

CNAViz improves copy-number segmentation in DNA sequencing data by combining local and global approaches, achieving better accuracy than existing methods in simulated and real data.

Jumper improves transcript assembly for Nidovirales by addressing discontinuous transcription, outperforming existing methods and identifying non-canonical transcripts.

CORSID identifies transcription regulatory sequences and genes in unannotated coronavirus genomes without prior information.

This paper introduces DeCiFer, a method to more accurately estimate cancer cell fractions and infer tumor evolution by addressing limitations of existing methods in the presence of copy-number aberrations and mutation losses.

PhyDOSE optimizes follow-up single-cell sequencing experiments using bulk data to reduce costs while maintaining accurate tumor phylogeny reconstruction.

This study identifies multiple SARS-CoV-2 strains within and across hosts using bulk RNA sequencing and consensus sequences, revealing within-host diversity, recombination, and geographic strain variation.

TiTUS samples and summarizes transmission trees for multi-strain infections using SATISFIABILITY, demonstrating accuracy on simulated and HIV data.

SharpTNI counts and samples parsimonious transmission networks under weak bottlenecks using timed phylogenies, accurately identifying co-transmissions in Ebola outbreaks.