Publications

Preprints and Working papers   |   Peer-reviewed articles   |   Book chapters  |   Google Scholar  |  MyBibliography

Key: * equal contribution; Valdar Lab member.

Preprints and working papers

  • Harigaya Y, Matoba N, Le BD, Valone JM, Stein JL, Love MI*, Valdar W* (2024+) Probabilistic classification of gene-by-treatment interactions on molecular count phenotypes bioRxiv preprint DOI:10.1101/2024.08.03.605142 [code]
  • Lenarcic AB, Valdar W (2019+) Algorithmic Bayesian group Gibbs selection arXiv preprint arXiv: 1901.02945 [code]
  • Lenarcic AB, Calaway JD, Pardo-Manuel de Villena F, Valdar W (2018+) Bayesian manifold-constrained-prior model for an experiment to locate Xce arXiv preprint arXiv:1812.08863
  • Keele GR, Maurizio PL, Oreper D, Valdar W (2018+) Bayesian decision theoretic design of two-founder experimental crosses given diallel data bioRxiv 489682; doi: https://doi.org/10.1101/489682
  • Roach J, Valdar W (2018) Permutation tests of non-exchangeable null models. arXiv preprint arXiv:1808.10483

Peer-reviewed, published articles

  1. Leist SR*, Schäfer A*, Risemberg EL*, Bell TA, Hock P, Zweigart MR, Linnertz CL, Miller DR, Shaw GD, Pardo-Manuel de Villena F, Ferris MT*, Valdar W*, Baric RS* (2024) Sarbecovirus disease susceptibility is conserved across viral and host models. Virus Research 346:199399 PMID:38823688 PMCID:PMC11225686
  2. Knuth MM, Xue J, Elnagheeb M, Gharaibeh RZ, Schoenrock S, McRitchie S, Brouwer C, Sumner SJ, Tarantino L, Valdar W, Rector RS, Simon J, Ideraabdullah FY (2024) Early life exposure to vitamin D deficiency impairs molecular mechanisms that regulate liver cholesterol biosynthesis, energy metabolism, inflammation, and detoxification. Frontiers in Endocrinology 15:1335855 PMID:38800476
  3. Risemberg EL, Smeekens JM, Cruz Cisneros MC, Hampton BK, Hock P, Linnertz CL, Miller DR, Orgel K, Shaw GD, Pardo Manuel de Villena F, Burks AW, Valdar W*, Kulis MD*, Ferris MT* (2024) A mutation in Themis contributes to peanut-induced oral anaphylaxis in CC027 mice. Journal of Allergy and Clinical Immunology. 154(2):387-397 PMID:38670234 PMCID:PMC11323216
  4. Salvador AC, Huda MN, Arends D, Elsaadi AM, Gacasan CA, Brockmann GA, Valdar W, Bennett BJ, Threadgill DW (2023) Analysis of strain, sex, and diet-dependent modulation of gut microbiota reveals candidate keystone organisms driving microbial diversity in response to American and ketogenic diets. Microbiome 11(1):220 PMID:37784178
  5. Payton A, Roell KR, Rebuli ME, Valdar W, Jaspers I, Rager JE (2023) Navigating the bridge between wet and dry lab toxicology research to address current challenges with high-dimensional data. Frontiers in Toxicology 5:1171175 PMID:37304253
  6. Le TH, Crouse WL, Keele GR, Holl K, Seshie O, Tschannen M, Craddock A, Das SK, McDonald B, Sharma NK, Key CC, Hawkins G, Valdar W, Mott R, Woods LCS (2023) Genetic mapping of multiple metabolic traits identifies novel genes for adiposity, lipids and insulin secretory capacity in outbred rats. Diabetes. 72(1):135-148 PMID:36219827
  7. Crouse WL†, Keele GR†, Gastonguay MS, Churchill GA*, Valdar W* (2022) A Bayesian model selection approach to mediation analysis. PLoS Genetics 18(5):e1010184 PMID:35533209 PMCID:PMC9129027 [bmediatR code]
  8. Crouse WL†, Das SK†, Le T, Keele G, Holl K, Seshie O, Craddock AL, Sharma NK, Comeau M, Langefeld CD, Hawkins G, Mott R, Valdar W*, Solberg Woods LC* (2022) Transcriptome-wide analyses of adipose tissue in outbred rats reveal genetic regulatory mechanisms relevant for human obesity. Physiological Genomics 54:206-219 PMID:35467982 PMCID:PMC9142160 [Selected for The American Physiological Society APSselect collection & as one the top 6 papers of Nov 2021-Nov 2022 for Physiological Genomics]
  9. Mosedale M*, Cai Y*, Eaddy JS, Kirby PJ, Wolenski FS, Dragan Y, Valdar W* (2021) Human-relevant mechanisms and risk factors for TAK-875-induced liver injury identified via a gene pathway-based approach in Collaborative Cross mice. Toxicology 461:152902 PMID:34418498 PMCID: PMC8936092
  10. Sun KY, Oreper D, Schoenrock SA, McMullan R, Giusti-Rodríguez P, Zhabotynsky V, Miller DR, Tarantino LM, Pardo-Manuel de Villena*, Valdar W* (2021) Bayesian modeling of skewed X inactivation in genetically diverse mice identifies a novel Xce allele associated with copy number changes. Genetics 218(1):iyab034 PMID:33693696 PMCID:PMC8128399 [talk]
  11. Keele GR*, Prokop JW*, He H, Holl K, Littrell J, Deal A, Kim Y, Kyle PB, Attipoe E, Johnson AC, Uhl KL, Sirpilla OL, Jahanbakhsh S, Robinson M, Levy S, Valdar W, Garrett MR, Woods LCS (2021) Sept8/SEPTIN8 involvement in cellular structure and kidney damage is identified by genetic mapping and a novel human tubule hypoxic model. Scientific Reports 11:2017 PMID:33483609 PMCID:PMC7822875
  12. Crouse WC, Kelada S, Valdar W (2020) Inferring the Allelic Series at QTL in Multiparental Populations. Genetics 216(4):957-983 [Selected for GSA’s 2020 Spotlight Collection] [code] PMID:33082282
  13. Sigmon JS, Blanchard MW, Baric RS, Bell TA, Brennan J, Brockmann GA, Burks AW, Calabrese JM, Caron KM, Cheney RE, Ciavatta D, Conlon F, Darr DB, Faber J, Franklin C, Gershon TR, Gralinski L, Gu B, Gaines CH, Hagan RS, Heimsath EG, Heise MT, Hock P, Ideraabdullah F, Jennette JC, Kafri T, Kashfeen A, Kulis M, Kumar V, Linnertz C, Livraghi-Butrico A, Lloyd KCK, Lutz C, Lynch RM, Magnuson T, Matsushima GK, McMullan R, Miller DR, Mohlke KL, Moy SS, Murphy C, Najarian M, O’Brien L, Palmer AA, Philpot BD, Randell SH, Reinholdt L, Ren Y, Rockwood S, Rogala AR, Saraswatula A, Sassetti CM, Schisler JC, Schoenrock SA, Shaw GD, Shorter JR, Smith CM, St Pierre CL, Tarantino LM, Threadgill DW, Valdar W, Vilen BJ, Wardwell K, Whitmire JK, Williams L, Zylka MJ, Ferris MT, McMillan L, Pardo-Manuel de Villena F, …, Ferris MT, McMillan L, Pardo-Manuel de Villena (2020) Content and Performance of the MiniMUGA Genotyping Array: A New Tool To Improve Rigor and Reproducibility in Mouse Research. Genetics 216(4):905-930 PMID:33067325
  14. Xue J, Hutchins EK, Elnagheeb M, Li Y, Valdar W, McRitchie S, Sumner S, Ideraabdullah FY (2020) Maternal Liver Metabolic Response to Chronic Vitamin D Deficiency Is Determined by Mouse Strain Genetic Background. Current Developments in Nutrition 4(8):nzaa106 PMID:32851199
  15. Keele GR*, Quach BC*, Israel JW, Chappell GA, Lewis L, Safi A, Simon JM, Cotney P, Crawford GE, Valdar W*, Rusyn I*, Furey TS* (2020) Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation. PLoS Genetics 16(1):e1008537 PMID:31961859 PMCID: PMC7010298
  16. Schoenrock SA, Kumar P, Gómez-A A, Dickson PE, Kim SM, Bailey L, Neira S, Riker KD, Farrington J, Gaines CH, Khan S, Wilcox TD, Roy TA, Leonardo MR, Olson AA, Gagnon LH, Philip VM, Valdar W, de Villena FP, Jentsch JD, Logan RW, McClung CA, Robinson DL, Chesler EJ, Tarantino LM (2020) Characterization of genetically complex Collaborative Cross mouse strains that model divergent locomotor activating and reinforcing properties of cocaine. Psychopharmacology (Berl) 237(4): 979–996 PMID:31897574
  17. Mosedale M*, Cai Y*, Eaddy JS, Corty RW, Nautiyal M, Watkins PB, Valdar W (2019) Identification of candidate risk factor genes for human idelalisib toxicity using a Collaborative Cross approach. Toxicological Sciences 172(2):265-278 PMID:31501888 PMCID:PMC6876541
  18. Keele GR*, Crouse WL*, Kelada SNP, Valdar W (2019) Determinants of QTL mapping power in the realized Collaborative Cross. G3: Genes, Genomes, Genetics 9(5):1707-1727 PMID:30914424 PMCID:PMC6505132
  19. Shorter JR*, Maurizio PL*, Bell TA, Shaw GD, Miller DR, Gooch TJ, Spence JS, McMillan L, Valdar W*, Pardo-Manuel de Villena F* (2019) A diallel of the mouse Collaborative Cross founders reveals strong strain-specific maternal effects on litter size. G3: Genes, Genomes, Genetics 9(5):1613-1622 PMID:30877080
  20. Corty RW, Valdar W (2018) vqtl: An R package for mean-variance QTL mapping. G3: Genes, Genomes, Genetics 8(12):3757-3766 PMID:30389795 PMC6288833
  21. Corty RW, Valdar W (2018) QTL mapping on a background of variance heterogeneity. G3: Genes, Genomes, Genetics 8(12):3767-3782 PMID:30389794 PMCID:PMC6288843
  22. Corty RW, Kumar V, Tarantino LM, Takahashi JS, Valdar W (2018) Mean-variance QTL mapping identifies novel QTL for circadian activity and exploratory behavior in mice. G3: Genes, Genomes, Genetics 8(12):3783-3790 PMID:30389793 PMCID:PMC6288835
  23. Xue J, Gharaibeh R, Pietryk E, Brouwer C, Tarantino LM, Valdar W, Ideraabdullah FY (2018) Impact of vitamin D depletion during development on mouse sperm DNA methylation. Epigenetics 13(9):959-974 PMID:30239288
  24. Oreper D, Schoenrock S, McMullan R, Ervin R, Farrington J, Miller D, Pardo-Manuel de Villena F, Valdar W*, Tarantino LM* (2018) Reciprocal F1 hybrids of two inbred mouse strains reveal parent-of-origin and perinatal diet effects on behavior and expression. G3: Genes, Genomes, Genetics 8(11):3447-3468 PMID:30171036 PMCID:PMC6222572
  25. 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
  26. 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: Genes, Genomes, Genetics 8(2):427-445 PMID:29187420 PMCID:PMC5919740
  27. 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: Genes, Genomes, Genetics 8(2):411-426 PMID:29187420
  28. 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
  29. 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 17(7):e12483 PMID:29125223
  30. 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: Genes, Genomes, Genetics 7(6):1623-1630 PMID:28592645 PMCID:PMC5473744
  31. Mosedale M*, Kim Y*, Brock WJ, Roth SE, Wiltshire T, Eaddy JS, Keele GR, Corty RW, Xie Y, Valdar W*, Watkins PB* (2017) Editors Highlight: 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 PMCID:6075566
  32. 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
  33. 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 [data]
  34. 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
  35. 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
  36. 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
  37. 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
  38. 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
  39. 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
  40. 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
  41. Zhang Z, Wang W, Valdar W (2014) Bayesian modeling of haplotype effects in multiparent populations. Genetics 198:139-156 PMID:25236455 PMCID:PMC4174926
  42. 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
  43. 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
  44. 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
  45. 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
  46. 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
  47. 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
  48. 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
  49. 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
  50. Ronnegard 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
  51. 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
  52. 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
  53. 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
  54. 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
  55. Collaborative Cross Consortium (2012) The genome architecture of the Collaborative Cross mouse genetic reference population. Genetics 190(2):389-401. PMID:22345608 PMCID:PMC3276630
  56. Ronnegard L, Valdar W (2011) Detecting major genetic loci controlling phenotypic variability in experimental crosses. Genetics 188:435-447. PMID:21467569 PMCID:PMC3122324
  57. 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
  58. 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
  59. 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
  60. 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
  61. 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
  62. 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
  63. 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
  64. 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
  65. 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
  66. 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
  67. 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
  68. 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
  69. 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.
  70. 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
  71. 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
  72. 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
  73. 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
  74. 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 NJ, 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
  75. 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
  76. 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
  77. Valdar W, Solberg LC, Gaugier D, Cookson WO, Rawlins JNP, Mott R, Flint J (2006) Genetic and environmental effects on complex traits in mice. Genetics 174(2):959-84. PMID:16888333 PMCID:PMC1602068
  78. 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
  79. Valdar W, Solberg LC, Gaugier D, Burnett S, Klenerman P, Cookson WO, Taylor M, Rawlins JNP, Mott R, Flint J (2006) Genome-wide genetic association of complex traits in outbred mice. Nature Genetics 38(8):879-87. PMID:16832355
  80. 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
  81. 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
  82. 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
  83. 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
  84. 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
  85. Valdar WSJ (2002) Scoring residue conservation. Proteins: Structure, Function, and Genetics 43(2): 227-241. PMID:12112692 Errata
  86. 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
  87. Valdar WSJ, Thornton JM (2001) Conservation helps to identify biologically relevant crystal contacts. Journal of Molecular Biology 313(2):399-416. PMID:11800565 Errata
  88. 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