Kirk Lohmueller*

Kirk Edward Lohmueller

Professor, Ecology And Evolutionary Biology, University of California Los Angeles

Professor, Human Genetics, University of California Los Angeles

Publications

  1. Mah JC, Lohmueller KE, Garud N. Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history.. bioRxiv : the preprint server for biology, 2023.
  2. Kyriazis CC, Robinson JA, Lohmueller KE. Using Computational Simulations to Model Deleterious Variation and Genetic Load in Natural Populations.. The American naturalist, 2023.
  3. Nigenda-Morales SF, Lin M, Nuñez-Valencia PG, Kyriazis CC, Beichman AC, Robinson JA, Ragsdale AP, Urbán R J, Archer FI, Viloria-Gómora L, Pérez-Álvarez MJ, Poulin E, Lohmueller KE, Moreno-Estrada A, Wayne RK. The genomic footprint of whaling and isolation in fin whale populations.. Nature communications, 2023.
  4. Wade EE, Kyriazis CC, Cavassim MIA, Lohmueller KE. Quantifying the fraction of new mutations that are recessive lethal.. Evolution; international journal of organic evolution, 2023.
  5. Barroso GV, Lohmueller KE. Inferring the mode and strength of ongoing selection.. Genome research, 2023.
  6. Leonard JA, von Holdt B, Smith TB, Sork VL, Shapiro B, Ostrander EA, Rieseberg LH, Van Valkenburgh B, Lohmueller KE. Remembering distinguished professor Robert K. Wayne.. Molecular ecology, 2023.
  7. Kyriazis CC, Robinson JA, Nigenda-Morales SF, Beichman AC, Rojas-Bracho L, Robertson KM, Fontaine MC, Wayne RK, Taylor BL, Lohmueller KE, Morin PA. Models based on best-available information support a low inbreeding load and potential for recovery in the vaquita.. Heredity, 2023.
  8. Kyriazis CC, Beichman AC, Brzeski KE, Hoy SR, Peterson RO, Vucetich JA, Vucetich LM, Lohmueller KE, Wayne RK. Genomic Underpinnings of Population Persistence in Isle Royale Moose.. Molecular biology and evolution, 2023.
  9. Mooney JA, Marsden CD, Yohannes A, Wayne RK, Lohmueller KE. Long-term Small Population Size, Deleterious Variation, and Altitude Adaptation in the Ethiopian Wolf, a Severely Endangered Canid.. Molecular biology and evolution, 2023.
  10. Zhang X, Kim B, Singh A, Sankararaman S, Durvasula A, Lohmueller KE. MaLAdapt Reveals Novel Targets of Adaptive Introgression From Neanderthals and Denisovans in Worldwide Human Populations.. Molecular biology and evolution, 2023.
  11. Robinson J, Kyriazis CC, Yuan SC, Lohmueller KE. Deleterious Variation in Natural Populations and Implications for Conservation Genetics.. Annual review of animal biosciences, 2022.
  12. Johri P, Eyre-Walker A, Gutenkunst RN, Lohmueller KE, Jensen JD. On the prospect of achieving accurate joint estimation of selection with population history.. Genome biology and evolution, 2022.
  13. Robinson JA, Kyriazis CC, Nigenda-Morales SF, Beichman AC, Rojas-Bracho L, Robertson KM, Fontaine MC, Wayne RK, Lohmueller KE, Taylor BL, Morin PA. The critically endangered vaquita is not doomed to extinction by inbreeding depression.. Science (New York, N.Y.), 2022.
  14. Sork VL, Cokus SJ, Fitz-Gibbon ST, Zimin AV, Puiu D, Garcia JA, Gugger PF, Henriquez CL, Zhen Y, Lohmueller KE, Pellegrini M, Salzberg SL. High-quality genome and methylomes illustrate features underlying evolutionary success of oaks.. Nature communications, 2022.
  15. Ortega-Del Vecchyo D, Lohmueller KE, Novembre J. Haplotype-based inference of the distribution of fitness effects.. Genetics, 2022.
  16. Beichman AC, Kalhori P, Kyriazis CC, DeVries AA, Nigenda-Morales S, Heckel G, Schramm Y, Moreno-Estrada A, Kennett DJ, Hylkema M, Bodkin J, Koepfli KP, Lohmueller KE, Wayne RK. Genomic analyses reveal range-wide devastation of sea otter populations.. Molecular ecology, 2022.
  17. Findley AS, Zhang X, Boye C, Lin YL, Kalita CA, Barreiro L, Lohmueller KE, Pique-Regi R, Luca F. A signature of Neanderthal introgression on molecular mechanisms of environmental responses.. PLoS genetics, 2021.
  18. Garcia JA, Lohmueller KE. Negative linkage disequilibrium between amino acid changing variants reveals interference among deleterious mutations in the human genome.. PLoS genetics, 2021.
  19. Mooney JA, Yohannes A, Lohmueller KE. The impact of identity by descent on fitness and disease in dogs.. Proceedings of the National Academy of Sciences of the United States of America, 2021.
  20. Durvasula A, Lohmueller KE. Negative selection on complex traits limits phenotype prediction accuracy between populations.. American journal of human genetics, 2021.
  21. Mitra I, Huang B, Mousavi N, Ma N, Lamkin M, Yanicky R, Shleizer-Burko S, Lohmueller KE, Gymrek M. Patterns of de novo tandem repeat mutations and their role in autism.. Nature, 2021.
  22. Kyriazis CC, Wayne RK, Lohmueller KE. Strongly deleterious mutations are a primary determinant of extinction risk due to inbreeding depression.. Evolution letters, 2020.
  23. Grujic O, Phung TN, Kwon SB, Arneson A, Lee Y, Lohmueller KE, Ernst J. Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations.. Nature communications, 2020.
  24. Zhen Y, Huber CD, Davies RW, Lohmueller KE. Greater strength of selection and higher proportion of beneficial amino acid changing mutations in humans compared with mice and Drosophila melanogaster.. Genome research, 2020.
  25. Adrion JR, Cole CB, Dukler N, Galloway JG, Gladstein AL, Gower G, Kyriazis CC, Ragsdale AP, Tsambos G, Baumdicker F, Carlson J, Cartwright RA, Durvasula A, Gronau I, Kim BY, McKenzie P, Messer PW, Noskova E, Ortega-Del Vecchyo D, Racimo F, Struck TJ, Gravel S, Gutenkunst RN, Lohmueller KE, Ralph PL, Schrider DR, Siepel A, Kelleher J, Kern AD. A community-maintained standard library of population genetic models.. eLife, 2020.
  26. Zhang X, Kim B, Lohmueller KE, Huerta-Sánchez E. The Impact of Recessive Deleterious Variation on Signals of Adaptive Introgression in Human Populations.. Genetics, 2020.
  27. Huber CD, Kim BY, Lohmueller KE. Population genetic models of GERP scores suggest pervasive turnover of constrained sites across mammalian evolution.. PLoS genetics, 2020.
  28. Beichman AC, Koepfli KP, Li G, Murphy W, Dobrynin P, Kliver S, Tinker MT, Murray MJ, Johnson J, Lindblad-Toh K, Karlsson EK, Lohmueller KE, Wayne RK. Aquatic Adaptation and Depleted Diversity: A Deep Dive into the Genomes of the Sea Otter and Giant Otter.. Molecular biology and evolution, 2019.
  29. Buckleton JS, Lohmueller KE, Inman K, Cheng K, Curran JM, Pugh SN, Bright JA, Taylor DA. Testing whether stutter and low-level DNA peaks are additive.. Forensic science international. Genetics, 2019.
  30. Sura SA, Smith LL, Ambrose MR, Amorim CEG, Beichman AC, Gomez ACR, Juhn M, Kandlikar GS, Miller JS, Mooney J, Mummah RO, Lohmueller KE, Lloyd-Smith JO. Ten simple rules for giving an effective academic job talk.. PLoS computational biology, 2019.
  31. Phung TN, Wayne RK, Wilson MA, Lohmueller KE. Complex patterns of sex-biased demography in canines.. Proceedings. Biological sciences, 2019.
  32. Robinson JA, Räikkönen J, Vucetich LM, Vucetich JA, Peterson RO, Lohmueller KE, Wayne RK. Genomic signatures of extensive inbreeding in Isle Royale wolves, a population on the threshold of extinction.. Science advances, 2019.
  33. vonHoldt BM, Kartzinel RY, Huber CD, Le Underwood V, Zhen Y, Ruegg K, Lohmueller KE, Smith TB. Growth factor gene IGF1 is associated with bill size in the black-bellied seedcracker Pyrenestes ostrinus.. Nature communications, 2018.
  34. Robinson JA, Brown C, Kim BY, Lohmueller KE, Wayne RK. Purging of Strongly Deleterious Mutations Explains Long-Term Persistence and Absence of Inbreeding Depression in Island Foxes.. Current biology : CB, 2018.
  35. Mooney JA, Huber CD, Service S, Sul JH, Marsden CD, Zhang Z, Sabatti C, Ruiz-Linares A, Bedoya G, Costa Rica/Colombia Consortium for Genetic Investigation of Bipolar Endophenotypes, Freimer N, Lohmueller KE. Understanding the Hidden Complexity of Latin American Population Isolates.. American journal of human genetics, 2018.
  36. Kim BY, Huber CD, Lohmueller KE. Deleterious variation shapes the genomic landscape of introgression.. PLoS genetics, 2018.
  37. Kim BY, Wei X, Fitz-Gibbon S, Lohmueller KE, Ortego J, Gugger PF, Sork VL. RADseq data reveal ancient, but not pervasive, introgression between Californian tree and scrub oak species (Quercus sect. Quercus: Fagaceae).. Molecular ecology, 2018.
  38. Chiang CWK, Marcus JH, Sidore C, Biddanda A, Al-Asadi H, Zoledziewska M, Pitzalis M, Busonero F, Maschio A, Pistis G, Steri M, Angius A, Lohmueller KE, Abecasis GR, Schlessinger D, Cucca F, Novembre J. Genomic history of the Sardinian population.. Nature genetics, 2018.
  39. Huber CD, Durvasula A, Hancock AM, Lohmueller KE. Gene expression drives the evolution of dominance.. Nature communications, 2018.
  40. Schweizer RM, Durvasula A, Smith J, Vohr SH, Stahler DR, Galaverni M, Thalmann O, Smith DW, Randi E, Ostrander EA, Green RE, Lohmueller KE, Novembre J, Wayne RK. Natural Selection and Origin of a Melanistic Allele in North American Gray Wolves.. Molecular biology and evolution, 2018.
  41. Beichman AC, Phung TN, Lohmueller KE. Comparison of Single Genome and Allele Frequency Data Reveals Discordant Demographic Histories.. G3 (Bethesda, Md.), 2017.
  42. Zhen Y, Harrigan RJ, Ruegg KC, Anderson EC, Ng TC, Lao S, Lohmueller KE, Smith TB. Genomic divergence across ecological gradients in the Central African rainforest songbird (Andropadus virens).. Molecular ecology, 2017.
  43. Huber CD, Kim BY, Marsden CD, Lohmueller KE. Determining the factors driving selective effects of new nonsynonymous mutations.. Proceedings of the National Academy of Sciences of the United States of America, 2017.
  44. Kim BY, Huber CD, Lohmueller KE. Inference of the Distribution of Selection Coefficients for New Nonsynonymous Mutations Using Large Samples.. Genetics, 2017.
  45. Pedersen CT, Lohmueller KE, Grarup N, Bjerregaard P, Hansen T, Siegismund HR, Moltke I, Albrechtsen A. The Effect of an Extreme and Prolonged Population Bottleneck on Patterns of Deleterious Variation: Insights from the Greenlandic Inuit.. Genetics, 2016.
  46. Phung TN, Huber CD, Lohmueller KE. Determining the Effect of Natural Selection on Linked Neutral Divergence across Species.. PLoS genetics, 2016.
  47. Ortega-Del Vecchyo D, Marsden CD, Lohmueller KE. PReFerSim: fast simulation of demography and selection under the Poisson Random Field model.. Bioinformatics (Oxford, England), 2016.
  48. Robinson JA, Ortega-Del Vecchyo D, Fan Z, Kim BY, vonHoldt BM, Marsden CD, Lohmueller KE, Wayne RK. Genomic Flatlining in the Endangered Island Fox.. Current biology : CB, 2016.
  49. Marsden CD, Rudin N, Inman K, Lohmueller KE. An assessment of the information content of likelihood ratios derived from complex mixtures.. Forensic science international. Genetics, 2016.
  50. Haned H, Gill P, Lohmueller K, Inman K, Rudin N. Validation of probabilistic genotyping software for use in forensic DNA casework: Definitions and illustrations.. Science & justice : journal of the Forensic Science Society, 2015.
  51. Marsden CD, Ortega-Del Vecchyo D, O'Brien DP, Taylor JF, Ramirez O, Vilà C, Marques-Bonet T, Schnabel RD, Wayne RK, Lohmueller KE. Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs.. Proceedings of the National Academy of Sciences of the United States of America, 2015.
  52. Inman K, Rudin N, Cheng K, Robinson C, Kirschner A, Inman-Semerau L, Lohmueller KE. Lab Retriever: a software tool for calculating likelihood ratios incorporating a probability of drop-out for forensic DNA profiles.. BMC bioinformatics, 2015.
  53. Zoledziewska M, Sidore C, Chiang CWK, Sanna S, Mulas A, Steri M, Busonero F, Marcus JH, Marongiu M, Maschio A, Ortega Del Vecchyo D, Floris M, Meloni A, Delitala A, Concas MP, Murgia F, Biino G, Vaccargiu S, Nagaraja R, Lohmueller KE, UK10K consortium, Timpson NJ, Soranzo N, Tachmazidou I, Dedoussis G, Zeggini E, Understanding Society Scientific Group, Uzzau S, Jones C, Lyons R, Angius A, Abecasis GR, Novembre J, Schlessinger D, Cucca F. Height-reducing variants and selection for short stature in Sardinia.. Nature genetics, 2015.
  54. Rohlfs RV, Aguiar VRC, Lohmueller KE, Castro AM, Ferreira ACS, Almeida VCO, Louro ID, Nielsen R. Fitting the Balding-Nichols model to forensic databases.. Forensic science international. Genetics, 2015.
  55. Brown R, Lee H, Eskin A, Kichaev G, Lohmueller KE, Reversade B, Nelson SF, Pasaniuc B. Leveraging ancestry to improve causal variant identification in exome sequencing for monogenic disorders.. European journal of human genetics : EJHG, 2015.
  56. Kim BY, Lohmueller KE. Selection and reduced population size cannot explain higher amounts of Neandertal ancestry in East Asian than in European human populations.. American journal of human genetics, 2015.
  57. Lohmueller KE. The distribution of deleterious genetic variation in human populations.. Current opinion in genetics & development, 2014.
  58. Lohmueller KE. Evolution. On the origin of Peter Rabbit.. Science (New York, N.Y.), 2014.
  59. DeGiorgio M, Lohmueller KE, Nielsen R. A model-based approach for identifying signatures of ancient balancing selection in genetic data.. PLoS genetics, 2014.
  60. Ko A, Cantor RM, Weissglas-Volkov D, Nikkola E, Reddy PM, Sinsheimer JS, Pasaniuc B, Brown R, Alvarez M, Rodriguez A, Rodriguez-Guillen R, Bautista IC, Arellano-Campos O, Muñoz-Hernández LL, Salomaa V, Kaprio J, Jula A, Jauhiainen M, Heliövaara M, Raitakari O, Lehtimäki T, Eriksson JG, Perola M, Lohmueller KE, Matikainen N, Taskinen MR, Rodriguez-Torres M, Riba L, Tusie-Luna T, Aguilar-Salinas CA, Pajukanta P. Amerindian-specific regions under positive selection harbour new lipid variants in Latinos.. Nature communications, 2014.
  61. Lohmueller KE. The impact of population demography and selection on the genetic architecture of complex traits.. PLoS genetics, 2014.
  62. Lohmueller KE, Rudin N, Inman K. Analysis of allelic drop-out using the Identifiler(®) and PowerPlex(®) 16 forensic STR typing systems.. Forensic science international. Genetics, 2014.
  63. Wilson Sayres MA, Lohmueller KE, Nielsen R. Natural selection reduced diversity on human y chromosomes.. PLoS genetics, 2014.
  64. 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, Degiorgio M, Jørgensen T, Sandbæk A, Lauritzen T, Brunak S, Kristiansen K, Li Y, Hansen T, Wang J, Nielsen R, Pedersen O. Whole-exome sequencing of 2,000 Danish individuals and the role of rare coding variants in type 2 diabetes.. American journal of human genetics, 2013.
  65. Lohmueller KE, Rudin N. Calculating the weight of evidence in low-template forensic DNA casework.. Journal of forensic sciences, 2012.
  66. 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, Lauritzen T, Hansen T, Pedersen O, Wang J, Nielsen R. Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome.. PLoS genetics, 2011.
  67. 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, De La Vega FM, Tridico S, Metspalu E, Nielsen K, Ávila-Arcos MC, Moreno-Mayar JV, Muller C, Dortch J, Gilbert MT, Lund O, Wesolowska A, Karmin M, Weinert LA, Wang B, Li J, Tai S, Xiao F, Hanihara T, van Driem G, Jha AR, Ricaut FX, de Knijff P, Migliano AB, Gallego Romero I, Kristiansen K, Lambert DM, Brunak S, Forster P, Brinkmann B, Nehlich O, Bunce M, Richards M, Gupta R, Bustamante CD, Krogh A, Foley RA, Lahr MM, Balloux F, Sicheritz-Pontén T, Villems R, Nielsen R, Wang J, Willerslev E. An Aboriginal Australian genome reveals separate human dispersals into Asia.. Science (New York, N.Y.), 2011.
  68. 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, 2011.
  69. Lohmueller KE, Bustamante CD, Clark AG. Detecting directional selection in the presence of recent admixture in African-Americans.. Genetics, 2010.
  70. Boyko AR, Quignon P, Li L, Schoenebeck JJ, Degenhardt JD, Lohmueller KE, Zhao K, Brisbin A, Parker HG, vonHoldt BM, Cargill M, Auton A, Reynolds A, Elkahloun AG, Castelhano M, Mosher DS, Sutter NB, Johnson GS, Novembre J, Hubisz MJ, Siepel A, Wayne RK, Bustamante CD, Ostrander EA. A simple genetic architecture underlies morphological variation in dogs.. PLoS biology, 2010.
  71. Lohmueller KE, Degenhardt JD, Keinan A. Sex-averaged recombination and mutation rates on the X chromosome: a comment on Labuda et al.. American journal of human genetics, 2010.
  72. Lohmueller KE, Bustamante CD, Clark AG. The effect of recent admixture on inference of ancient human population history.. Genetics, 2010.
  73. Vonholdt BM, Pollinger JP, Lohmueller KE, Han E, Parker HG, Quignon P, Degenhardt JD, Boyko AR, Earl DA, Auton A, Reynolds A, Bryc K, Brisbin A, Knowles JC, Mosher DS, Spady TC, Elkahloun A, Geffen E, Pilot M, Jedrzejewski W, Greco C, Randi E, Bannasch D, Wilton A, Shearman J, Musiani M, Cargill M, Jones PG, Qian Z, Huang W, Ding ZL, Zhang YP, Bustamante CD, Ostrander EA, Novembre J, Wayne RK. Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication.. Nature, 2010.
  74. Lohmueller KE. Graydon et al. provide no new evidence that forensic STR loci are functional.. Forensic science international. Genetics, 2009.
  75. Wall JD, Lohmueller KE, Plagnol V. Detecting ancient admixture and estimating demographic parameters in multiple human populations.. Molecular biology and evolution, 2009.
  76. Lohmueller KE, Bustamante CD, Clark AG. Methods for human demographic inference using haplotype patterns from genomewide single-nucleotide polymorphism data.. Genetics, 2009.
  77. Auton A, Bryc K, Boyko AR, Lohmueller KE, Novembre J, Reynolds A, Indap A, Wright MH, Degenhardt JD, Gutenkunst RN, King KS, Nelson MR, Bustamante CD. Global distribution of genomic diversity underscores rich complex history of continental human populations.. Genome research, 2009.
  78. 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, 2008.
  79. 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, 2008.
  80. Olshen AB, Gold B, Lohmueller KE, Struewing JP, Satagopan J, Stefanov SA, Eskin E, Kirchhoff T, Lautenberger JA, Klein RJ, Friedman E, Norton L, Ellis NA, Viale A, Lee CS, Borgen PI, Clark AG, Offit K, Boyd J. Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping.. BMC genetics, 2008.
  81. Lohmueller KE, Wong LJ, Mauney MM, Jiang L, Felder RA, Jose PA, Williams SM. Patterns of genetic variation in the hypertension candidate gene GRK4: ethnic variation and haplotype structure.. Annals of human genetics, 2006.
  82. Lohmueller KE, Mauney MM, Reich D, Braverman JM. Variants associated with common disease are not unusually differentiated in frequency across populations.. American journal of human genetics, 2005.
  83. Patterson N, Hattangadi N, Lane B, Lohmueller KE, Hafler DA, Oksenberg JR, Hauser SL, Smith MW, O'Brien SJ, Altshuler D, Daly MJ, Reich D. Methods for high-density admixture mapping of disease genes.. American journal of human genetics, 2004.
  84. Lohmueller KE, Pearce CL, Pike M, Lander ES, Hirschhorn JN. Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease.. Nature genetics, 2003.
  85. Hirschhorn JN, Lohmueller K, Byrne E, Hirschhorn K. A comprehensive review of genetic association studies.. Genetics in medicine : official journal of the American College of Medical Genetics, 2002.