Yu Lin

The paper introduces ConDiGA, a pipeline for constructing accurate protein sequence databases from metagenomic data to improve metaproteomics analysis, achieving deep coverage in synthetic and real microbiota samples.

VStrains reconstructs viral strains de novo from quasispecies by extracting strain-specific paths from assembly graphs, outperforming existing methods on simulated and real datasets.

MetaCoAG improves metagenomic binning by using assembly graphs, composition, and coverage, achieving higher quality bins than existing tools.

Kmer2SNP is a reference-free SNP caller that uses k-mer frequency and graph matching to improve speed and accuracy over existing methods.

The paper introduces a new network mining algorithm to identify pathway-centric interactions in cancer data, revealing dense between-pathway interactions with therapeutic potential.

Building the repeat graph from fast, possibly misassembled contigs lets Flye resolve repeats and produce more contiguous long-read assemblies, with fewer errors than Canu on human and worm genomes.

HaploJuice improves haplotype assembly accuracy by estimating sub-sample proportions and using dynamic programming, outperforming existing methods on simulated and real data.

This paper introduces a de Bruijn graph-based assembler for long error-prone reads, achieving more accurate genome reconstructions than existing methods.