publications
book
Broman KW, Sen Ś (2009) A Guide to QTL Mapping with R/qtl. Springer, New York
journal articles
2023
Zhang Q, Linke V, Overmyer KA, Traeger LL, Kasahara K, Miller IJ, Manson DE, Polaske TJ,
Kerby RL, Kemis JH, Trujillo EA, Reddy TR, Russell JD, Schueler KL, Stapleton DS,
Rabaglia ME, Seldin M, Gatti DM, Keele GR, Pham DT, Gerdt JP, Vivas EI, Lusis AJ,
Keller MP, Churchill GA, Blackwell HE, Broman KW, Attie AD, Coon
JJ, Rey FE (2023)
Genetic mapping of microbial and host traits reveals production of
immunomodulatory lipids by Akkermansia muciniphila in the murine gut.
Nat Microbiol 8:424-440
2022
Yoshihara T, Miller ND, Rabanal FA, Myles H, Kwak I-Y, Broman KW,
Sadkhin B, Baxter I, Dilkes BP, Hudson ME, Spalding EP (2022)
Leveraging orthology within maize and Arabidopsis QTL to identify
genes affecting natural variation in gravitropism.
Proc Natl Acad Sci USA 119: e2212199119
Vincent M, Gyuricza IG, Keele GR, Gatti DM, Keller MP, Broman KW,
Churchill GA (2022) QTLViewer: An interactive webtool for genetic
analysis in the Collaborative Cross and Diversity Outbred mouse
populations. G3
(Bethesda) 12:jkac146
Michel KJ, Lima DC, Hundley H, Singan V, Yoshinaga Y, Daum C, Barry K,
Broman KW, Buell CR, de Leon N, Kaeppler SM (2022) Genetic mapping and
prediction of flowering time and plant height in a maize Stiff Stalk
MAGIC population. Genetics 221:iyac063
Broman KW (2022) A generic hidden Markov model
for multi-parent populations. G3
(Bethesda) 12:jkab396
2021
Trotter C, Kim H, Farage G, Prins P, Williams RW, Broman KW, Sen
Ś (2021) Speeding up eQTL scans in the BXD population using GPUs.
G3 (Bethesda) 11:jkab254
Lobo AK, Traeger LL, Keller MP, Attie AD, Rey FE, Broman KW (2021)
Identification of sample mix-ups and mixtures in microbiome data in
Diversity Outbred mice. G3
(Bethesda) 11:jkab308
Tran Q, Broman KW (2021)
Treatment of the X chromosome in mapping multiple quantitative trait
loci.
G3 (Bethesda) 11:jkab005
Hassold T, Maylor-Hagen H, Wood A, Gruhn J, Hoffmann E, Broman KW,
Hunt P (2021) Failure to recombine is a common feature of human
oogenesis. Am J Hum Genet 108:16-24
2020
Linke V, Overmyer KA, Miller IJ, Brademan DR, Hutchins PD, Trujillo
EA, Reddy TR, Russell JD, Cushing EM, Schueler DL, Stapleton DS,
Rabaglia ME, Keller MP, Gatti DM, Keele GR, Pham D, Broman KW,
Churchill GA, Attie AD, Coon JJ (2020) A large-scale genome-lipid
association map guides lipid identification. Nat
Metab 2:1149-1162
Schwerbel K, Kamitz A, Krahmer N, Hallahan N, Jähnert M, Gottmann P,
Lebek S, Schallschmidt T, Arends D, Schumacher F, Kleuser B, Haltenhof
T, Heyd F, Gancheva S, Broman KW, Roden M, Joost HG, Chadt A,
Al-Hasani H, Vogel H, Jonas W, Schürmann A (2020) Immunity-related
GTPase induces lipophagy to prevent excess hepatic lipid accumulation.
J Hepatol 73:771-782
Broman KW (2020) Reproducibility report: Identifying essential genes by mutagenesis.
ReScience C 6 (1): #12
Rodriguez-Gil JL, Watkins-Chow DE, Baxter LL, Elliot G, Harper UL,
Wincovitch SM, Wedel JC, Incao AA, Huebecker M, Boehm FJ, Garver WS,
Porter FD, Broman KW, Platt FM, Pavan BJ (2020) Genetic background
modifies phenotypic severity and longevity in a mouse model of
Niemann-Pick Disease Type C1.
Dis Model Mech 13:dmm042614
2019
Kemis JH, Linke V, Barrett KL, Boehm FJ, Traeger LL, Keller MP,
Rabaglia ME, Schueler KL, Stapleton DS, Gatti DM, Churchill GA,
Amador-Noguez D, Russell JD, Yandell BS, Broman KW, Coon JJ, Attie
AD, Rey FE (2019) Genetic determinants of gut microbiota composition
and bile acid profiles in mice. PLoS Genet
15:e1008073
Keller MP, Rabaglia ME, Schueler KL, Stapleton DS, Gatti DM, Vincent
M, Mitok KA, Wang Z, Ishimura T, Simonett SP, Emfinger CH, Das R, Beck
T, Kendziorski C, Broman KW, Yandell BS, Churchill GA, Attie AD (2019)
Gene loci associated with insulin secretion in islets from
non-diabetic mice. J Clin Invest 130:4419-4432
Boehm FJ, Chesler EJ, Yandell BS, Broman KW (2019)
Testing pleiotropy vs. separate QTL in multiparental populations.
G3 (Bethesda) 9:2317-2324
Boehm F, Yandell B, Broman KW (2019) qtl2pleio: Testing pleiotropy
vs. separate QTL in multiparental populations. J Open Source
Software 4(38):1435
Broman KW, Gatti DM, Svenson KL, Sen Ś, Churchill GA (2019)
Cleaning genotype data from Diversity Outbred mice.
G3 (Bethesda) 9:1571-1579
Broman KW, Gatti DM, Simecek P, Furlotte NA, Prins P, Sen Ś,
Yandell BS, Churchill GA (2019)
R/qtl2: software for mapping quantitative trait loci with
high-dimensional data and multi-parent populations.
Genetics 211:495-502
2018
Palus M, Sohrabi Y, Broman KW, Strnad H, Šíma M, Růžek D, Volkova
V, Slapničková M, Vojtíšková J, Mrázková L, Salát J, Lipoldová M
(2018) A novel locus on mouse chromosome 7 that influences survival
after infection with tick-borne encephalitis virus. BMC
Neurosci 19:39
Keller MP, Gatti DM, Schueler KL, Rabaglia ME, Stapleton DS, Simecek
P, Vincent M, Allen S, Broman AT, Bacher R, Kendziorski C, Broman
KW, Yandell BS, Churchill GA, Attie AD (2018) Genetic drivers of
pancreatic islet function. Genetics 209:335-356
Broman KW, Woo KH (2018) Data organization in spreadsheets.
Am Stat 72:2-10
Keele GR, Prokop JW, He H, Holl K, Littrell J, Deal A, Francic S, Cui
L, Gatti DM, Broman KW, Tschannen M, Tsaih S-W, Zagloul M, Kim Y,
Baur B, Fox J, Robinson M, Levy S, Flister MJ, Mott R, Valdar W,
Solberg Woods LC (2018) Genetic fine-mapping and identification of candidate
genes and variants for adiposity traits in outbred rats.
Obesity 26:213-222
2017
Florek NW, Kamlangdee A, Mutschler JP, Kingstad-Bakke B,
Schultz-Darken N, Broman KW, Osorio JE, Friedrich TC (2017)
A modified vaccinia Ankara vaccine vector expressing a mosaic H5
hemagglutinin reduces viral shedding in rhesus macaques.
PLoS ONE 12:e0181738
Wang RJ, Gray MM, Parmenter MD, Broman KW, Payseur
BA (2017) Recombination rate variation in mice from an isolated
island. Mol Ecol
26:457-470
2016
Keller MP, Paul PK, Rabaglia ME, Stapleton DS, Schueler KL, Broman AT,
Ye SI, Leng N, Brandon CJ, Neto EC, Plaisier CL, Simonett SP, Kebede
MA, Sheynkman GM, Klein MA, Baliga NS, Smith LM, Broman KW, Yandell
BS, Kendziorski C, Attie AD (2016) The transcription factor Nfatc2
regulates β-cell proliferation and genes associated with type 2
diabetes in mouse and human islets. PLoS Genet 12:e1006466
Parmenter MD, Gray MM, Hogan CA, Ford IN, Broman KW, Vinyard CJ,
Payseur BA (2016) Genetics of skeletal evolution in unusually large mice
from Gough Island. Genetics 204:1559-1572
Zigler JS Jr, Hodgkinson CA, Wright M, Klise A, Sundin O, Broman KW,
Hejtmancik F, Huang H, Patek B, Sergeev Y, Hose S, Brayton C,
Xaiodong J, Vasquez D, Maragakis N, Mori S, Goldman D, Hoke A,
Sinha D (2016) A spontaneous missense mutation in branched chain keto
acid dehydrogenase kinase in the rat affects both the central and
peripheral nervous systems. PLoS ONE 11:e0160447
Sloan Z, Arends D, Broman KW, Centeno A, Furlotte N, Nijveen H,
Yan L, Zhou X, Williams RW, Prins P (2016) GeneNetwork: framework for
web-based genetics. J Open Source Software 1(2):25
De Simone M, Spagnuolo L, Lorè NI, Cigana C, De Fino I, Broman KW,
Iraqi FA, Bragonzi A (2016) Mapping genetic determinants of host
susceptibility to Pseudomonas aeruginosa lung infection in
mice. BMC Genomics 17:351
Tian J, Keller MP, Broman AT, Kendziorski C, Yandell BS, Attie AD,
Broman KW (2016) The dissection of expression quantitative trait locus
hotspots.
Genetics 202:1563-1574
Gruhn JR, Al-Asmar N, Fasnacht R, Maylor-Hagen H, Peinado V,
Rubio C, Broman KW, Hunt PA, Hassold T (2016)
Correlations between synaptic initiation and meiotic recombination: A study of humans and mice.
Am J Hum Genet 98:102-115
Kwak I-Y, Moore CR, Spalding EP, Broman KW (2016) Mapping quantitative
trait loci underlying function-valued traits using functional
principal component analysis and multi-trait mapping.
G3 (Bethesda) 6:79-86
2015
Tian J, Keller MP, Oler AT, Rabaglia ME, Schueler KL, Stapleton DS, Broman
AT, Zhao W, Kendziorski C, Yandell BS, Hagenbuch B, Broman KW,
Attie AD (2015) Identification of the bile acid transporter Slco1a6 as a
candidate gene that broadly affects gene expression in mouse
pancreatic islets. Genetics 201:1253-1262
Broman KW, Keller MP, Broman
AT, Kendziorski C, Yandell BS, Sen Ś, Attie AD (2015)
Identification and correction of sample mix-ups in expression
genetic data: A case study. G3 (Bethesda)
5:2177-2186
Gray MM, Parmenter MD, Hogan CA, Ford I, Cuthbert RJ, Ryan PG, Broman
KW, Payseur BA (2015) Genetics of rapid and extreme size evolution in
island mice. Genetics 201:213-228
Whitney KD, Broman KW, Kane NC, Hovick SM, Randell RA, Rieseberg
LH (2015) Quantitative trait locus mapping identifies candidate alleles involved in adaptive
introgression and range expansion in a wild
sunflower. Mol Ecol
24:2194-2211
Broman KW (2015) R/qtlcharts: interactive graphics for quantitative
trait locus mapping.
Genetics 199:359-361
2014
Florek NW, Weinfurter JT, Jegaskanda S, Brewoo JN, Powell TD, Young
GR, Das SC, Hatta M, Broman KW, Hungnes O, Dudman SG, Kawaoka Y,
Kent SJ, Stinchcomb DT, Osorio JE, Friedrich TC (2014)
Modified vaccinia Ankara encoding influenza virus hemagglutinin
induces heterosubtypic immunity in macaques.
J Virol 88:13418-13428
Gatti DM, Svenson KL, Shabalin A, Wu L-Y, Valdar W, Simecek P, Goodwin
N, Cheng R, Pomp D, Palmer A, Chesler EJ, Broman KW, Churchill GA
(2014) Quantitative trait locus mapping methods for Diversity Outbred
mice. G3 (Bethesda) 4:1623-1633
Street VA, Kujawa SG, Manichaikul A, Broman KW, Kallman JC, Shilling DJ, Iwata AJ,
Robinson LC, Robbins CA, Li J, Liberman MC, Tempel BL (2014) Resistance to
noise-induced hearing loss in 129S6 and MOLF mice: Identification
of independent, overlapping, and interacting chromosomal regions.
J Assoc Res Otolaryngol 15:721-738
Kwak I-Y, Moore CR, Spalding EP, Broman KW (2014) A simple
regression-based method to map quantitative trait loci underlying
function-valued phenotypes. Genetics 197:
1409-1416
Broman KW (2014) Fourteen years of R/qtl: Just barely sustainable.
J Open Res Softw 2(1):e11
Rowsey R, Gruhn J, Broman KW, Hunt PA, Hassold T (2014)
Examining variation in recombination levels in the human female: A
test of the production line hypothesis. Am J Hum Genet 95:108-112
Huang BE, Raghavan C, Mauleon R, Broman
KW, Leung H (2014) Efficient imputation of missing markers in
low-coverage genotyping-by-sequencing data from multi-parent
crosses. Genetics 197:401-404
Baier B, Hunt P, Broman KW, Hassold T (2014) Variation in genome-wide levels of meiotic recombination is established at the onset of prophase in mammalian males. PLoS Genet 10:e1004125
2013
Gruhn JR, Rubio C, Broman KW, Hunt PA, Hassold T (2013) Cytological studies of human meiosis: sex-specific differences in recombination originate at, or prior to, establishment of double-strand breaks. PLoS ONE 8:e85075
Moore CR, Johnson LS, Kwak I-Y, Livny M,
Broman KW, Spalding EP (2013)
High-throughput computer vision introduces the time axis to a quantitative trait map of a plant growth response.
Genetics 195:1077-1086
Bautz DJ, Broman KW, Threadgill DW (2013)
Identification of a novel polymorphism in X-linked sterol-4-alpha-carboxylate 3-dehydrogenase (Nsdhl) associated with reduced HDL cholesterol levels in I/LnJ mice.
G3 (Bethesda) 3: 1819-1825
Harris M, Burns CM, Becker EA, Braasch AT, Gostick E, Johnson RC,
Broman KW, Price DA, Friedrich TC, O’Connor SL (2013) Acute-phase CD8 T cell
responses that select for escape variants are needed to control live
attenuated simian immunodeficiency virus. J Virol 87:9353-9364
Maenner MJ, Baker MW, Broman KW, Tian J, Barnes JK, Atkins A, McPherson E, Hong J, Brilliant MH, Mailick MR
(2013) FMR1 CGG expansions: Prevalence and sex ratios. Am
J Med Genet B Neuropsychiatr Genet 162:466-473
2012
Broman KW, Kim S, Sen
Ś, Ané C, Payseur BA (2012) Mapping quantitative trait loci
onto a phylogenetic tree. Genetics 192:267-279
Rice CA, Riehl J, Broman K, Soukup JW, Gengler WR (2012) Comparing the degree of exothermic polymerization in commonly used acrylic and provisional composite resins for intraoral appliances. J Vet Dent 29: 78-83
Galvan A, Colombo F, Noci S, Pazzaglia S, Mancuso M, Manenti G, Broman KW, Saran A, Dragani TA (2012) The Lsktm1 locus modulates lung and skin tumorigenesis in the mouse. G3 (Bethesda) 2:1041-1046
Greene JM, Chin EN, Budde ML, Lhost JJ, Hines PJ, Burwitz BJ, Broman KW, Nelson JE, Friedrich TC, O’Connor DH (2012) Ex vivo SIV-specific CD8 T cell responses in heterozygous animals are primarily directed against peptides presented by a single MHC haplotype. PLoS ONE 7:e43690
Neto EC, Keller MP, Broman AF, Attie AD,
Jansen RC, Broman KW, Yandell BS (2012)
Quantile-based permutation thresholds for quantitative trait loci hotspots.
Genetics 191:1355-1365
King EG, Merkes CM, McNeil CL, Hoofer SR, Sen S, Broman KW, Long AD, Macdonald SJ (2012) Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource. Genome Res 22:1558-1566
Wang CY, Stapleton DS, Schueler KL, Rabaglia ME, Oler AT, Keller MP, Kendziorski CM, Broman KW, Yandell BS, Schadt EE, Attie ED (2012) Tsc2, a positional candidate gene underlying a quantitative trait locus for hepatic steatosis. J Lipid Res 53:1493-1501
Arends D, van der Velde KJ, Prins P, Broman KW, Möller S, Jansen RC, Swertz MA (2012) xQTL workbench: a web based environment for xQTL analysis. Bioinformatics 28:1042-1044
Amlin-Van Schaick JC, Kim S, Broman KW, Reilly KM (2012) Scram1 is a modifier of spinal cord resistance for astrocytoma on mouse chromosome 5. Mamm Genome 23:277-285
Broman KW (2012) Genotype probabilities at intermediate generations in the construction of recombinant inbred lines. Genetics 190:403-412
Broman KW (2012) Haplotype probabilities in advanced intercross populations. G3 (Bethesda) 2:199-202
Collaborative Cross Consortium [97 authors] (2012) The genome architecture of the Collaborative Cross mouse genetic reference population. Genetics 190:389-401
Amlin-Van Schaick JC, Kim S, DiFabio C, Lee M-H, Broman KW, Reilly KM (2012) Arlm1 is a male-specific modifier of astrocytoma resistance on mouse chr 12. Neuro Oncol 14:160-174
Davis RC, Van Nas A, Castellani LW, Zhao Y, Zhou Z, Wen P, Yu S, Qi H, Rosales M, Schadt EE, Broman KW, Peterfy M, Lusis AJ (2012) Systems genetics of susceptibility to obesity-induced diabetes in mice. Physiol Genomics 44:1-13
2011
Weinfurter JT, Brunner K, Capuano SV III, Li C, Broman KW, Kawaoka Y, Friedrich T (2011) Cross-reactive T cells are involved in rapid clearance of 2009 pandemic H1N1 influenza virus in nonhuman primates. PLoS Pathog 7:e1002381
Aylor DL, Valdar W, Foulds-Mathes W, Buus RJ,
Verdugo RA, Baric RS, Ferris MT, Frelinger JA, Heise M,
Frieman MB, Gralinski LE, Bell TA, Didion JD, Hua K,
Nehrenberg DL, Powell CL, Steigerwalt J, Xie Y, Kelada SNP,
Collins F, Yang IV, Schwartz DA, Branstetter LA,
Chesler EJ, Miller DR, Spence J, Liu EY, McMillan L,
Sarkar A, Wang J, Wang W, Zhang Q, Broman KW, Korstanje R,
Durrant C, Mott R, Iraqi FA, Pomp D, Threadgill D,
Pardo-Manuel de Villena F, Churchill GA (2011) Genetic analysis of complex traits in the emerging Collaborative Cross. Genome Res 21: 1213-1222
Greene JM, Wiseman RW, Lank SM, Bimber BN, Karl JA, Burwitz BJ, Lhost JJ, Hawkins OE, Kunstman KJ, Broman KW, Wolinsky SM, Hildebrand WH, O’Connor DH (2011) Differential MHC class I expression in distinct leukocyte subsets. BMC Immunol 12:39
Bradley KM, Breyer JP, Melville DB, Broman KW, Knapik EW, Smith JR (2011) An SNP-based linkage map for zebrafish reveals sex determination loci. G3 (Bethesda) 1:3-9
Moreland AJ, Guethlein LA, Reeves RK, Broman KW, Johnson RP, Parham P, O’Connor DH, Bimber BN (2011) Characterization of killer immunoglobulin-like receptor genetics and comprehensive genotyping by pyrosequencing in rhesus macaques. BMC Genomics 12:295
Svetec N, Werzner A, Wilches R, Pavlidis P, Álvarez-Castro JM, Broman KW, Metzler D, Stephan W (2011) Identification
of X-linked quantitative trait loci affecting cold tolerance in Drosophila
melanogaster and fine-mapping by selective sweep analysis.
Mol Ecol 20:530-544
2010
Murdoch B, Owen N, Shirley S, Crumb S, Broman KW, Hassold T (2010) Multiple loci contribute
to genome-wide recombination levels in male mice. Mamm Genome 21:550-555
Billings T, Sargent EE, Szatkiewicz JP, Leahy N, Kwak I-Y, Bektassova N, Walker M, Hassold T, Graber JH, Broman KW, Petkov PM (2010) Patterns of recombination activity on mouse chromosome 11 revealed by high resolution mapping. PLoS ONE 5:e15340
Arends D, Prins P, Jansen RC, Broman KW (2010) R/qtl: High-throughput multiple QTL mapping. Bioinformatics 26:2990-2992
Bader HL, Ruhe AL, Wang LW, Wong AK, Walsh KF, Packer RA, Mitelman J, Robertson KR, O’Brien DP, Broman KW, Shelton GD, Apte SS, Neff MW (2010) An ADAMTSL2 founder mutation causes Musladin-Lueke Syndrome, a heritable disorder of beagle dogs, featuring stiff skin and joint contractures. PLoS ONE 5:e12817
Jurisic G, Sundberg JP, Bleich A, Leiter EH, Broman KW, Buechler G, Alley L, Vestweber D, Detmar M (2010) Quantitative lymphatic vessel trait analysis suggests Vcam1 as candidate modifier gene of inflammatory bowel disease. Genes Immun 11:219-231
Burrage LC, Baskin-Hill AE, Sinasac DS, Singer JB, Croniger CM, Kirby A, Kulbokas EJ, Daly MJ, Lander ES, Broman KW, Nadeau JH (2010) Genetic resistance to diet-induced obesity in chromosome substitution strains of mice. Mamm Genome 21:115-129
Greene JM, Lhost JJ, Burwitz BJ, Budde ML, Macnair CE, Weiker MK, Gostick E, Friedrich TC, Broman KW, Price DA, O’Connor SL, O’Connor DH (2010) Extralymphoid CD8+ T cells resident in tissue from Simian Immunodeficiency Virus SIVmac239Δnef-vaccinated macaques suppress SIVmac239 replication ex vivo. J Virol 84:3362-3372
Wong AK, Ruhe AL, Dumont BL, Robertson KR, Guerrero G, Shull SM, Ziegle JS, Millon LV, Broman KW, Payseur BA, Neff MW (2010) A comprehensive linkage map of the dog genome. Genetics 184:595-605
2009
Shavit JA, Manichaikul A, Lemmerhirt HL, Broman KW, Ginsburg D (2009)
Modifiers of von Willebrand factor identified by natural variation in inbred strains of mice. Blood 114:5368-5374
Cheng EY, Hunt PA, Naluai-Cecchini TA, Fligner CL, Fujimoto VY, Pasternack TL, Schwartz JM, Steinauer JE, Woodruff TJ, Cherry SM, Hansen TA, Vallente RU, Broman KW, Hassold TJ (2009) Meiotic recombination in human oocytes. PLoS Genet 5:e1000661
Fledel-Alon A, Wilson DJ, Broman K, Wen X, Ober C, Coop G, Przeworski M (2009) Broad-scale recombination patterns underlying proper disjunctions in humans. PLoS Genet 5:e1000658
Cox A, Ackert-Bicknell CL, Dumont BL, Ding Y,
Bell JT, Brockmann GA, Wergedal JE, Bult C, Paigen B, Flint J, Tsaih
S-W, Churchill GA, Broman KW (2009) A new
standard genetic map for the laboratory mouse. Genetics 182:1335-1344
Dumont BL, Broman KW,
Payseur BA (2009) Variation in genomic recombination rates among
heterogeneous stock mice. Genetics 182:1345-1349
Manichaikul A, Broman KW (2009) Binary trait mapping in experimental crosses with selective genotyping. Genetics 182:863-874
Venkatesan M, Broman KW, Sellers M, Rasgon JL (2009) An initial linkage map of the West Nile Virus vector Culex tarsalis. Insect Mol Biol 18:453-463
Sen Ś, Johannes F, Broman KW (2009) Selective genotyping and phenotyping strategies in a complex trait context.
Genetics 181:1613-1626
Manichaikul A, Moon JY, Sen Ś, Yandell BS, Broman KW (2009) A model selection approach for the
identification of quantitative trait loci in experimental crosses,
allowing epistasis. Genetics 181:1077-1086
[Erratum: Genetics 184:607, 2010
]
2008
Shao H, Burrage LC, Sinasac DS, Hill AE, Ernest SR, O’Brien W, Courtland HW, Jepsen KJ, Kirby A, Kulbokas EJ, Daly MJ, Broman KW, Lander ES, Nadeau JH (2008)
Genetic architecture of complex traits: Large phenotypic effects and pervasive epistasis.
Proc Natl Acad Sci USA 105:19910-19914
Hill M, Broman KW, Stupka E, Smith WC, Jiang D, Sidow A (2008)
The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution. Genome Res 18:1369-1379
Lupi I, Broman KW, Tzuo S-C, Gutenberg A, Martino E, Caturegli P (2008) Novel autoantigens in autoimmune hypophysitis. Clin Endocrinol 69:269-278
Paigen K, Szatkiewicz JP, Sawyer K, Leahy N, Parvanov ED, Ng SH, Graber JH, Broman KW, Petkov PM (2008) The recombinational anatomy of a mouse chromosome. PLoS Genet 4(7):e1000119
Bjornsson HT, Albert TJ, Ladd-Acosta CM, Green RD, Rongione MA,
Middle CM, Irizarry RA, Broman KW, Feinberg AP (2008) SNP-specific array-based allele-specific expression analysis. Genome Res 18:771-779
Peirce JL, Broman KW, Lu L, Chesler EJ,
Zhou G, Airey DC, Birmingham AE, Williams RW (2008) Genome Reshuffling for Advanced Intercross Permutation (GRAIP): Simulation and permutation for advanced intercross population analysis. PLoS ONE 3(4):e1977
Roy-Gagnon M-H, Mathias RA, Fallin MD, Jee SH, Broman KW, Wilson AF (2008) An extension of the
regression of offspring on mid-parent to test for association and
estimate locus-specific heritability: The revised ROMP method.
Ann Hum Genet 72:115-125
Sinha D, Klise A, Sergeev Y, Hose S, Bhutto IA,
Hackler L, Malpic-Ilanos T, Samtani S, Grebe R, Goldberg MF,
Hejtmancik JF, Nath A, Zack DJ, Fariss RN, McLeod DS, Sundin O, Broman KW, Lutty GA, Zigler JS
Jr (2008) βA3/A1-crystallin in astroglial cells regulates retinal
vascular remodeling during development. Mol
Cell Neurosci 37:85-95
2007
Rajagopal SK, Ma Q, Obler D, Shen J, Manichaikul A,
Tomita-Mitchell A, Boardman K, Briggs C, Garg V, Srivastava D,
Goldmuntz E, Broman KW, Benson DW,
Smoot LB, Pu, WT (2007) Spectrum of heart disease associated with murine
and human GATA4 mutation. J Mol
Cell Cardiol 43:677-685
Manichaikul A, Palmer AA, Sen Ś, Broman KW (2007) Significance thresholds for
quantitative trait locus mapping under selective genotyping.
Genetics 177:1963-1966
Petkov PM, Broman KW,
Szatkiewicz JP, Paigen K (2007) Crossover interference underlies sex
differences in recombination rates. Trends Genet 23:539-542
Peirce JL, Broman KW, Lu L, Williams RW (2007) A simple method for combining genetic mapping data from multiple crosses and experimental designs. PLoS ONE 2(10):e1036
Teuscher F, Broman KW (2007)
Haplotype probabilities for multiple-strain recombinant inbred lines.
Genetics 175:1267-1274
Sen Ś, Satagopan JM, Broman KW, Churchill GA (2007) R/qtlDesign: Inbred
line cross experimental design. Mamm
Genome 18:87-93
Lemmerhirt HL, Broman
KW, Shavit JA, Ginsburg D (2007) Genetic regulation of plasma von
Willebrand factor levels: Quantitative trait loci analysis in a mouse model. J Thromb
Haemost 5:329-335
Nichols KM, Broman KW, Sundin K, Young JM,
Wheeler PA, Thorgaard GH (2007) Quantitative trait loci by maternal
cytoplasmic environment interaction for development rate in Oncorhynchus
mykiss. Genetics 175:335-347
2006
Broman KW, Sen Ś, Owens SE,
Manichaikul A, Southard-Smith EM, Churchill GA (2006) The X chromosome
in quantitative trait locus mapping. Genetics 174:2151-2158
Shrestha S, Smith MW, Broman KW,
Farzadegan H, Vlahov D, Strathdee SA (2006)
Multiperson use of syringes among injection drug users in a needle
exchange program: A gene based molecular epidemiological analysis.
J Acquir Immune Defic Syndr
43:335-343
Kess D, Lindqvist AK, Peters T, Wang H, Zamek J,
Nischt R, Broman KW, Blakytny R, Krieg
T, Holmdahl R, Scharffetter-Kochanek K (2006) Identification of
susceptibility loci for skin disease in a murine psoriasis model.
J Immunol 177:4612-4619
Manichaikul A, Dupuis J, Sen Ś, Broman KW (2006) Poor performance of bootstrap
confidence intervals for the location of a quantitative trait
locus. Genetics 174:481-489
Sundin OH, Broman KW,
Chang HH, Vito ECL, Stark WJ, Gottsch JD (2006)
A common locus for late-onset Fuchs corneal dystrophy
maps to 18q21.2-q21.32.
Invest Ophthalmol Vis Sci
47:3919-3926
Feenstra B, Skovgaard IM, Broman KW (2006) Mapping quantitative trait loci
by an extension of the Haley-Knott regression method using estimating
equations. Genetics 173:2269-2282
Chadwick LH, Pertz L, Broman
KW, Bartolomei MS, Willard HF (2006) Genetic control of X
chromosome inactivation in mice: Definition of the Xce candidate
interval. Genetics 173:2111-2119
Grant GR, Robinson SW, Edwards RE, Clothier B, Davies R, Judah DJ,
Broman KW, Smith AG (2006)
Multiple polymorphic genes determine ‘normal’ hepatic and splenic iron
status in mice. Hepatology 44:174-185
Orgogozo V, Broman KW, Stern DL (2006)
High-resolution QTL mapping reveals sign epistasis controlling
ovariole number between two Drosophila species. Genetics 173:197-205
Shrestha S, Strathdee SA, Broman KW,
Smith MW (2006) Unknown biological
mixtures evaluation using STR analytical quantification.
Electrophoresis
27:409-415
Reilly KM, Broman KW, Bronson RT,
Tsang S, Loisel DA, Christy ES, Sun Z, Diehl J, Munroe DJ, Tuskan RG
(2006) An imprinted locus epistatically influences Nstr1 and
Nstr2 to control resistance to nerve sheath tumors in a
neurofibromatosis type 1 mouse model. Cancer Res 66:62-68
Sundin OH, Jun AS, Broman KW, Liu SH, Sheehan SE, Vito ECL, Stark WJ,
Gottsch JD (2006)
Linkage of late-onset Fuchs corneal dystrophy
to a novel locus at 13pTel-13q12.13.
Invest Ophthalmol Vis Sci 47:140-145
2005
Sundin OH, Leppert GS, Silva ED, Yang J-M, Dharmaraj S, Maumenee
IH, Santos LC, Parsa CF, Traboulsi EI, Broman KW, DiBernardo C, Sunness JS, Toy J,
Weinberg EM (2005) Extreme hyperopia is the result of null mutations in MFRP,
which encodes a Frizzled-related protein.
Proc Natl Acad Sci USA 102:9553-9558
Gottsch JD, Sundin OH, Liu SH, Jun AS, Broman KW, Stark WJ, Vito
EC, Narang AK, Thompson JM, Magovern M (2005) Inheritance of a novel
COL8A2 mutation defines a distinct early-onset subtype of Fuchs
corneal dystrophy. Invest Ophthalmol Vis Sci
46:1934-1939
Owens SE, Broman KW,
Wiltshire T, Elmore JB, Bradley KM, Smith JR, Southard-Smith EM (2005)
Genome-wide linkage identifies novel modifier loci of aganglionosis
in the Sox10Dom model of Hirschsprung
disease. Hum Mol Genet 14:1549-1558
Broman KW (2005) The genomes of
recombinant inbred lines. Genetics 169:1133-1146
[Erratum: Genetics 173:2419, 2006
]
Guler ML, Ligons DL, Wang Y, Bianco M, Broman
KW, Rose NR (2005) Two autoimmune diabetes loci influencing T
cell apoptosis control susceptibility to experimental autoimmune
myocarditis. J Immunol 174:2167-2173
Congdon N, Broman KW, Lai H, Munoz B, Bowie H, Gilbert D,
Wojciechowski R, West SK (2005) Cortical, but not posterior
subcapsular, cataract shows significant familial aggregation in an
older population after adjustment for possible shared environmental
factors. Ophthalmology 112:73-77
Chen WM, Broman KW, Liang KY (2005) Power
and robustness of linkage tests for quantitative traits in general
pedigrees. Genet
Epidemiol 28:11-23
2004
Boyadjiev SA, Dodson JL, Radford CL, Ashrafi GH, Beaty TH, Mathews
RI, Broman KW, Gearhart JP (2004)
Clinical and molecular characterization of the bladder
exstrophy-epispadias complex: Analysis of 232 families. BJU
International 94:1337-1343
The Complex Trait Consortium [113 authors (2004) The
Collaborative Cross, a community resource for the genetic analysis of
complex traits. Nat Genet 36:1133-1137
Chen S, Wang W, Broman KW,
Katki HA, Parmigiani G (2004) BayesMendel: An R environment for Mendelian risk
prediction. Stat Appl Genet
Mol Biol 3(1): article 21
Neff MW, Robertson KR, Wong AK, Safra N, Broman KW, Slatkin M, Mealey KL, Pedersen NC (2004)
Breed distribution and history of canine mdr1-1Δ, a pharmacogenetic
mutation that marks the emergence of breeds from the collie lineage.
Proc Natl Acad Sci USA 101:11725-11730
Tankersley CG, Broman KW (2004)
Interactions in hypoxic and hypercapnic breathing
are genetically linked to mouse chromosomes 1 and 5. J Appl Physiol 97:77-84
Congdon N, Broman KW, Lai H, Munoz B,
Bowie H, Gilbert D, Wojciechowski R, Alston C, West SK (2004) Nuclear
cataract shows significant familial aggregation in an older population
after adjustment for possible shared environmental factors. Invest Ophthalmol Vis Sci
45:2182-2186
Tankersley CG, Campen M, Bierman A, Flanders SE, Broman KW, Rabold R (2004) Particle effects on
heart-rate regulation in senescent mice. Inhal Toxicol 16:381-390
Sivagnanasundaram S, Broman KW, Liu M,
Petronis A (2004) Quasi-linkage: A confounding factor in linkage analysis of
complex diseases? Hum
Genet 114:588-593
Chen WM, Broman KW, Liang KY (2004)
Quantitative trait linkage analysis by generalized estimating
equations: Unification of variance components and Haseman-Elston
regression. Genet
Epidemiol 26:265-272
Kieffer TL, Finucane MM, Nettles RE, Quinn TC, Broman KW, Ray SC,
Persaud D, Siliciano RF (2004) Genotypic analysis of HIV-1 drug
resistance at the limit of detection: Virus production without
evolution in treated adults with undetectable HIV loads. J Infect Dis 189:1452-1456
2003
Lidman O, Swanberg M, Horvath L, Broman
KW, Olsson T, Piehl F (2003) Discrete gene loci regulate
neurodegeneration, lymphocyte infiltration and major
histocompatibility complex class II expression in the CNS. J Neurosci 23:9817-9823
Glaser RL, Broman KW, Shulman RL,
Eskenazi B, Wyrobek AJ, Jabs EW (2003) The paternal age effect in Apert
syndrome is due in part to the increased frequency of mutations in
sperm. Am J Hum Genet 73:939-947
Denny P, Hopes E, Gingles N, Broman
KW, McPheat W, Morten J, Alexander J, Andrew PW, Brown SDM (2003) A
major locus conferring susceptibility to infection by Streptococcus
pneumoniae in mice. Mamm
Genome 14:448-453
Lamichhane G, Zignol M, Blades NJ, Geiman DE, Dougherty A, Broman KW, Bishai WR (2003) A post-genomic method
for predicting essential genes at subsaturation levels of mutagenesis:
application to Mycobacterium tuberculosis. Proc Natl Acad Sci USA 100:7213-7218
Broman KW, Wu H, Sen Ś, Churchill
GA (2003) R/qtl: QTL mapping in experimental crosses.
Bioinformatics 19:889-890
Broman KW (2003) Mapping quantitative trait loci
in the case of a spike in the phenotype distribution. Genetics 163:1169-1175
Becanovic K, Wallstrom E, Kornek B, Glaser A, Broman KW, Dahlman I, Olofsson P, Holmdahl R,
Luthman H, Lassmann H, Olsson T (2003) New loci regulating rat myelin
oligodendrocyte glycoprotein-induced experimental autoimmune
encephalomyelitis. J Immunol
170:1062-1069
2002
Broman KW, Speed TP (2002) A model
selection approach for the identification of quantitative trait loci
in experimental crosses. J Roy Stat Soc
B 64:641-656
Jun AS, Broman KW, Do DV, Akpek EK,
Stark WJ, Gottsch JD (2002) Endothelial dystrophy, iris hypoplasia,
congenital cataract, and stromal thinning (EDICT) syndrome maps to
chromosome 15q22.1-q25.3. Am J Ophthalmol 134:172-176
Broman KW, Rowe LB, Churchill GA,
Paigen K (2002) Crossover interference in the mouse. Genetics
160:1123-1131
2001
Hunter KW, Broman KW, Le Voyer T,
Lukes L, Cozma D, Debies MT, Rouse J, Welch DR (2001)
Predisposition to efficient mammary tumor metastatic progression is
linked to the breast cancer metastasis suppressor gene Brms1.
Cancer
Research 61:8866-8872
Ravenel JD, Broman KW, Perlman EJ,
Niemitz EL, Jayawardena TM,
Bell DW, Haber DA, Uejima H, Feinberg AP (2001) Loss of imprinting of
Insulin-Like Growth Factor-II (IGF2) gene in distinguishing specific
biologic subtypes of Wilms tumor.
J Natl Cancer Inst 93:1698-1703
Broman KW (2001) Review of
statistical methods for QTL mapping in experimental crosses.
Lab
Animal 30(7):44-52
Note: The publisher
requires that I make the following statement: “The paper can only be
downloaded for personal study use and cannot be copied for commercial
purposes without the permission of the publisher.”
Broman KW (2001) Estimation of allele frequencies with data on
sibships. Genet Epidemiol 20:307-315
[Erratum: Genet Epidemiol 23:465-466, 2002
]
Giglio S, Broman KW, Matsumoto N,
Calvari V, Gimelli G, Neumann T, Ohashi H, Voullaire L, Larizza D,
Giorda R, Weber JL, Ledbetter DH, Zuffardi O (2001) Olfactory
receptor-gene clusters, genomic-inversion polymorphisms, and
common chromosome rearrangements. Am J Hum Genet 68:874-883
Boyartchuk VL, Broman KW, Mosher RE,
D’Orazio SEF, Starnbach MN, Dietrich WF (2001) Multigenic control of
Listeria monocytogenes susceptibility in mice. Nat Genet 27:259-260
Yu A, Zhao C, Fan Y, Jang W, Mungall AJ, Deloukas P, Olsen A,
Doggett NA, Ghebranious N, Broman KW, Weber JL (2001)
Comparison of human genetic and sequence-based physical maps. Nature
409:951-953
Lichter-Konecki U, Broman KW, Blau EB, Konecki DS (2001) Genetic
and physical mapping of the locus for autosomal dominant renal Fanconi
syndrome, on chromosome 15q15.3 Am J Hum Genet 68:264-268
2000
Kissebah AH, Sonnenberg GE, Myklebust J, Goldstein M, Broman K,
James RG, Marks JA, Krakower GR, Jacob HJ, Weber J, Martin L, Blangero
J, Comuzzie AG (2000) Quantitative trait loci on chromosomes 3 and 17
influence phenotypes of the metabolic syndrome. Proc Natl Acad Sci
USA 97:14478-14483
Witte JS, Goddard KAB, Conti DV, Elston RC, Lin J, Suarez BK,
Broman KW, Burmester JK, Weber JL, Catalona WJ (2000) Genomewide scan
for prostate cancer-aggressiveness loci. Am J Hum Genet 67:92-99
Broman KW, Weber JL (2000) Characterization of human crossover
interference. Am J Hum Genet 66:1911-1926
Suarez BK, Lin J, Burmester JK, Broman KW, Weber JL, Banerjee TK,
Goddard KAB, Witte JS, Elston RC, Catalona WJ (2000) A genome
screen of multiplex prostate cancer sibships. Am J Hum Genet 66:933-944
Brown AS, Feingold E, Broman KW, Sherman SL (2000) Genome-wide
variation in recombination in female meiosis: A risk factor for
non-disjunction of chromosome 21. Hum Mol Genet
9:515-523
1999
Broman KW, Weber JL (1999) Long homozygous chromosomal
segments in reference families from the Centre d’Étude du
Polymorphisme Humain. Am J Hum Genet 65:1493-1500
[Errata]
Broman KW, Weber JL (1999) Method for constructing
confidently ordered linkage
maps. Genet Epidemiol
16:337-343
Neff MW, Broman KW, Mellersh CS, Ray K, Acland GM, Aguirre GD,
Ziegle JS, Ostrander EA, Rine J (1999) A
second-generation genetic linkage map of the domestic dog, Canis
familiaris. Genetics 151:803-820
1998
Broman KW, Murray JC, Sheffield VC, White RL, Weber JL
(1998) Comprehensive human genetic maps: Individual and sex-specific
variation in recombination. Am J Hum Genet 63:861-869
Broman K, Speed T, Tigges M (1998) Estimation of
antigen-responsive T cell frequencies in PBMC from human
subjects. Stat Sci 13:4-8
1996
Broman K, Speed T, Tigges M (1996) Estimation of
antigen-responsive T cell frequencies in PBMC from human
subjects. J Immunol Meth 198:119-132
Dernburg AF, Broman KW, Fung JC, Marshall WF, Philips J,
Agard DA, Sedat JW (1996) Perturbation of nuclear architecture by
long-distance chromosome interactions. Cell 85:745-759
editorials
Broman KW (2005) Mapping expression in
randomized rodent genomes. Nat
Genet 37:209-210
Broman KW, Feingold E (2004) SNPs made routine. Nat Methods 1:104-105
letters
Sieberts SK, Broman KW, Gudbjartsson
DF (2004) “Biased towards the null” means reduced power. Am J Hum
Genet 75:720-722
(Response to Schork and Greenwood, Am J Hum Genet
74:306-316, 2004)
Broman KW, Caffo BS (2003) Simulation-based
P values: Response to North et al. Am J Hum
Genet 72:496
(Response to North
et al., Am J Hum Genet 71:439-441, 2002)
Ravenel JD, Perlman EJ, Broman KW,
Feinberg AP (2002) Response: Re: Loss of imprinting of Insulin-Like
Growth Factor-II (IGF2) gene in distinguishing specific biologic
subtypes of Wilms tumor. J Natl Cancer
Inst 94:1809-1810
(Response to Morison
et al., J Natl Cancer Inst 94:1809, 2002)
Broman KW, Weber JL (1998) Estimation of pairwise
relationships in the presence of genotyping errors. Am J Hum Genet
63:1563-1564
proceedings and book chapters
Broman KW (2012) Applied statistics and exposition (commentary). In: Dudoit S (ed) Selected Works of Terry Speed, Springer, pp 353-355
González-Recio O, López de
Maturana E, Vega AT, Engelman CD, Broman KW (2009) Detecting
single-nucleotide polymorphism by single-nucleotide polymorphism
interactions in rheumatoid arthritis by a two-step approach with
machine learning and a Bayesian threshold least absolute shrinkage and
selection operator (LASSO) model. BMC Proc 3(Suppl 7):S63
Broman KW, Heath SC (2007) Managing and
manipulating genetic data. In: Barnes MR,
Gray IC (eds) Bioinformatics for Geneticists, 2nd edition,
Wiley, pp. 17-31
Broman KW, Matsumoto N, Giglio S,
Martin CL, Roseberry JA, Zuffardi O, Ledbetter DH, Weber JL (2003)
Common long human inversion polymorphism on chromosome 8p. In:
Goldstein DR (ed) Science and Statistics: A Festschrift for Terry
Speed. IMS Lecture Notes-Monograph Series, Vol 40, pp 237-245
Weber JL, Broman KW (2001) Genotyping for human whole-genome
scans: Past, present, and future. In: Rao DC, Province MA (eds)
Genetic Dissection of Complex Traits. Vol 42: Advances in Genetics.
Academic Press, New York, pp 77-96
Broman KW (1999) Cleaning genotype data. In: Goldin L, Amos CI,
Chase GA, Goldstein AM, Jarvik GP, Martinez MM, Suarez BK, Weeks DE,
Wijsman EM, MacCluer JE. Genetics Workshop 11: Analysis of genetic and
environmental factors in common diseases. Genet Epidemiol
17(Supp 1):S79-S83
Broman KW, Speed TP (1999) A review of methods for
identifying QTLs in experimental crosses. In: Seillier-Moiseiwitsch F
(ed) Statistics in Molecular Biology and Genetics. IMS Lecture
Notes-Monograph Series, Vol 33, pp 114-142
technical reports and preprints
Yu Z, Farage G, Williams RW, Broman KW, Sen Ś (2023) BulkLMM:
Real-time genome scans for multiple quantitative traits using linear
mixed models. bioRxiv
doi:10.1101/2023.12.20.572698
Litichevskiy L, Considine M, Gill J, Shandar V, Cox TO, Descamps HC,
Wright KM, Amses KR, Dohnalová L, Liou MJ, Tetlak M, Galindo-Fiallos
MR, Wong AC, Lundgren P, Kim J, Uhr GT, Rahman RJ, Mason S, Merenstein
C, Bushman FD, Raj A, Harding F, Chen Z, Prateek GV, Mullis M, Deighan
AG, Robinson L, Tanes C, Bittinger K, Chakraborty M, Bhatt AS, Li H,
Barnett I, Davenport ER, Broman KW, Cohen RL, Botstein D, Freund A, Di
Francesco A, Churchill GA, Li M, Thaiss CA (2023) Interactions between
the gut microbiome, dietary restriction, and aging in genetically
diverse mice. bioRxiv
doi:10.1101/2023.11.28.568137
Broman KW (2010) Genetic map construction with R/qtl. Technical report #214, Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison
Broman KW (2006) Use of hidden Markov models
for QTL mapping. Working paper 125, Department of Biostatistics,
Johns Hopkins University, Baltimore, MD
Blades NJ, Broman KW (2002)
Estimating the number of essential genes in a genome by random
transposon mutagenesis. Technical Report MS02-20, Department of Biostatistics,
Johns Hopkins University, Baltimore, MD
Bowman KO, Shenton LR, Kastenbaum MA, Broman K (1992)
Overdispersion: Notes on discrete distributions. Technical Report
ORNL/TM-12167, Oak Ridge National Laboratory
dissertation
Broman KW (1997) Identifying quantitative trait loci in
experimental crosses. PhD dissertation, Department of Statistics,
University of California, Berkeley