Publications

Kirk’s Google Scholar Profile  

Lohmueller Lab members are listed in Bold.

Preprints:

Zhen Y, Huber CD, Davies RW, Lohmueller KE. Stronger and higher proportion of beneficial amino acid changing mutations in humans compared to mice and flies, BioRxiv. 

Phung TN, Wayne RK, Wilson Sayres MA*, Lohmueller KE*. Complex patterns of sex-biased demography in canines, (*Contributed equally). BioRxiv.

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). BioRxiv

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 KEDetermining 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 KEPReFerSim: 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 foxCurr 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 illustrationsSci 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 KEBottlenecks 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 profilesBMC 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 disordersEur 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 SardiniaNat 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 populationsCurr 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 systemsForensic 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