Magnus Rattray

The paper shows that miR-9 levels increase stepwise during zebrafish neurogenesis through sequential activation of distinct pri-mir-9 loci, which helps overcome adaptation in Her6 dynamics.

HiChIP-Peaks improves HiChIP peak calling by focusing on re-ligation sites, enhancing reliability and enabling differential peak analysis across samples.

The paper uses deep learning to identify tissue-specific TF binding sites by analyzing ChIP-seq data from MEIS and HOXA2 in mouse branchial arches.

The paper uses live imaging and mathematical modeling to show HES5 protein dynamics correlate with cell-state transitions and fate decisions in murine neurogenesis.

OscoNet improves upon Oscope by providing a statistical criterion for selecting oscillatory genes and a more accurate pseudo-time estimation method.

The paper introduces Scasat, a pipeline for analyzing single-cell ATAC-seq data, and shows it can identify cell types by analyzing open chromatin regions.

GrandPrix improves the Bayesian GPLVM for single-cell data by scaling it to large datasets and enabling pseudotime inference with branching dynamics.

BGP identifies gene-specific branching dynamics in single-cell data using a non-parametric model and demonstrates its effectiveness on synthetic and hematopoiesis data.