Rasmus Nielsen

This paper presents a statistical framework for correcting SARS-CoV-2 genomic sequences using phylogenetic priors, improving call rate and accuracy in challenging regions.

STEM-LM uses masked language modeling to predict multi-species distributions by treating species presence as tokens in a spatio-temporal 'sentence', achieving high discrimination on ecological datasets.

The paper corrects an overcounting issue in the unresolved FBD model for tip-dating and demonstrates its application to empirical datasets.

DICAROS improves ancestral shape reconstruction by modeling shape correlations using diffeomorphic dynamics, outperforming traditional methods on non-symmetric trees.

This study introduces a stochastic framework for phylogenetic shape analysis using diffusion processes and applies it to butterfly wing data.

The paper introduces D+ and D* statistics to improve detection of gene flow by addressing saturation bias in deeper phylogenies using multiallelic site patterns.

The paper introduces ratePlacer, a method for dating ancient environmental DNA by accounting for DNA damage, showing it outperforms existing methods but highlights challenges in age estimation.

This paper introduces a Bayesian framework for inferring transmission networks from polyclonal infections, demonstrating its application to Plasmodium falciparum with high precision and recall in simulations.

WASTER infers shallow phylogenies from low-coverage short reads without assembly or alignment, achieving accuracy comparable to traditional methods at lower costs.

This paper introduces DICAROS, a method for ancestral shape reconstruction that outperforms existing methods by combining LDDMM and Felsensteins Independent Contrasts, and applies it to swallowtail butterflies.

This study identifies genetic factors underlying color and pattern variation in Oophaga pumilio frogs from Bocas del Toro, finding key genes involved in different polymorphisms and evidence of selective sweeps.

This paper introduces POLEGON, a method for estimating branch lengths in Ancestral Recombination Graphs using uninformative priors, showing improved coalescence time estimates and population size inferences.

This study evaluates how well four ARG inference tools perform with phasing errors, finding they remain robust despite inaccuracies in haplotype phasing.

The paper analyzes exome sequencing data from coast redwood to identify genetic structure and adaptation loci, revealing a population break south of San Francisco Bay.

ngsAMOVA provides a probabilistic framework for analyzing molecular variance and divergence with low-depth sequencing data, improving accuracy over genotype calling methods.

This study investigates aneuploidy prevalence in coast redwood using an MCMC method, finding higher aneuploidy in second-growth trees and chromosome loss in tissue culture plants.

vcfgl simulates genotype likelihoods to study uncertainties and biases in genetic data, aiding in benchmarking GL-based methods.

The paper evaluates five methods for detecting ecological interactions from sedimentary ancient DNA data and finds high false discovery rates and poor detection performance under realistic conditions.

The paper challenges a previously reported 900 kya bottleneck in African ancestry, arguing it is a statistical artifact rather than a true demographic event.

The paper uses ancient DNA and strontium isotope analyses to show a deep east-west divergence in steppe ancestry in Southern Europe, supporting specific linguistic divergence models for Indo-European languages.

The paper develops methods for analyzing low-depth NIPT sequencing data to accurately estimate allele frequencies and genetic effect sizes, enabling population genetic studies.

The paper introduces a fast approximate likelihood method for phylogenetic assignment of DNA sequences, showing improved accuracy in taxonomic classification compared to existing methods.

The paper presents a chromosome-level genome assembly for the snowy owl and identifies evolutionary new centromeres seeded by a transposable element, showing lineage-specific centromere evolution.

SINGER improves ARG reconstruction accuracy and uncertainty quantification for large genomic samples by enabling efficient posterior sampling.

ngsBriggs estimates postmortem DNA damage using a fast regression method, outperforming existing tools in speed and accuracy for ancient DNA authentication.

The paper introduces a Bayesian MCMC method for inferring admixture graphs and applies it to Native American and Arctic populations, finding that the Koryak population, not Saqqaq, is the best proxy for gene flow into Athabascans.

This study identifies the genetic basis of phenotypic diversity in betta fish using GWAS and genome sequencing, revealing loci associated with coloration, sex determination, and aggression.

SCONCE2 jointly infers single cell copy number profiles and tumor evolutionary distances, showing higher accuracy than existing methods in simulations and real data.

The paper develops a method to estimate multiple admixture events using 3-locus linkage disequilibrium, demonstrating its accuracy on simulated data and applying it to Colombian and Mexican populations.

This study benchmarks three ARG inference methods for estimating coalescence times using simulations, finding ARGweaver most accurate but less scalable than Relate and tsinfer+tsdate.