Rasmus Nielsen, Ph.D. - Publications

Integrative Biology University of California, Berkeley, Berkeley, CA 
Population Genomics

273 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Jin Y, Aguilar-Gómez D, Brandt DYC, Square TA, Li J, Liu Z, Wang T, Sudmant PH, Miller CT, Nielsen R. Population genomics of variegated toad-headed lizard Phrynocephalus versicolor and its adaptation to the colorful sand of the Gobi Desert. Genome Biology and Evolution. PMID 35679302 DOI: 10.1093/gbe/evac076  0.725
2022 Zhang Z, Zhang Y, Wang Y, Zhao Z, Yang M, Zhang L, Zhou B, Xu B, Zhang H, Chen T, Dai W, Zhou Y, Shi S, Nielsen R, Li SC, et al. The Tibetan-Yi region is both a corridor and a barrier for human gene flow. Cell Reports. 39: 110720. PMID 35476999 DOI: 10.1016/j.celrep.2022.110720  0.829
2022 Guerra G, Nielsen R. Covariance of pairwise differences on a multi-species coalescent tree and implications for . Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 377: 20200415. PMID 35430886 DOI: 10.1098/rstb.2020.0415  0.326
2022 Chen C, Parejo M, Momeni J, Langa J, Nielsen RO, Shi W, Vingborg R, Kryger P, Bouga M, Estonba A, Meixner M. Population Structure and Diversity in European Honey Bees ( L.)-An Empirical Comparison of Pool and Individual Whole-Genome Sequencing. Genes. 13. PMID 35205227 DOI: 10.3390/genes13020182  0.346
2021 Chen ZH, Xu YX, Xie XL, Wang DF, Aguilar-Gómez D, Liu GJ, Li X, Esmailizadeh A, Rezaei V, Kantanen J, Ammosov I, Nosrati M, Periasamy K, Coltman DW, Lenstra JA, ... Nielsen R, et al. Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep. Communications Biology. 4: 1307. PMID 34795381 DOI: 10.1038/s42003-021-02817-4  0.312
2021 Cheng JY, Stern AJ, Racimo F, Nielsen R. Detecting selection in multiple populations by modelling ancestral admixture components. Molecular Biology and Evolution. PMID 34626111 DOI: 10.1093/molbev/msab294  0.824
2021 Zhang X, Witt KE, Bañuelos MM, Ko A, Yuan K, Xu S, Nielsen R, Huerta-Sanchez E. The history and evolution of the Denisovan- haplotype in Tibetans. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34050022 DOI: 10.1073/pnas.2020803118  0.353
2021 Margaryan A, Lawson DJ, Sikora M, Racimo F, Rasmussen S, Moltke I, Cassidy LM, Jørsboe E, Ingason A, Pedersen MW, Korneliussen T, Wilhelmson H, Buś MM, de Barros Damgaard P, Martiniano R, ... ... Nielsen R, et al. Author Correction: Population genomics of the Viking world. Nature. PMID 33707634 DOI: 10.1038/s41586-021-03328-2  0.81
2021 Svedberg J, Shchur V, Reinman S, Nielsen R, Corbett-Detig R. Inferring Adaptive Introgression Using Hidden Markov Models. Molecular Biology and Evolution. PMID 33502512 DOI: 10.1093/molbev/msab014  0.339
2020 Pipes L, Wang H, Huelsenbeck JP, Nielsen R. Assessing uncertainty in the rooting of the SARS-CoV-2 phylogeny. Molecular Biology and Evolution. PMID 33295605 DOI: 10.1093/molbev/msaa316  0.549
2020 Margaryan A, Lawson DJ, Sikora M, Racimo F, Rasmussen S, Moltke I, Cassidy LM, Jørsboe E, Ingason A, Pedersen MW, Korneliussen T, Wilhelmson H, Buś MM, de Barros Damgaard P, Martiniano R, ... ... Nielsen R, et al. Population genomics of the Viking world. Nature. 585: 390-396. PMID 32939067 DOI: 10.1038/S41586-020-2688-8  0.84
2020 Márquez R, Linderoth TP, Mejía-Vargas D, Nielsen R, Amézquita A, Kronforst MR. Divergence, gene flow and the origin of leapfrog geographic distributions: The history of color pattern variation in Phyllobates poison-dart frogs. Molecular Ecology. PMID 32814358 DOI: 10.1111/Mec.15598  0.409
2020 Pei J, Zhang Y, Nielsen R, Wu Y. Inferring the ancestry of parents and grandparents from genetic data. Plos Computational Biology. 16: e1008065. PMID 32797037 DOI: 10.1371/Journal.Pcbi.1008065  0.407
2020 Shchur V, Svedberg J, Medina P, Corbett-Detig R, Nielsen R. On the Distribution of Tract Lengths During Adaptive Introgression. G3 (Bethesda, Md.). PMID 32763953 DOI: 10.1534/G3.120.401616  0.416
2020 Todesco M, Owens GL, Bercovich N, Légaré JS, Soudi S, Burge DO, Huang K, Ostevik KL, Drummond EBM, Imerovski I, Lande K, Pascual-Robles MA, Nanavati M, Jahani M, Cheung W, ... ... Nielsen R, et al. Massive haplotypes underlie ecotypic differentiation in sunflowers. Nature. PMID 32641831 DOI: 10.1038/S41586-020-2467-6  0.72
2020 Setter D, Mousset S, Cheng X, Nielsen R, DeGiorgio M, Hermisson J. VolcanoFinder: Genomic scans for adaptive introgression. Plos Genetics. 16: e1008867. PMID 32555579 DOI: 10.1371/Journal.Pgen.1008867  0.466
2020 Wang MS, Wang S, Li Y, Jhala Y, Thakur M, Otecko NO, Si JF, Chen HM, Shapiro B, Nielsen R, Zhang YP, Wu DD. Ancient hybridization with an unknown population facilitated high altitude adaptation of canids. Molecular Biology and Evolution. PMID 32384152 DOI: 10.1093/Molbev/Msaa113  0.474
2020 Corbett-Detig R, Russell S, Nielsen R, Losos J. Phenotypic convergence is not mirrored at the protein level in a lizard adaptive radiation. Molecular Biology and Evolution. PMID 32027369 DOI: 10.1093/Molbev/Msaa028  0.426
2020 da Fonseca RR, Couto A, Machado AM, Brejova B, Albertin CB, Silva F, Gardner P, Baril T, Hayward A, Campos A, Ribeiro ÂM, Barrio-Hernandez I, Hoving HJ, Tafur-Jimenez R, Chu C, ... ... Nielsen R, et al. A draft genome sequence of the elusive giant squid, Architeuthis dux. Gigascience. 9. PMID 31942620 DOI: 10.1093/Gigascience/Giz152  0.372
2020 Barrett A, Arbeithuber B, Zaidi A, Wilton P, Paul IM, Nielsen R, Makova KD. Pronounced somatic bottleneck in mitochondrial DNA of human hair. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 375: 20190175. PMID 31787049 DOI: 10.1098/Rstb.2019.0175  0.65
2019 Zaidi AA, Wilton PR, Su MS, Paul IM, Arbeithuber B, Anthony K, Nekrutenko A, Nielsen R, Makova KD. Bottleneck and selection in the germline and maternal age influence transmission of mitochondrial DNA in human pedigrees. Proceedings of the National Academy of Sciences of the United States of America. PMID 31757848 DOI: 10.1073/Pnas.1906331116  0.653
2019 Ling G, Miller D, Nielsen R, Stern A. A Bayesian framework for inferring the influence of sequence context on point mutations. Molecular Biology and Evolution. PMID 31651955 DOI: 10.1093/Molbev/Msz248  0.39
2019 Exposito-Alonso M, Burbano HA, Bossdorf O, Nielsen R, Weigel D. Publisher Correction: Natural selection on the Arabidopsis thaliana genome in present and future climates. Nature. PMID 31570884 DOI: 10.1038/S41586-019-1626-0  0.795
2019 Stern AJ, Wilton PR, Nielsen R. An approximate full-likelihood method for inferring selection and allele frequency trajectories from DNA sequence data. Plos Genetics. 15: e1008384. PMID 31518343 DOI: 10.1371/Journal.Pgen.1008384  0.396
2019 Moreno-Mayar JV, Korneliussen TS, Dalal J, Renaud G, Albrechtsen A, Nielsen R, Malaspinas AS. A likelihood method for estimating present-day human contamination in ancient male samples using low-depth X-chromosome data. Bioinformatics (Oxford, England). PMID 31504166 DOI: 10.1093/Bioinformatics/Btz660  0.724
2019 Exposito-Alonso M, Burbano HA, Bossdorf O, Nielsen R, Weigel D. Natural selection on the Arabidopsis thaliana genome in present and future climates. Nature. PMID 31462776 DOI: 10.1038/S41586-019-1520-9  0.818
2019 Sikora M, Pitulko VV, Sousa VC, Allentoft ME, Vinner L, Rasmussen S, Margaryan A, de Barros Damgaard P, de la Fuente C, Renaud G, Yang MA, Fu Q, Dupanloup I, Giampoudakis K, Nogués-Bravo D, ... ... Nielsen R, et al. The population history of northeastern Siberia since the Pleistocene. Nature. PMID 31168093 DOI: 10.1038/S41586-019-1279-Z  0.812
2019 Ko A, Nielsen R. Joint Estimation of Pedigrees and Effective Population Size Using Markov Chain Monte Carlo. Genetics. PMID 31123041 DOI: 10.1534/Genetics.119.302280  0.37
2019 Bi K, Linderoth T, Singhal S, Vanderpool D, Patton JL, Nielsen R, Moritz C, Good JM. Temporal genomic contrasts reveal rapid evolutionary responses in an alpine mammal during recent climate change. Plos Genetics. 15: e1008119. PMID 31050681 DOI: 10.1371/Journal.Pgen.1008119  0.452
2019 Prohaska A, Racimo F, Schork AJ, Sikora M, Stern AJ, Ilardo M, Allentoft ME, Folkersen L, Buil A, Moreno-Mayar JV, Korneliussen T, Geschwind D, Ingason A, Werge T, Nielsen R, et al. Human Disease Variation in the Light of Population Genomics. Cell. 177: 115-131. PMID 30901534 DOI: 10.1016/J.Cell.2019.01.052  0.824
2019 Alves JM, Carneiro M, Cheng JY, Lemos de Matos A, Rahman MM, Loog L, Campos PF, Wales N, Eriksson A, Manica A, Strive T, Graham SC, Afonso S, Bell DJ, Belmont L, ... ... Nielsen R, et al. Parallel adaptation of rabbit populations to myxoma virus. Science (New York, N.Y.). PMID 30765607 DOI: 10.1126/Science.Aau7285  0.395
2019 Harris K, Zhang Y, Nielsen R. Genetic rescue and the maintenance of native ancestry Conservation Genetics. 20: 59-64. DOI: 10.1007/S10592-018-1132-1  0.47
2018 Chen H, Alvarez JJS, Ng SH, Nielsen R, Zhai W. Passage adaptation correlates with the reduced efficacy of the influenza vaccine. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 30561532 DOI: 10.1093/Cid/Ciy1065  0.587
2018 Rascovan N, Sjögren KG, Kristiansen K, Nielsen R, Willerslev E, Desnues C, Rasmussen S. Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline. Cell. PMID 30528431 DOI: 10.1016/J.Cell.2018.11.005  0.427
2018 Rogers RL, Zhou L, Chu C, Márquez R, Corl A, Linderoth T, Freeborn L, MacManes MD, Xiong Z, Zheng J, Guo C, Xun X, Kronforst MR, Summers K, Wu Y, ... ... Nielsen R, et al. Genomic Takeover by Transposable Elements in the Strawberry Poison Frog. Molecular Biology and Evolution. 35: 2913-2927. PMID 30517748 DOI: 10.1093/Molbev/Msy185  0.587
2018 Moreno-Mayar JV, Vinner L, de Barros Damgaard P, de la Fuente C, Chan J, Spence JP, Allentoft ME, Vimala T, Racimo F, Pinotti T, Rasmussen S, Margaryan A, Iraeta Orbegozo M, Mylopotamitaki D, Wooller M, ... ... Nielsen R, et al. Early human dispersals within the Americas. Science (New York, N.Y.). PMID 30409807 DOI: 10.1126/Science.Aav2621  0.818
2018 Liu S, Huang S, Chen F, Zhao L, Yuan Y, Francis SS, Fang L, Li Z, Lin L, Liu R, Zhang Y, Xu H, Li S, Zhou Y, Davies RW, ... ... Nielsen R, et al. Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History. Cell. 175: 347-359.e14. PMID 30290141 DOI: 10.1016/J.Cell.2018.08.016  0.808
2018 Medina P, Thornlow B, Nielsen R, Corbett-Detig R. Estimating the Timing of Multiple Admixture Pulses During Local Ancestry Inference. Genetics. PMID 30206187 DOI: 10.1534/Genetics.118.301411  0.386
2018 Corl A, Bi K, Luke C, Challa AS, Stern AJ, Sinervo B, Nielsen R. The Genetic Basis of Adaptation following Plastic Changes in Coloration in a Novel Environment. Current Biology : Cb. PMID 30197088 DOI: 10.1016/J.Cub.2018.06.075  0.429
2018 de Barros Damgaard P, Marchi N, Rasmussen S, Peyrot M, Renaud G, Korneliussen T, Moreno-Mayar JV, Pedersen MW, Goldberg A, Usmanova E, Baimukhanov N, Loman V, Hedeager L, Pedersen AG, Nielsen K, ... ... Nielsen R, et al. Author Correction: 137 ancient human genomes from across the Eurasian steppes. Nature. PMID 30166629 DOI: 10.1038/S41586-018-0488-1  0.732
2018 Ilardo M, Nielsen R. Human adaptation to extreme environmental conditions. Current Opinion in Genetics & Development. 53: 77-82. PMID 30077046 DOI: 10.1016/J.Gde.2018.07.003  0.369
2018 Shchur V, Nielsen R. On the number of siblings and p-th cousins in a large population sample. Journal of Mathematical Biology. PMID 29876645 DOI: 10.1007/S00285-018-1252-8  0.314
2018 Wu DD, Ding XD, Wang S, Wójcik JM, Zhang Y, Tokarska M, Li Y, Wang MS, Faruque O, Nielsen R, Zhang Q, Zhang YP. Pervasive introgression facilitated domestication and adaptation in the Bos species complex. Nature Ecology & Evolution. PMID 29784979 DOI: 10.1038/S41559-018-0562-Y  0.442
2018 Damgaard PB, Marchi N, Rasmussen S, Peyrot M, Renaud G, Korneliussen T, Moreno-Mayar JV, Pedersen MW, Goldberg A, Usmanova E, Baimukhanov N, Loman V, Hedeager L, Pedersen AG, Nielsen K, ... ... Nielsen R, et al. 137 ancient human genomes from across the Eurasian steppes. Nature. PMID 29743675 DOI: 10.1038/S41586-018-0094-2  0.415
2018 de Barros Damgaard P, Martiniano R, Kamm J, Moreno-Mayar JV, Kroonen G, Peyrot M, Barjamovic G, Rasmussen S, Zacho C, Baimukhanov N, Zaibert V, Merz V, Biddanda A, Merz I, Loman V, ... ... Nielsen R, et al. The first horse herders and the impact of early Bronze Age steppe expansions into Asia. Science (New York, N.Y.). PMID 29743352 DOI: 10.1126/Science.Aar7711  0.643
2018 Ilardo MA, Moltke I, Korneliussen TS, Cheng J, Stern AJ, Racimo F, de Barros Damgaard P, Sikora M, Seguin-Orlando A, Rasmussen S, van den Munckhof ICL, Ter Horst R, Joosten LAB, Netea MG, Salingkat S, ... Nielsen R, et al. Physiological and Genetic Adaptations to Diving in Sea Nomads. Cell. 173: 569-580.e15. PMID 29677510 DOI: 10.1016/J.Cell.2018.03.054  0.817
2018 Zhou X, Guang X, Sun D, Xu S, Li M, Seim I, Jie W, Yang L, Zhu Q, Xu J, Gao Q, Kaya A, Dou Q, Chen B, Ren W, ... ... Nielsen R, et al. Population genomics of finless porpoises reveal an incipient cetacean species adapted to freshwater. Nature Communications. 9: 1276. PMID 29636446 DOI: 10.1038/S41467-018-03722-X  0.457
2018 Zhou X, Sun D, Guang X, Ma S, Fang X, Mariotti M, Nielsen R, Gladyshev VN, Yang G. Molecular Footprints of Aquatic Adaptation Including Bone Mass Changes in Cetaceans. Genome Biology and Evolution. 10: 967-975. PMID 29608729 DOI: 10.1093/Gbe/Evy062  0.367
2018 Schroeder H, Sikora M, Gopalakrishnan S, Cassidy LM, Maisano Delser P, Sandoval Velasco M, Schraiber JG, Rasmussen S, Homburger JR, Ávila-Arcos MC, Allentoft ME, Moreno-Mayar JV, Renaud G, Gómez-Carballa A, Laffoon JE, ... ... Nielsen R, et al. Origins and genetic legacies of the Caribbean Taino. Proceedings of the National Academy of Sciences of the United States of America. PMID 29463742 DOI: 10.1073/Pnas.1716839115  0.81
2018 Wilton PR, Zaidi A, Makova K, Nielsen R. A Population Phylogenetic View of Mitochondrial Heteroplasmy. Genetics. PMID 29343499 DOI: 10.1534/Genetics.118.300711  0.658
2018 Moreno-Mayar JV, Potter BA, Vinner L, Steinrücken M, Rasmussen S, Terhorst J, Kamm JA, Albrechtsen A, Malaspinas AS, Sikora M, Reuther JD, Irish JD, Malhi RS, Orlando L, Song YS, ... Nielsen R, et al. Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans. Nature. 553: 203-207. PMID 29323294 DOI: 10.1038/Nature25173  0.719
2018 Song J, Han S, Amaru R, Quispe T, Kim D, Crawford JE, Stehlik J, Nielsen R, Lee Y, Prchal JT. Novel Form of Alternative Splicing of NFKB1. Its Role in Polycythemia and Adaptation to High Altitude in Andean Aymara Blood. 132: 2316-2316. DOI: 10.1182/Blood-2018-99-117463  0.347
2017 Crawford JE, Amaru R, Song J, Julian CG, Racimo F, Cheng JY, Guo X, Yao J, Ambale-Venkatesh B, Lima JA, Rotter JI, Stehlik J, Moore LG, Prchal JT, Nielsen R. Natural Selection on Genes Related to Cardiovascular Health in High-Altitude Adapted Andeans. American Journal of Human Genetics. 101: 752-767. PMID 29100088 DOI: 10.1016/J.Ajhg.2017.09.023  0.804
2017 Sikora M, Seguin-Orlando A, Sousa VC, Albrechtsen A, Korneliussen T, Ko A, Rasmussen S, Dupanloup I, Nigst PR, Bosch MD, Renaud G, Allentoft ME, Margaryan A, Vasilyev SV, Veselovskaya EV, ... ... Nielsen R, et al. Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers. Science (New York, N.Y.). PMID 28982795 DOI: 10.1126/Science.Aao1807  0.6
2017 Harris K, Nielsen R. Q&A: Where did the Neanderthals go? Bmc Biology. 15: 73. PMID 28859637 DOI: 10.1186/S12915-017-0414-2  0.395
2017 Ko A, Nielsen R. Composite likelihood method for inferring local pedigrees. Plos Genetics. 13: e1006963. PMID 28827797 DOI: 10.1371/Journal.Pgen.1006963  0.353
2017 Figueiró HV, Li G, Trindade FJ, Assis J, Pais F, Fernandes G, Santos SHD, Hughes GM, Komissarov A, Antunes A, Trinca CS, Rodrigues MR, Linderoth T, Bi K, Silveira L, ... ... Nielsen R, et al. Genome-wide signatures of complex introgression and adaptive evolution in the big cats. Science Advances. 3: e1700299. PMID 28776029 DOI: 10.1126/Sciadv.1700299  0.472
2017 Wang H, Vieira FG, Crawford JE, Chu C, Nielsen R. Asian wild rice is a hybrid swarm with extensive gene flow and feralization from domesticated rice. Genome Research. PMID 28385712 DOI: 10.1101/Gr.204800.116  0.382
2017 Cheng YJ, Mailund T, Nielsen R. Fast admixture analysis and population tree estimation for SNP and NGS data. Bioinformatics (Oxford, England). PMID 28334108 DOI: 10.1093/Bioinformatics/Btx098  0.394
2017 Buckley MT, Racimo F, Allentoft ME, Jensen MK, Jonsson A, Huang H, Hormozdiari F, Sikora M, Marnetto D, Eskin E, Jørgensen ME, Grarup N, Pedersen O, Hansen T, Kraft P, ... ... Nielsen R, et al. Selection in Europeans on fatty acid desaturases associated with dietary changes. Molecular Biology and Evolution. PMID 28333262 DOI: 10.1093/Molbev/Msx103  0.784
2017 Nielsen R, Akey JM, Jakobsson M, Pritchard JK, Tishkoff S, Willerslev E. Tracing the peopling of the world through genomics. Nature. 541: 302-310. PMID 28102248 DOI: 10.1038/Nature21347  0.469
2017 Corbett-Detig R, Nielsen R. A Hidden Markov Model Approach for Simultaneously Estimating Local Ancestry and Admixture Time Using Next Generation Sequence Data in Samples of Arbitrary Ploidy. Plos Genetics. 13: e1006529. PMID 28045893 DOI: 10.1371/Journal.Pgen.1006529  0.448
2017 Amaru R, Song J, Reading NS, Gordeuk VR, Quispe T, Moore L, Nielsen R, Prchal JT. Erythroid and Cardiovascular High Altitude-Selected Haplotypes in Andean Aymaras and Tibetans Blood. 130: 2205-2205. DOI: 10.1182/Blood.V130.Suppl_1.2205.2205  0.349
2016 Racimo F, Gokhman D, Fumagalli M, Ko A, Hansen T, Moltke I, Albrechtsen A, Carmel L, Huerta-Sánchez E, Nielsen R. Archaic adaptive introgression in TBX15/WARS2. Molecular Biology and Evolution. PMID 28007980 DOI: 10.1093/Molbev/Msw283  0.818
2016 Nielsen R. Fumio Tajima and the Origin of Modern Population Genetics. Genetics. 204: 389-390. PMID 27729488 DOI: 10.1534/Genetics.116.195271  0.366
2016 Malaspinas AS, Westaway MC, Muller C, Sousa VC, Lao O, Alves I, Bergström A, Athanasiadis G, Cheng JY, Crawford JE, Heupink TH, Macholdt E, Peischl S, Rasmussen S, Schiffels S, ... ... Nielsen R, et al. A genomic history of Aboriginal Australia. Nature. PMID 27654914 DOI: 10.1038/Nature18299  0.816
2016 Pagani L, Lawson DJ, Jagoda E, Mörseburg A, Eriksson A, Mitt M, Clemente F, Hudjashov G, DeGiorgio M, Saag L, Wall JD, Cardona A, Mägi R, Sayres MA, Kaewert S, ... ... Nielsen R, et al. Genomic analyses inform on migration events during the peopling of Eurasia. Nature. PMID 27654910 DOI: 10.1038/Nature19792  0.522
2016 Wang H, Xu X, Vieira FG, Xiao Y, Li Z, Wang J, Nielsen R, Chu C. The Power of Inbreeding: NGS Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication. Molecular Plant. PMID 27179918 DOI: 10.1016/J.Molp.2016.04.018  0.449
2016 DeGiorgio M, Huber CD, Hubisz MJ, Hellmann I, Nielsen R. SweepFinder2: increased sensitivity, robustness and flexibility. Bioinformatics (Oxford, England). PMID 27153702 DOI: 10.1093/Bioinformatics/Btw051  0.307
2016 Vieira FG, Albrechtsen A, Nielsen R. Estimating IBD tracts from low coverage NGS data. Bioinformatics (Oxford, England). PMID 27153648 DOI: 10.1093/Bioinformatics/Btw212  0.311
2016 Harris K, Nielsen R. The Genetic Cost of Neanderthal Introgression. Genetics. PMID 27038113 DOI: 10.1534/Genetics.116.186890  0.414
2016 Chu C, Nielsen R, Wu Y. REPdenovo: Inferring De Novo Repeat Motifs from Short Sequence Reads. Plos One. 11: e0150719. PMID 26977803 DOI: 10.1371/Journal.Pone.0150719  0.388
2016 Crawford JE, Riehle MM, Markianos K, Bischoff E, Guelbeogo WM, Gneme A, Sagnon N, Vernick KD, Nielsen R, Lazzaro BP. Evolution of GOUNDRY, a cryptic subgroup of Anopheles gambiae s.l., and its impact on susceptibility to Plasmodium infection. Molecular Ecology. PMID 26846876 DOI: 10.1111/Mec.13572  0.455
2015 da Fonseca RR, Smith BD, Wales N, Cappellini E, Skoglund P, Fumagalli M, Samaniego JA, Carøe C, Ávila-Arcos MC, Hufnagel DE, Korneliussen TS, Vieira FG, Jakobsson M, Arriaza B, Willerslev E, ... Nielsen R, et al. The origin and evolution of maize in the Southwestern United States. Nature Plants. 1: 14003. PMID 27246050 DOI: 10.1038/Nplants.2014.3  0.41
2015 Crawford JE, Riehle MM, Guelbeogo WM, Gneme A, Sagnon N, Vernick KD, Nielsen R, Lazzaro BP. Reticulate Speciation and Barriers to Introgression in the Anopheles gambiae Species Complex. Genome Biology and Evolution. 7: 3116-3131. PMID 26615027 DOI: 10.1093/Gbe/Evv203  0.388
2015 Librado P, Der Sarkissian C, Ermini L, Schubert M, Jónsson H, Albrechtsen A, Fumagalli M, Yang MA, Gamba C, Seguin-Orlando A, Mortensen CD, Petersen B, Hoover CA, Lorente-Galdos B, Nedoluzhko A, ... ... Nielsen R, et al. Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments. Proceedings of the National Academy of Sciences of the United States of America. PMID 26598656 DOI: 10.1073/Pnas.1513696112  0.823
2015 Rasmussen S, Allentoft ME, Nielsen K, Orlando L, Sikora M, Sjögren KG, Pedersen AG, Schubert M, Van Dam A, Kapel CM, Nielsen HB, Brunak S, Avetisyan P, Epimakhov A, Khalyapin MV, ... ... Nielsen R, et al. Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago. Cell. 163: 571-82. PMID 26496604 DOI: 10.1016/J.Cell.2015.10.009  0.399
2015 Fumagalli M, Moltke I, Grarup N, Racimo F, Bjerregaard P, Jørgensen ME, Korneliussen TS, Gerbault P, Skotte L, Linneberg A, Christensen C, Brandslund I, Jørgensen T, Huerta-Sánchez E, Schmidt EB, ... ... Nielsen R, et al. Greenlandic Inuit show genetic signatures of diet and climate adaptation. Science (New York, N.Y.). 349: 1343-7. PMID 26383953 DOI: 10.1126/Science.Aab2319  0.788
2015 Huber CD, DeGiorgio M, Hellmann I, Nielsen R. Detecting recent selective sweeps while controlling for mutation rate and background selection. Molecular Ecology. PMID 26290347 DOI: 10.1111/Mec.13351  0.371
2015 Raghavan M, Steinrücken M, Harris K, Schiffels S, Rasmussen S, DeGiorgio M, Albrechtsen A, Valdiosera C, Ávila-Arcos MC, Malaspinas AS, Eriksson A, Moltke I, Metspalu M, Homburger JR, Wall J, ... ... Nielsen R, et al. Genomic evidence for the Pleistocene and recent population history of Native Americans. Science (New York, N.Y.). PMID 26198033 DOI: 10.1126/Science.Aab3884  0.765
2015 Rohlfs RV, Aguiar VR, Lohmueller KE, Castro AM, Ferreira AC, Almeida VC, Louro ID, Nielsen R. Fitting the Balding-Nichols model to forensic databases. Forensic Science International. Genetics. 19: 86-91. PMID 26186694 DOI: 10.1016/J.Fsigen.2015.05.005  0.348
2015 Rohlfs RV, Nielsen R. Phylogenetic ANOVA: The Expression Variance and Evolution Model for Quantitative Trait Evolution. Systematic Biology. 64: 695-708. PMID 26169525 DOI: 10.1093/Sysbio/Syv042  0.346
2015 Rasmussen M, Sikora M, Albrechtsen A, Korneliussen TS, Moreno-Mayar JV, Poznik GD, Zollikofer CP, Ponce de León MS, Allentoft ME, Moltke I, Jónsson H, Valdiosera C, Malhi RS, Orlando L, Bustamante CD, ... ... Nielsen R, et al. The ancestry and affiliations of Kennewick Man. Nature. PMID 26087396 DOI: 10.1038/Nature14625  0.574
2015 Allentoft ME, Sikora M, Sjögren KG, Rasmussen S, Rasmussen M, Stenderup J, Damgaard PB, Schroeder H, Ahlström T, Vinner L, Malaspinas AS, Margaryan A, Higham T, Chivall D, Lynnerup N, ... ... Nielsen R, et al. Population genomics of Bronze Age Eurasia. Nature. 522: 167-72. PMID 26062507 DOI: 10.1038/Nature14507  0.725
2015 Cao H, Wu H, Luo R, Huang S, Sun Y, Tong X, Xie Y, Liu B, Yang H, Zheng H, Li J, Li B, Wang Y, Yang F, Sun P, ... ... Nielsen R, et al. De novo assembly of a haplotype-resolved human genome. Nature Biotechnology. 33: 617-22. PMID 26006006 DOI: 10.1038/Nbt.3200  0.423
2015 Racimo F, Sankararaman S, Nielsen R, Huerta-Sánchez E. Evidence for archaic adaptive introgression in humans. Nature Reviews. Genetics. 16: 359-71. PMID 25963373 DOI: 10.1038/Nrg3936  0.834
2015 Vestergaard JS, Twomey E, Larsen R, Summers K, Nielsen R. Number of genes controlling a quantitative trait in a hybrid zone of the aposematic frog Ranitomeya imitator. Proceedings. Biological Sciences / the Royal Society. 282: 20141950. PMID 25925096 DOI: 10.1098/Rspb.2014.1950  0.357
2015 Winther RG, Millstein RL, Nielsen R. Introduction: Genomics and philosophy of race. Studies in History and Philosophy of Biological and Biomedical Sciences. 52: 1-4. PMID 25861858 DOI: 10.1016/J.Shpsc.2015.03.003  0.368
2015 Karmin M, Saag L, Vicente M, Wilson Sayres MA, Järve M, Talas UG, Rootsi S, Ilumäe AM, Mägi R, Mitt M, Pagani L, Puurand T, Faltyskova Z, Clemente F, Cardona A, ... ... Nielsen R, et al. A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome Research. 25: 459-66. PMID 25770088 DOI: 10.1101/Gr.186684.114  0.761
2015 Moon S, Kim TH, Lee KT, Kwak W, Lee T, Lee SW, Kim MJ, Cho K, Kim N, Chung WH, Sung S, Park T, Cho S, Groenen MA, Nielsen R, et al. A genome-wide scan for signatures of directional selection in domesticated pigs. Bmc Genomics. 16: 130. PMID 25765548 DOI: 10.1186/S12864-015-1330-X  0.437
2015 Winther RG, Giordano R, Edge MD, Nielsen R. The mind, the lab, and the field: Three kinds of populations in scientific practice. Studies in History and Philosophy of Biological and Biomedical Sciences. PMID 25753677 DOI: 10.1016/J.Shpsc.2015.01.009  0.361
2015 Foote AD, Liu Y, Thomas GW, Vina? T, Alföldi J, Deng J, Dugan S, van Elk CE, Hunter ME, Joshi V, Khan Z, Kovar C, Lee SL, Lindblad-Toh K, Mancia A, ... Nielsen R, et al. Convergent evolution of the genomes of marine mammals. Nature Genetics. 47: 272-5. PMID 25621460 DOI: 10.1038/Ng.3198  0.427
2015 Ai H, Fang X, Yang B, Huang Z, Chen H, Mao L, Zhang F, Zhang L, Cui L, He W, Yang J, Yao X, Zhou L, Han L, Li J, ... ... Nielsen R, et al. Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing. Nature Genetics. 47: 217-25. PMID 25621459 DOI: 10.1038/Ng.3199  0.469
2015 Moltke I, Fumagalli M, Korneliussen TS, Crawford JE, Bjerregaard P, Jørgensen ME, Grarup N, Gulløv HC, Linneberg A, Pedersen O, Hansen T, Nielsen R, Albrechtsen A. Uncovering the genetic history of the present-day Greenlandic population. American Journal of Human Genetics. 96: 54-69. PMID 25557782 DOI: 10.1016/J.Ajhg.2014.11.012  0.448
2015 Westesson O, Nielsen R, John JS, Caulin A, Hahner N, Stewart S, Foo C, Lung K, Catalano J, Lee M, Giannikopoulos P, Polkinghorn W, Wiessman J, Regev A, Bivona T. Abstract 2173: Robust estimation of mutation burden Cancer Research. 75: 2173-2173. DOI: 10.1158/1538-7445.Am2015-2173  0.322
2015 Racimo F, Sankararaman S, Nielsen R, Huerta-Sánchez E. Evidence for archaic adaptive introgression in humans Nature Reviews Genetics. 16: 359-371. DOI: 10.1038/nrg3936  0.777
2014 Schubert M, Jónsson H, Chang D, Der Sarkissian C, Ermini L, Ginolhac A, Albrechtsen A, Dupanloup I, Foucal A, Petersen B, Fumagalli M, Raghavan M, Seguin-Orlando A, Korneliussen TS, Velazquez AM, ... ... Nielsen R, et al. Prehistoric genomes reveal the genetic foundation and cost of horse domestication. Proceedings of the National Academy of Sciences of the United States of America. 111: E5661-9. PMID 25512547 DOI: 10.1073/Pnas.1416991111  0.672
2014 Malaspinas AS, Lao O, Schroeder H, Rasmussen M, Raghavan M, Moltke I, Campos PF, Sagredo FS, Rasmussen S, Gonçalves VF, Albrechtsen A, Allentoft ME, Johnson PL, Li M, Reis S, ... ... Nielsen R, et al. Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil. Current Biology : Cb. 24: R1035-7. PMID 25455029 DOI: 10.1016/J.Cub.2014.09.078  0.818
2014 Jónsson H, Schubert M, Seguin-Orlando A, Ginolhac A, Petersen L, Fumagalli M, Albrechtsen A, Petersen B, Korneliussen TS, Vilstrup JT, Lear T, Myka JL, Lundquist J, Miller DC, Alfarhan AH, ... ... Nielsen R, et al. Speciation with gene flow in equids despite extensive chromosomal plasticity. Proceedings of the National Academy of Sciences of the United States of America. 111: 18655-60. PMID 25453089 DOI: 10.1073/Pnas.1412627111  0.41
2014 Clemente FJ, Cardona A, Inchley CE, Peter BM, Jacobs G, Pagani L, Lawson DJ, Antão T, Vicente M, Mitt M, DeGiorgio M, Faltyskova Z, Xue Y, Ayub Q, Szpak M, ... ... Nielsen R, et al. A Selective Sweep on a Deleterious Mutation in CPT1A in Arctic Populations. American Journal of Human Genetics. 95: 584-589. PMID 25449608 DOI: 10.1016/J.Ajhg.2014.09.016  0.83
2014 Moreno-Mayar JV, Rasmussen S, Seguin-Orlando A, Rasmussen M, Liang M, Flåm ST, Lie BA, Gilfillan GD, Nielsen R, Thorsby E, Willerslev E, Malaspinas AS. Genome-wide ancestry patterns in Rapanui suggest pre-European admixture with Native Americans. Current Biology : Cb. 24: 2518-25. PMID 25447991 DOI: 10.1016/J.Cub.2014.09.057  0.706
2014 Korneliussen TS, Albrechtsen A, Nielsen R. ANGSD: Analysis of Next Generation Sequencing Data. Bmc Bioinformatics. 15: 356. PMID 25420514 DOI: 10.1186/S12859-014-0356-4  0.307
2014 Seguin-Orlando A, Korneliussen TS, Sikora M, Malaspinas AS, Manica A, Moltke I, Albrechtsen A, Ko A, Margaryan A, Moiseyev V, Goebel T, Westaway M, Lambert D, Khartanovich V, Wall JD, ... ... Nielsen R, et al. Genomic structure in Europeans dating back at least 36,200 years Science. 346: 1113-1118. PMID 25378462 DOI: 10.1126/Science.Aaa0114  0.742
2014 Key FM, Peter B, Dennis MY, Huerta-Sánchez E, Tang W, Prokunina-Olsson L, Nielsen R, Andrés AM. Selection on a variant associated with improved viral clearance drives local, adaptive pseudogenization of interferon lambda 4 (IFNL4). Plos Genetics. 10: e1004681. PMID 25329461 DOI: 10.1371/Journal.Pgen.1004681  0.805
2014 Rebolledo-Jaramillo B, Su MS, Stoler N, McElhoe JA, Dickins B, Blankenberg D, Korneliussen TS, Chiaromonte F, Nielsen R, Holland MM, Paul IM, Nekrutenko A, Makova KD. Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA. Proceedings of the National Academy of Sciences of the United States of America. 111: 15474-9. PMID 25313049 DOI: 10.1073/Pnas.1409328111  0.633
2014 Raghavan M, DeGiorgio M, Albrechtsen A, Moltke I, Skoglund P, Korneliussen TS, Grønnow B, Appelt M, Gulløv HC, Friesen TM, Fitzhugh W, Malmström H, Rasmussen S, Olsen J, Melchior L, ... ... Nielsen R, et al. The genetic prehistory of the New World Arctic. Science (New York, N.Y.). 345: 1255832. PMID 25170159 DOI: 10.1126/Science.1255832  0.781
2014 DeGiorgio M, Lohmueller KE, Nielsen R. A model-based approach for identifying signatures of ancient balancing selection in genetic data. Plos Genetics. 10: e1004561. PMID 25144706 DOI: 10.1371/Journal.Pgen.1004561  0.431
2014 Stern A, Bianco S, Yeh MT, Wright C, Butcher K, Tang C, Nielsen R, Andino R. Costs and benefits of mutational robustness in RNA viruses. Cell Reports. 8: 1026-36. PMID 25127138 DOI: 10.1016/J.Celrep.2014.07.011  0.338
2014 Harris K, Nielsen R. Error-prone polymerase activity causes multinucleotide mutations in humans. Genome Research. 24: 1445-54. PMID 25079859 DOI: 10.1101/Gr.170696.113  0.403
2014 Huerta-Sánchez E, Jin X, Asan, Bianba Z, Peter BM, Vinckenbosch N, Liang Y, Yi X, He M, Somel M, Ni P, Wang B, Ou X, Huasang, Luosang J, ... ... Nielsen R, et al. Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature. 512: 194-7. PMID 25043035 DOI: 10.1038/Nature13408  0.831
2014 Malaspinas AS, Tange O, Moreno-Mayar JV, Rasmussen M, DeGiorgio M, Wang Y, Valdiosera CE, Politis G, Willerslev E, Nielsen R. bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS) Bioinformatics (Oxford, England). 30: 2962-2964. PMID 24974206 DOI: 10.1093/Bioinformatics/Btu410  0.682
2014 Liu S, Lorenzen ED, Fumagalli M, Li B, Harris K, Xiong Z, Zhou L, Korneliussen TS, Somel M, Babbitt C, Wray G, Li J, He W, Wang Z, Fu W, ... ... Nielsen R, et al. Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears. Cell. 157: 785-94. PMID 24813606 DOI: 10.1016/J.Cell.2014.03.054  0.413
2014 Liang M, Nielsen R. The lengths of admixture tracts. Genetics. 197: 953-67. PMID 24770332 DOI: 10.1534/Genetics.114.162362  0.329
2014 Qanbari S, Pausch H, Jansen S, Somel M, Strom TM, Fries R, Nielsen R, Simianer H. Classic selective sweeps revealed by massive sequencing in cattle. Plos Genetics. 10: e1004148. PMID 24586189 DOI: 10.1371/Journal.Pgen.1004148  0.471
2014 Ferrer-Admetlla A, Liang M, Korneliussen T, Nielsen R. On detecting incomplete soft or hard selective sweeps using haplotype structure. Molecular Biology and Evolution. 31: 1275-91. PMID 24554778 DOI: 10.1093/Molbev/Msu077  0.432
2014 Rasmussen M, Anzick SL, Waters MR, Skoglund P, DeGiorgio M, Stafford TW, Rasmussen S, Moltke I, Albrechtsen A, Doyle SM, Poznik GD, Gudmundsdottir V, Yadav R, Malaspinas AS, White SS, ... ... Nielsen R, et al. The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature. 506: 225-9. PMID 24522598 DOI: 10.1038/Nature13025  0.772
2014 Olalde I, Allentoft ME, Sánchez-Quinto F, Santpere G, Chiang CW, DeGiorgio M, Prado-Martinez J, Rodríguez JA, Rasmussen S, Quilez J, Ramírez O, Marigorta UM, Fernández-Callejo M, Prada ME, Encinas JM, ... Nielsen R, et al. Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European. Nature. 507: 225-8. PMID 24463515 DOI: 10.1038/Nature12960  0.704
2014 Fumagalli M, Vieira FG, Linderoth T, Nielsen R. ngsTools: methods for population genetics analyses from next-generation sequencing data. Bioinformatics (Oxford, England). 30: 1486-7. PMID 24458950 DOI: 10.1093/Bioinformatics/Btu041  0.399
2014 Li S, Besenbacher S, Li Y, Kristiansen K, Grarup N, Albrechtsen A, Sparsø T, Korneliussen T, Hansen T, Wang J, Nielsen R, Pedersen O, Bolund L, Schierup MH. Variation and association to diabetes in 2000 full mtDNA sequences mined from an exome study in a Danish population. European Journal of Human Genetics : Ejhg. 22: 1040-5. PMID 24448545 DOI: 10.1038/Ejhg.2013.282  0.401
2014 Wilson Sayres MA, Lohmueller KE, Nielsen R. Natural Selection Reduced Diversity on Human Y Chromosomes Plos Genetics. 10. PMID 24415951 DOI: 10.1371/Journal.Pgen.1004064  0.766
2014 Raghavan M, Skoglund P, Graf KE, Metspalu M, Albrechtsen A, Moltke I, Rasmussen S, Stafford TW, Orlando L, Metspalu E, Karmin M, Tambets K, Rootsi S, Mägi R, Campos PF, ... ... Nielsen R, et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature. 505: 87-91. PMID 24256729 DOI: 10.1038/Nature12736  0.449
2014 Rohlfs RV, Harrigan P, Nielsen R. Modeling gene expression evolution with an extended Ornstein-Uhlenbeck process accounting for within-species variation. Molecular Biology and Evolution. 31: 201-11. PMID 24113538 DOI: 10.1093/Molbev/Mst190  0.342
2014 Key FM, Peter B, Dennis MY, Huerta-Sanchez E, Tang W, Prokunina-Olsson L, Nielsen R, Andrés AM. ABC results and inferred parameter estimates for the SDN model. Plos Genetics. DOI: 10.1371/Journal.Pgen.1004681.T003  0.759
2014 Lohmueller KE, Sparsø T, Li Q, Andersson E, Korneliussen T, Albrechtsen A, Banasik K, Grarup N, Hallgrimsdottir I, Kiil K, Kilpeläinen TO, Krarup NT, Pers TH, Sanchez G, Hu Y, ... ... Nielsen R, et al. Erratum: Whole-exome sequencing of 2,000 Danish individuals and the role of rare coding variants in type 2 diabetes (The American Journal of Human Genetics (2013) 93 (1072-1086)) American Journal of Human Genetics. 94. DOI: 10.1016/J.Ajhg.2014.02.002  0.327
2013 Lohmueller KE, Sparsø T, Li Q, Andersson E, Korneliussen T, Albrechtsen A, Banasik K, Grarup N, Hallgrimsdottir I, Kiil K, Kilpeläinen TO, Krarup NT, Pers TH, Sanchez G, Hu Y, ... ... Nielsen R, et al. Whole-exome sequencing of 2,000 Danish individuals and the role of rare coding variants in type 2 diabetes. American Journal of Human Genetics. 93: 1072-86. PMID 24290377 DOI: 10.1016/J.Ajhg.2013.11.005  0.318
2013 Crawford JE, Nielsen R. Detecting adaptive trait loci in nonmodel systems: divergence or admixture mapping? Molecular Ecology. 22: 6131-48. PMID 24128338 DOI: 10.1111/Mec.12562  0.328
2013 Bi K, Linderoth T, Vanderpool D, Good JM, Nielsen R, Moritz C. Unlocking the vault: next-generation museum population genomics. Molecular Ecology. 22: 6018-32. PMID 24118668 DOI: 10.1111/Mec.12516  0.484
2013 Korneliussen TS, Moltke I, Albrechtsen A, Nielsen R. Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data. Bmc Bioinformatics. 14: 289. PMID 24088262 DOI: 10.1186/1471-2105-14-289  0.402
2013 Li YH, Zhao SC, Ma JX, Li D, Yan L, Li J, Qi XT, Guo XS, Zhang L, He WM, Chang RZ, Liang QS, Guo Y, Ye C, Wang XB, ... ... Nielsen R, et al. Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. Bmc Genomics. 14: 579. PMID 23984715 DOI: 10.1186/1471-2164-14-579  0.482
2013 Fumagalli M, Vieira FG, Korneliussen TS, Linderoth T, Huerta-Sánchez E, Albrechtsen A, Nielsen R. Quantifying population genetic differentiation from next-generation sequencing data. Genetics. 195: 979-92. PMID 23979584 DOI: 10.1534/Genetics.113.154740  0.45
2013 Vieira FG, Fumagalli M, Albrechtsen A, Nielsen R. Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation. Genome Research. 23: 1852-61. PMID 23950147 DOI: 10.1101/Gr.157388.113  0.324
2013 Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert M, Cappellini E, Petersen B, Moltke I, Johnson PL, Fumagalli M, Vilstrup JT, Raghavan M, Korneliussen T, ... ... Nielsen R, et al. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature. 499: 74-8. PMID 23803765 DOI: 10.1038/Nature12323  0.806
2013 Grarup N, Sulem P, Sandholt CH, Thorleifsson G, Ahluwalia TS, Steinthorsdottir V, Bjarnason H, Gudbjartsson DF, Magnusson OT, Sparsø T, Albrechtsen A, Kong A, Masson G, Tian G, Cao H, ... ... Nielsen R, et al. Genetic architecture of vitamin B12 and folate levels uncovered applying deeply sequenced large datasets. Plos Genetics. 9: e1003530. PMID 23754956 DOI: 10.1371/Journal.Pgen.1003530  0.406
2013 Harris K, Nielsen R. Inferring demographic history from a spectrum of shared haplotype lengths. Plos Genetics. 9: e1003521. PMID 23754952 DOI: 10.1371/Journal.Pgen.1003521  0.46
2013 Somel M, Sayres MAW, Jordan G, Huerta-Sanchez E, Fumagalli M, Ferrer-Admetlla A, Nielsen R. A scan for human-specific relaxation of negative selection reveals unexpected polymorphism in proteasome genes Molecular Biology and Evolution. 30: 1808-1815. PMID 23699470 DOI: 10.1093/Molbev/Mst098  0.435
2013 Huerta-Sánchez E, Degiorgio M, Pagani L, Tarekegn A, Ekong R, Antao T, Cardona A, Montgomery HE, Cavalleri GL, Robbins PA, Weale ME, Bradman N, Bekele E, Kivisild T, Tyler-Smith C, ... Nielsen R, et al. Genetic signatures reveal high-altitude adaptation in a set of ethiopian populations. Molecular Biology and Evolution. 30: 1877-88. PMID 23666210 DOI: 10.1093/Molbev/Mst089  0.433
2013 Albrechtsen A, Grarup N, Li Y, Sparsø T, Tian G, Cao H, Jiang T, Kim SY, Korneliussen T, Li Q, Nie C, Wu R, Skotte L, Morris AP, Ladenvall C, ... ... Nielsen R, et al. Exome sequencing-driven discovery of coding polymorphisms associated with common metabolic phenotypes. Diabetologia. 56: 298-310. PMID 23160641 DOI: 10.1007/S00125-012-2756-1  0.319
2012 Peter BM, Huerta-Sanchez E, Nielsen R. Distinguishing between selective sweeps from standing variation and from a de novo mutation. Plos Genetics. 8: e1003011. PMID 23071458 DOI: 10.1371/Journal.Pgen.1003011  0.809
2012 Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F, Liang S, Zhang W, Guan Y, Shen D, Peng Y, Zhang D, Jie Z, Wu W, Qin Y, ... ... Nielsen R, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature. 490: 55-60. PMID 23023125 DOI: 10.1038/Nature11450  0.386
2012 Nielsen R, Korneliussen T, Albrechtsen A, Li Y, Wang J. SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing data. Plos One. 7: e37558. PMID 22911679 DOI: 10.1371/Journal.Pone.0037558  0.315
2012 Zhai W, Nielsen R, Goldman N, Yang Z. Looking for Darwin in genomic sequences--validity and success of statistical methods. Molecular Biology and Evolution. 29: 2889-93. PMID 22490825 DOI: 10.1093/Molbev/Mss104  0.662
2012 Li J, Liu Y, Xin X, Kim TS, Cabeza EA, Ren J, Nielsen R, Wrana JL, Zhang Z. Evidence for positive selection on a number of MicroRNA regulatory interactions during recent human evolution. Plos Genetics. 8: e1002578. PMID 22457636 DOI: 10.1371/Journal.Pgen.1002578  0.312
2012 Wang Y, Nielsen R. Estimating population divergence time and phylogeny from single-nucleotide polymorphisms data with outgroup ascertainment bias. Molecular Ecology. 21: 974-86. PMID 22211450 DOI: 10.1111/J.1365-294X.2011.05413.X  0.428
2012 Xu X, Liu X, Ge S, Jensen JD, Hu F, Li X, Dong Y, Gutenkunst RN, Fang L, Huang L, Li J, He W, Zhang G, Zheng X, Zhang F, ... ... Nielsen R, et al. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotechnology. 30: 105-11. PMID 22158310 DOI: 10.1038/Nbt.2050  0.658
2011 Fumagalli M, Sironi M, Pozzoli U, Ferrer-Admetlla A, Ferrer-Admettla A, Pattini L, Nielsen R. Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution. Plos Genetics. 7: e1002355. PMID 22072984 DOI: 10.1371/Journal.Pgen.1002355  0.46
2011 Lorenzen ED, Nogués-Bravo D, Orlando L, Weinstock J, Binladen J, Marske KA, Ugan A, Borregaard MK, Gilbert MT, Nielsen R, Ho SY, Goebel T, Graf KE, Byers D, Stenderup JT, et al. Species-specific responses of Late Quaternary megafauna to climate and humans. Nature. 479: 359-64. PMID 22048313 DOI: 10.1038/Nature10574  0.79
2011 Lohmueller KE, Albrechtsen A, Li Y, Kim SY, Korneliussen T, Vinckenbosch N, Tian G, Huerta-Sanchez E, Feder AF, Grarup N, Jørgensen T, Jiang T, Witte DR, Sandbæk A, Hellmann I, ... ... Nielsen R, et al. Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome. Plos Genetics. 7: e1002326. PMID 22022285 DOI: 10.1371/Journal.Pgen.1002326  0.464
2011 Brawand D, Soumillon M, Necsulea A, Julien P, Csárdi G, Harrigan P, Weier M, Liechti A, Aximu-Petri A, Kircher M, Albert FW, Zeller U, Khaitovich P, Grützner F, Bergmann S, ... Nielsen R, et al. The evolution of gene expression levels in mammalian organs. Nature. 478: 343-8. PMID 22012392 DOI: 10.1038/Nature10532  0.34
2011 Yan G, Zhang G, Fang X, Zhang Y, Li C, Ling F, Cooper DN, Li Q, Li Y, van Gool AJ, Du H, Chen J, Chen R, Zhang P, Huang Z, ... ... Nielsen R, et al. Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nature Biotechnology. 29: 1019-23. PMID 22002653 DOI: 10.1038/Nbt.1992  0.458
2011 Rasmussen M, Guo X, Wang Y, Lohmueller KE, Rasmussen S, Albrechtsen A, Skotte L, Lindgreen S, Metspalu M, Jombart T, Kivisild T, Zhai W, Eriksson A, Manica A, Orlando L, ... ... Nielsen R, et al. An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (New York, N.Y.). 334: 94-8. PMID 21940856 DOI: 10.1126/Science.1211177  0.752
2011 Kim SY, Lohmueller KE, Albrechtsen A, Li Y, Korneliussen T, Tian G, Grarup N, Jiang T, Andersen G, Witte D, Jorgensen T, Hansen T, Pedersen O, Wang J, Nielsen R. Estimation of allele frequency and association mapping using next-generation sequencing data. Bmc Bioinformatics. 12: 231. PMID 21663684 DOI: 10.1186/1471-2105-12-231  0.351
2011 Nielsen R, Paul JS, Albrechtsen A, Song YS. Genotype and SNP calling from next-generation sequencing data. Nature Reviews. Genetics. 12: 443-51. PMID 21587300 DOI: 10.1038/Nrg2986  0.4
2011 Moltke I, Albrechtsen A, Hansen TVO, Nielsen FC, Nielsen R. A method for detecting IBD regions simultaneously in multiple individuals - With applications to disease genetics Genome Research. 21: 1168-1180. PMID 21493780 DOI: 10.1101/Gr.115360.110  0.385
2010 Beaumont MA, Nielsen R, Robert C, Hey J, Gaggiotti O, Knowles L, Estoup A, Panchal M, Corander J, Hickerson M, Sisson SA, Fagundes N, Chikhi L, Beerli P, Vitalis R, et al. In defence of model-based inference in phylogeography. Molecular Ecology. 19: 436-446. PMID 29284924 DOI: 10.1111/J.1365-294X.2009.04515.X  0.802
2010 Nielsen R. Genomics: In search of rare human variants Nature. 467: 1050-1051. PMID 20981085 DOI: 10.1038/4671050A  0.436
2010 Andrés AM, Dennis MY, Kretzschmar WW, Cannons JL, Lee-Lin SQ, Hurle B, Schwartzberg PL, Williamson SH, Bustamante CD, Nielsen R, Clark AG, Green ED. Balancing selection maintains a form of ERAP2 that undergoes nonsense-mediated decay and affects antigen presentation. Plos Genetics. 6: e1001157. PMID 20976248 DOI: 10.1371/Journal.Pgen.1001157  0.532
2010 Li Y, Vinckenbosch N, Tian G, Huerta-Sanchez E, Jiang T, Jiang H, Albrechtsen A, Andersen G, Cao H, Korneliussen T, Grarup N, Guo Y, Hellman I, Jin X, Li Q, ... ... Nielsen R, et al. Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nature Genetics. 42: 969-72. PMID 20890277 DOI: 10.1038/Ng.680  0.383
2010 Yi X, Liang Y, Huerta-Sanchez E, Jin X, Cuo ZX, Pool JE, Xu X, Jiang H, Vinckenbosch N, Korneliussen TS, Zheng H, Liu T, He W, Li K, Luo R, ... ... Nielsen R, et al. Sequencing of 50 human exomes reveals adaptation to high altitude. Science (New York, N.Y.). 329: 75-8. PMID 20595611 DOI: 10.1126/Science.1190371  0.748
2010 Albrechtsen A, Moltke I, Nielsen R. Natural selection and the distribution of identity-by-descent in the human genome Genetics. 186: 295-308. PMID 20592267 DOI: 10.1534/Genetics.110.113977  0.473
2010 Albrechtsen A, Nielsen FC, Nielsen R. Ascertainment biases in SNP chips affect measures of population divergence Molecular Biology and Evolution. 27: 2534-2547. PMID 20558595 DOI: 10.1093/Molbev/Msq148  0.472
2010 Kim SY, Li Y, Guo Y, Li R, Holmkvist J, Hansen T, Pedersen O, Wang J, Nielsen R. Design of association studies with pooled or un-pooled next-generation sequencing data Genetic Epidemiology. 34: 479-491. PMID 20552648 DOI: 10.1002/Gepi.20501  0.397
2010 Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, ... ... Nielsen R, et al. A draft sequence of the Neandertal genome. Science (New York, N.Y.). 328: 710-22. PMID 20448178 DOI: 10.1126/Science.1188021  0.811
2010 Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, Metspalu M, Metspalu E, Kivisild T, Gupta R, Bertalan M, Nielsen K, Gilbert MT, Wang Y, Raghavan M, ... ... Nielsen R, et al. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature. 463: 757-62. PMID 20148029 DOI: 10.1038/Nature08835  0.457
2010 Axelsson E, Albrechtsen A, van AP, Li L, Megens HJ, Vereijken AL, Crooijmans RP, Groenen MA, Ellegren H, Willerslev E, Nielsen R. Segregation distortion in chicken and the evolutionary consequences of female meiotic drive in birds. Heredity. 105: 290-8. PMID 20104236 DOI: 10.1038/Hdy.2009.193  0.323
2010 Pool JE, Hellmann I, Jensen JD, Nielsen R. Population genetic inference from genomic sequence variation. Genome Research. 20: 291-300. PMID 20067940 DOI: 10.1101/Gr.079509.108  0.809
2010 Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W, Li J, Wei F, ... ... Nielsen R, et al. The sequence and de novo assembly of the giant panda genome. Nature. 463: 311-7. PMID 20010809 DOI: 10.1038/Nature08696  0.433
2010 Yi X, Liang Y, Huerta-Sanchez E, Jin X, Cuo ZXP, Pool JE, Xu X, Jiang H, Vinckenbosch N, Korneliussen TS, Zheng H, Liu T, He W, Li K, Luo R, ... ... Nielsen R, et al. Archaeology Augments Tibet's Genetic History--Response Science. 329: 1467-1468. DOI: 10.1126/Science.329.5998.1467-B  0.73
2010 Beaumont MA, Nielsen R, Robert C, Hey J, Gaggiotti O, Knowles L, Estoup A, Panchal M, Corander J, Hickerson M, Sisson SA, Fagundes N, Chikhi L, Beerli P, Vitalis R, et al. In defence of model-based inference in phylogeography Molecular Ecology. 19: 436-446. DOI: 10.1111/j.1365-294X.2009.04515.x  0.764
2010 Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W, Li J, Wei F, ... ... Nielsen R, et al. Erratum: The sequence and de novo assembly of the giant panda genome Nature. 463: 1106-1106. DOI: 10.1038/Nature08846  0.367
2009 Haile J, Froese DG, Macphee RD, Roberts RG, Arnold LJ, Reyes AV, Rasmussen M, Nielsen R, Brook BW, Robinson S, Demuro M, Gilbert MT, Munch K, Austin JJ, Cooper A, et al. Ancient DNA reveals late survival of mammoth and horse in interior Alaska. Proceedings of the National Academy of Sciences of the United States of America. 106: 22352-7. PMID 20018740 DOI: 10.1073/Pnas.0912510106  0.805
2009 Nielsen R. Adaptionism - 30 years after gould and lewontin Evolution. 63: 2487-2490. PMID 19744124 DOI: 10.1111/J.1558-5646.2009.00799.X  0.432
2009 Xia Q, Guo Y, Zhang Z, Li D, Xuan Z, Li Z, Dai F, Li Y, Cheng D, Li R, Cheng T, Jiang T, Becquet C, Xu X, Liu C, ... ... Nielsen R, et al. Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science (New York, N.Y.). 326: 433-6. PMID 19713493 DOI: 10.1126/Science.1176620  0.664
2009 Andrés AM, Hubisz MJ, Indap A, Torgerson DG, Degenhardt JD, Boyko AR, Gutenkunst RN, White TJ, Green ED, Bustamante CD, Clark AG, Nielsen R. Targets of balancing selection in the human genome. Molecular Biology and Evolution. 26: 2755-64. PMID 19713326 DOI: 10.1093/Molbev/Msp190  0.611
2009 Nielsen R, Hubisz MJ, Hellmann I, Torgerson D, Andrés AM, Albrechtsen A, Gutenkunst R, Adams MD, Cargill M, Boyko A, Indap A, Bustamante CD, Clark AG. Darwinian and demographic forces affecting human protein coding genes. Genome Research. 19: 838-49. PMID 19279335 DOI: 10.1101/Gr.088336.108  0.578
2009 Nielsen R, Beaumont MA. Statistical inferences in phylogeography. Molecular Ecology. 18: 1034-47. PMID 19207258 DOI: 10.1111/J.1365-294X.2008.04059.X  0.322
2009 Ramírez-Soriano A, Nielsen R. Correcting Estimators of θ and Tajima's D for Ascertainment Biases Caused by the Single-Nucleotide Polymorphism Discovery Process Genetics. 181: 701-710. PMID 19087964 DOI: 10.1534/Genetics.108.094060  0.376
2009 Pool JE, Nielsen R. Inference of historical changes in migration rate from the lengths of migrant tracts. Genetics. 181: 711-9. PMID 19087958 DOI: 10.1534/Genetics.108.098095  0.687
2009 Albrechtsen A, Korneliussen TS, Moltke I, van Overseem Hansen T, Nielsen FC, Nielsen R. Relatedness mapping and tracts of relatedness for genome-wide data in the presence of linkage disequilibrium Genetic Epidemiology. 33: 266-274. PMID 19025785 DOI: 10.1002/Gepi.20378  0.338
2009 Zhai W, Nielsen R, Slatkin M. An investigation of the statistical power of neutrality tests based on comparative and population genetic data. Molecular Biology and Evolution. 26: 273-83. PMID 18922762 DOI: 10.1093/Molbev/Msn231  0.783
2008 Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, Fan W, Zhang J, Li J, Zhang J, Guo Y, Feng B, Li H, Lu Y, Fang X, ... ... Nielsen R, et al. The diploid genome sequence of an Asian individual. Nature. 456: 60-5. PMID 18987735 DOI: 10.1038/Nature07484  0.726
2008 Munch K, Boomsma W, Huelsenbeck JP, Willerslev E, Nielsen R. Statistical assignment of DNA sequences using Bayesian phylogenetics. Systematic Biology. 57: 750-7. PMID 18853361 DOI: 10.1080/10635150802422316  0.79
2008 Munch K, Boomsma W, Willerslev E, Nielsen R. Fast phylogenetic DNA barcoding. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 363: 3997-4002. PMID 18852104 DOI: 10.1098/Rstb.2008.0169  0.782
2008 Kosiol C, Vinař T, Da Fonseca RR, Hubisz MJ, Bustamante CD, Nielsen R, Siepel A. Patterns of positive selection in six mammalian genomes Plos Genetics. 4. PMID 18670650 DOI: 10.1371/Journal.Pgen.1000144  0.573
2008 Axelsson E, Willerslev E, Gilbert MTP, Nielsen R. The effect of ancient DNA damage on inferences of demographic histories. Molecular Biology and Evolution. 25: 2181-2187. PMID 18653730 DOI: 10.1093/Molbev/Msn163  0.401
2008 Boyko AR, Williamson SH, Indap AR, Degenhardt JD, Hernandez RD, Lohmueller KE, Adams MD, Schmidt S, Sninsky JJ, Sunyaev SR, White TJ, Nielsen R, Clark AG, Bustamante CD. Assessing the evolutionary impact of amino acid mutations in the human genome. Plos Genetics. 4: e1000083. PMID 18516229 DOI: 10.1371/Journal.Pgen.1000083  0.598
2008 Pool JE, Nielsen R. The impact of founder events on chromosomal variability in multiply mating species. Molecular Biology and Evolution. 25: 1728-36. PMID 18511425 DOI: 10.1093/Molbev/Msn124  0.694
2008 Bollback JP, York TL, Nielsen R. Estimation of 2Nes from temporal allele frequency data. Genetics. 179: 497-502. PMID 18493066 DOI: 10.1534/Genetics.107.085019  0.729
2008 Hellmann I, Mang Y, Gu Z, Li P, De La Vega FM, Clark AG, Nielsen R. Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals Genome Research. 18: 1020-1029. PMID 18411405 DOI: 10.1101/Gr.074187.107  0.479
2008 Lohmueller KE, Indap AR, Schmidt S, Boyko AR, Hernandez RD, Hubisz MJ, Sninsky JJ, White TJ, Sunyaev SR, Nielsen R, Clark AG, Bustamante CD. Proportionally more deleterious genetic variation in European than in African populations. Nature. 451: 994-7. PMID 18288194 DOI: 10.1038/Nature06611  0.538
2008 Yang Z, Nielsen R. Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Molecular Biology and Evolution. 25: 568-79. PMID 18178545 DOI: 10.1093/Molbev/Msm284  0.357
2007 Singh ND, Bauer DuMont VL, Hubisz MJ, Nielsen R, Aquadro CF. Patterns of mutation and selection at synonymous sites in Drosophila. Molecular Biology and Evolution. 24: 2687-97. PMID 18000010 DOI: 10.1093/Molbev/Msm196  0.603
2007 Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, ... ... Nielsen R, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/Nature06341  0.745
2007 Pool JE, Nielsen R. Population size changes reshape genomic patterns of diversity. Evolution; International Journal of Organic Evolution. 61: 3001-6. PMID 17971168 DOI: 10.1111/J.1558-5646.2007.00238.X  0.731
2007 Nielsen R, Hellmann I, Hubisz M, Bustamante C, Clark AG. Recent and ongoing selection in the human genome. Nature Reviews. Genetics. 8: 857-68. PMID 17943193 DOI: 10.1038/Nrg2187  0.604
2007 Caicedo AL, Williamson SH, Hernandez RD, Boyko A, Fledel-Alon A, York TL, Polato NR, Olsen KM, Nielsen R, McCouch SR, Bustamante CD, Purugganan MD. Genome-wide patterns of nucleotide polymorphism in domesticated rice. Plos Genetics. 3: 1745-56. PMID 17907810 DOI: 10.1371/Journal.Pgen.0030163  0.573
2007 Zhai W, Slatkin M, Nielsen R. Exploring variation in the d(N)/d(S) ratio among sites and lineages using mutational mappings: applications to the influenza virus. Journal of Molecular Evolution. 65: 340-8. PMID 17846819 DOI: 10.1007/S00239-007-9019-7  0.764
2007 Johnson SS, Hebsgaard MB, Christensen TR, Mastepanov M, Nielsen R, Munch K, Brand T, Gilbert MT, Zuber MT, Bunce M, Rønn R, Gilichinsky D, Froese D, Willerslev E. Ancient bacteria show evidence of DNA repair. Proceedings of the National Academy of Sciences of the United States of America. 104: 14401-5. PMID 17728401 DOI: 10.1073/Pnas.0706787104  0.775
2007 Petersen L, Bollback JP, Dimmic M, Hubisz M, Nielsen R. Genes under positive selection in Escherichia coli. Genome Research. 17: 1336-43. PMID 17675366 DOI: 10.1101/Gr.6254707  0.737
2007 Wong WSW, Nielsen R. Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models Bioinformatics. 23: 2031-2037. PMID 17550911 DOI: 10.1093/Bioinformatics/Btm299  0.325
2007 Williamson SH, Hubisz MJ, Clark AG, Payseur BA, Bustamante CD, Nielsen R. Localizing recent adaptive evolution in the human genome. Plos Genetics. 3: e90. PMID 17542651 DOI: 10.1371/Journal.Pgen.0030090  0.606
2007 Albrechtsen A, Castella S, Andersen G, Hansen T, Pedersen O, Nielsen R. A Bayesian multilocus association method: allowing for higher-order interaction in association studies. Genetics. 176: 1197-1208. PMID 17435250 DOI: 10.1534/Genetics.107.071696  0.348
2007 Hernandez RD, Hubisz MJ, Wheeler DA, Smith DG, Ferguson B, Rogers J, Nazareth L, Indap A, Bourquin T, McPherson J, Muzny D, Gibbs R, Nielsen R, Bustamante CD. Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques. Science (New York, N.Y.). 316: 240-3. PMID 17431170 DOI: 10.1126/Science.1140462  0.56
2007 Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, ... ... Nielsen R, et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science (New York, N.Y.). 316: 222-34. PMID 17431167 DOI: 10.1126/Science.1139247  0.744
2007 Pastene LA, Goto M, Kanda N, Zerbini AN, Kerem D, Watanabe K, Bessho Y, Hasegawa M, Nielsen R, Larsen F, Palsbøll PJ. Radiation and speciation of pelagic organisms during periods of global warming: The case of the common minke whale, Balaenoptera acutorostrata Molecular Ecology. 16: 1481-1495. PMID 17391271 DOI: 10.1111/J.1365-294X.2007.03244.X  0.411
2007 Hey J, Nielsen R. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proceedings of the National Academy of Sciences of the United States of America. 104: 2785-90. PMID 17301231 DOI: 10.1073/Pnas.0611164104  0.548
2007 Binladen J, Gilbert MT, Bollback JP, Panitz F, Bendixen C, Nielsen R, Willerslev E. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. Plos One. 2: e197. PMID 17299583 DOI: 10.1371/Journal.Pone.0000197  0.737
2007 Shapiro JA, Huang W, Zhang C, Hubisz MJ, Lu J, Turissini DA, Fang S, Wang HY, Hudson RR, Nielsen R, Chen Z, Wu CI. Adaptive genic evolution in the Drosophila genomes. Proceedings of the National Academy of Sciences of the United States of America. 104: 2271-6. PMID 17284599 DOI: 10.1073/Pnas.0610385104  0.463
2007 Haile J, Holdaway R, Oliver K, Bunce M, Gilbert MT, Nielsen R, Munch K, Ho SY, Shapiro B, Willerslev E. Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor? Molecular Biology and Evolution. 24: 982-9. PMID 17255121 DOI: 10.1093/Molbev/Msm016  0.774
2007 Nielsen R, Bauer DuMont VL, Hubisz MJ, Aquadro CF. Maximum likelihood estimation of ancestral codon usage bias parameters in Drosophila. Molecular Biology and Evolution. 24: 228-35. PMID 17041152 DOI: 10.1093/Molbev/Msl146  0.581
2006 Nightingale KK, Lyles K, Ayodele M, Jalan P, Nielsen R, Wiedmann M. Novel method to identify source-associated phylogenetic clustering shows that Listeria monocytogenes includes niche-adapted clonal groups with distinct ecological preferences. Journal of Clinical Microbiology. 44: 3742-51. PMID 17021104 DOI: 10.1128/Jcm.00618-06  0.343
2006 Wong WS, Sainudiin R, Nielsen R. Identification of physicochemical selective pressure on protein encoding nucleotide sequences. Bmc Bioinformatics. 7: 148. PMID 16542458 DOI: 10.1186/1471-2105-7-148  0.336
2006 Nielsen R. Comparative genomics: difference of expression. Nature. 440: 161-161. PMID 16525458 DOI: 10.1038/440161A  0.345
2005 Nielsen R. Molecular Signatures of Natural Selection Annual Review of Genetics. 39: 197-218. PMID 16285858 DOI: 10.1146/Annurev.Genet.39.073003.112420  0.458
2005 Nielsen R, Williamson S, Kim Y, Hubisz MJ, Clark AG, Bustamante C. Genomic scans for selective sweeps using SNP data. Genome Research. 15: 1566-75. PMID 16251466 DOI: 10.1101/Gr.4252305  0.557
2005 Clark AG, Hubisz MJ, Bustamante CD, Williamson SH, Nielsen R. Ascertainment bias in studies of human genome-wide polymorphism. Genome Research. 15: 1496-502. PMID 16251459 DOI: 10.1101/Gr.4107905  0.552
2005 Bustamante CD, Fledel-Alon A, Williamson S, Nielsen R, Hubisz MT, Glanowski S, Tanenbaum DM, White TJ, Sninsky JJ, Hernandez RD, Civello D, Adams MD, Cargill M, Clark AG. Natural selection on protein-coding genes in the human genome. Nature. 437: 1153-7. PMID 16237444 DOI: 10.1038/Nature04240  0.564
2005 Matz MV, Nielsen R. A likelihood ratio test for species membership based on DNA sequence data. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 360: 1969-74. PMID 16214754 DOI: 10.1098/Rstb.2005.1728  0.319
2005 Wang Y, van der Hoeven RS, Nielsen R, Mueller LA, Tanksley SD. Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 112: 72-84. PMID 16208505 DOI: 10.1007/S00122-005-0107-Z  0.411
2005 York TL, Durrett RT, Tanksley S, Nielsen R. Bayesian and maximum likelihood estimation of genetic maps Genetical Research. 85: 159-168. PMID 16174334 DOI: 10.1017/S0016672305007494  0.311
2005 Zhang J, Nielsen R, Yang Z. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Molecular Biology and Evolution. 22: 2472-9. PMID 16107592 DOI: 10.1093/Molbev/Msi237  0.313
2005 Dimmic MW, Hubisz MJ, Bustamante CD, Nielsen R. Detecting coevolving amino acid sites using Bayesian mutational mapping. Bioinformatics (Oxford, England). 21: i126-35. PMID 15961449 DOI: 10.1093/Bioinformatics/Bti1032  0.476
2005 Williamson SH, Hernandez R, Fledel-Alon A, Zhu L, Nielsen R, Bustamante CD. Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proceedings of the National Academy of Sciences of the United States of America. 102: 7882-7. PMID 15905331 DOI: 10.1073/Pnas.0502300102  0.579
2005 Sainudiin R, Wong WS, Yogeeswaran K, Nasrallah JB, Yang Z, Nielsen R. 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. Journal of Molecular Evolution. 60: 315-26. PMID 15871042 DOI: 10.1007/S00239-004-0153-1  0.302
2005 Nielsen R, Bustamante C, Clark AG, Glanowski S, Sackton TB, Hubisz MJ, Fledel-Alon A, Tanenbaum DM, Civello D, White TJ, J Sninsky J, Adams MD, Cargill M. A scan for positively selected genes in the genomes of humans and chimpanzees. Plos Biology. 3: e170. PMID 15869325 DOI: 10.1371/Journal.Pbio.0030170  0.538
2005 Nielsen R. Human genomics: disclosure of variation. Nature. 434: 288-289. PMID 15772636 DOI: 10.1038/434288A  0.419
2005 Yang Z, Wong WS, Nielsen R. Bayes empirical bayes inference of amino acid sites under positive selection. Molecular Biology and Evolution. 22: 1107-18. PMID 15689528 DOI: 10.1093/Molbev/Msi097  0.348
2005 Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, Nielsen R, Thornton K, Hubisz MJ, Chen R, Meisel RP, Couronne O, Hua S, Smith MA, Zhang P, Liu J, et al. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Research. 15: 1-18. PMID 15632085 DOI: 10.1101/Gr.3059305  0.396
2005 Semon M, Nielsen R, Jones MP, McCouch SR. 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. Genetics. 169: 1639-47. PMID 15545652 DOI: 10.1534/Genetics.104.033175  0.358
2005 Whelan S, Nielsen R. Statistical Methods in Molecular Evolution Systematic Biology. 55: 698-700. DOI: 10.1080/10635150600899780  0.405
2004 Jobson RW, Nielsen R, Laakkonen L, Wikström M, Albert VA. Adaptive evolution of cytochrome c oxidase: Infrastructure for a carnivorous plant radiation Proceedings of the National Academy of Sciences of the United States of America. 101: 18064-18068. PMID 15596720 DOI: 10.1073/Pnas.0408092101  0.324
2004 Nielsen R. Population genetic analysis of ascertained SNP data. Human Genomics. 1: 218-224. PMID 15588481 DOI: 10.1186/1479-7364-1-3-218  0.385
2004 Wong WS, Yang Z, Goldman N, Nielsen R. Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics. 168: 1041-51. PMID 15514074 DOI: 10.1534/Genetics.104.031153  0.327
2004 Sainudiin R, Durrett RT, Aquadro CF, Nielsen R. Microsatellite mutation models: insights from a comparison of humans and chimpanzees. Genetics. 168: 383-95. PMID 15454551 DOI: 10.1534/Genetics.103.022665  0.618
2004 Nielsen R, Hubisz MJ, Clark AG. Reconstituting the Frequency Spectrum of Ascertained Single-Nucleotide Polymorphism Data Genetics. 168: 2373-2382. PMID 15371362 DOI: 10.1534/Genetics.104.031039  0.344
2004 Kim Y, Nielsen R. Linkage disequilibrium as a signature of selective sweeps. Genetics. 167: 1513-24. PMID 15280259 DOI: 10.1534/Genetics.103.025387  0.347
2004 Wong WSW, Nielsen R. Detecting selection in noncoding regions of nucleotide sequences. Genetics. 167: 949-958. PMID 15238543 DOI: 10.1534/Genetics.102.010959  0.341
2004 Hey J, Nielsen R. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics. 167: 747-60. PMID 15238526 DOI: 10.1534/Genetics.103.024182  0.611
2004 Zhai W, Todd MJ, Nielsen R. Is haplotype block identification useful for association mapping studies? Genetic Epidemiology. 27: 80-3. PMID 15185406 DOI: 10.1002/Gepi.20014  0.608
2004 Durrett R, Nielsen R, York TL. Bayesian estimation of genomic distance. Genetics. 166: 621-9. PMID 15020449 DOI: 10.1534/Genetics.166.1.621  0.363
2004 Hey J, Won YJ, Sivasundar A, Nielsen R, Markert JA. Using nuclear haplotypes with microsatellites to study gene flow between recently separated Cichlid species. Molecular Ecology. 13: 909-19. PMID 15012765 DOI: 10.1046/J.1365-294X.2003.02031.X  0.627
2004 Palsbøll PJ, Bérubé M, Aguilar A, Notarbartolo-Di-Sciara G, Nielsen R. Discerning between recurrent gene flow and recent divergence under a finite-site mutation model applied to North Atlantic and Mediterranean Sea fin whale (Balaenoptera physalus) populations. Evolution. 58: 670-675. DOI: 10.1111/J.0014-3820.2004.Tb01691.X  0.38
2003 Clark AG, Glanowski S, Nielsen R, Thomas P, Kejariwal A, Todd MJ, Tanenbaum DM, Civello D, Lu F, Murphy B, Ferriera S, Wang G, Zheng X, White TJ, Sninsky JJ, et al. Positive selection in the human genome inferred from human-chimp-mouse orthologous gene alignments. Cold Spring Harbor Symposia On Quantitative Biology. 68: 471-7. PMID 15338650 DOI: 10.1101/Sqb.2003.68.479  0.403
2003 Clark AG, Glanowski S, Nielsen R, Thomas PD, Kejariwal A, Todd MA, Tanenbaum DM, Civello D, Lu F, Murphy B, Ferriera S, Wang G, Zheng X, White TJ, Sninsky JJ, et al. Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science (New York, N.Y.). 302: 1960-3. PMID 14671302 DOI: 10.1126/Science.1088821  0.395
2003 Nielsen R, Tarpy DR, Reeve HK. Estimating effective paternity number in social insects and the effective number of alleles in a population. Molecular Ecology. 12: 3157-64. PMID 14629394 DOI: 10.1046/J.1365-294X.2003.01994.X  0.329
2003 Clark AG, Nielsen R, Signorovitch J, Matise TC, Glanowski S, Heil J, Winn-Deen ES, Holden AL, Lai E. Linkage disequilibrium and inference of ancestral recombination in 538 single-nucleotide polymorphism clusters across the human genome. American Journal of Human Genetics. 73: 285-300. PMID 12844287 DOI: 10.1086/377138  0.446
2003 Nielsen R, Yang Z. Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA. Molecular Biology and Evolution. 20: 1231-9. PMID 12777508 DOI: 10.1093/Molbev/Msg147  0.388
2003 Huelsenbeck JP, Nielsen R, Bollback JP. Stochastic mapping of morphological characters. Systematic Biology. 52: 131-58. PMID 12746144 DOI: 10.1080/10635150390192780  0.769
2003 Nielsen R, Signorovitch J. Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium Theoretical Population Biology. 63: 245-255. PMID 12689795 DOI: 10.1016/S0040-5809(03)00005-4  0.355
2003 Bustamante CD, Nielsen R, Hartl DL. Maximum likelihood and Bayesian methods for estimating the distribution of selective effects among classes of mutations using DNA polymorphism data. Theoretical Population Biology. 63: 91-103. PMID 12615493 DOI: 10.1016/S0040-5809(02)00050-3  0.545
2002 York TL, Durrett R, Nielsen R. Bayesian estimation of the number of inversions in the history of two chromosomes. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 9: 805-18. PMID 12614548 DOI: 10.1089/10665270260518281  0.305
2002 Nielsen R. Mapping Mutations on Phylogenies Systematic Biology. 51: 729-739. PMID 12396587 DOI: 10.1080/10635150290102393  0.301
2002 Cai S, Kabuki DY, Kuaye AY, Cargioli TG, Chung MS, Nielsen R, Wiedmann M. Rational design of DNA sequence-based strategies for subtyping Listeria monocytogenes. Journal of Clinical Microbiology. 40: 3319-25. PMID 12202573 DOI: 10.1128/Jcm.40.9.3319-3325.2002  0.381
2002 Yang Z, Nielsen R. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Molecular Biology and Evolution. 19: 908-17. PMID 12032247 DOI: 10.1093/Oxfordjournals.Molbev.A004148  0.346
2002 Bustamante CD, Nielsen R, Sawyer SA, Olsen KM, Purugganan MD, Hartl DL. The cost of inbreeding in Arabidopsis. Nature. 416: 531-4. PMID 11932744 DOI: 10.1038/416531A  0.573
2002 Signorovitch J, Nielsen R. PATRI-paternity inference using genetic data. Bioinformatics. 18: 341-342. PMID 11847091 DOI: 10.1093/Bioinformatics/18.2.341  0.322
2002 Bustamante CD, Nielsen R, Hartl DL. A maximum likelihood method for analyzing pseudogene evolution: implications for silent site evolution in humans and rodents. Molecular Biology and Evolution. 19: 110-7. PMID 11752196 DOI: 10.1093/Oxfordjournals.Molbev.A003975  0.55
2001 Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP. Bayesian inference of phylogeny and its impact on evolutionary biology. Science (New York, N.Y.). 294: 2310-4. PMID 11743192 DOI: 10.1126/Science.1065889  0.803
2001 Wakeley J, Nielsen R, Liu-Cordero SN, Ardlie K. The Discovery of Single-Nucleotide Polymorphisms—and Inferences about Human Demographic History American Journal of Human Genetics. 69: 1332-1347. PMID 11704929 DOI: 10.1086/324521  0.798
2001 Nielsen R. Statistical tests of selective neutrality in the age of genomics Heredity. 86: 641-647. PMID 11595044 DOI: 10.1046/J.1365-2540.2001.00895.X  0.427
2000 Nielsen R, Slatkin M. Likelihood analysis of ongoing gene flow and historical association. Evolution; International Journal of Organic Evolution. 54: 44-50. PMID 10937182 DOI: 10.1111/J.0014-3820.2000.Tb00006.X  0.707
2000 Yang Z, Nielsen R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Molecular Biology and Evolution. 17: 32-43. PMID 10666704 DOI: 10.1093/Oxfordjournals.Molbev.A026236  0.361
1999 Huelsenbeck JP, Nielsen R. Effect of nonindependent substitution on phylogenetic accuracy. Systematic Biology. 48: 317-28. PMID 12066710 DOI: 10.1080/106351599260319  0.598
1999 Nielsen R, Palsbøll PJ. Single-locus tests of microsatellite evolution: multi-step mutations and constraints on allele size. Molecular Phylogenetics and Evolution. 11: 477-484. PMID 10196086 DOI: 10.1006/Mpev.1998.0597  0.322
1999 Huelsenbeck JP, Nielsen R. Variation in the pattern of nucleotide substitution across sites. Journal of Molecular Evolution. 48: 86-93. PMID 9873080 DOI: 10.1007/Pl00006448  0.616
1999 Yang Z, Nielsen R, Hasegawa M. Models of amino acid substitution and applications to mitochondrial protein evolution. Molecular Biology and Evolution. 15: 1600-11. PMID 9866196 DOI: 10.1093/Oxfordjournals.Molbev.A025888  0.312
1998 Nielsen R, Mountain JL, Huelsenbeck JP, Slatkin M. MAXIMUM-LIKELIHOOD ESTIMATION OF POPULATION DIVERGENCE TIMES AND POPULATION PHYLOGENY IN MODELS WITHOUT MUTATION. Evolution; International Journal of Organic Evolution. 52: 669-677. PMID 28565245 DOI: 10.1111/J.1558-5646.1998.Tb03692.X  0.77
1998 Rannala B, Huelsenbeck JP, Yang Z, Nielsen R. Taxon sampling and the accuracy of large phylogenies. Systematic Biology. 47: 702-10. PMID 12066312 DOI: 10.1080/106351598260680  0.581
1998 Nielsen R. Maximum Likelihood Estimation of Population Divergence Times and Population Phylogenies under the Infinite Sites Model Theoretical Population Biology. 53: 143-151. PMID 9615473 DOI: 10.1006/Tpbi.1997.1348  0.379
1998 Yang Z, Nielsen R. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. Journal of Molecular Evolution. 46: 409-18. PMID 9541535 DOI: 10.1007/Pl00006320  0.364
1997 Nielsen R. Site-by-site estimation of the rate of substitution and the correlation of rates in mitochondrial DNA. Systematic Biology. 46: 346-353. PMID 11975345 DOI: 10.1093/Sysbio/46.2.346  0.327
1997 Nielsen R. Robustness of the Estimator of the Index of Dispersion for DNA Sequences Molecular Phylogenetics and Evolution. 7: 346-351. PMID 9187093 DOI: 10.1006/Mpev.1997.0411  0.325
1997 Nielsen R. The ratio of replacement to silent divergence and tests of neutrality Journal of Evolutionary Biology. 10: 217-231. DOI: 10.1046/J.1420-9101.1997.10020217.X  0.363
1996 Huelsenbeck JP, Hillis DM, Nielsen R. A Likelihood-Ratio Test of Monophyly Systematic Biology. 45: 546-558. DOI: 10.1093/Sysbio/45.4.546  0.585
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