Rasmus

Research Expertise and Interest

evolution., molecular evolution, population genetics, human variation, human genetics, phylogenetics, applied statistics, genetics, evolutionary processes, evolutionary biology

Research Description

Dr. Nielsen received his Ph.D. from UC-Berkeley in 1998, did postdoctoral research at Harvard University and worked as an assistant professor at Cornell University from 2000-2004.  From 2004 he has been a Professor of Biology at the University of Copenhagen and he joined the faculty at the departments of Integrative Biology and Statistics at Berkeley in Jan. 2008.

His work is on statistical and population genetic analyses of genomic data, in particular methods for detecting natural selection, describing population genetic variation, inferring demography, and methods for association mapping. Much of his current research concerns statistical analysis of next-generation sequencing data, both in the context of medical genetics and population genetics. Many of the methods he has developed are heavily used by other researchers, including the phylogeny based methods for detecting positive selection implemented in PAML, the methods for inferring demographic histories implemented in the IM and IMa programs, the method for detecting selective sweeps implemented in SweepFinder, and the methods for analysing Next Generation Sequencing (NGS) data implemented in ANGSD. 

One of the central problems he has been interested in is the molecular basis of evolutionary adaptation.  What happens at the molecular levels as one species is transformed into another over evolutionary time? To address this question he has developed a number of computational methods and applied them to large scale genomic data, such as genomic comparisons of humans and chimpanzees.  

He has also worked on understanding human genetic variation.  He uses both classical statistical methods and evolutionary inferences to identify genetic variants that affect phenotypic variability in humans, including genetic adaptations to diet and local environmental factors. He has studied the genetic basis of human adaption to high altitude, changes in diet, and cold climates.  He has also worked extensively on analyses of ancient DNA derived from fossils to understand human origins and diversification.

He teaches courses in population genetics, human genetics, and statistics.

Example publications:

  • E Huerta-Sánchez, X Jin, Z Bianba, BM Peter, N Vinckenbosch, Y Liang, X Yi, M He, M Somel, P Ni, B Wang, X Ou, J Luosang, Z Xi Ping Cuo, K Li, G Gao, Y Yin, W Wang, X Zhang, X Xu, H Yang, Y Li, J Wang, J Wang, R Nielsen (2014). Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature 512: 194-197.
  • I Moltke, N Grarup, ME Jørgensen, et al. (2014). A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes. Nature 512: 190-193
  • R Nielsen, JS Paul, A Albrechtsen, YS Song (2011). Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet. 12 (6): 443-451.
  • Hey J. and R. Nielsen. 2007. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc Natl Acad Sci U S A. 104: 2785–2790.

For more information see: https://nielsen-lab.github.io

In the News

Tales from 141,430 and one genomes

Analysis of the world’s largest set of genome data from pregnant women, totaling 141,431 expectant mothers from across China, has uncovered unsuspected associations between genes and birth outcomes, including the birth of twins and a woman’s age at first pregnancy.

What the Inuit can tell us about omega-3 fats and ‘paleo’ diets

The traditional diet of Greenland natives – the Inuit – is held up as an example of how high levels of omega-3 fatty acids can counterbalance the bad health effects of a high-fat diet, but a new study hints that what’s true for the Inuit may not be true for everyone else.

Genome Analysis Pinpoints Arrival and Spread of First Americans

The original Americans came from Siberia in a single wave no more than 23,000 years ago, at the height of the last Ice Age, and apparently hung out in the north – perhaps for thousands of years – before spreading in two distinct populations throughout North and South America, according to a new genomic analysis.

Extinct human cousin gave Tibetans advantage at high elevation

Tens of thousands of years ago, the common ancestors of Han Chinese and Tibetans interbred with a mysterious human-like group known as Denisovans and picked up a unique variant of a gene for hemoglobin regulation that later helped them adapt to a low-oxygen environment on the high Tibetan plateau, reports UC Berkeley professor of integrative biology Rasmus Nielsen

Tibetans adapted to high altitude in less than 3,000 years

UC Berkeley's Rasmus Nielsen teamed up with Chinese researchers to compare the genomes of Tibetans living above 14,000 feet to Han Chinese living at essentially sea level. They found that within the last 3,000 years, Tibetans evolved genetic mutations in a number of genes having to do with how the body deals with oxygen, making it possible for Tibetans to thrive at high altitudes while their Han relatives cannot.

Featured in the Media

Please note: The views and opinions expressed in these articles are those of the authors and do not necessarily reflect the official policy or positions of UC Berkeley.
June 3, 2019

Mutation That Protects Against HIV Raises Death Rate

New York Times
Malcolm Ritter, Associated Press
When a Chinese doctor edited the genomes of twin embryos using CRISPR-Cas9 technology, he intended to reduce their risk of HIV. The scientific community was incensed by the prematurity of the experiment, and, indeed, a new Berkeley study finds that the mutation he used is associated with heightened risk of early death from other causes, including flu. "You should consider all the effects of mutations you induce," says integrative biology professor Rasmus Nielsen, senior author of the new paper, co-authored by postdoctoral researcher Xinzhu Wei. They made the discovery by studying data on some 400,000 people who'd signed up for the UK Biobank, which has tracked their health since. Roughly 4,000 participants carried the mutation in both copies of their CCR5 gene, and 151 had died -- a death rate about 20 percent higher than that of other subjects. For more on this, see our press release at Berkeley News. Stories on this topic appeared in more than 400 sources around the world, including Scientific American, The Scientist, New Scientist, Los Angeles Times, The Atlantic, Wired, BBC News, National Geographic, Bloomberg News, LiveScience, Financial Times (UK), EuroNews (France), Cosmos (Australia), Vaaju (Singapore), Ärzte Zeitung (Germany), and NPR--link to audio.
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