Genetical Genomics: Spotlight on QTL Hotspots

1. SchadtEE

MonksSA

DrakeTA

LusisAJ

CheN

2003 Genetics of gene expression surveyed in maize, mouse and man. Nature 422 297 302

2. de KoningDJ

HaleyCS

2005 Genetical genomics in humans and model organisms. Trends Genet 21 377 381

3. EmilssonV

ThorleifssonG

ZhangB

LeonardsonAS

ZinkF

2008 Genetics of gene expression and its effect on disease. Nature 452 423 428

4. KeurentjesJJ

FuJ

TerpstraIR

GarciaJM

van den AckervekenG

2007 Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci. Proc Natl Acad Sci U S A 104 1708 1713

5. WuC

DelanoDL

MitroN

SuSV

JanesJ

2008 Gene set enrichment in eQTL data identifies novel annotations and pathway regulators. PLoS Genet 4(5) e1000070 doi:10.1371/journal.pgen.1000070

6. WesselJ

ZapalaMA

SchorkNJ

2007 Accommodating pathway information in expression quantitative trait locus analysis. Genomics 90 132 142

7. PengJ

WangP

TangH

2007 Controlling for false positive findings of trans-hubs in expression quantitative trait loci mapping. BMC Proc 1Suppl 1 S157

8. Perez-EncisoM

2004 In silico study of transcriptome genetic variation in outbred populations. Genetics 166 547 554

9. WangS

ZhengT

WangY

2007 Transcription activity hot spot, is it real or an artifact? BMC Proc 1Suppl 1 S94

10. ChurchillGA

DoergeRW

2008 Naive application of permutation testing leads to inflated type I error rates. Genetics 178 609 610

11. StylianouIM

AffourtitJP

ShockleyKR

WilpanRY

AbdiFA

2008 Applying gene expression, proteomics and single-nucleotide polymorphism analysis for complex trait gene identification. Genetics 178 1795 1805

12. ZhuJ

ZhangB

SmithEN

DreesB

BremRB

2008 Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat Genet 40 854 861

13. YvertG

BremRB

WhittleJ

AkeyJM

FossE

2003 Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat Genet 35 57 64

14. Le RouzicA

CarlborgO

2008 Evolutionary potential of hidden genetic variation. Trends Ecol Evol 23 33 37

15. GibsonG

WagnerG

2000 Canalization in evolutionary genetics: a stabilizing theory? Bioessays 22 372 380

16. GibsonG

DworkinI

2004 Uncovering cryptic genetic variation. Nat Rev Genet 5 681 690

17. CarlborgO

HaleyCS

2004 Epistasis: too often neglected in complex trait studies? Nat Rev Genet 5 618 625

18. QueitschC

SangsterTA

LindquistS

2002 Hsp90 as a capacitor of phenotypic variation. Nature 417 618 624

19. RutherfordSL

LindquistS

1998 Hsp90 as a capacitor for morphological evolution. Nature 396 336 342

20. BergmanA

SiegalML

2003 Evolutionary capacitance as a general feature of complex gene networks. Nature 424 549 552

21. IyengarSK

ElstonRC

2007 The genetic basis of complex traits: rare variants or “common gene, common disease”? Methods Mol Biol 376 71 84

22. BodmerW

BonillaC

2008 Common and rare variants in multifactorial susceptibility to common diseases. Nat Genet 40 695 701

23. BremRB

YvertG

ClintonR

KruglyakL

2002 Genetic dissection of transcriptional regulation in budding yeast. Science 296 752 755

24. KirstM

MyburgAA

De LeonJP

KirstME

ScottJ

2004 Coordinated genetic regulation of growth and lignin revealed by quantitative trait locus analysis of cDNA microarray data in an interspecific backcross of eucalyptus. Plant Physiol 135 2368 2378

25. MonksSA

LeonardsonA

ZhuH

CundiffP

PietrusiakP

2004 Genetic inheritance of gene expression in human cell lines. Am J Hum Genet 75 1094 1105

26. MorleyM

MolonyCM

WeberTM

DevlinJL

EwensKG

2004 Genetic analysis of genome-wide variation in human gene expression. Nature 430 743 747

27. CheungVG

SpielmanRS

EwensKG

WeberTM

MorleyM

2005 Mapping determinants of human gene expression by regional and genome-wide association. Nature 437 1365 1369

28. StrangerBE

ForrestMS

ClarkAG

MinichielloMJ

DeutschS

2005 Genome-wide associations of gene expression variation in humans. PLoS Genet 1 e78 doi:10.1371/journal.pgen.0010078

29. CheslerEJ

LuL

ShouS

QuY

GuJ

2005 Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nat Genet 37 233 242

30. BystrykhL

WeersingE

DontjeB

SuttonS

PletcherMT

2005 Uncovering regulatory pathways that affect hematopoietic stem cell function using ‘genetical genomics’. Nat Genet 37 225 232

31. HubnerN

WallaceCA

ZimdahlH

PetrettoE

SchulzH

2005 Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease. Nat Genet 37 243 253

32. MehrabianM

AllayeeH

StocktonJ

LumPY

DrakeTA

2005 Integrating genotypic and expression data in a segregating mouse population to identify 5-lipoxygenase as a susceptibility gene for obesity and bone traits. Nat Genet 37 1224 1233

33. DeCookR

LallS

NettletonD

HowellSH

2006 Genetic regulation of gene expression during shoot development in Arabidopsis. Genetics 172 1155 1164

34. LanH

ChenM

FlowersJB

YandellBS

StapletonDS

2006 Combined expression trait correlations and expression quantitative trait locus mapping. PLoS Genet 2 e6 doi:10.1371/journal.pgen.0020006

35. WangS

YehyaN

SchadtEE

WangH

DrakeTA

2006 Genetic and genomic analysis of a fat mass trait with complex inheritance reveals marked sex specificity. PLoS Genet 2 e15 doi:10.1371/journal.pgen.0020015

36. LiY

AlvarezOA

GuttelingEW

TijstermanM

FuJ

2006 Mapping determinants of gene expression plasticity by genetical genomics in C. elegans. PLoS Genet 2 e222 doi:10.1371/journal.pgen.0020222

37. McClurgP

JanesJ

WuC

DelanoDL

WalkerJR

2007 Genomewide association analysis in diverse inbred mice: power and population structure. Genetics 176 675 683

38. SchadtEE

MolonyC

ChudinE

HaoK

YangX

2008 Mapping the genetic architecture of gene expression in human liver. PLoS Biol 6 e107 doi:10.1371/journal.pbio.0060107

39. GhazalpourA

DossS

KangH

FarberC

WenPZ

2008 High-resolution mapping of gene expression using association in an outbred mouse stock. PLoS Genet 4 e1000149 doi:10.1371/journal.pgen.1000149