Valdar Lab Publications

Literature

Preprints and Working papers   |   Peer-reviewed articles  |   Book chapters

Key: * equal contribution; Valdar Lab member;

Preprints and working papers

Peer-reviewed, published articles

  1. Kafkafi N, Agassi J, Chesler EJ, Crabbe JC, Crusio WE, Eilam D, Gerlai R, Golani I, Gomez-Marin A, Heller R, Iraqi F, Jaljuli I, Karp NA, Morgan H, Nicholson G, Pfaff DW, Richter HS, Stark PB, Stiedl O, Stodden V, Tarantino LM, Tucci V, Valdar W, Williams RW, Wurbel H, Benjamini Y (2018) Reproducibility and replicability of rodent phenotyping in preclinical studies. Neuroscience and Biobehavioral Reviews 87:218-232 PMID:29357292
  2. Maurizio PL, Ferris MT, Keele GR, Miller DR, Shaw GD, Whitmore AC, West A, Morrison CR, Noll KE, Plante KS, Cockrell AS, Threadgill DW, Pardo-Manuel de Villena F, Baric RS, Heise MT, Valdar W (2018) Bayesian diallel analysis reveals Mx1-dependent and Mx1-independent effects on response to influenza A virus in mice. G3 (Bethesda) 8(2):427-445 PMID:29187420
  3. Turner SD, Maurizio PL, Valdar W, Yandell BS, Simon PW (2018) Dissecting the genetic architecture of shoot growth in carrot (Daucus carota, L.) using a diallel mating design. G3 (Bethesda) 8(2):411-426 PMID:29187420
  4. Keele GR, Prokop JW, He H, Holl K, Littrell J, Deal A, Francic S, Cui L, Gatti DM, Broman KW, Tschannen M, Tsaih S, Zagloul M, Kim Y, Baur B, Fox J, Robinson M, Levy S, Flister M, 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(1):213-222 PMID:29193816 PMCID:PMC5740008
  5. Schoenrock S, Oreper DG, McMullan R, Farrington J, Ervin R, Miller D, Pardo-Manuel de Villena F, Valdar W, Tarantino LM (2018) Perinatal nutrition interacts with genetic background to alter behavior in a parent-of-origin dependent manner in adult Collaborative Cross mice. Genes, Brain and Behavior (Epub 2017) PMID:29125223
  6. Oreper DG, Cai Y, Tarantino LM, Pardo-Manual de Villena F, Valdar W (2017) Inbred Strain Variant Database (ISVdb): A repository for probabilistically informed sequence differences among the Collaborative Cross strains and their founders. G3 (Bethesda) 7(6):1623-1630 PMID:28592645 PMCID:PMC5473744
  7. Mosedale M*, Kim Y*, Brock WJ, Roth SE, Wiltshire T, Eaddy JS, Keele GR, Corty RW, Xie Y, Valdar W*, Watkins PB* (2017) Candidate Risk Factors and Mechanisms for Tolvaptan-Induced Liver Injury Are Identified Using a Collaborative Cross Approach. Toxicological Sciences 156(2):438-454 PMID:28115652
  8. Xue J, Schoenrock SA, Valdar W, Tarantino LM, Ideraabdullah FY (2016) Maternal vitamin D depletion alters DNA methylation at imprinted loci in multiple generations. Clinical Epigenetics 8:107 PMID:27777636 PMCID:PMC5062906
  9. Schoenrock SA*, Oreper D*, Young N, Ervin RB, Bogue MA, Valdar W*, Tarantino LM* (2016) Ovariectomy results in inbred strain-specific increases in anxiety-like behavior in mice. Physiology and Behavior 167:404-412 PMID:27693591
  10. Xie Y, Liu Y, Valdar W (2016) Joint estimation of multiple dependent Gaussian graphical models with applications to mouse genomics. Biometrika 103(3):493-511 PMID:29038606 PMCID:PMC5640885 doi:10.1093/biomet/asw035
  11. Gralinski LE, Ferris MT, Aylor DL, Whitmore AC, Green R, Frieman M, Deming D, Menachery VD, Miller DR, Buus RJ, Bell TA, Churchill GA, Threadgill DW, Katze MG, McMillan L, Valdar W, Heise MT, Baric RS (2015) Genome wide identification of SARS-CoV susceptibility loci using the Collaborative Cross. PLoS Genetics 11(10):e1005504. PMID:26452100 PMCID:PMC4599853
  12. Li J, Lange LA, Sabourin J, Duan Q, Valdar W, Willis MS, Li Y, Wilson JG, Lange EM (2015) Genome-wide and Exome-wide Association Study of Serum Lipoprotein (a) in the Jackson Heart Study. Journal of Human Genetics 60(12):755-61. PMID:26377243 PMC -- in process
  13. Durda P, Sabourin J, Lange EM, Nalls MA, Mychaleckyj JC, Jenny NS, Li J, Walston J, Harris TB, Psaty BM, Valdar W, Liu Y, Cushman M, Reiner AP, Tracy* RP, Lange* LA (2015) Plasma levels of sIL-2Rα: associations with clinical cardiovascular events and genome-wide association scan. Arteriosclerosis, Thrombosis, and Vascular Biology 35(10):2246-53. PMID:26293465 PMC -- in process
  14. Sabourin J, Valdar W, Nobel AB (2015) A permutation approach for selecting the penalty parameter in penalized model selection. Biometrics 71(4):1185-94. PMID:26243050 PMCID:PMC4314429
  15. Crowley JJ, Zhabotynsky V, Sun W, Huang S, Pakatci IK, Kim Y, Wang JR, Morgan AP, Calaway JD, Aylor DL, Yun Z, Bell TA, Buus RJ, Calaway ME, Didion JP, Gooch TJ, Hansen SD, Robinson NN, Shaw GD, Spence JS, Quackenbush CR, Barrick CJ, Nonneman RaJ, Kim K, Xenakis J, Xie Y, Valdar W, Lenarcic AB, Wang W, Welsh CE, Fu C, Zhang Z, Holt J, Guo Z, Threadgill DW, Tarantino LM, Miller DR, Zou F, McMillan L, Sullivan PF, Pardo Manuel de Villena F (2015) Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance. Nature Genetics 47(4):353-60 PMID:25730764 PMCID:PMC4380817
  16. Sabourin J, Nobel AB, Valdar W (2015) Fine-mapping additive and dominant SNP effects using group-LASSO and Fractional Resample Model Averaging Genetic Epidemiology 39(2):77-88 PMID:25417853 PMCID:PMC4314429
  17. Zhang Z, Wang W, Valdar W (2014) Bayesian modeling of haplotype effects in multiparent populations. Genetics 198:139-156 PMID:25236455 PMCID:PMC4174926
  18. Gatti DM, Svenson KL, Shabalin A, Wu L, 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: Genes, Genomes, Genetics 4(9):1623-1633 PMID:25237114 PMCID:PMC4169154
  19. Matson BC, Corty RW, Karpinich NO, Murtha AP, Valdar W, Grotegut CA, Caron KM. (2014) Midregional pro-adrenomedullin plasma concentrations are blunted in severe preeclampsia. Placenta 35(9):780-3 PMID:25043691 PMCID:PMC4143458
  20. Leamy LJ, Elo K, Nielsen MK, Thorn SR, Valdar W, Pomp D (2014) Quantitative trait loci for energy balance traits in an advanced intercross line derived from mice divergently selected for heat loss. PeerJ 2:e392 PMID:24918027
  21. Crowley JJ*, Kim Y*, Lenarcic AB*, Quackenbush CR, Barrick C, Adkins DE, Shaw GS, Miller DR, Pardo Manuel de Villena F, Sullivan PF, Valdar W (2014) Genetics of adverse reactions to haloperidol in a mouse diallel: A drug-placebo experiment and Bayesian causal analysis. Genetics 196(1):321-47 PMID:24240528 PMCID:PMC3872195
  22. Phillippi J*, Xie Y*, Miller DR, Bell TA, Zhang Z, Lenarcic AB, Aylor DL, Krovi SH, Threadgill DW, Pardo-Manuel de Villena F, Wang W, Valdar W*, Frelinger JA* (2014) Using the Collaborative Cross to probe the immune system. Genes and Immunity 15(1):38-46 PMID:24195963 PMCID:PMC4004367
  23. Calaway J, Lenarcic AB, Didion JP, Wang JR, Searle JB, McMillan L, Valdar W, Pardo-Manuel de Villena F (2013) Genetic architecture of skewed X inactivation in the laboratory mouse. PLoS Genetics 9(10):e1003853 PMID:24098153 PMCID:PMC3789830
  24. Ferris MT, Aylor DL, Bottomly D, Whitmore AC, Aicher LD, Bell TA, Bradel-Tretheway B, Bryan JT, Buus RJ, Gralinski LE, Haagmans BL, McMillan L, Miller DR, Rosenzweig E, Valdar W, Wang J, Churchill GA, Threadgill DW, McWeeney SK, Katze MG, Pardo-Manuel de Villena F, Baric RS, Heise MT (2013) Modeling host genetic regulation of influenza pathogenesis in the Collaborative Cross. PLoS Pathogens 9(2):e1003196 PMID:23468633 PMCID:PMC3585141
  25. Solberg Woods LC, Holl KL, Oreper D, Xie Y, Tsaih S-W, Valdar W (2012) Fine-mapping diabetes-related traits, including insulin resistance, in heterogeneous stock rats. Physiological Genomics 44(21):1013-26 PMID:22947656 PMCID:PMC3524769
  26. Rönnegård L, Valdar W (2012) Recent developments in statistical methods for detecting genetic loci affecting phenotypic variability. BMC Genetics 13(1):63 PMID:22827487 PMCID:PMC3493319
  27. Valdar W*, Sabourin J*, Nobel A, Holmes C (2012) Reprioritizing genetic associations in hit regions using LASSO-based resample model averaging. Genetic Epidemiology 36(5):451-462 PMID:22549815 PMCID:PMC3470705
  28. Lenarcic AB, Svenson KL, Churchill GA, Valdar W (2012) A general Bayesian approach to analyzing diallel crosses of inbred strains. Genetics 190(2):413-435. PMID:22345610 PMCID:PMC3276624
  29. Svenson KL, Gatti DM, Valdar W, Welsh CE, Cheng R, Chesler EJ, Palmer AA, McMillan L, Churchill GA (2012) The Mouse Diversity Outbred Population. Genetics 190(2):437-447. PMID:22345611 PMCID:PMC3276626
  30. Zhang W, Korstanje R, Thaisz J, Staedtler F, Harttman N, Xu L, Feng M, Yanas L, Yang H, Valdar W, Churchill GA, DiPetrillo K (2012) Genomewide association mapping of quantitative traits in outbred mice. G3: Genes, Genomes, Genetics 2(2):167-174. PMID:22384395 PMCID:PMC3284324
  31. Collaborative Cross Consortium (2012) The genome architecture of the Collaborative Cross mouse genetic reference population. Genetics 190(2):389-401. PMID:22345608 PMCID:PMC3276630
  32. Rönnegård L, Valdar W (2011) Detecting major genetic loci controlling phenotypic variability in experimental crosses. Genetics 188:435-447. PMID:21467569 PMCID:PMC3122324
  33. Johnsen AK*, Valdar W*, Golden L, Ortiz-Lopez A, Hitzemann R, Flint J, Mathis D, Benoist C (2011) Genetics of arthritis severity: a genome-wide and species-wide dissection in HS mice. Arthritis & Rheumatism 63(9):2630-2640. PMID:21560115 PMCID:PMC3371645
  34. 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 JP, Hua K, Nehrenberg DL, Powell CL, Steigerwalt J, Xie Y, Kelada SNP, Collins FS, 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 Research 21(8):1213-1222. PMID:21406540 PMCID:PMC3149489
  35. Ahlqvist E, Ekman D, Lindvall T, Popovic M, Förster M, Hultqvist M, Klaczkowska D, Teneva I, Johannesson M, Flint J, Valdar W, Nandakumar KS, Holmdahl R (2011) High resolution mapping of a complex disease, a model for rheumatoid arthritis, using heterogeneous stock mice. Human Molecular Genetics 20(15):3031-3041. PMID:21565963
  36. Solberg Woods L, Holl K, Tschannen M, Valdar W (2010) Fine-mapping a locus for glucose tolerance using heterogeneous stock rats. Physiological Genomics 41(1):102-8. PMID:20068026 PMCID:PMC2841497
  37. Valdar W, Holmes CC, Mott R, Flint J (2009) Mapping in structured populations by resample model averaging. Genetics 182(4):1263-77. PMID:19474203 PMCID:PMC2728864
  38. Kover PX, Valdar W, Trakalo J, Scarcelli N, Ehrenreich IM, Purugganan MD, Durrant C, Mott R (2009) A Multiparent Advanced Generation Inter-Cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genetics 5(7):e1000551 PMID:19593375 PMCID:PMC2700969
  39. Huang GJ, Shifman S, Valdar W, Johannesson M, Yalcin B, Taylor MS, Taylor JM, Mott R, Flint J (2009) High resolution mapping of expression QTLs in heterogeneous stock mice in multiple tissues. Genome Research 19(6):1133-40. PMID:19376938 PMCID:PMC2694476
  40. Ramagopalan SV, Valdar W, Criscuoli M, Deluca GC, Dyment DA, Orton SM, Yee IM, Ebers GC, Sadovnick AD; for the Canadian Collaborative Study Group (2009) Age of puberty and the risk of multiple sclerosis: a population based study. Eur J Neurol 16(3):342-7. PMID:19170744
  41. Ramagopalan SV, Valdar W, Dyment DA, DeLuca GC, Yee IM, Giovannoni G, Ebers GC, Sadovnick AD; Canadian Collaborative Study Group (2009) Association of infectious mononucleosis with multiple sclerosis: a population-based study. Neuroepidemiology 32(4):257-62. PMID:19209005
  42. Bice P, Valdar W, Zhang L, Liu L, Lai D, Grahame N, Flint J, Li TK, Lumeng L, Foroud T (2009) Genomewide SNP Screen to Detect Quantitative Trait Loci for Alcohol Preference in the High Alcohol Preferring and Low Alcohol Preferring Mice. Alcohol Clin Exp Res 33(3):531-7. PMID:19120064 PMCID:PMC2867232
  43. López-Aumatell R, Vicens-Costa E, Guitart-Masip M, Martínez-Membrives E, Valdar W, Johannesson M, Cañete T, Blázquez G, Driscoll P, Flint J, Tobeña A, Fernández-Teruel A (2009) Unlearned anxiety predicts learned fear: a comparison among heterogeneous rats and the Roman rat strains. Behav Brain Res. 202(1):92-101. PMID:19447285
  44. Willis-Owen SAG, Valdar W (2009) Deciphering gene-environment interactions through mouse models of allergic asthma. Journal of Allergy and Clinical Immunology 123(1):14-23. PMID:18926561
  45. Johannesson M, Lopez-Aumatell R, Stridh P, Diez M, Tuncel J, Blázquez G, Martinez-Membrives E, Cañete T, Vicens-Costa E, Graham D, Copley RR, Hernandez-Pliego P, Beyeen AD, Ockinger J, Fernández-Santamaría C, Gulko PS, Brenner M, Tobeña A, Guitart-Masip M, Giménez-Llort L, Dominiczak A, Holmdahl R, Gauguier D, Olsson T, Mott R, Valdar W, Redei EE, Fernández-Teruel A, Flint J (2009) A resource for the simultaneous high-resolution mapping of multiple quantitative trait loci in rats: the NIH heterogeneous stock. Genome Res 19(1):150-8. PMID:18971309 PMCID:PMC2612958.
  46. Ramagopalan SV, Herrera BM, Valdar W, Dyment DA, Orton SM, Yee IM, Criscuoli M, Atkins K, Ebers GC, Sadovnick AD (2008) No Effect of Birth Weight on the Risk of Multiple Sclerosis. A Population-Based Study. Neuroepidemiology 31(3):181-184. PMID:18784417
  47. Ramagopalan SV, Valdar W, Dyment DA, DeLuca GC, Orton SM, Yee IM, Criscuoli M, Ebers GC, Sadovnick AD; Canadian Collaborative Study Group (2008) No effect of preterm birth on the risk of multiple sclerosis: a population based study. BMC Neurology 8:30 PMID:18673559
  48. Lopez-Aumatell R, Guitart-Masip M, Vicens-Costa E, Gimenez-Llort L, Valdar W, Johannesson M, Flint J, Tobeña A, Fernandez-Teruel A (2008) Fearfulness in a large N/Nih genetically heterogeneous rat stock: differential profiles of timidity and defensive flight in males and females. Behav Brain Res 188(1):41-55. PMID:18079010
  49. Ramagopalan SV, Dyment DA, Valdar W, Herrera BM, Criscuoli M, Yee IM, Sadovnick AD, Ebers GC; Canadian Collaborative Study Group (2007) Autoimmune disease in families with multiple sclerosis: a population-based study. Lancet Neurology 6(7):604-10 PMID:17560172
  50. Keays DA, Tian G, Poirier K, Huang GJ, Siebold C, Cleak J, Oliver PL, Fray M, Harvey RJ, Molnár Z, Piñon MC, Dear N, Valdar W, Brown SD, Davies KE, Rawlins span class="pubjournal", Cowan NJ, Nolan P, Chelly J, Flint J (2007) Mutations in α-Tubulin Cause Abnormal Neuronal Migration in Mice and Lissencephaly in Humans. Cell 128(1):45-57. PMID:17218254
  51. Taylor M, Valdar W, Flint J, Mott R (2007) Management, presentation and interpretation of genome scans using GSCANDB. Bioinformatics 15;23(12):1545-9 PMID:17400728
  52. Keays DA, Clark TG, Campbell TG, Broxholme J, Valdar W (2007) Estimating the number of coding mutations in genotypic and phenotypic driven N-ethyl-N-nitrosourea (ENU) screens: Revisited. Mammalian Genome 18(2):123-4 PMID:17347895
  53. Valdar W, Solberg LC, Gaugier D, Cookson WO, Rawlins span class="pubjournal"P, Mott R, Flint J (2006) Genetic and environmental effects on complex traits in mice. Genetics 174(2):959-84. PMID:16888333 PMCID:PMC1602068
  54. Orton S, Herrera BM, Yee IM, Valdar W, Ramaglopalan SV, Sadovnick AD, Ebers GC Canadian Collaborative Study Group (2006) Lancet Neurology 5(11):932-6. PMID:17052660
  55. Valdar W, Solberg LC, Gaugier D, Burnett S, Klenerman P, Cookson WO, Taylor M, Rawlins span class="pubjournal"P, Mott R, Flint J (2006) Genome-wide genetic association of complex traits in outbred mice. Nature Genetics 38(8):879-87. PMID:16832355
  56. Solberg LC, Valdar W, Gauguier D, Nunez G, Taylor A, Hernandez P, Davidson S, Burns P, Cookson W, Deacon R, Rawlins span class="pubjournal"P, Mott R, Flint J (2006) A protocol for high throughput phenotyping, suitable for quantitative trait analysis in mice. Mammalian Genome 17(2):129-46 PMID:16465593
  57. Valdar W, Mott R, Flint J (2006) Simulating the collaborative cross: power of QTL detection and mapping resolution in large sets of recombinant inbred strains of mice. Genetics 172(3):1783-97. PMID:16361245 PMCID:PMC1456308
  58. Flint J, Valdar W, Shifman S, Mott R (2005) Experimental strategies for mapping and cloning quantitative trait genes in rodents. Nature Reviews Genetics 6(4):271-286. PMID:15803197
  59. Churchill GA, Airey DC, Allayee H, Angel JM, Attie AD, Beatty J, Beavis WD, Belknap JK, Bennett B, Berrettini W, Bleich A, Bogue M, Broman KW, Buck KJ, Buckler E, Burmeister M, Chesler EJ, Cheverud JM, Clapcote S, Cook MN, Cox RD, Crabbe JC, Crusio WE, Darvasi A, Deschepper CF, Doerge RW, Farber CR, Forejt J, Gaile D, Garlow SJ, Geiger H, Gershenfeld H, Gordon T, Gu J, Gu W, de Haan G, Hayes NL, Heller C, Himmelbauer H, Hitzemann R, Hunter K, Hsu HC, Iraqi FA, Ivandic B, Jacob HJ, Jansen RC, Jepsen KJ, Johnson DK, Johnson TE, Kempermann G, Kendziorski C, Kotb M, Kooy RF, Llamas B, Lammert F, Lassalle JM, Lowenstein PR, Lu L, Lusis A, Manly KF, Marcucio R, Matthews D, Medrano JF, Miller DR, Mittleman G, Mock BA, Mogil JS, Montagutelli X, Morahan G, Morris DG, Mott R, Nadeau JH, Nagase H, Nowakowski RS, O'Hara BF, Osadchuk AV, Page GP, Paigen B, Paigen K, Palmer AA, Pan HJ, Peltonen-Palotie L, Peirce J, Pomp D, Pravenec M, Prows DR, Qi Z, Reeves RH, Roder J, Rosen GD, Schadt EE, Schalkwyk LC, Seltzer Z, Shimomura K, Shou S, Sillanpaa MJ, Siracusa LD, Snoeck HW, Spearow JL, Svenson K, Tarantino LM, Threadgill D, Toth LA, Valdar W, de Villena FP, Warden C, Whatley S, Williams RW, Wiltshire T, Yi N, Zhang D, Zhang M, Zou F; Complex Trait Consortium (2004) The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nature Genetics 36(11):1133-7. PMID:15514660
  60. Valdar WSJ , Mott R, Flint J (2003) QTL fine-mapping with recombinant-inbred heterogeneous stocks and in-vitro heterogeneous stocks. Mammalian Genome 14(12):830-838. PMID:14724734
  61. Valdar WSJ (2002) Scoring residue conservation. Proteins: Structure, Function, and Genetics 43(2): 227-241. PMID:12112692 Errata
  62. Nobeli I, Laskowski RA, Valdar WSJ, Thornton JM (2001) On the molecular discrimination between adenine and guanine in proteins. Nucleic Acids Research 29(21):4294-4309. PMID:11691917
  63. Valdar WSJ, Thornton JM (2001) Conservation helps to identify biologically relevant crystal contacts. Journal of Molecular Biology 313(2):399-416. PMID:11800565 Errata
  64. Valdar WSJ, Thornton JM (2001) Protein-protein interfaces: analysis of amino acid conservation in homodimers. Proteins: Structure, Function, and Genetics 42(1):108-124. PMID:11093265

Book Chapters

Valdar WSJ, Jones DT (2002) Amino acid residue conservation. In Bioinformatics: Sequence, Structure, Function (Orengo CA, Thornton JM, Jones DT Eds). BIOS Scientific Publishers Ltd, Oxford. Amazon