Rasmus Nielsen

Rasmus Nielsen

Professor

ORCID: 0000-0003-0513-6591

Publication year:
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201 - 250 out of 255Page size: 50
  1. 2007
  2. Published

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

    Hey, J. & Nielsen, Rasmus, 2007, In: Proceedings of the National Academy of Science of the United States of America. 104, 8, p. 2785-90 5 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  3. Published

    Localizing recent adaptive evolution in the human genome

    Williamson, S. H., Hubisz, M. J., Clark, A. G., Payseur, B. A., Bustamante, C. D. & Nielsen, Rasmus, 2007, In: PLoS Genetics. 3, 6, p. e90

    Research output: Contribution to journal › Journal article › Research › peer-review

  4. Published

    Maximum likelihood estimation of ancestral codon usage bias parameters in Drosophila

    Nielsen, Rasmus, Bauer DuMont, V. L., Hubisz, M. J. & Aquadro, C. F., 2007, In: Molecular Biology and Evolution. 24, 1, p. 228-35 7 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  5. Published

    Patterns of mutation and selection at synonymous sites in Drosophila

    Singh, N. D., Bauer DuMont, V. L., Hubisz, M. J., Nielsen, Rasmus & Aquadro, C. F., 2007, In: Molecular Biology and Evolution. 24, 12, p. 2687-97 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  6. Published

    Population size changes reshape genomic patterns of diversity

    Pool, J. E. & Nielsen, Rasmus, 2007, In: Evolution. 61, 12, p. 3001-6 5 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  7. Published

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

    Pastene, L. A., Goto, M., Kanda, N., Zerbini, A. N., Kerem, D., Watanabe, K., Bessho, Y., Hasegawa, M., Nielsen, Rasmus, Larsen, F. & Palsbøll, P. J., 2007, In: Molecular Ecology. 16, 7, p. 1481-1495 15 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  8. Published

    Recent and ongoing selection in the human genome

    Nielsen, Rasmus, Hellmann, I., Hubisz, M., Bustamante, C. & Clark, A. G., 2007, In: Nature Reviews. Genetics. 8, 11, p. 857-68 11 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  9. Published

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

    Binladen, J., Gilbert, M Thomas P, Bollback, J. P., Panitz, F., Bendixen, C., Nielsen, Rasmus & Willerslev, Eske, 2007, In: PLoS ONE. 2, 2, p. e197

    Research output: Contribution to journal › Journal article › Research › peer-review

  10. 2006
  11. Published

    Comparative genomics: Difference of expression

    Nielsen, Rasmus, 2006, In: Nature. 440, 7081, p. 161-161

    Research output: Contribution to journal › Journal article › Research › peer-review

  12. Published

    CpG + CpNpG Analysis of Protein-Coding Sequences from Tomato

    Hobolth, A., Nielsen, Rasmus, Wang, Y., Wu, F. & Tanksley, S. D., 2006, In: Molecular Biology and Evolution. 23, 6, p. 1318-1323

    Research output: Contribution to journal › Journal article › Research › peer-review

  13. Published

    Identification of physicochemical selective pressure on protein encoding nucleotide sequences

    Wong, W. S. W., Sainudiin, R. & Nielsen, Rasmus, 2006, In: BMC Bioinformatics. 7, 10 p., 148.

    Research output: Contribution to journal › Journal article › Research › peer-review

  14. Published

    Novel Method To Identify Source-Associated Phylogenetic Clustering Shows that Listeria monocytogenes Includes Niche-Adapted Clonal Groups with Distinct Ecological Preferences

    Nightingale, K. K., Lyles, K., Ayodele, M., Jalan, P., Nielsen, Rasmus & Wiedmann, M., 2006, In: Journal of Clinical Microbiology. 44, 10, p. 3742-3751

    Research output: Contribution to journal › Journal article › Research › peer-review

  15. Published

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

    Nielsen, Rasmus, 2006, In: Evolution. 60, 1, p. 208-209

    Research output: Contribution to journal › Review › Research

  16. Published

    Statistical Approaches for DNA Barcoding

    Nielsen, Rasmus & Matz, M., 2006, In: Systematic Biology. 55, 1, p. 162-169

    Research output: Contribution to journal › Journal article › Research › peer-review

  17. Published

    Why Sex?

    Nielsen, Rasmus, 2006, In: Science. 311, 5763, p. 960-961

    Research output: Contribution to journal › Journal article › Research › peer-review

  18. 2005
  19. Published

    A Scan for Positively Selected Genes in the Genomes of Humans and Chimpanzees

    Nielsen, Rasmus, Bustamente, C., Clark, A. G., Glanowski, S., Sackton, T. B., Hubisz, M. J., Fledel-Alon, A., Tanenbaum, D. M., Civello, D., White, T. J., Sninsky, J. J., Adams, M. D. & Cargill, M., 2005, In: PLoS - Biology. 3, 6, p. e170

    Research output: Contribution to journal › Journal article › Research › peer-review

  20. Published

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

    Matz, M. V. & Nielsen, Rasmus, 2005, In: Philosophical Transactions of the Royal Society of London. Biological Sciences. 360, 1462, p. 1969-1974

    Research output: Contribution to journal › Journal article › Research › peer-review

  21. Published

    Ascertainment bias in studies of human genome-wide polymorphism

    Clark, A. G., Hubisz, M. J., Bustamente, C. D., Williamson, S. H. & Nielsen, Rasmus, 2005, In: Genome Research. 15, 11, p. 1496-1502

    Research output: Contribution to journal › Journal article › Research › peer-review

  22. Published

    Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection

    Yang, Z., Wong, W. S. W. & Nielsen, Rasmus, 2005, In: Molecular Biology and Evolution. 22, 4, p. 1107-1118

    Research output: Contribution to journal › Journal article › Research › peer-review

  23. Published

    Bayesian and maximum likelihood estimation of genetic maps

    York, T. L., Durrett, R. T., Tanksley, S. & Nielsen, Rasmus, 2005, In: Genetics Research. 85, 2, p. 159-168

    Research output: Contribution to journal › Journal article › Research › peer-review

  24. Published

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

    Wang, Y., van der Hoeven, R. S., Nielsen, Rasmus, Mueller, L. A. & Tanksley, S. D., 2005, In: Theoretical and Applied Genetics. 112, 1, p. 72-84

    Research output: Contribution to journal › Journal article › Research › peer-review

  25. Published

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

    Richards, S., Liu, Y., Bettencourt, B. R., Hradecky, P., Letovsky, S., Nielsen, Rasmus & et al., 2005, In: Genome Research. 15, 1, p. 1-18

    Research output: Contribution to journal › Journal article › Research › peer-review

  26. Published

    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

    Sainudiin, R., Wong, W. S. W., Yogeeswaran, K., Nasrallah, J. B., Yang, Z. & Nielsen, Rasmus, 2005, In: Journal of Molecular Evolution. 60, 3, p. 315-326

    Research output: Contribution to journal › Journal article › Research › peer-review

  27. Published

    Detecting coevolving amino acid sites using Bayesian mutational mapping

    Dimmic, M. W., Hubisz, M. J., Bustamente, C. D. & Nielsen, Rasmus, 2005, In: Bioinformatics. 21, 1, p. i126-i135

    Research output: Contribution to journal › Journal article › Research › peer-review

  28. Published

    Detecting selection needs comparative data

    Nielsen, Rasmus & Hubisz, M. J., 2005, In: Nature. 433, 7023, p. E6

    Research output: Contribution to journal › Journal article › Research › peer-review

  29. Published

    Disclosure of variation

    Nielsen, Rasmus, 2005, In: Nature. 434, 7031, p. 288-289

    Research output: Contribution to journal › Journal article › Research › peer-review

  30. Published

    Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level

    Zhang, J., Nielsen, Rasmus & Yang, Z., 2005, In: Molecular Biology and Evolution. 22, 12, p. 2472-2479

    Research output: Contribution to journal › Journal article › Research › peer-review

  31. Published

    Genomic scans for selective sweeps using SNP data

    Nielsen, Rasmus, Williamson, S., Kim, Y., Hubisz, M. J., Clark, A. G. & Bustamente, C., 2005, In: Genome Research. 15, 11, p. 1566-1575

    Research output: Contribution to journal › Journal article › Research › peer-review

  32. Published

    Mapping Mutations on Phylogenies

    Nielsen, Rasmus, 2005, Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Dunn, M. J., Jorde, L. B., Little, P. F. R. & Subramaniam, S. (eds.). Wiley

    Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research

  33. Published

    Molecular Signatures of Natural Selection

    Nielsen, Rasmus, 2005, In: Annual Review of Genetics. 39, p. 197-218

    Research output: Contribution to journal › Journal article › Research › peer-review

  34. Published

    Natural selection on protein-coding genes in the human genome

    Bustamente, C. D., Fledel-Alon, A., Williamson, S., Nielsen, Rasmus, Hubisz, M., Glanowski, S., Tanenbaum, D. M., White, T. J., Sninsky, J. J., Hernandez, R. D., Civello, D., Adams, M. D., Cargill, M. & Clark, A. G., 2005, In: Nature. 437, 7062, p. 1153-1157

    Research output: Contribution to journal › Letter › Research

  35. Published

    Peopling the Americas

    Nielsen, Rasmus, 2005, In: European Journal of Human Genetics. 13, 10, p. 1100-1101

    Research output: Contribution to journal › Comment/debate › Research

  36. Published

    Simultaneous inference of selection and population growth from patterns of variation in the human genome

    Williamson, S. H., Hernandez, R., Fledel-Alon, A., Zhu, L., Nielsen, Rasmus & Bustamente, C. D., 2005, In: Proceedings of the National Academy of Science of the United States of America. 102, 22, p. 7882-7887

    Research output: Contribution to journal › Journal article › Research › peer-review

  37. Published

    Statistical Methods in Molecular Evolution

    Nielsen, Rasmus (ed.), 2005, New York: Springer. 508 p. (Statistics for Biology and Health).

    Research output: Book/Report › Book › Research › peer-review

  38. Published

    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

    Semon, M., Nielsen, Rasmus, Jones, M. P. & McCouch, S. R., 2005, In: Genetics. 169, 3, p. 1639-1647

    Research output: Contribution to journal › Journal article › Research › peer-review

  39. 2004
  40. Published

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

    Jobson, R. W., Nielsen, Rasmus, Laakkonen, L., Wikström, M. & Albert, V. A., 2004, In: Proceedings of the National Academy of Sciences of the United States of America. 101, 52, p. 18064-18068 5 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  41. 2003

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

    Nielsen, Rasmus & Signorovitch, J., 2003, In: Theoretical Population Biology. 63, 3, p. 245-255 11 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  43. Positive Selection in the Human Genome Inferred from Human-Chimp-Mouse Orthologous Gene Alignments

    Clark, A. G., Glanowski, S., Nielsen, Rasmus, Thomas, P., Kejariwal, A., Todd, M. J., Tanenbaum, D. M., Civello, D., Lu, F., Murphy, B., Ferriera, S., Wang, G., Zheng, X., White, T. J., Sninsky, J. J., Adams, M. D. & Cargill, M., 2003, In: Cold Spring Harbor Symposia on Quantitative Biology. 68, 1, p. 479-486 8 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  44. 2002

  45. Bayesian estimation of the number of inversions in the history of two chromosomes

    York, T. L., Durrett, R. & Nielsen, Rasmus, 1 Dec 2002, In: Journal of Computational Biology. 9, 6, p. 805-818 14 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  46. 2001

  47. Distinguishing Migration From Isolation: A Markov Chain Monte Carlo Approach

    Nielsen, Rasmus & Wakeley, J., 2001, In: Genetics. 158, 2, p. 885-896 12 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  48. The discovery of Single-Nucleotide Polymorphisms: and Inferences about Human Demographic History

    Wakeley, J., Nielsen, Rasmus, Liu-Cordero, S. N. & Ardlie, K., 2001, In: American Journal of Human Genetics. 69, 6, p. 1332-1347 16 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  49. 1999

  50. Changes in ds/dn in the HIV-1 env Gene

    Nielsen, Rasmus, 1999, In: MOLECULAR BIOLOGY AND EVOLUTION . 16, 5, p. 711-714 4 p.

    Research output: Contribution to journal › Letter › Research › peer-review

  51. Effect of nonindependent substitution on phylogenetic accuracy

    Huelsenbeck, J. P. & Nielsen, Rasmus, 1999, In: Systematic Biology. 48, 2, p. 317-328 12 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  52. Published

    Evidence for a Na+/Ca2+ exchange mechanism in frog skin epithelium

    Madsen, K. H., Larsen, Birger Brodin & Nielsen, Rasmus, 1999, In: Pflügers Archiv - European Journal of Physiology. 437, 2, p. 175-81 7 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  53. Published

    Single-Locus Tests of Microsatellite Evolution: Multi-Step Mutations and Constraints on Allele Size

    Nielsen, Rasmus & Palsbøll, P. J., 1999, In: Molecular Phylogenetics and Evolution. 11, 3, p. 477-484 8 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  54. 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, 22-26 June 1999

    Nielsen, Rasmus, 1999, In: Trends in Genetics. 15, 11, p. 442-443 2 p.

    Research output: Contribution to journal › Conference article › Research › peer-review

  55. Variation in the pattern of nucleotide substitution across sites

    Huelsenbeck, J. P. & Nielsen, Rasmus, 1999, In: Journal of Molecular Evolution. 48, 1, p. 86-93 8 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  56. 1998

  57. Synonymous and nonsynonymous rate variation in nuclear genes of mammals

    Yang, Z. & Nielsen, Rasmus, 23 Apr 1998, In: Journal of Molecular Evolution. 46, 4, p. 409-418 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  58. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene

    Nielsen, Rasmus & Yang, Z., 1 Mar 1998, In: Genetics. 148, 3, p. 929-936 8 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  59. Maximum-likelihood estimation of population divergence times and population phylogeny in models without mutation

    Nielsen, Rasmus, Mountain, J. L., Huelsenbeck, J. P. & Slatkin, M., 1 Jan 1998, In: Evolution. 52, 3, p. 669-677 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

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