Kirk’s Google Scholar Profile

Lohmueller Lab members are listed in Bold.

Preprints: 

• Martinez I Zurita A, Kyriazis CC, Lohmueller KE. The impact of non-neutral synonymous mutations when inferring selection on non-synonymous mutations, bioRxiv, doi: 10.1101/2024.02.07.579314.

• 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, doi: https://doi.org/10.1101/2023.11.09.566454 (*Co-corresponding authors)

• Huang B, Durvasula A, Mousavi N, Ziaei-Jam H, Maksimov M, Lohmueller KE*, Melissa Gymrek.* Genome-wide selection inference at short taem repeats, bioRxiv  (*Contributed equally)

2024

• Kyriazis CC, Serieys LEK, Bishop JM, Drouilly M, Viljoen S, Wayne RK, Lohmueller KE. The influence of gene flow on population viability in an isolated urban caracal population, Mol Ecol, in press. bioRxiv doi: https://doi.org/10.1101/2023.07.20.549918

2023

• Kyriazis CC, Robinson JA, Lohmueller KE. Using computational simulations to model deleterious variation and genetic load in natural populations. Am Nat. 2023; 202:747-752.
• Nigenda-Morales SF*, Lin M*, Nunez-Valencia PG, Kyriazis CC, Beichman AC, Robinson JA, Ragsdale AP, Urban J, Archer FI, Viloria-Gomora L, Perez-Alvarez MJ, Poulin E, Lohmueller KE*, Moreno-Estrada A*, Wayne RK. The genomic footprint of whaling and isolation in fin whale populations. Nat Commun. 2023; 14:5465. (*Co-corresponding authors)
• Leonard J, von Holdt B, Smith TB, Sork VL, Shapiro B, Ostrander EA, Rieseberg LH, Van Valkenburgh B, Lohmueller KE. Remembering distinguished professor Robert K. Wayne. Mol Ecol. 2023;32:2364-2368.
• Barroso GV & Lohmueller KE. Inferring the mode and strength of ongoing selection. Genome Research. 2023; 33:632-643.
• Wade EE, Kyriazis CC, Cavassim MIA, & Lohmueller KE. Quantifying the fraction of new mutations that are recessive lethal. Evolution. 2023; 77:1539-1549.
• 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 (Edinb). 2023; Mar 20. (*Co-corresponding authors)
• 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, Mol Biol Evol. 2023; 40(1):msad001 (*Contributed equally)
• 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, Mol Biol Evol. 2023;40(2):msad021 (*Contributed equally)
• 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. Mol Biol Evol. 2023;40(1):msac277. 
• Robinson J, Kyriazis CC, Yuan SC, Lohmueller KE. Deleterious variation in natural populations and implications for conservation genetics, Annu Rev Anim Biosci. 2023;11:93-114.

2022

• 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. 2022 May 6;376(6593):635-639. (*Co-corresponding authors)
• 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. Nat Commun. 2022 Apr 19;13(1):2047
• Ortega-Del Vecchyo D, Lohmueller KE, Novembre J. Haplotype-based inference of the distribution of fitness effects. Genetics. 2022 Apr 4;220(4):iyac002.
• 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. Mol Ecol. 2021 Dec 30. (*Contributed equally)

2021

• 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; 17(9): e1009493.
• Garcia JA and Lohmueller KE. Negative linkage disequilibrium between amino acid changing variants reveals interference among deleterious mutations in the human genome, PLoS Genetics 2021; 17(7): e1009676.
• Mooney JA, Yohannes A, and Lohmueller KE. The impact of identity by descent on fitness and disease in dogs, Proc Natl Acad Sci U S A. 2021; 118(16):e2019116118.
• Durvasula A, Lohmueller KE. Negative selection on complex traits limits phenotype prediction accuracy between populations, Am J Hum Genet  2021; 108(4):620-631.
• 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, 2021; 31:110-120.
• 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 autismNature, 2021; 589,246-250. (*Co-corresponding authors)

2020

• 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. Natue Communications 2020; 11:6168.
• Kyriazis CC, Wayne RK, Lohmueller KE. Strongly deleterious mutations are a primary determinant of extinction risk due to inbreeding depression. Evolution Letters 2020.
• Adrion JR, et al., (including Kyriazis K, Durvasula A, Lohmueller KE). A community-maintained standard library of population genetic models. eLife 2020; 9:e54967.
• Zhang X, Kim BY, Lohmueller KE*, Huerta-Sanchez E*. The impact of recessive deleterious variation on signals of adaptive introgression in human populations. Genetics 2020; 215: 799-812.  (*Contributed equally)
• Huber CD, Kim BY, Lohmueller KE. Population genetic models of GERP scores suggest pervasive turnover of constrained sites across mammalian evolution. PLoS Genetics 2020; 16(5): e100882714.

2019

• 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 Sci Int Genet, 2019; 43:102166.
• 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 Comput Biol, 2019; 15:e1007163.
• Beichman A, Koepfli KP, Li G; Murphy W, Dobrynin P, Kilver 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 (Enhydra lutris) and giant otter (Pteronura brasiliensis), Mol Bio Evol, 2019; 36:2631-2655. (*Contributed equally).
• Phung TN, Wayne RK, Wilson Sayres MA*, Lohmueller KE*. Complex patterns of sex-biased demography in canines, (*Contributed equally). Proc Royal Soc B, 2019; 286:20181976.
• Robinson JA, Räikkönen J, Vucetich LM, Vucetich JA, Hedrick PW, Peterson RO, Lohmueller KE*, Wayne RK*. Genomic signatures of extensive inbreeding in Isle Royale wolves, a population on the threshold of extinction, (*Contributed equally). Sci Adv, 2019; 5:eaau0757.

2018

• Mooney JA, Huber CD, Service S, Sul JH, Marsden CD, Zhang Z, Sabatti C, Ruiz-Linares A, Bedoy G, Costa Rica/Colombia Consortium for Genetic Investigation of Bipolar Endophenotypes, Freimer N, Lohmueller KE. Understanding the hidden complexity of Latin American population isolates. Am J Hum Genet, 2018; 103:707-726.
• 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, 2018; 28: 3487-94. (*Contributed equally).
• Kim BY, Huber CD, Lohmueller KE. Deleterious variation mimics signatures of genomic incompatibility and adaptive introgression. PLoS Genetics 2018; 14 e1007741.
• Kim BY, Wei X, Fitz-Gibbon S, Lohmueller KE, Ortego J, Gugger PF, Sork VL. RADseq data reveal pervasive, but not promiscuous, ancient introgression within Californian white oak species (Quercus: Fagaceae). Mol Ecol, 2018; 27: 4556-4571.
• Beichman AC, Huerta-Sanchez E, and Lohmueller KE. Using genomic data to infer historic population dynamics of non-model organisms, Annu Rev Ecol Evol Syst, 2018; 49: 433-456.
• 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. Nat Commun, 2018; 9: 4855.
• Huber CD, Durvasula A, Hancock AM, Lohmueller KE. Gene expression drives the evolution of dominance, Nat Commun, 2018; 9: 2750.
• 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, and Novembre J. Genomic history of the Sardinian population, Nat Genet, 2018; 50: 1426-1434.
• 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. Mol Biol Evol. 2018; 35(5):1190-1209.

2017

• Beichman AC, Phung TN, Lohmueller KE. Comparison of Single Genome and Allele Frequency Data Reveals Discordant Demographic Histories. G3 (Bethesda). 2017; 7(11):3605-3620.
• 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). Mol Ecol. 2017; 26(19):4966-4977.
• Kim BY, Huber CD, Lohmueller KE. Inference of the Distribution of Selection Coefficients for New Nonsynonymous Mutations Using Large Samples. Genetics 2017; 206(1):345-361.
• Huber CD, Kim BY, Marsden CD, Lohmueller KE. Determining the factors driving selective effects of new nonsynonymous mutations. Proc Natl Acad Sci U S A. 2017; 114(17):4465-4470.
• 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 2017; 205(2):787-801.

2016

• Phung TN, Huber CD, Lohmueller KE. Determining the effect of natural selection on linked neutral divergence across species, PLoS Genetics 2016; 12: e1006199.
• Ortega-Del Vecchyo D, Marsden CD, Lohmueller KE. PReFerSim: Fast simulation of demography and selection under the Poisson Random Field model. Bioinformatics. 2016 Jul 19.
• 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. Curr Biol. 2016 May 9;26(9):1183-9. (*Contributed equally).
• Marsden CD, Rudin N, Inman K, Lohmueller KE. An assessment of the information content of likelihood ratios derived from complex mixtures. Forensic Sci Int Genet. 2016 May;22:64-72.
• Haned H, Gill P, Lohmueller K, Inman K, Rudin N. Validation of probabilistic genotyping software for use in forensic DNA casework: Definitions and illustrations. Sci Justice. 2016 Mar;56(2):104-8.
• 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. Proc Natl Acad Sci U S A. 2016 Jan 5;113(1):152-7.

2015

• 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 Sep 18;16:298.
• 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. Eur J Hum Genet. 2015 Apr 22. doi: 10.1038/ejhg.2015.68.
• Zoledziewska M*, Sidore C*, Chiang CW*, Sanna S*, Mulas A, Steri M, Busonero F, Marcus JH, Marongiu M, Maschio A, Del Vecchyo DO, 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. Nat Genet. 2015 Nov;47(11):1352-6. (*Contributed equally).
• 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 Sci Int Genet, 2015 Nov;19:86-91
• Kim BY and Lohmueller KE. Selection and reduced population size cannot explain higher amounts of Neandertal ancestry in East Asian than in European human popualtions. Am J Hum Genet 2015 Mar 5;96(3):454-61.

2014

• Lohmueller KE. The distribution of deleterious genetic variation in human populations. Curr Opin Genet Dev 2014 Oct 13;29C:139-146.
• Lohmueller KE. Evolution. On the origin of Peter Rabbit. Science 2014 Aug 29;345(6200):1000-1
• DeGiorgio M, Lohmueller KE, Nielsen R. A model-based approach for identifying signatures of ancient balancing selection in genetic data. PLoS Genet. 2014 Aug 21;10(8):e1004561.
• Ko A, Cantor RM, Weissglas-Volkov D, Nikkola E, Linga Reddy PVM, 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, Rodriguez-Torres M, Riba L, Tusie-Luna T, Aguilar-Salinas CA, Pajukanta P. Amerindian-specific regions under positive selection harbor new lipid variants in Latinos. Nat Commun 2014; 5: 3983.
• Lohmueller KE. The impact of population demography and selection on the genetic architecture of complex traits. PLoS Genetics 2014; 10: e1004379.
• Lohmueller KE, Rudin N, Inman K. Analysis of allelic drop-out using the Identifiler® and PowerPlex® 16 forensic STR typing systems.  Forensic Sci Int Genet 2014; 12C:1-11.
• Wilson Sayres M, Lohmueller KE, Nielsen R. Natural selection reduced diversity on human Y chromosomes. PLoS Genetics 2014; 10: e1004064.

2013

• Lohmueller KE*, Sparsø T*, Li Q,  Andersson E, Korneliussen T, Albrechtsen A, Banasik K, Grarup N, Hallgrimsdottir I, Kiil K, Kilpeläinen T, Krarup N, Pers T, Sanchez G, Jørgensen T, Sandbæk A, Lauritzen T, Kristiansen K, Brunak S, Li Y, Hansen T, Wang J, Nielsen R, Pedersen O. Whole exome sequencing of 2,000 Danish individuals and the role of low-frequency coding variants in type 2 diabetes. Am J Hum Genet 2013; 93:1072-1086. (*Contributed equally).
• Lohmueller KE, Rudin N.  Calculating the weight of evidence in low-template forensic DNA casework. Journal of Forensic Sciences, 2013; 58 Suppl 1:S243-9.

2011

• Rasmussen M*, Guo X*, Wang Y*, Lohmueller KE*, and 54 additional co-authors. Aboriginal Australian genomic sequence obtained from hundred-year-old lock of hair reveals separate human dispersals into Asia. Science 2011; 334:94-98 (*Contributed equally).
• Lohmueller KE, Albrechtsen A, Li Y, Kim SY, Korneliussen T, Vinckenbosch N, Tian G, Huerta-Sanchez E, Feder A, 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; 7:e1002326.
• Kim SY, Lohmueller KE, Albrechtsen A, Li Y, Korneliussen T, Tian G, Grarup N, Jiang T, Andersen G, Witt 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; 12:231.
• Lohmueller KE, Bustamante CD, Clark AG.  Detecting directional selection in the presence of recent admixture in African Americans. Genetics 2011; 187:823-835.

Older Publications