Guillaume J. P. Filion

A novel High-Throughput Ligase-Independent Mapping method to detect Viral Integration Sites

The paper introduces Terminal Mapping, a high-throughput method to detect viral integration sites without restriction enzymes or ligation, showing improved recovery of HIV-1 insertion sites compared to inverse PCR.

CodonTransformer: a multispecies codon optimizer using context-aware neural networks

CodonTransformer optimizes DNA sequences for protein expression across species by learning from natural codon usage patterns and generating sequences with appropriate regulatory features.

Strand asymmetry influences mismatch resolution during single-strand annealing

The paper shows that strand asymmetry affects mismatch resolution during single-strand annealing in mouse chromatin, with the break position determining the repair bias.

Chromosome Compartments on the Inactive X Guide TAD Formation Independently of Transcription during X-Reactivation

The paper shows that TAD formation on the inactive X occurs before transcription during X-reactivation, independent of transcriptional activity.

Calibrating seed-based alignment heuristics with Sesame

This paper develops a theoretical framework to calibrate seeding heuristics in DNA sequencing alignment and provides an open-source implementation called Sesame.

Mapping short reads, faithfully

This paper introduces a method to map short reads with higher faithfulness by estimating reference repetitiveness, achieving competitive performance with existing tools.

Spatially clustered loci with multiple enhancers are frequent targets of HIV-1

The paper identifies spatially clustered genes with multiple enhancers as frequent targets of HIV-1 integration in T cells.

Experimental assay of a fitness landscape on a macroevolutionary scale

The paper experimentally assays a fitness landscape on a macroevolutionary scale by analyzing the effects of amino acid substitutions in yeast His3 orthologs.

OneD: increasing reproducibility of Hi-C Samples with abnormal karyotypes

OneD improves Hi-C reproducibility for samples with abnormal karyotypes by addressing copy number variations, outperforming existing methods while maintaining performance on normal karyotypes.

Transcription Factors Orchestrate Dynamic Interplay Between Genome Topology And Gene Regulation During Cell Reprogramming

The paper shows transcription factors drive genome topology changes before gene expression during cell reprogramming.

Analytic combinatorics for bioinformatics I: seeding methods

The paper introduces a theoretical framework using analytic combinatorics to estimate the success rate and error rates of seeding heuristics in bioinformatics.

Parallel sequencing lives, or what makes large sequencing projects successful

The paper compares two Hi-C samples, showing how adherence to FAIR principles leads to successful sequencing projects.

Structural features of the fly chromatin colors revealed by automatic three-dimensional modeling.

The paper introduces TADbit, a computational framework for 3D chromatin modeling, and applies it to fly genomic domains to reveal structural differences linked to chromatin colors.

Distinct structural transitions of chromatin topological domains coordinate hormone-induced gene regulation

The paper examines how hormone-induced changes in gene regulation are coordinated by structural transitions of chromatin topological domains in breast cancer cells.