Search filters

List of works by Rasmus Nielsen

100 ancient genomes show repeated population turnovers in Neolithic Denmark

scientific article published on 10 January 2024

35th Annual Meeting of the European Association for the Study of Diabetes

article

35th Annual Meeting of the European Association for the Study of Diabetes : Brussels, Belgium, 28 September-2 October 1999

article

A Bayesian multilocus association method: allowing for higher-order interaction in association studies

scientific article published on 15 April 2007

A Draft Sequence of the Neandertal Genome

scientific article

A Likelihood-Ratio Test of Monophyly

article

A Population Phylogenetic View of Mitochondrial Heteroplasmy.

scientific article published on 17 January 2018

A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations

scientific article

A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes

scientific article

A genome-wide scan for signatures of directional selection in domesticated pigs

scientific article

A hidden Markov model approach for simultaneously estimating local ancestry and admixture time using next generation sequence data in samples of arbitrary ploidy

article

A likelihood ratio test for species membership based on DNA sequence data

scientific article

A map of climate change-driven natural selection in Arabidopsis thaliana

scholarly article published 14 May 2018

A metagenome-wide association study of gut microbiota in type 2 diabetes

scientific article (publication date: 4 October 2012)

A method for detecting IBD regions simultaneously in multiple individuals--with applications to disease genetics

scientific article

A model-based approach for identifying signatures of ancient balancing selection in genetic data

scientific article (publication date: August 2014)

A recent bottleneck of Y chromosome diversity coincides with a global change in culture

scientific article

A scan for human-specific relaxation of negative selection reveals unexpected polymorphism in proteasome genes

scientific article published on 22 May 2013

A scan for positively selected genes in the genomes of humans and chimpanzees

scientific article

A scientific note on the revised estimates of effective paternity frequency in Apis

article

ANGSD: Analysis of Next Generation Sequencing Data.

scientific article

Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites

scientific article

Acquired generalized lipoatrophy (AGL): highly selective MR lipid imaging and localized (1)H-MRS

scientific article published on 01 August 2000

Adaptionism-30 years after Gould and Lewontin

scientific article published on 30 July 2009

Adaptive evolution of cytochrome c oxidase: Infrastructure for a carnivorous plant radiation

scientific article

Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA

scientific article (publication date: 14 August 2014)

An Aboriginal Australian genome reveals separate human dispersals into Asia

scientific article (publication date: 7 October 2011)

An investigation of the statistical power of neutrality tests based on comparative and population genetic data

scientific article

Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor?

scientific article

Ancient DNA reveals late survival of mammoth and horse in interior Alaska

scholarly article

Ancient bacteria show evidence of DNA repair

scientific article

Ancient biomolecules from deep ice cores reveal a forested southern Greenland

scientific article

Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers

scientific article published on 5 October 2017

Ancient human genome sequence of an extinct Palaeo-Eskimo

scientific article

Ascertainment bias in studies of human genome-wide polymorphism.

scientific article

Ascertainment biases in SNP chips affect measures of population divergence

scientific article

Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice

scientific article

Assessing the evolutionary impact of amino acid mutations in the human genome

scientific article

Association Mapping for Compound Heterozygous Traits Using Phenotypic Distance and Integer Programming

Bacterial natural transformation by highly fragmented and damaged DNA ⬇️

scientific article (publication date: 3 December 2013)

Bayesian and maximum likelihood estimation of genetic maps

scientific article published on 01 April 2005

CCR5-∆32 is deleterious in the homozygous state in humans

scientific article published on 03 June 2019

Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data.

scientific article

Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments

Classic selective sweeps revealed by massive sequencing in cattle

scientific article

Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution

scientific article

Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx).

scientific article

Composite likelihood method for inferring local pedigrees

scientific article

Convergent evolution of increased urine concentrating ability in desert mammals

scientific article published on 13 September 2020

Convergent evolution of the genomes of marine mammals

scientific article published on 26 January 2015

Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium

scientific article

Costs and benefits of mutational robustness in RNA viruses

scientific article

Darwinian and demographic forces affecting human protein coding genes

scientific article published on 11 March 2009

De novo assembly of a haplotype-resolved human genome.

scientific article

Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques

scientific article

Demography: peopling the Americas

scientific article published in October 2005

Dependence of paracentric inversion rate on tract length

scientific article

Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European

scientific article

Design of association studies with pooled or un-pooled next-generation sequencing data

scientific article

Detecting Selection in Protein Coding Genes Using the Rate of Nonsynonymous and Synonymous Divergence

article

Detecting Site-Specific Physicochemical Selective Pressures: Applications to the Class I HLA of the Human Major Histocompatibility Complex and the SRK of the Plant Sporophytic Self-Incompatibility System

article

Detecting adaptive trait loci in nonmodel systems: divergence or admixture mapping?

scientific article published on 26 November 2013

Detecting coevolving amino acid sites using Bayesian mutational mapping

scientific article published in June 2005

Detecting recent selective sweeps while controlling for mutation rate and background selection

scientific article published on 20 August 2015

Diabetic intestinal growth adaptation and glucagon-like peptide 2 in the rat: effects of dietary fibre.

scientific article

Difference of expression

journal article; published in Nature on 2006-03-08

Distinguishing between selective sweeps from standing variation and from a de novo mutation

scientific article

EVOLUTION: Why Sex?

scientific article published in Science

Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago

scientific article

Early human dispersals within the Americas

scientific article published in Science

Effect of Nonindependent Substitution on Phylogenetic Accuracy

article

Elevated genetic risk for multiple sclerosis emerged in steppe pastoralist populations

scientific article published on 10 January 2024

Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline

scientific article published on 06 December 2018

Enhanced glucagon-like peptide-1 (GLP-1) response to oral glucose in glucose-intolerant HIV-infected patients on antiretroviral therapy

scientific article

Erratum: The origin and evolution of maize in the Southwestern United States

scholarly article published in Nature Plants

Erratum: The sequence and de novo assembly of the giant panda genome

scientific article published in Nature

Error-prone polymerase activity causes multinucleotide mutations in humans

scientific article

Estimating IBD tracts from low coverage NGS data

scientific article

Estimating effective paternity number in social insects and the effective number of alleles in a population

scientific article published in November 2003

Estimating population divergence time and phylogeny from single-nucleotide polymorphisms data with outgroup ascertainment bias

scientific article

Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA.

scientific article

Estimating the timing of multiple admixture events using 3-locus Linkage Disequilibrium

article

Estimation of 2Nes from temporal allele frequency data

scientific article

Estimation of allele frequency and association mapping using next-generation sequencing data

scientific article

Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level

scientific article (publication date: December 2005)

Evidence for archaic adaptive introgression in humans

scientific article

Evidence for positive selection on a number of MicroRNA regulatory interactions during recent human evolution

scientific article

Evolution of GOUNDRY, a cryptic subgroup of Anopheles gambiae s.l., and its impact on susceptibility to Plasmodium infection

scientific article published on 4 February 2016

Evolution of genes and genomes on the Drosophila phylogeny

scientific article

Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

scientific article

Evolutionary genomics: detecting selection needs comparative data.

scientific article

Exome sequencing-driven discovery of coding polymorphisms associated with common metabolic phenotypes.

scientific article published on 19 November 2012

Exploring variation in the d(N)/d(S) ratio among sites and lineages using mutational mappings: applications to the influenza virus

scientific article published on 11 September 2007

Fast admixture analysis and population tree estimation for SNP and NGS data

scientific article

Fast phylogenetic DNA barcoding

scientific article (publication date: 27 December 2008)

Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models

scientific article

Fitting the Balding-Nichols model to forensic databases

scientific article

Fumio Tajima and the Origin of Modern Population Genetics

scientific article

Genes under positive selection in Escherichia coli.

scientific article

Genetic architecture of vitamin B12 and folate levels uncovered applying deeply sequenced large datasets

scientific article

Genetic signatures reveal high-altitude adaptation in a set of ethiopian populations ⬇️

scientific article

Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques

scientific article published on 16 October 2011

Genome-wide ancestry patterns in Rapanui suggest pre-European admixture with Native Americans

scientific article

Genome-wide patterns of nucleotide polymorphism in domesticated rice

scientific article

Genome-wide signatures of complex introgression and adaptive evolution in the big cats.

scientific article

Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History

Genomic Takeover by Transposable Elements in the Strawberry Poison Frog

article

Genomic analyses inform on migration events during the peopling of Eurasia

scientific article (publication date: 13 October 2016)

Genomic scans for selective sweeps using SNP data

scientific article

Genotype and SNP calling from next-generation sequencing data

scientific article

Greenlandic Inuit show genetic signatures of diet and climate adaptation

scientific article

Human Disease Variation in the Light of Population Genomics

scientific article published on 01 March 2019

Human genomics: disclosure of variation

scientific article published on 01 March 2005

Human-Mediated Admixture and Selection Shape the Diversity on the Modern Swine (Sus scrofa) Y Chromosomes

scientific article published on 01 October 2021

Identification of physicochemical selective pressure on protein encoding nucleotide sequences

scientific article published on 16 March 2006

Impact of IDDM2 on disease pathogenesis and progression in children with newly diagnosed type 1 diabetes: reduced insulin antibody titres and preserved beta cell function

scientific article published on 23 November 2005

In defence of model-based inference in phylogeography.

scientific article

In defense of statistical methods for detecting positive selection

scientific article published on 31 August 2009

Increased mortality in a Danish cohort of young people with Type 1 diabetes mellitus followed for 24 years

scientific article

Inference of historical changes in migration rate from the lengths of migrant tracts

scientific article published on 15 December 2008

Inferring Adaptive Introgression Using Hidden Markov Models

scientific article published on 01 May 2021

Inferring demographic history from a spectrum of shared haplotype lengths

scientific article

Inferring the ancestry of parents and grandparents from genetic data

scientific article published on 14 August 2020

Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics

scientific article (publication date: 20 February 2007)

Introduction: Genomics and philosophy of race

scientific article published on 7 April 2015

Investigate the origins of COVID-19

scientific article

Is haplotype block identification useful for association mapping studies?

scientific article published in July 2004

Joint Estimation of Pedigrees and Effective Population Size Using Markov Chain Monte Carlo

scientific article published on 22 May 2019

Linkage disequilibrium as a signature of selective sweeps

scientific article

Looking for Darwin in genomic sequences--validity and success of statistical methods

scientific article published on 3 April 2012

MAXIMUM-LIKELIHOOD ESTIMATION OF POPULATION DIVERGENCE TIMES AND POPULATION PHYLOGENY IN MODELS WITHOUT MUTATION.

scientific article

Mapping mutations on phylogenies

scientific article published on 01 October 2002

Massive haplotypes underlie ecotypic differentiation in sunflowers

scientific article published on 08 July 2020

Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA.

scientific article published on 13 October 2014

Maximum Likelihood Estimation of Population Divergence Times and Population Phylogenies under the Infinite Sites Model ⬇️

scientific article published on April 1, 1998

Maximum likelihood and Bayesian methods for estimating the distribution of selective effects among classes of mutations using DNA polymorphism data.

scientific article published in March 2003

Maximum likelihood estimation of ancestral codon usage bias parameters in Drosophila.

scientific article

Modeling gene expression evolution with an extended Ornstein-Uhlenbeck process accounting for within-species variation

scientific article published on 10 October 2013

Molecular Footprints of Aquatic Adaptation Including Bone Mass Changes in Cetaceans.

scientific article

Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing

scientific article

Molecular signatures of natural selection

scientific article (publication date: 2005)

Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage

scientific article published on 03 January 2008

Nationwide reduction in the frequency of severe hypoglycemia by half.

scientific article published on 21 December 2014

Natural Selection on Genes Related to Cardiovascular Health in High-Altitude Adapted Andeans

scientific article

Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome.

scientific article

Natural selection and the distribution of identity-by-descent in the human genome

scientific article

Natural selection on protein-coding genes in the human genome

scientific article (publication date: 20 October 2005)

Neutrophil Gelatinase-Associated Lipocalin (NGAL) and Kidney Injury Molecule 1 (KIM1) in patients with diabetic nephropathy: a cross-sectional study and the effects of lisinopril.

scientific article published on October 2010

No association between vitamin D levels around time of birth and later risk of developing oligo- and polyarticular juvenile idiopathic arthritis: a Danish case-cohort study.

scientific article published on 27 July 2016

No statistical evidence for an effect of CCR5-∆32 on lifespan in the UK Biobank cohort

scientific article published on 23 December 2019

North African fox genomes show signatures of repeated introgression and adaptation to life in deserts

scientific article published in 2023

Novel method to identify source-associated phylogenetic clustering shows that Listeria monocytogenes includes niche-adapted clonal groups with distinct ecological preferences

scientific article

Number of genes controlling a quantitative trait in a hybrid zone of the aposematic frog Ranitomeya imitator

article

Offending prior to first psychiatric contact: a population-based register study

scientific article published on 25 April 2012

Ohana, a tool set for population genetic analyses of admixture components

On The Number Of Siblings Andp-th Cousins In A Large Population Sample

On detecting incomplete soft or hard selective sweeps using haplotype structure

scientific article published on 18 February 2014

On the number of siblings and p-th cousins in a large population sample

scientific article published on 06 June 2018

Origins and genetic legacies of the Caribbean Taino

scientific article published on 20 February 2018

Paleogenomics. Genomic structure in Europeans dating back at least 36,200 years

scientific article

Parallel adaptation of rabbit populations to myxoma virus

scientific article published on 14 February 2019

Patterns of mutation and selection at synonymous sites in Drosophila.

scientific article published on 13 November 2007

Patterns of positive selection in six Mammalian genomes

scientific article

Peptide YY and glucagon-like peptide-1 contribute to decreased food intake after Roux-en-Y gastric bypass surgery.

scientific article published on 30 August 2016

Pervasive introgression facilitated domestication and adaptation in the Bos species complex

Phylogenetic ANOVA: The Expression Variance and Evolution Model for Quantitative Trait Evolution

scientific article

Physiological and Genetic Adaptations to Diving in Sea Nomads

scientific article

Population genetic analysis of ascertained SNP data

scientific article

Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals

scientific article published on 14 April 2008

Population genetic inference from genomic sequence variation

scientific article

Population genomics of Bronze Age Eurasia

scientific article published on June 2015

Population genomics of finless porpoises reveal an incipient cetacean species adapted to freshwater.

scientific article published on 10 April 2018

Population genomics of post-glacial western Eurasia

scientific article published on 10 January 2024

Population genomics of the Viking world

scientific article published on 16 September 2020

Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears

scientific article

Population size changes reshape genomic patterns of diversity

scientific article

Positive selection on apoptosis related genes

scientific article published on 22 December 2009

Postglacial viability and colonization in North America's ice-free corridor.

scientific article

Prehistoric genomes reveal the genetic foundation and cost of horse domestication

scientific article

Proportionally more deleterious genetic variation in European than in African populations.

scientific article

Purifying Selection: Action on Silent Sites

Q&A: Where did the Neanderthals go?

scientific article

Q&A;: who is H. sapiens really, and how do we know?

scientific article (publication date: 31 March 2011)

Quantifying population genetic differentiation from next-generation sequencing data

scientific article

REDUCING AN INTELLECTUAL DEFICIT: COALESCENT THEORY FOR (ALMOST) EVERYONE1

article by Rasmus Nielsen published 2006 in Evolution

REPdenovo: Inferring De Novo Repeat Motifs from Short Sequence Reads

scientific article

Radiation and speciation of pelagic organisms during periods of global warming: the case of the common minke whale, Balaenoptera acutorostrata

scientific article

Radiation of extant cetaceans driven by restructuring of the oceans

scientific article

Rational design of DNA sequence-based strategies for subtyping Listeria monocytogenes

scientific article

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

scientific article

Recent and ongoing selection in the human genome

scientific article

Relatedness mapping and tracts of relatedness for genome-wide data in the presence of linkage disequilibrium

scientific article

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

article

Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants

Reticulate Speciation and Barriers to Introgression in the Anopheles gambiae Species Complex

scientific article

Reticulate speciation and adaptive introgression in the Anopheles gambiae species complex

Retraction Note: CCR5-∆32 is deleterious in the homozygous state in humans

scientific article published on 01 November 2019

Robustness of the estimator of the index of dispersion for DNA sequences

scientific article published in June 1997

SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing data

scientific article (publication date: 2012)

SNP discovery using Next Generation Transcriptomic Sequencing in Atlantic herring (Clupea harengus)

scientific article

Segregation distortion in chicken and the evolutionary consequences of female meiotic drive in birds

scientific article published on 27 January 2010

Selection in Europeans on Fatty Acid Desaturases Associated with Dietary Changes

scientific article

Selection on a variant associated with improved viral clearance drives local, adaptive pseudogenization of interferon lambda 4 (IFNL4)

scientific article

Selection on the FADS region in Europeans

Sequencing of 50 human exomes reveals adaptation to high altitude

scientific article

Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution

scientific article

Single-locus tests of microsatellite evolution: multi-step mutations and constraints on allele size.

scientific article published on April 1999

Site-by-site estimation of the rate of substitution and the correlation of rates in mitochondrial DNA.

scientific article published in June 1997

Speciation with gene flow in equids despite extensive chromosomal plasticity

scientific article

Species-specific responses of Late Quaternary megafauna to climate and humans

scientific article (publication date: 2 November 2011)

Statistical Methods in Molecular Evolution

Statistical approaches for DNA barcoding

scientific article published on February 2006

Statistical assignment of DNA sequences using Bayesian phylogenetics

scientific article published in October 2008

Statistical inferences in phylogeography

scientific article

Statistical tests of selective neutrality in the age of genomics

scientific article

Stochastic Mapping of Morphological Characters

scientific article (publication date: April 2003)

SweepFinder2: increased sensitivity, robustness and flexibility.

scientific article published on 15 February 2016

Synonymous and nonsynonymous rate variation in nuclear genes of mammals.

scientific article

Targets of balancing selection in the human genome

scientific article published on 27 August 2009

Temporal genomic contrasts reveal rapid evolutionary responses in an alpine mammal during recent climate change

scientific article published on 03 May 2019

Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans.

scientific article

The Evolutionary Pathway to Virulence of an RNA Virus

scientific article published on March 2017

The Genetic Basis of Adaptation following Plastic Changes in Coloration in a Novel Environment

scientific article published on 06 September 2018

The Genetic Cost of Neanderthal Introgression

scientific article

The Power of Inbreeding: NGS-Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication

scientific article

The ancestry and affiliations of Kennewick Man

scientific article

The diploid genome sequence of an Asian individual

scientific article

The discovery of single-nucleotide polymorphisms--and inferences about human demographic history

scientific article

The effect of ancient DNA damage on inferences of demographic histories

scientific article published on 24 July 2008

The evolution of gene expression levels in mammalian organs

scientific article (publication date: 19 October 2011)

The first horse herders and the impact of early Bronze Age steppe expansions into Asia

scientific article

The genetic architecture of sporadic and multiple consecutive miscarriage

scientific article published on 25 November 2020

The genetic prehistory of the New World Arctic

scientific article

The genome of a Late Pleistocene human from a Clovis burial site in western Montana

scientific article

The impact of founder events on chromosomal variability in multiply mating species ⬇️

scientific article published on 28 May 2008

The lengths of admixture tracts

scientific article

The mind, the lab, and the field: Three kinds of populations in scientific practice

scientific article published on 07 March 2015

The molecular clock is gone but not forgotten What about Molecular Clocks? Symposium at the Annual Meeting of the Society for the Study of Evolution (SSE), Madison, Wisconsin, USA, 22â 26 June 1999

The origin and evolution of maize in the American Southwest

The origin and evolution of maize in the Southwestern United States

scientific article

The population history of northeastern Siberia since the Pleistocene

scientific article published on 05 June 2019

The population structure of African cultivated rice oryza glaberrima (Steud.): evidence for elevated levels of linkage disequilibrium caused by admixture with O. sativa and ecological adaptation

scientific article

The selection landscape and genetic legacy of ancient Eurasians

scientific article published on 10 January 2024

The sequence and de novo assembly of the giant panda genome

scientific article

The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing

scientific article

Tracing the peopling of the world through genomics

scientific article

Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments

scientific article

Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil

scientific article

Uncovering the genetic history of the present-day Greenlandic population. ⬇️

scientific article

Understanding Admixture Fractions

Unlocking the vault: next-generation museum population genomics

scientific article

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

scientific article

Using nuclear haplotypes with microsatellites to study gene flow between recently separated Cichlid species

scientific article published on April 2004

Variation and association to diabetes in 2000 full mtDNA sequences mined from an exome study in a Danish population

scientific article published on 22 January 2014

Variation in the pattern of nucleotide substitution across sites

scientific article

Whole-Exome Sequencing of 2,000 Danish Individuals and the Role of Rare Coding Variants in Type 2 Diabetes

Whole-exome sequencing of 2,000 Danish individuals and the role of rare coding variants in type 2 diabetes

scientific article

bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS).

scientific article

ngsTools: methods for population genetics analyses from next-generation sequencing data

scientific article

Paulina is supported by:

About Paulina

Help