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diff --git a/general/references/references.md b/general/references/references.md new file mode 100644 index 0000000..039b49e --- /dev/null +++ b/general/references/references.md @@ -0,0 +1,1191 @@ +### References + +## Papers and References to GeneNetwork +[Highlighted References](#New)| +[Key References](#Key) | +[Background References](#Background) | + +| [2020](#2020) | [2019](#2019) | [2018](#2018) | [2017](#2017) | [2016](#2016) | [2015](#2015) | [2014](#2014) | [2013](#2013) |[2012](#2012) | [2011](#2011) | [2010](#2010) |[2009](#2009) | [2008](#2008) |[2007](#2007) |[2006](#2006) | [2005](#2005) | [2004](#2004) | [2003](#2003) | + +Google Scholar search for _"genenetwork" OR "webqtl"_ generated: +1. 1430 hits on 2016/09/08 +2. 1730 hits on 2017/10/17 +3. 2020 hits on 2019/05/13 + + +[Google Scholar](https://scholar.google.com/scholar?as_q=&as_epq=&as_oq=genenetwork.org&as_eq=&as_occt=any&as_sauthors=&as_publication=&as_ylo=&as_yhi=&btnG=&hl=en&as_sdt=0%2C5) search for *genenetwork.org* generated: +1. 1030 hits on 2019/05/13 +2. 105 hits from 2018/01/01 to 2019/05/13 + + + +<div id="New"> </div> + +> ## Highlighted References + + #### **_Please send us citations to articles that we may have missed._** + +1. Mulligan MK, Mozhui K, Prins P, Williams RW [2017](https://ncbi.nlm.nih.gov/pubmed/27933521) GeneNetwork: A Toolbox for Systems Genetics. In *Systems Genetics*, Methods in Molecular Biology 1488:75-120 +[An updated primer in using GeneNetwork for molecular analysis of mouse and human cohorts.] + - <small>[PDF version](/images/upload/Mulligan_How_To_Use_GeneNetwork_2017_v1.pdf)</small> + +2. Williams RW, Williams EG [2017](/images/upload/Williams_ResourcesSystemsGenetics_MethodsMolBio_2016.pdf) Resources for Systems Genetics. In *Systems Genetics*, Methods in Molecular Biology 1488:3-29. +[This review is intended to help you when making the hard choices about types of resources to use in system genetic studies. The short answer: embrace diversity in your resources. The computational barriers to joint analysis are now minimal.] + - <small>[PDF version](/images/upload/Williams_ResourcesSystemsGenetics_MethodsMolBio_2016.pdf)</small> + + +3. Williams RW [2009](http://journal.frontiersin.org/article/10.3389/neuro.01.016.2009/full) Herding cats: the sociology of data integration. Frontier in Neuroscience 3(2):154-6. +[An short but amusing commentary on predictive (someday perhaps even precision) medicine and how to get there using genetic reference populations such as the BXD and Collaborative Cross families.] + - <small>[PDF version](http://journal.frontiersin.org/article/10.3389/neuro.01.016.2009/full)</small> + + +4. Pinelli M, Carissimo A, Cutillo L, Lai CH, Mutarelli M, Moretti MN, Singh MV, Karali M, Carrella D, Pizzo M, Russo F, Ferrari S, Ponzin D, Angelini C, Banfi S, di Bernardo D [2016](https://ncbi.nlm.nih.gov/pubmed/27235414) An atlas of gene expression and gene co-regulation in the human retina.Nucleic Acids Res. 2016 Jul 8;44(12):5773-84 + - <small>[RETINA database](http://retina.tigem.it)</a>, and see the [PDF](/images/upload/Pinelli_diBerardo_2016_AtlasHumanRetina.pdf). These data are now in GeneNetwork (Species = Human, Group = Retina). + </small> + + +5. Williams EG, Wu Y, Pooja J, Dubuis S, Blattmann P, Argmann CA, Houten SM, Amariuta T, Wolski W, Zamboni N, Aebersold R, Auwerx J [2016](https://ncbi.nlm.nih.gov/pubmed/27284200) Systems proteomics and trans-omic integration illuminate new mechanisms in mitochondrial function. Science 352(6291):aad0189 + - <small>[HTML version](http://science.sciencemag.org/content/352/6291/aad0189.full) + - [PDF](/images/upload/WilliamsEG_Auwerx_Systems_Science-2016.pdf) + </small> + + +6. Sloan Z, Arends D, Broman KW, Centeno A, Furlotte N, Nijveen H, Yan L, Zhou X, Williams RW, Prins P (2016) GenetNetwork: framework for web-based genetics. The Journal of Open Source Software http://joss.theoj.org/papers/10.21105/joss.00025 (http://dx.doi.org/10.21105/joss.00025) + - <small>[HTML version](http://joss.theoj.org/papers/10.21105/joss.00025) + </small> + +7. Alam G, Miller DB, O'Callaghan JP, Lu L, Williams RW, Jones BC [2016](https://ncbi.nlm.nih.gov/pubmed/27182044) MPTP neurotoxicity is highly concordant between the sexes among BXD recombinant inbred mouse strains. Neurotoxicology in press +<small>[PDF version](/images/upload/Alam_Jones_MPTP_Neurotox_2016.pdf) +</small> + + +8. Merkwirth C, Jovaisaite V, Durieux J, Matilainen O, Jordan SD, Quiros PM, Steffen KK, Williams EG, Mouchiroud L, Tronnes SU, Murillo V, Wolff SC, Shaw RJ, Auwerx J, Dillin A [2016](https://ncbi.nlm.nih.gov/pubmed/27133168) Two conserved histone demethylases regulate mitochondrial stress-induced longevity. Cell 165:1209-1223 + + +9. Wang X, Pandey AK, Mulligan MK, Williams EG, Mozhui K, Li Z, Jovaisaite V, Quarles LD, Xiao Z, Huang J, Capra JA, Chen Z, Taylor WL, Bastarache L, Niu X, Pollard KS, Ciobanu DC, Reznik AO, Tishkov AV, Zhulin IB, Peng J, Nelson SF, Denny JC, Auwerx J, Lu L, Williams RW [2016]("https://ncbi.nlm.nih.gov/pubmed/26833085). Joint mouse-human phenome-wide association to test gene function and disease risk. Nature Communications 7:10464 +[Best reference on the BXD family of strains and the wide range of phenotypes that have been generated over the past 40 years.] + - <small>[PDF version](/images/upload/Wang_PheWas_NatComm_2016.pdf) and the + [Supplementary Tables in one Excel file](/images/upload/Wang_SupplementalTables_NatComm_2016.xlsx) </small> + +10. Xue Y, Li J, Yan L, Lu L, Liao FF [2015](https://ncbi.nlm.nih.gov/pubmed/26092713) Genetic variability to diet-induced hippocampal dysfunction in BXD recombinant inbred (RI) mouse strains. Behav Brain Res 292:83-94 + + +11. Chaum E, Winborn CS, Bhattacharya S [2015](https://ncbi.nlm.nih.gov/pubmed/25963977) Multilayered genetic and omics dissection of mitochondrial activity in a mouse reference population. Mamm Genome 26:210-221 + +12. Cheng Q, Seltzer Z, Sima C, Lakschevitz FS, Glogauer M. [2015](https://ncbi.nlm.nih.gov/pubmed/25942439). Quantitative Trait Loci and Candidate Genes for Neutrophil Recruitment in Sterile Inflammation Mapped in AXB-BXA Recombinant Inbred Mice. PLoS One 10:e0124117 + +13. Scott RE, Ghule PN, Stein JL, Stein GS [2015](https://ncbi.nlm.nih.gov/pubmed/25215496). Cell cycle gene expression networks discovered using systems biology: Significance in carcinogenesis. J Cell Physiol 230:2533-42 + + +14. Williams EG, Auwerx J [2015](https://ncbi.nlm.nih.gov/pubmed/26140590). The convergence of systems and reductionist approaches in complex trait analysis. Cell 162:23-32. + + +15. Wu Y, Williams EG, Dubuis S, Mottis A, Jovaisaite V, Houten SM, Argmann CA, Faridi P, Wolski W, Kutalik Z, Zamboni N, Auwerx J, Aebersold R [2014](https://ncbi.nlm.nih.gov/pubmed/25215496). Multilayered genetic and omics dissection of mitochondrial activity in a mouse reference population. Cell 158:1415-1430 + +16. Hayes SK, Hager R, Grencis RK (2014) Sex-dependent genetics effects on immune responses to parasitic nematodes. BMC Genomics 15:193 + + +17. Harenza JL, Muldoon PP, De Biasi M, Damaj MI, Miles MF (2014) Genetic variation within the Chrna7 gene modulates nicotine reward-like phenotypes in mice. Genes Brain Behav 13:213-225 + + +18. Ye R, Carneiro AM, Airey D, Sanders-Bush E, Williams RW, Lu L, Wang J, Zhang B, Blakely RD [2014](https://ncbi.nlm.nih.gov/pubmed/24102824). Evaluation of heritable determinants of blood and brain serotonin homeostasis using recombinant inbred mice. Genes Brain Behav. 13:247-260 + +19. Houtkooper RH, Mouchiroud L, Ryu D, Moullan N, Katsyuba E, Knott G, Williams RW, Auwerx J [2013](https://ncbi.nlm.nih.gov/pubmed/23698443). Mitonuclear protein imbalance as a conserved longevity mechanism. Nature 497:451-457 [PDF Version](/images/upload/Houtkooper_Williams_Auwerx_Nature_2013.pdf) + + + + +<div id="Key"> <div/> + +> ## Key References + +The first section lists key technical papers that are appropriate references when citing GeneNetwork and WebQTL. The second section lists publications and other resources that have made use of GeneNetwork. + + +1. Mulligan MK, Mozhui K, Prins P, Williams RW [2016](https://ncbi.nlm.nih.gov/pubmed/26092713). GeneNetwork – A toolbox for systems genetics. In *Systems Genetics*, Methods in Molecular Biology; Schughart K, Williams RW eds.; Humana Press, in press +[This is a currently the most comprehensive protocol and guide (20 Mb) for GeneNetwork.] + + - <small>[PDF Version](/images/upload/Mulligan_How_To_Use_GeneNetwork_2016_v1.pdf)</small> + + + + +2. Williams RW, Mulligan MK [2012](https://ncbi.nlm.nih.gov/pubmed/23195314). Genetic and molecular network analysis of behavior. Int Rev Neurobiol. 104:135-57. [Explains the use of GeneNetwork in behavioral neurogenetics] + - <small><a href="/images/upload/Williams_Mulligan_Bioinformatics of Brain Short 2012.pdf" target="_blank" >PDF version</A> +</small> + + +3. Williams EG, Auwerx J [2015](https://ncbi.nlm.nih.gov/pubmed/26140590). The convergence of systems and reductionist approaches in complex trait analysis. Cell 162:23-32. [Research into the genetic and environmental factors behind complex trait variation has traditionally been segregated into distinct scientific camps. The reductionist approach aims to decrypt phenotypic variability bit by bit, founded on the underlying hypothesis that genome-to-phenome relations are largely constructed from the additive effects of their molecular players. In contrast, the systems approach aims to examine large-scale interactions of many components simultaneously, on the premise that interactions in gene networks can be both linear and non-linear. Both approaches are complementary, and they are becoming increasingly intertwined due to developments in gene editing tools, omics technologies, and population resources. Together, these strategies are beginning to drive the next era in complex trait research, paving the way to improve agriculture and toward more personalized medicine.] + - <small>[PDF version](/images/upload/WilliamsEG_Auwerx_Cell2015.pdf)</small> + +4. Wang J, Williams RW, Manly KF ([2003](http://journals.humanapress.com/ArticleDetail.pasp?issn=1539-2791&acode=NI:1:4:299)) WebQTL: Web-based complex trait analysis. Neuroinformatics 1: 299-308 [*Full Text PDF Version*](http://www.genenetwork.org/pdf/webqtl.pdf). [A good technical reference to WebQTL and GeneNetwork] + +5. Williams RW, Gu J, Qi S, Lu L ([2003](http://journals.humanapress.com/ArticleDetail.pasp?issn=1539-2791&acode=NI:1:4:299)) The genetic structure of recombinant inbred mice: high-resolution consensus maps for complex trait analysis. Genome Biology 2(11) [*Full Text Version*](http://genomebiology.com/content/2/11/RESEARCH0046). [A detailed analysis of the genetics of recombinant inbred strains] + +6. Chesler EJ, Wang J, Lu L, Qu Y, Manly KF, Williams RW ([2003](http://journals.humanapress.com/ArticleDetail.pasp?issn=1539-2791&acode=NI:1:4:343)) Genetic correlates of gene expression in recombinant inbred strains: a relational model to explore for neurobehavioral phenotypes. Neuroinformatics 1: 343-357.[*Full Text PDF Version*](http://www.nervenet.org/pdf/Genetic_Correlation_webQTL.pdf). [Best reference regarding interpretation of genetic correlations.] + +7. Chesler EJ, Lu L, Wang J, Williams RW, Manly KF ([2004](http://www.nature.com/cgi-taf/DynaPage.taf?file=/neuro/journal/v7/n5/full/nn0504-485.html)) WebQTL: rapid exploratory analysis of gene expression and genetic networks for brain and behavior. Nature Neuroscience 7: 485-486.[*Full Text PDF Version*](http://www.genenetwork.org/pdf/nn0504-485.pdf) [A short review] + +8. Chesler EJ, Williams RW ([2004](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15474587)) Brain gene expression: genomics and genetics. International Review of Neurobiology 60:59-95. (*DNA Arrays in Neurobiology*, edited by MF Miles, Elsevier, Amsterdam). [A longer discussion, both statistical and conceptual, on the genetic analysis of gene expression and relations to higher order behavioral phenotypes]</a> + +9. Bystrykh L, Weersing E, Dontje B, Sutton S, Pletcher MT, Wiltshire T, Su AI, Vellenga E, Wang J, Manly KF, Lu L, Chesler EJ, Alberts R, Jansen RC, Williams RW, Cooke M, de Haan G ([2005](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15711547)) Uncovering regulatory pathways affecting hematopoietic stem cell function using "genetical genomics." Nature Genetics 37:225-232. [Please cite this article if you have used the GNF-Groningen hematopoietic stem cell data set.] + +10. Chesler EJ, Lu L, Shou S, Qu Y, Gu J, Wang J, Hsu HC, Mountz JD, Baldwin N, Langston MA, Threadgill DW, Manly KF, Williams RW ([2005](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15711545)) Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nature Genetics 37: 233-242. [Please cite this article if you have used one of the UTHSC brain data sets.] + +11. Damerval C, Maurice A, Josse JM, de Vienne D ([1994](http://www.genetics.org/cgi/content/abstract/137/1/289)) Quantitative trait loci underlying gene product variation: a novel perspective for analyzing regulation of genome expression. Genetics 137: 289-301 [*Full Text PDF Version* ](http://www.genetics.org/cgi/reprint/137/1/289) [The first published paper on system genetics. Impressive; before its time.] + + > <small>[Damerval et al., 1994 abstract] A methodology to dissect the genetic architecture of quantitative variation of numerous gene products simultaneously is proposed. For each individual of a segregating progeny, proteins extracted from a given organ are separated using two-dimensional electrophoresis, and their amounts are estimated with a computer-assisted system for spot quantification. Provided a complete genetic map is available, statistical procedures allow determination of the number, effects and chromosomal locations of factors controlling the amounts of individual proteins. This approach was applied to anonymous proteins of etiolated coleoptiles of maize, in an F(2) progeny between two distant lines. The genetic map included both restriction fragment length polymorphism and protein markers. Minimum estimates of one to five unlinked regulatory factors were found for 42 of the 72 proteins analyzed, with a large diversity of effects. Dominance and epistasis interactions were involved in the control of 38% and 14% of the 72 proteins, respectively. Such a methodology might help understanding the architecture of regulatory networks and the possible adaptive or phenotypic significance of the polymorphism of the genes involved. + </small> + + + + +12. Grisham W, Schottler NA, Valli-Marill J, Beck L, Beatty J ([2010](http://www.ncbi.nlm.nih.gov/pubmed/20516355)) Teaching bioinformatics and neuroinformatics by using free web-based tools. CBE--Life Sciences Education 9: 98-107 [*Full Text PDF Version*](http://www.lifescied.org/content/9/2/98.full.pdf+html) + + - <small> A terrific introduction to a wide range of bioinformatic resources, including GeneNetwork, that have been assembled as a coherent teaching module. A detailed student/instructor’s manual, PDFs of handouts, PowerPoint slides, and sample exams are available for free at [http://mdcune.psych.ucla.edu/modules/bioinformatics](http://mdcune.psych.ucla.edu/modules/bioinformatics).<br/> + - **Youtube videos of Dr. William Grisham teaching neurogenetics at UCLA** + - [Part 1](http://www.youtube.com/watch?v=5UniEc_pzs0) + + - [Part 2](http://www.youtube.com/watch?v=zjdOWC7zxt0) + - [Part 3](http://www.youtube.com/watch?v=caC0YGhDoo8) + - [Part 4](http://www.youtube.com/watch?v=eTzIcM3aspM) + - [Part 5](http://www.youtube.com/watch?v=Dnq7w4RIAXI) + + </small> + +13. Grisham W ([2009](http://www.funjournal.org/downloads/200981/grisham81.pdf)) Modular digitial course in undergraduate neuroscience education (MDCUNE): A website offering free digital tools for neuroscience educators. Journal of Undergraduate Neuroscience Education 8:A26-A31 [*Full Text PDF Version*](http://www.funjournal.org/downloads/200981/grisham81.pdf) + + - > <small>An excellent example of how resources such as GeneNetwork and the Mouse Brain Library can be used in class room labs.</small> + + +14. Hübner N, Wallace CA, Zimdahl H, Petretto E, Schulz H, Maciver F, Mueller M, Hummel O, Monti J, Zidek V, Musilova A, Kren V, Causton H, Game L, Born G, Schmidt S, Muller A, Cook SA, Kurtz TW, Whittaker J, Pravenec M, Aitman TJ ([2005]("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15711544)) Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease. Nature Genetics 37: 243-253. [Please cite this article if you have used one of the rat HXB kidney or peritoneal fat data sets.] + +15. Kang HM, Ye C, Eskin E (2008) Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots. Genetics 180:1909-1925 +[*Full Text PDF Version*](http://www.genetics.org/cgi/content/abstract/genetics.108.094201v1). [An important method that can greatly improve the ability to resolve true genetic interactions in expression genetic studies.] + +16. Ljungberg K, Holmgren S, Carlborg O ([2004](http://bioinformatics.oupjournals.org/cgi/content/abstract/bth175?ijkey=21Pp0pgOuBL6Q&keytype=ref)) Simultaneous search for multiple QTL using the global optimization algorithm DIRECT. Bioinformatics 20:1887-1895. [Please review and cite this article if you have exploited the DIRECT pair-scan tool and output graphs in WebQTL.] + +17. Manly KF, Wang J, Williams RW ([2005](http://genomebiology.com/2005/6/3/R27)) Weighting by heritability for detection of quantitative trait loci with microarray estimates of gene expression. Genome Biology 6: R27 [*Full Text HTML and PDF Version*](http://genomebiology.com/2005/6/3/R27). [Please cite this article if you have used one of the HWT (Heritability Weighted Transform) data sets.] + +18. Manly K, Williams RW (2001) WEBQTL—WWW service for mapping quantitative trait loci. International Mouse Genome Conference 15: 74. [First published abstract on WebQTL, presented Oct 2001, Edinburgh; also see [2002](http://www.complextrait.org/archive/2002/HTML/manly.html) CTC abstract] + +19. Taylor BA, Heiniger HJ, Meier H ([1973](http://www.ncbi.nlm.nih.gov/pubmed/4719448)) Genetic analysis of resistance to cadmium-induced teticular damage in mice. Proc Soc Exp Biol Med 143:629-33 [This is one of the first full paper on the use of recombinant inbred strains in biomedical research and the first paper to use BXD lines of mice. The *cdm* locus that they mapped to distal Chr 3 was subsequently defined as the *Slc38a8* metal testicular metal ion transporter. [Full text](/images/upload/Taylor_1973.pdf) + +20. Webster JA, Gibbs JR, Clarke J, Ray M, Zhang W, Holmans P, Rohrer K, Zhao A, Marlowe L, Kaleem M, McCorquodale DS 3rd, Cuello C, Leung D, Bryden L, Nath P, Zismann VL, Joshipura K, Huentelman MJ, Hu-Lince D, Coon KD, Craig DW, Pearson JV; NACC-Neuropathology Group, Heward CB, Reiman EM, Stephan D, Hardy J, Myers AJ ([2009](http://www.ncbi.nlm.nih.gov/pubmed/19361613)) Genetic control of human brain transcript expression in Alzheimer disease. Am J Hum Genet 84:445-58. [Please review and cite this article if you have used the HUMAN data set by Myers and colleagues in GeneNetwork.] + +21. Williams RW, Shou S, Lu L, Wang J, Manly KF, Hsu HC, Mountz J, Threadgill DW ([2002](http://www.complextrait.org/ctc2002/williams.html)) Genomic analysis of transcriptional networks: combining microarrays with complex trait analysis. Complex Trait Consortium 1 [One of the first published abstracts on system genetic analysis of microarray data sets, presented May 2002.] + +22. Zhang B, Schmoyer D, Kirov S, Snoddy J ([2004](http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=14975175)) GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies. BMC Bioinformatics 5:16. [This reference describes GOTM--the predecessor of WebGestalt that is now used to analyze sets of covarying transcripts.] + + +<div id="2019"> </div> + +> ### GeneNetwork (2019) </A> (not complete) + + + +1. Théberge ET, Baker JA, Dubose C, Boyle JK, Balce K, Goldowitz D, Hamre KM ([2019](https://ncbi.nlm.nih.gov/pubmed/30589433)) Genetic influences on the amount of cell death in the neural tube of BXD mice exposed to acute ethanol at midgestation. Alcohol Clin Exp Res 43:439-452 + +2. Roy S, Zaman KI, Williams RW, Homayouni R ([2019](https://ncbi.nlm.nih.gov/pubmed/30871457) Evaluation of Sirtuin-3 probe quality and co-expressed genes using literature cohesion. BMC Bioinformatics 20(Suppl 2):104 + + + + + +<div id="2018"> </div> + +> ### GeneNetwork (2018) </A> (not complete) + +1. Ashbrook DG, Mulligan MK, Williams RW Post-genomic behavioral genetics: From revolution to routine ([2018](https://ncbi.nlm.nih.gov/pubmed/29193773)) Genes Brain Behav 17:e12441 + +2. de Vries M, Faiz A, Woldhuis RR, Postma DS, de Jong TV, Sin DD, Bossé Y, Nickle DC, Guryev V, Timens W, van den Berge M, Brandsma CA ([2018](https://ncbi.nlm.nih.gov/pubmed/29212667)) Lung tissue gene-expression signature for the ageing lung in COPD. Thorax 73:609-617 + +3. Diessler S, Jan M, Emmenegger Y, Guex N, Middleton B, Skene DJ, Ibberson M, Burdet F, Götz L, Pagni M, Sankar M, Liechti R, Hor CN, Xenarios I, Franken P (2018[](https://ncbi.nlm.nih.gov/pubmed/30091978)) A systems genetics resource and analysis of sleep regulation in the mouse. PLoS Biology 16(8):e2005750 + +4. King R, Struebing FL, Li Y, Wang J, Koch AA, Cooke Bailey JN, Gharahkhani P; International Glaucoma Genetics Consortium; NEIGHBORHOOD Consortium, MacGregor S, Allingham RR, Hauser MA, Wiggs JL, Geisert EE ([2018](https://ncbi.nlm.nih.gov/pubmed/29370175)) Genomic locus modulating corneal thickness in the mouse identifies POU6F2 as a potential risk of developing glaucoma. PLoS Genet 14:e1007145 + +5. Lu Y, Zhou D, King R, Zhu S, Simpson CL, Jones BC, Zhang W, Geisert EE, Lu L ([2018](https://ncbi.nlm.nih.gov/pubmed/30619460)) The genetic dissection of Myo7a gene expression in the retinas of BXD mice. Mol Vis 24:115-126 + +6. Struebing FL, King R, Li Y, Cooke Bailey JN; NEIGHBORHOOD consortium, Wiggs JL, Geisert EE ([2018](https://ncbi.nlm.nih.gov/pubmed/29421330)) Genomic loci modulating retinal ganglion cell death following elevated IOP in the mouse. Exp Eye Res 169:61-67 + + + +<div id="2017"> </div> + +> ### GeneNetwork (2017) (not complete) + +1. Baker JA, Li J, Zhou D, Yang M, Cook MN, Jones BC, Mulligan MK, Hamre KM, Lu L ([2017](https://ncbi.nlm.nih.gov/pubmed/28027852)) Analyses of differentially expressed genes after exposure to acute stress, acute ethanol, or a combination of both in mice. Alcohol 58:139-151 + +2. Baud A, Mulligan MK, Casale FP, Ingels JF, Bohl CJ, Callebert J, Launay JM, Krohn J, Legarra A, Williams RW, Stegle O ([2017](https://ncbi.nlm.nih.gov/pubmed/28121987)) Genetic variation in the social environment contributes to health and disease. PLoS Genet 13(1):e1006498 +3. Brockmann GA, Arends D, Heise S, Dogan A ([2017](https://ncbi.nlm.nih.gov/pubmed/27933540)) Systems genetics of obesity. Methods Mol Biol. 2017;1488:481-497 + +4. Grisham W, Brumberg JC, Gilbert T, Lanyon L, Williams RW, Olivo R ([2017](https://ncbi.nlm.nih.gov/pubmed/29371844)) Teaching with Big Data: Report from the 2016 Society for Neuroscience Teaching Workshop. J Undergrad Neurosci Educ 16:A68-A76 + + +5. Jones BC, Jellen LC ([2017](https://ncbi.nlm.nih.gov/pubmed/27933539)) Systems genetics analysis of iron and its regulation in brain and periphery. Methods Mol Biol 1488:467-480 + +6. Lopez MF, Miles MF, Williams RW, Becker HC (<a href="https://ncbi.nlm.nih.gov/pubmed/27793543" target="_blank" >2017</a>) Variable effects of chronic intermittent ethanol exposure on ethanol drinking in a genetically diverse mouse cohort. Alcohol 58:73-82 + +7. Parker CC, Dickson PE, Philip VM, Thomas M, Chesler EJ ([2017](https://ncbi.nlm.nih.gov/pubmed/28398643)) Curr Protoc Neurosci 79:8.39.1-8.39.20 + +8. Porcu P, O'Buckley TK, Lopez MF, Becker HC, Miles MF, Williams RW, Morrow AL ([2017](https://ncbi.nlm.nih.gov/pubmed/27884493)) Initial genetic dissection of serum neuroactive steroids following chronic intermittent ethanol across BXD mouse strains. Alcohol 58:107-125 + +9. Rinker JA, Fulmer DB, Trantham-Davidson H, Smith ML, Williams RW, Lopez MF, Randall PK, Chandler LJ, Miles MF, Becker HC, Mulholland PJ ([2017](https://ncbi.nlm.nih.gov/pubmed/27884493)) Differential potassium channel gene regulation in BXD mice reveals novel targets for pharmacogenetic therapies to reduce heavy alcohol drinking. Alcohol 58:33-45 + +10. van der Vaart AD, Wolstenholme JT, Smith ML, Harris GM, Lopez MF, Wolen AR, Becker HC, Williams RW, Miles MF ([2017](https://ncbi.nlm.nih.gov/pubmed/27838001)) The allostatic impact of chronic ethanol on gene expression: A genetic analysis of chronic intermittent ethanol treatment in the BXD cohort. Alcohol 58:93-106 + + +<div id="2016"> </div> + +> ### GeneNetwork (2016) + +1. Alam G, Miller DB, O'Callaghan JP, Lu L, Williams RW, Jones BC ([2016](https://ncbi.nlm.nih.gov/pubmed/27182044)) MPTP neurotoxicity is highly concordant between the sexes among BXD recombinant inbred mouse strains. Neurotoxicology 55:40-7 + +2. Chintalapudi SR, Wang X, Li H, Lau YH, Williams RW, Jablonski MM ([2016](https://ncbi.nlm.nih.gov/pubmed/27881906)) Genetic and immunohistochemical analysis of HSPA5 in mouse and human retinas. Molecular Vision 22:1318-1331 + +3. Lu H, Lu L, Williams RW, Jablonski MM ([2016](https://ncbi.nlm.nih.gov/pubmed/27011731)) Iris transillumination defect and its gene modulators do not correlate with intraocular pressure in the BXD family of mice. Molecular Vision 22:224-233 + +4. Merkwirth C, Jovaisaite V, Durieux J, Matilainen O, Jordan SD, Quiros PM, Steffen KK, Williams EG, Mouchiroud L, Tronnes SU, Murillo V, Wolff SC, Shaw RJ, Auwerx J, Dillin A ([2016](https://ncbi.nlm.nih.gov/pubmed/27133168)) Two conserved histone demethylases regulate mitochondrial stress-induced longevity. Cell 165:1209-1223 + +5. Neuner SM, Garfinkel BP, Wilmott LA, Ignatowska-Jankowska BM, Citri A, Orly J, Lu L, Overall RW, Mulligan MK, Kempermann G, Williams RW, O'Connell KM, Kaczorowski CC ([2016]("https://ncbi.nlm.nih.gov/pubmed/27460150)) Systems genetics identifies Hp1bp3 as a novel modulator of cognitive aging. Neurobiol Aging 46:58-67 + +6. 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Ashbrook DG, Williams RW, Lu L, Hager R ([2015](https://ncbi.nlm.nih.gov/pubmed/26190982)) A cross-species genetic analysis identifies candidate genes for mouse anxiety and human bipolar disorder. Frontiers in Behavioral Neuroscience 9:171 + +3. Chaum E, Winborn CS, Bhattacharya S ([2015](https://ncbi.nlm.nih.gov/pubmed/25963977)) Genomic regulation of senescence and innate immunity signaling in the retinal pigment epithelium. Mammalian Genome 26:210-221 [Full text](/images/upload/ChaumMammGenome2015.pdf) + +4. Cheng Q, Seltzer Z, Sima C, Lakschevitz FS, Glogauer M ([2015](https://ncbi.nlm.nih.gov/pubmed/25608512)) Quantitative trait loci and candidate genes for neutrophil recruitment in sterile inflammation mapped in AXB-BXA recombinant inbred mice. PLoS One 10:e0124117 + +5. Cook MN, Baker JA, Heldt SA, Williams RW, Hamre KM, Lu L ([2015](https://ncbi.nlm.nih.gov/pubmed/25991709)) Identification of candidate genes that underlie the QTL on chromosome 1 that mediates genetic differences in stress-ethanol interactions. Physiol Genomics 47:308-317 + +6. Delprato A, Bonheur B, Algéo MP, Rosay P, Lu L, Williams RW, Crusio WE ([2015](https://ncbi.nlm.nih.gov/pubmed/26449520)) Systems genetic analysis of hippocampal neuroanatomy and spatial learning in mice. Genes Brain Behav 14(8):591-606 + +7. Ferguson B, Ram R, Handoko HY, Mukhopadhyay P, Muller HK, Soyer HP, Morahan G, Walker GJ ([2015](https://ncbi.nlm.nih.gov/pubmed/25088201)) Melanoma susceptibility as a complex trait: genetic variation controls all stages of tumor progression. Oncogene 34:2879-86 + +8. King R, Lu L, Williams RW, Geisert EE. ([2015](https://ncbi.nlm.nih.gov/pubmed/26604663)) Transcriptome networks in the mouse retina: An exon level BXD RI database. Mol Vis 21:1235-1251 + +9. Lee J, Seol MY, Jeong S, Kwon HJ, Lee CR, Ku CR, Kang SW, Jeong JJ, Shin DY, Nam KH, Lee EJ, Chung WY, Jo YS ([2015](https://ncbi.nlm.nih.gov/pubmed/25942439)) KSR1 is coordinately regulated with Notch signaling and oxidative phosphorylation in thyroid cancer. J Mol Endocrinol 54:115-124 + +10. Padula AE, Griffin WC 3rd, Lopez MF, Nimitvilai S, Cannady R, McGuier NS, Chesler EJ, Miles MF, Williams RW, Randall PK, Woodward JJ, Becker HC, Mulholland PJ ([2015](https://ncbi.nlm.nih.gov/pubmed/25942439)) KCNN genes that encode small-conductance Ca(2+)-activated K(+) channels influence alcohol and drug addiction. Neuropsychopharmacology 40:1928-1939 + +11. Scott RE, Ghule PN, Stein JL, Stein GS ([2015](https://ncbi.nlm.nih.gov/pubmed/25662840)) Cell cycle gene expression networks discovered using systems biology: Significance in carcinogenesis. J Cell Physiol 230:2533-42 + +12. 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Emery FD, Parvathareddy J, Pandey AK, Cui Y, Williams RW, Miller MA ([2014](https://ncbi.nlm.nih.gov/pubmed/24687986)) Genetic control of weight loss during pneumonic Burkholderia pseudomallei infection. Pathog Dis 71:249-264 + +5. Goldowitz D, Lussier AA, Boyle JK, Wong K, Lattimer SL, Dubose C, Lu L, Kobor MS, Hamre KM ([2014]("https://ncbi.nlm.nih.gov/pubmed/25076964)) Molecular pathways underpinning ethanol-induced neurodegeneration. Front Genet 5:203 + +6. Graybeal C, Bachu M, Mozhui K, Saksida LM, Bussey TJ, Sagalyn E, Williams RW, Holmes A ([2014](https://ncbi.nlm.nih.gov/pubmed/24586288)) Strains and stressors: an analysis of touchscreen learning in genetically diverse mouse strains. PLoS One 9(2):e87745 + +7. Hall RA, Liebe R, Hochrath K, Kazakov A, Alberts R, Laufs U, Böhm M, Fischer HP, Williams RW, Schughart K, Weber SN, Lammert F ([2014]("https://ncbi.nlm.nih.gov/pubmed/24586654)) Systems genetics of liver fibrosis: Identification of fibrogenic and expression quantitative trait loci in the BXD murine reference population.PLoS One 9(2):e89279 + +8. Harenza JL, Muldoon PP, Biasi MD, Imad Damaj M, Miles MF ([2014](https://ncbi.nlm.nih.gov/pubmed/24289814)) Genetic variation within the Chrna7 gene modulates nicotine reward-like phenotypes in mice. Genes, Brain & Behavior 13:213-225 + +9. Hayes SK, Hager R, Grencis RK ([2014](https://ncbi.nlm.nih.gov/pubmed/24628794)) Sex-dependent genetics effects on immune responses to parasitic nematodes. BMC Genomics 15:193 + +10. Huang Y, Zhu X, Wang L, Liu X, Lu L, Gu W, Jiao Y ([2014](https://ncbi.nlm.nih.gov/pubmed/25133246)) Genome wide analysis of sex difference in gene expression profiles of bone formations using sfx mice and BXD RI strains. 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Davies MN, Lawn S, Whatley S, Fernandes C, Williams RW, Schalkwyk LC ([2009](http://frontiersin.org/neurogenomics/paper/10.3389/neuro.15/002.2009/)) To what extent is blood a reasonable surrogate for brain gene expression studies: estimation from mouse hippocampus and spleen. Front. Neurogen. 1:2. doi:10.3389/neuro.15.002.2009 + +7. Foreman JE, Lionikas A, Lang DH, Gyekis JP, Krishnan M, Sharkey NA, Gerhard GS, Grant MD, Vogler GP, Mack HA, Stout JT, Griffith JW, Lakoski JM, Hofer SM, McClearn GE, Vandenbergh DJ, Blizard DA ([2009]("http://www.ncbi.nlm.nih.gov/pubmed/19671078)) Genetic architecture for hole-board behaviors across substantial time intervals in young, middle-aged and old mice. Genes Brain Behav 8:714-27 + +8. Gaglani SM, Lu L, Williams RW, Rosen GD ([2009](http://www.ncbi.nlm.nih.gov/pubmed/19426526)) The genetic control of neocortex volume and covariation with patterns of gene expression in mice. BMC Neuroscience 10:44 +[*Full Text HTML Version*](http://www.biomedcentral.com/1471-2202/10/44), +[*Full Text PDF Version*](http://www.biomedcentral.com/content/pdf/1471-2202-10-44.pdf) + +9. Gatti DM, Harrill AH, Wright FA, Threadgill DW, Rusyn I. ([2009](http://www.ncbi.nlm.nih.gov/pubmed/19609828)) Replication and narrowing of gene expression quantitative trait loci using inbred mice. Mamm Genome 20:437-46. + +10. Geisert EE, Lu L, Freeman-Anderson ME, Wang X, Gu W, Jiao Y, Williams RW ([2009](http://www.molvis.org/molvis/v15/a185)) Gene expression landscape of the mammalian eye: A global survey and database of mRNAs of 103 strains of mice. *Molecular Vision* 15:1730-1763 PMID:19727342 [*Full Text HTML Version*](http://www.molvis.org/molvis/v15/a185), +[*Full Text PDF Version*](http://www.molvis.org/molvis/v15/a185/mv-v15-a185-geisert.pdf) + + +11. Grisham W ([2009](http://www.funjournal.org/downloads/200981/grisham81.pdf)) Modular digitial course in undergraduate neuroscience education (MDCUNE): A website offering free digital tools for neuroscience educators. Journal of Undergraduate Neuroscience Education 8:A26-A31 [*Full Text PDF Version*](http://www.funjournal.org/downloads/200981/grisham81.pdf) +<BR><SMALL> +An excellent example of how resources such as GeneNetwork and the Mouse Brain Library can be used in class room labs. +</SMALL> + +12. Jellen LC, Beard JL, Jones BC ([2009](http://www.ncbi.nlm.nih.gov/pubmed/19393285)) Systems genetics analysis of iron regulation. Biochemie in press. +19393285 + +13. Koutnikova H, Markku L, Lu L, Combe R, Paananen J, Kuulasmaa T, Kuusisto J, Häring H, Hansen T, Pedersen,O, Smith U, Hanefel M, Williams RW, Auwerx J ([2009](http://www.ncbi.nlm.nih.gov/pubmed/19662162)) Identification of UBP1 as a critical blood pressure determinant. 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Overall RW, Kempermann G, Peirce J, Lu L, Goldowitz D, Gage FH, Goodwin S, Smit AB, Airey DC, Rosen GD, Schalkwyk LC, Sutter TR, Nowakowski RS, Whatley S, Williams RW ([2009](http://www.ncbi.nlm.nih.gov/pubmed/20582282)) Genetics of the hippocampal transcriptome in mice: a systematic survey and online neurogenomic resource. Frontiers in Neuroscience 3:55 +[*Full Text HTML Version*](http://www.frontiersin.org/neurogenomics/10.3389/neuro.15.003.2009/full), +<a href="javascript:__doPostBack('ctl00$ContentAreaRightMenu$ArchiveRightMenu$lnkPDF','')" target="_blank" >*Full Text PDF Version*</a> + +16. Overton JD, Adams GS, McCall RD, Kinsey ST ([2009](http://www.ncbi.nlm.nih.gov/pubmed/19100334)) High energy phosphate concentrations and AMPK phosphorylation in skeletal muscle from mice with inherited differences in hypoxic exercise tolerance. Comp Biochem Physiol A Mol Integr Physiol 152:478-85 + +17. Philip VM, Duvvuru S, Gomero B, Ansah TA, Blaha CD, Cook MN, Hamre KM, Laviviere WR, Matthews DB, Mittleman G, Goldowitz D, Chesler EJ ([2009](http://www.ncbi.nlm.nih.gov/pubmed/19958391)) High-throughput behavioral phenotyping in the expanded panel of BXD recombinant inbred strains. Genes, Brain and Behavior 8:in press PMID: 19958391 [*Full Text HTML Version*](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2855868/) + +18. Ruden DM, Chen L, Possidente D, Possidente B, Rasouli P, Wang L, Lu X, Garfinkel MD, Hirsch HV, Page GP ([2009](http://www.ncbi.nlm.nih.gov/pubmed/19737576)) Genetical toxicogenomics in Drosophila identifies master-modulatory loci that are regulated by developmental exposure to lead. Neurotoxicology 30:898-914 + +19. Rosen GL, Pung C, Owens C, Caplow J, Kim H, Lu L, Williams RW ([2009](http://www.ncbi.nlm.nih.gov/pubmed/19191878)) Genetic modulation of striatal volume in BXD recombinant inbred mice. Genes, Brain & Behavior 8:296-308 + +20. Saccone SF, Bierut LJ, Chesler EJ, Kalivas PW, Lerman C, Saccone NL, Uhl GR, Li CY, Philip VM, Edenberg HJ, Sherry ST, Feolo M, Moyzis RK, Rutter JL ([2009](http://www.ncbi.nlm.nih.gov/pubmed/19381300)) Supplementing high-density SNP microarrays for additional coverage of disease-related genes: addiction as a paradigm. PLoS ONE 4:e5225. [*Full Text HTML Version*]("http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005225), +[*Full Text PDF Version*](http://www.plosone.org/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0005225&representation=PDF). [Supplementary table 1 provides links to many transcripts and genes, some of which were mined from an analysis of GeneNetwork data sets.] + +21. Silva GL, Junta CM, Sakamoto-Hojo ET, Donadi EA, Louzada-Junior P, Passos GA ([2009](http://www.ncbi.nlm.nih.gov/pubmed/19758195)) Genetic susceptibility loci in rheumatoid arthritis establish transcriptional regulatory networks with other genes. Ann N Y Acad Sci 1173:521-37 + +22. Tapocik JD, Letwin N, Mayo CL, Frank B, Luu T, Achinike O, House C, Williams R, Elmer GI, Lee NH ([2009](http://www.ncbi.nlm.nih.gov/pubmed/19386926)) Identification of candidate genes and gene networks specifically associated with analgesic tolerance to morphine. J Neurosci 2:5295-307 [*Full Text HTML*](http://www.jneurosci.org/cgi/content/full/29/16/5295) + +23. Thomas C, Gioiello A, Noriega L, Strehle A, Oury J, Rizzo G, Macchiarulo A, Yamamoto H, Mataki C, Pruzanski M, Pellicciari R, Auwerx J, Schoonjans K ([2009]("http://www.ncbi.nlm.nih.gov/pubmed/19723493)) TGR5-mediated bile acid sensing controls glucose homeostasis. Cell Metab 10:167-77 +[*Full Text PDF*](http://www.genenetwork.org/images/upload/Thomas_Auwerx_2009.pdf) + +24. Webb BT, McClay JL, Vargas-Irwin C, York TP, van den Oord EJCG ([2009](http://www.ncbi.nlm.nih.gov/pubmed/19723493)) In silico whole genome association scan for murine prepulse inhibition. PLoS ONE 4: e5246. doi:10.1371/journal.pone.0005246 +[*Full Text HTML*](http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0005246), +[*Full Text HTML*](http://www.plosone.org/article/fetchObjectAttachment.action;jsessionid=18CBF1DF825C97C45A98D0256635C650?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0005246&representation=PDF) + + + +25. Weng J, Symons MN, Singh SM ([2009](http://www.ncbi.nlm.nih.gov/pubmed/19107586)) Studies on syntaxin 12 and alcohol preference involving C57BL/6J and DBA/2J strains of mice. Behav Genet. 39:183-191 +[*Full Text HTML Version*](http://www.iovs.org/cgi/content/abstract/50/5/1996) + +26. Whitney IE, Raven MA, Ciobanu DC, Williams RW, Reese BE ([2009](http://www.iovs.org/cgi/content/abstract/50/5/1996)) Multiple genes on chromosome 7 regulate dopaminergic amacrine cell number in the mouse. Investigative Ophthalmology & Visual Science 50:1996-2003. +[*Full Text HTML Version*](http://www.iovs.org/cgi/content/abstract/50/5/1996). + +27. Wu S, Lusis AJ, Drake TA ([2009](http://www.jlr.org/cgi/reprint/R800067-JLR200v1.pdf)) A systems-based framework for understanding complex metabolic and cardiovascular disorders. Journal of Lipid Research, in press [*Full Text PDF*](http://www.jlr.org/cgi/reprint/R800067-JLR200v1.pdf) + +28. Zheng QY, Ding D, Yu H, Salvi RJ, Johnson KR ([2009](http://www.ncbi.nlm.nih.gov/pubmed/18280008)) A locus on distal chromosome 10 (*ahl4*) affecting age-related hearing loss in A/J mice. Neurobiol Aging. 2009 Oct;30(10):1693-705. + + +<div id="2008"> </div> + +> ### GeneNetwork (2008) + + +1. Abdeltawab NF, Aziz RK, Kansal R, Rowe SL, Su Y, Gardner L, Brannen C, Nooh MM, Attia RR, Abdelsamed HA, Taylor WL, Williams RW, Kotb M (2008) An unbiased systems genetics approach to mapping genetic loci modulating susceptibility to severe streptococcal sepsis. PLoS Pathogens 4:e1000042 +[*Full Text HTML Version*](http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1000042), +[*Full Text PDF Version*](http://www.plospathogens.org/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.ppat.1000042&representation=PDF) + + +2. Bertrand L, Fan Y, Nissanov J, Rioux L (2008) Genetic regulation of the anatomy of the olfactory bulb. Society for Neuroscience [2008](http://www.sfn.org/skins/main/pdf/abstracts/am2008/poster_presentations/tuesday_pm.pdf) + + +3. Bhoumik A, Singha N, O'Connell MJ, Ronai ZA ([2008](http://www.ncbi.nlm.nih.gov/pubmed/18397884)) Regulation of TIP60 by ATF2 modulates ATM activation. J Biol Chem 283:17605-14 +[*Full Text HTML Version*](http://www.jbc.org/content/283/25/17605.long), [*Full Text PDF Version*](http://www.jbc.org/content/early/2008/04/08/jbc.M802030200.full.pdf) + + +4. Bjork K, Rimondini R, Hansson AC, Terasmaa A, Hyytiä P, Heilig M, Sommer WH ([2008](http://www.ncbi.nlm.nih.gov/pubmed/18367649)) Modulation of voluntary ethanol consumption by beta-arrestin 2. FASEB J 22:2552-60 +[*Full Text HTML Version*](http://www.fasebj.org/cgi/content/full/22/7/2552), +[*Full Text PDF Version*](http://www.fasebj.org/cgi/reprint/22/7/2552.pdf) + + +5. Boone EM, Hawks BW, Li W, Garlow SJ ([2008](http://www.ncbi.nlm.nih.gov/pubmed/18199428)) Genetic regulation of hypothalamic cocaine and amphetamine-regulated transcript (CART) in BxD inbred mice. Brain Res 1194:1-7 + +6. Crawford NP, Alsarraj J, Lukes L, Walker RC, Officewala JS, Yang HH, Lee MP, Ozato K, Hunter KW (2008) Bromodomain 4 activation predicts breast cancer survival. Proc Natl Acad Sci USA 105:6380-6385 +[*Full Text HTML Version*](http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18427120) + +7. Crawford NP, Walker RC, Lukes L, Officewala JS, Williams RW, Hunter KW ([2008](http://www.ncbi.nlm.nih.gov/pubmed/18301994)) The Diasporin Pathway: a tumor progression-related transcriptional network that predicts breast cancer survival. Clin Exp Metastasis 25:357-69 +[*Full Text HTML Version*](http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18301994) + +8. Danciger M, Ogando D, Yang H, Matthes MT, Yu N, Ahern K, Yasumura D, Williams RW, Lavail MM ([2008](http://www.ncbi.nlm.nih.gov/pubmed/18344445)) Genetic modifiers of retinal degeneration in the *rd3* mouse. Invest Ophthalmol Vis Sci 49:2863-2869 +[*Full Text HTML Version*](http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18344445) + + +9. Druka A, Druka I, Centeno AG, Li H, Sun Z, Thomas WT, Bonar N, Steffenson BJ, Ullrich SE, Kleinhofs A, Wise RP, Close TJ, Potokina E, Luo Z, Wagner C, Schweizer GF, Marshall DF, Kearsey MJ, Williams RW, Waugh R ([2008](http://www.ncbi.nlm.nih.gov/pubmed/19017390)) Towards systems genetic analyses in barley: Integration of phenotypic, expression and genotype data into GeneNetwork. BMC Genet 9:73 +[*Full Text HTML Version*]("http://www.biomedcentral.com/1471-2156/9/73) + +10. Dykstra B, de Haan G ([2008](http://www.ncbi.nlm.nih.gov/pubmed/18008087)) Hematopoietic stem cell aging and self-renewal. Cell Tissue Res 331:91-101 + +11. Ferrara CT, Wang P, Neta EC, Stevenes RD, Bain JR, Wenner BR, Ilkayeva OR, Keller MP, Blasiole DA, Kendziorski C, Yandell BS, Newgard CB, Attie AD (2008) Genetic networks of liver metabolism revealed by integration of metabolic and transcriptional profiling. PLoS Genetics 4: e1000034. doi:10.1371/journal.pgen.1000034 +[*Full Text HTML Version*](http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000034) + +12. Gerrits A, Dykstra B, Otten M, Bystrykh L, de Haan G ([2008](http://www.ncbi.nlm.nih.gov/pubmed/18560825)) Combining transcriptional profiling and genetic linkage analysis to uncover gene networks operating in hematopoietic stem cells and their progeny. Immunogenetics. 60:411-22. + +13. Grieve IC, Dickens NJ, Pravenec M, Kren V, Hubner N, Cook SA, Aitman TJ, Petretto E, Mangion J ([2008](http://www.ncbi.nlm.nih.gov/pubmed/19112506)) Genome-wide co-expression analysis in multiple tissues. PLoS One. 3:e4033. PMID: 19706712 [*Full Text HTML Version*](http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0004033), +[*Full Text PDF Version*](http://www.plosone.org/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0004033&representation=PDF) + +14. Hall R, Hillebrandt S, Hochrath K, Gruenhage F, Weber S, Schwartz S, Yildiz Y , Sauerbruch T, Lammert F (2008) BXD recombinant inbred mouse lines–a genetic reference population for dissection of the complex genetics of liver fibrosis. Zeitschrift fur Gastroenterologie 46:in press +[*Full Text PDF Version*](http://www.thieme-connect.com/ejournals/abstract/zfg/doi/10.1055/s-2008-1037508) + +15. Han B, Altman NS, Mong JA, Klein LC, Pfaff DW, Vandenbergh DJ (2008) Comparing quantitative trait loci and gene expression data. Advances in Bioinformatics, doi:10.1155/2008/719818. +[*Full Text PDF Version*](http://hindawi.com/RecentlyAcceptedArticlePDF.aspx?journal=ABI&number=719818) and [*Full Text HTML Version*](http://www.hindawi.com/journals/abi/2008/719818.html) + + +16. Hayat Y, Yang J, Xu HM, Zhu J ([2008](http://www.ncbi.nlm.nih.gov/pubmed/19067460)) Influence of outliers on QTL mapping for complex traits. J Zhejiang Univ Sci B. 9:931-7 + +17. Heimel JA, Hermans JM, Sommeijer JP; Neuro-Bsik Mouse Phenomics consortium, Levelt CN ([2008](http://www.ncbi.nlm.nih.gov/pubmed/18700840)) Genetic control of experience-dependent plasticity in the visual cortex. Genes Brain Behav 7:915-23. +[*Full Text PDF Version*](http://www.genenetwork.org/images/upload/Heimel_2008_BXDVisualCortex.pdf) + + +18. Jan TA, Lu L, Li CX, Williams RW, Waters RS ([2008](http://www.biomedcentral.com/1471-2202/9/3)) Genetic analysis of posterior medial barrel subfield (PMBSF) size in somatosensory cortex (SI) in recombinant inbred strains of mice. BMC Neuroscience 9:3 +[*Full Text PDF Version*](http://www.biomedcentral.com/content/pdf/1471-2202-9-3.pdf) + +19. Johnson KR, Longo-Guessa C, Gagnona LH, Yub H, Zhengb QY ([2008](http://www.ncbi.nlm.nih.gov/pubmed/18662770)) A locus on distal chromosome 11 (*ahl8*) and its interaction with *Cdh23 ahl* underlie the early onset, age-related hearing loss of DBA/2J mice. Genomics 92:219-225 + +20. Jones LC, Beard JL, Jones BC ([2008](http://www.ncbi.nlm.nih.gov/pubmed/18189309)) Genetic analysis reveals polygenic influences on iron, copper, and zinc in mouse hippocampus with neurobiological implications. Hippocampus 18:398-410 +[*Full Text PDF Version*](images/upload/Jones_2008_Hippocampus.pdf) + + +21. Jones LC, Earley CJ, Allen RP, Jones BC ([2008](http://www.ncbi.nlm.nih.gov/pubmed/18189309)) Of mice and men, periodic limb movements and iron: how the human genome informs the mouse genome. Genes, Brain and Behavior 7:513-514. +[*Full Text PDF Version*](/images/upload/Jones_OfMiceandMen.pdf) + +22. Kang HM, Ye C, Eskin E ([2008](http://www.ncbi.nlm.nih.gov/pubmed/18791227)) Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots. Genetics doi:10.1534/genetics.108.094201 +[*Full Text PDF Version*](http://www.genetics.org/cgi/content/abstract/genetics.108.094201v1). [An important method that can greatly improve the ability to resolve true genetic interactions in expression genetic studies.] + +23. Kadarmideen HN ([2008](http://www.ncbi.nlm.nih.gov/pubmed/19045837)) Genetical systems biology in livestock: Application to gonadotrophin releasing hormone and reproduction. IET Systems Biology 2:423-441 +[*Full Text PDF Version*](/images/upload/Kadarmideen_2008.pdf) + + +24. Kerns RT, Miles MF (2008) Microarray analysis of ethanol-induced changes in gene expression. Alcohol: Methods and Protocols. In: Methods in Molecular Biology 447:395-410 +[*Full Text PDF Version*](http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-242-7_26) + + +25. Kotb M, Fathey N, Aziz R, Rowe S, Williams RW, Lu L ([2008](http://www.ncbi.nlm.nih.gov/pubmed/18972751)) Unbiased forward genetics and systems biology approaches to understanding how gene-environment interactions work to predict susceptibility and outcomes of infections. Novartis Found Symp 293:156-165; discussion pp 165-167, 181-183 + +26. Loos M (2008) The PhenoTyper automated home cage environment as a high throughput tool to detect behavioral abnormalities in mutant mice. Proceeding of Measuring Behavior (Maastricht, The Netherlands, Aug 26-29, 2008). +[*Full Text PDF Version*](http://www.neurobsik.nl/Loos_2008.pdf) + + +27. Loudet O, Michael TP, Burger BT, Le Metté C, Mockler TC, Weigel D, Chory J ([2008](http://www.ncbi.nlm.nih.gov/pubmed/18971337)) A zinc knuckle protein that negatively controls morning-specific growth in Arabidopsis thaliana. Proc Natl Acad Sci USA 105:17193-8 +[*Full Text HTML Version*](http://www.pnas.org/content/105/44/17193.long) , and [*Full Text Supplement*](http://www.pnas.org/content/suppl/2008/10/29/0807264105.DCSupplemental/0807264105SI.pdf) + +28. Lu L, Wei L, Peirce JL, Wang X, Zhou J, Homayouni R, Williams RW, Airey DC (2008) Using gene expression databases for classical trait QTL candidate gene discovery in the BXD recombinant inbred genetic reference population: mouse forebrain weight. BMC Genomics 9:444 +[*Full Text HTML Version*](http://www.biomedcentral.com/1471-2164/9/444), and [*Full Text PDF Version*](http://www.biomedcentral.com/content/pdf/1471-2164-9-444.pdf) + +29. Macedo C, Magalhaes DA, Tonani M, Marques MC, Junta CM, Passos GA ([2008](http://www.ncbi.nlm.nih.gov/pubmed/18597059)) Genes that code for T cell signaling proteins establish transcriptional regulatory networks during thymus ontogeny. +Mol Cell Biochem 318:63-71 + +30. Morahan G, Peeva V, Munish M, Williams R (2008) Systems genetics can provide new insights in to immune regulation and autoimmunity. Journal of Autoimmunity 31:233-236. +[*Full Text PDF Version*](http://www.genenetwork.org/images/upload/Morahan_2008.pdf) + +31. Mozhui RT, Ciobanu DC, Schikorski T, Wang XS, Lu L, Williams RW (2008) Dissection of a QTL hotspot on mouse distal chromosome 1 that modulates neurobehavioral phenotypes and gene expression. PLoS Genetics 4: e1000260. doi:10.1371/journal.pgen.1000260 +[*Full Text HTML Version*](http://www.plosgenetics.org/article/info:doi%2F10.1371%2Fjournal.pgen.1000260) + + +32. New J, Kendall W, Huang J, Chesler E ([2008](http://www.computer.org/portal/web/csdl/doi/10.1109/TVCG.2008.61)) Dynamic visualization of coexpression in systems genetics data. IEEE Trans Visualization & Computer Graphics 14:1081-1095. + +33. Pravenec M, Petretto E ([2008](http://www.ncbi.nlm.nih.gov/pubmed/18541997)) Insight into the genetics of hypertension, a core component of the metabolic syndrome. +Genes and cell metabolism. Curr Opin Clin Nutr Metab Care 11:393-397 +[*Full Text HTML Version*](http://www.plosgenetics.org/article/info:doi%2F10.1371%2Fjournal.pgen.1000260) + + +34. Pritchard M, Reeves RH, Dierssen M, Patterson D, Gardiner KJ ([2008](http://www.ncbi.nlm.nih.gov/pubmed/18544929)) Down syndrome and the genes of human chromosome 21: current knowledge and future potentials. Cytogenetics and Genome Research 121:67-77 + +35. Reiner DJ, Jan TA, Boughter JD Jr, Li CX, Lu L, Williams RW, Waters RS ([2008](http://www.ncbi.nlm.nih.gov/pubmed/18653645)) Genetic analysis of tongue size and taste papillae number and size in recombinant inbred strains of mice. Chemical Senses 33:693-707 + +36. Swertz MA, Tesson BM, Scheltema RA, Vera G, Jansen RC (2008) MOLGENIS for genetical genomics. Chapter 5. MGG: a customizable software infrastructure for genetical genomics. +[*Full Text PDF Version*](http://dissertations.ub.rug.nl/FILES/faculties/science/2008/m.a.swertz/05_c5.pdf) + + +37. Williams RW, Lu L ([2008](http://pubs.niaaa.nih.gov/publications/arh313/275-277.pdf)) Integrative genetic analysis of alcohol dependence using the GeneNetwork web resources. In Pathways to Alcohol Dependence: Alcohol Research & Health 31:275-277 +[*Full Text PDF Version*](http://pubs.niaaa.nih.gov/publications/arh313/275-277.pdf) + + +38. Woo JH, Zheng T, Kim JH ([2008](http://inderscience.metapress.com/app/home/contribution.asp?referrer=parent&backto=issue,7,8;journal,3,6;linkingpublicationresults,1:121101,1)) DACE: Differential Allelic Co-Expression test for estimating regulatory associations of SNP and biological pathway. International Journal of Functional Informatics and Personalised Medicine 1:407-418 + +39. Yang RJ, Mozhui K, Karlsson RM, Cameron HA, Williams RW, Holmes A ([2008](http://www.ncbi.nlm.nih.gov/pubmed/18185497)) Variation in mouse basolateral amygdala volume is associated with differences in stress reactivity and fear learning. Neuropsychopharmacology. 33:2595-604 +[*Full Text HTML Version*](http://www.nature.com/npp/journal/v33/n11/full/1301665a.html), +[*Full Text PDF Version*]("http://www.nature.com/npp/journal/v33/n11/pdf/1301665a.pdf) + +40. Zhang Y, Maksakova IA, Gagnier L , van de Lagemaat LN, Mager DL (2008) Genome-wide assessments reveal extremely high levels of polymorphism of two active families of mouse endogenous retroviral elements. PLoS Genet 4(2): e1000007. doi:10.1371/journal.pgen.1000007 +[*Full Text HTML Version*](http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000007) + + +<div id="2007"> </div> + +> ### GeneNetwork (2007) + + +1. Aziz RK, Kansal R, Abdeltawab NF, Rowe SL, Su Y, Carrigan D, Nooh MM, Attia RR, Brannen C, Gardner LA, Lu L, Williams RW, Kotb M ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17525705)) Susceptibility to severe Streptococcal sepsis: use of a large set of isogenic mouse lines to study genetic and environmental factors. Genes and Immunity 8:404-415 + +2. Bao L, Peirce JL, Zhou M, Li H, Goldowitz D, Williams RW, Lu L, Cui Y ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17428815)) An integrative genomics strategy for systematic characterization of genetic loci modulating phenotypes. Hum Mol Genet 16:1381-1390 + +3. Bao L, Zhou M, Wu L, Lu L, Goldowitz D, Williams RW, Cui Y ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17099235)) PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits. Nucleic Acids Res. 35(Database issue):D51-54 +[*Full Text PDF Version*](http://nar.oxfordjournals.org/cgi/reprint/35/suppl_1/D51), +[Full Text HTML Version*](http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D51) + +4. Benhamou JP, Rizzetto M, Reichen J, Rodés J ([2007](http://books.google.com/books?id=taE276KCyecC&dq=genenetwork+webqtl)) Textbook of hepatology: from basic science to clinical practice. Blackwell Publishing, p. [379]("http://books.google.com/books?id=taE276KCyecC&pg=PA379&lpg=PA379&dq=genenetwork+webqtl&source=web&ots=2CjGbbDh3B&sig=tXdbQ7KAGOyxOee9TECF40GXyywl)), ISBN 1405127414 + +5. Bennett B, Downing C, Carosone-Link P, Ponicsan H, Ruf C, Johnson TE ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17250610)) Quantitative trait locus mapping for acute functional tolerance to ethanol in the L x S recombinant inbred panel. Alcohol Clin Exp Res. 31:200-208. [Phenotype data described in this paper are accessible in GeneNetwork in the LXS Phenotype database; ID numbers 10126, 10127, 10132, 10134, 10138, and 10139 (select Species=MOUSE, Group=LXS, Type=PHENOTYPES and search the ALL field with the term "functional" or just enter the ID numbers above.] + +6. Cervino ACL, Darvasi A, Fallah Mi, Mader CC, Tsinoremas NF ([2007](http://www.genetics.org/cgi/content/full/175/1/321)) An integrated in silico gene mapping strategy in inbred mice. Genetics 175:321-333 +[*Full Text PDF Version*](http://www.genetics.org/cgi/reprint/175/1/321) + + + +7. Chesler EJ ([2007](http://www3.interscience.wiley.com/cgi-bin/summary/114171173/SUMMARY)) Bioinformatics of behavior. In Neurobehavioral Genetics, ed Jones BC, Mormede P +CRC Press ISBN 084931903X InterScience +[95-114](http://books.google.com/books?id=ZNYE-FcvYloC&pg=PA102&lpg=PA102&dq=genenetwork+webqtl&source=web&ots=q3RfjmnLjt&sig=sDjpfmvzdx2lKigtJKqbb-H8Di8&hl=en&sa=X&oi=book_result&resnum=3&ct=result#PPA95,M1)), ISBN 1405127414 + +8. Chesler EJ ([2007](http://www3.interscience.wiley.com/cgi-bin/summary/114171173/SUMMARY)) Combining quantitative trait and gene-expression data. In Bioinformatics of Geneticists, ed Barnes MR, Wiley InterScience + +9. Coppin H, Darnaud V, Kautz L, Meynard D, Aubry M, Mosser J, Martinez M, Roth MP ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17945001)) Gene expression profiling of Hfe-/- liver and duodenum in mouse strains with differing susceptibilities to iron loading: identification of transcriptional regulatory targets of Hfe and potential hemochromatosis modifiers. Genome Biology 8:R221 +[*Full Text PDF Version*](http://www.plosgenetics.org/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pgen.0030214&representation=PDF) +[*Full Text HTML Version*](http://genomebiology.com/2007/8/10/R221) + +10. Crawford NP, Qian X, Ziogas A, Papageorge AG, Boersma BJ, Walker RC, Lukes L, Rowe WL, Zhang J, Ambs S, Lowy DR, Anton-Culver H, Hunter KW ([2007](http://www.ncbi.nlm.nih.gov/pubmed/18081427)) Rrp1b, a new candidate susceptibility gene for breast cancer progression and metastasis. PLoS Genetics 3: e214 +[*Full Text PDF Version*](http://www.plosgenetics.org/article/fetchObjectAttachment.action?uri=info%3Adoi%2F10.1371%2Fjournal.pgen.0030214&representation=PDF), +[*Full Text HTML Version*](http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030214) + + +11. Dong H, Martin MV, Colvin J, Ali Z, Wang L, Lu L, Williams RW, Rosen GD, Csernansky JG, Cheverud JM ([2007]("http://www.ncbi.nlm.nih.gov/pubmed/17406662)) Quantitative trait loci linked to thalamus and cortex gray matter volumes in BXD recombinant inbred mice. Heredity 99:62-69 + +12. Fox JG, Barthold SW, Davisson MT, Newcomer CE ([2007](http://books.google.com/books?id=vnRpW-gI9JMC)) The mouse in biomedical research. (2nd ed). Academic Press, p. 530. + +13. French L, Pavlidis P ([2007](http://bib.oxfordjournals.org/cgi/content/abstract/8/6/446)) Informatics in neuroscience. Briefings in Bioinformatics 8:446-456 + +14. Gatti D, Maki A, Chesler EJ, Kirova R, Kosyk O, Lu L, Manly KF, Williams RW, Perkins A, Langston MA, Threadgill DW, Rusyn I ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17542012)) Genome-level analysis of genetic regulation of liver gene expression networks. Hepatology 46:548-557 + [*Full Text PDF Version*](/images/upload/Gatti_Rusyn_2007.pdf) + +15. Grice DE, Reenila I, Mannisto PT, Brooks Ai, Smith GG, Golden GT, Buxbaum JD, Berrettini WH (2007) Transcriptional profiling of C57 and DBA strains of mice in the absence and presence of morphine. BMC Genomics 8:76 +[*Full Text PDF Version*](http://www.biomedcentral.com/content/pdf/1471-2164-8-76.pdf), +[*Full Text HTML Version*]("http://www.biomedcentral.com/1471-2164/8/76) + +16. Hancock JM, Mallon AM ([2007](http://www.ncbi.nlm.nih.gov/pubmed/18192320)) Phenobabelomics--mouse phenotype data resources. Brief Funct Genomic Proteomic 6:292-301 + +17. Hawes JJ, Tuskan RG, Reilly KM ([2007](http://www.ingentaconnect.com/content/klu/10048/2007/00000008/00000002/00000078;jsessionid=1m2u56h1a4lj2.alice)) *Nf1* expression is dependent on strain background: implications for tumor suppressor haploinsufficiency studies. Neurogenetics 8: 121-130. [Nf1 expression in whole brain (INIA data set) and in striatum (Rosen data set) was used to catalyze a detailed study of the degree of NPcis (Nf1 + Trp53) haploinsufficiency. Email: kreilly@ncifcrf.gov] + +18. Hofstetter JR, Svihla-Jones DA, Mayeda AR ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17974007)) A QTL on mouse chromosome 12 for the genetic variance in free-running circadian period between inbred strains of mice. J Circadian Rhythms 5:7 +[*Full Text PDF Version*](http://www.jcircadianrhythms.com/content/pdf/1740-3391-5-7.pdf), +[*Full Text HTML Version*](http://www.jcircadianrhythms.com/content/5/1/7) + +19. Hsu HC, Lu L, Yi N, Van Zant G, Williams RW, Mountz JD ([2007](http://books.google.com/books?id=fbTsCdQv7cEC&dq=genenetwork+webqtl&source=gbs_summary_s&cad=0)) Quantitative trait locus mapping in aging systems. In: Methods in Molecular Biology (Vol 371). Biological Aging: Methods and Protocols, ed Tollefsbol TO, Humana Press, Inc., Netlibrary, Springer +[*Google Book Search*](http://books.google.com/books?id=fbTsCdQv7cEC&pg=RA4-PA332&lpg=RA4-PA332&dq=genenetwork+webqtl&source=web&ots=PawLDYAUam&sig=hOHsKDfumr3U-ZEUtT7Ag6gJAYg&hl=en&sa=X&oi=book_result&resnum=9&ct=result#PRA4-PA321,M1) + +20. Jawad M, Giotopoulos G, Fitch S, Cole C, Plumb M, Talbot CJ ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17185011)) Mouse bone marrow and peripheral blood erythroid cell counts are regulated by different autosomal genetic loci. Blood Cells Mol Disease 38:69-77 + +21. Jessberger S, Gage FH ([2007](http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1800354)) ZOOMING IN: a new high-resolution gene expression atlas of the brain. Mol Syst Biol. 3:75 + +22. Jones BC, Beard JL, Gibson JN, Unger EL, Allen RP, McCarthy KA, Earley CJ ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17475678)) Systems genetic analysis of peripheral iron parameters in the mouse. American Journal of Physiology Regul Integr Comp Physiol 293: R116-124 +[*Full Text HTML Version*]("http://ajpregu.physiology.org/cgi/content/full/293/1/R116), and see <a href="http://www.genenetwork.org/images/upload/Jones et al 1999 Pharmacogenetics3-0.pdf" target="_blank" >*full text of Jones et al., 1999.*</a> + +23. Jones BC and Mormede JP (2007) Neurobehavioral genetics: methods and applications. ([2007](http://books.google.com/books?id=P85FPhRKFVMC&pg=PA102&lpg=PA102&dq=genenetwork+webqtl&source=web&ots=-qg3S-C0xQ&sig=HoOCQpZrV3i45I0vPfDb3PfDMvY)) CRC Press, Taylor & Francis Group, Boca Raton, Florida, p. 102, ISBN 084931903X + +24. Kadarmideen HN, Reverter A (2007) Combined genetic, genomic and transcriptomic methods in the analysis of animal traits. CABI Review: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources 2: No. 042 (16 pp) +[*Full Text PDF Version*](/images/upload/Kadarmideen_Reverter_2007.pdf) + +25. Korostynski M, Piechota M, Kaminska D, Solecki W. Przewlocki R ([2007](http://genomebiology.com/2007/8/6/R128)) Morphine effects on striatal transcriptome in mice. Genome Biology 8:R128 + +26. Lad HV, Liu L, Payá-Cano JL, Fernandes C, Schalkwyk LC ([2007](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1998875/?tool=pubmed)) Quantitative traits for the tail suspension test: automation, optimization, and BXD RI mapping. Mamm Genome. 2007 Jul;18(6-7):482-91 +[*Full Text PubMed Central version*](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1998875/?tool=pubmed) + + +27. Liang Y, Jansen M, Aronow B, Geiger H, Van Zant G ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17220891)) The quantitative trait gene latexin influences the size of the hematopoietic stem cell population in mice. Nature Genetics 39:141-142 (doi: 10.1038/ng1938). [Using the BXD mouse strains, Liang, Van Zant and colleagues, demonstrate that sequence variants in *Lxn* modulate cell cycling kinetics of bone marrow stem cells. High expression of *Lxn* mRNA and protein is associated with the C57BL/6J allele and with lower proliferative activity. The authors made good use of the [BXD Hematopoietic Stem Cell](http://www.genenetwork.org/dbdoc/HC_U_0304_R.html) data set and *Lxn* Affymetrix probe set 96065_at. Figures 1 and 5 were generated using GeneNetwork.] + +28. Llamas B, Bélanger S, Picard S, Deschepper CF ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17566079)) Cardiac mass and cardiomyocyte size are governed by different genetic loci on either autosomes or chromosome Y in recombinant inbred mice. Physiol Genomics 31:176-82 + +29. Meng PH, Macquet A, Loudet O, Marion-Poll A, North HM ([2007](http://mplant.oxfordjournals.org/cgi/content/full/ssm014v1)) Analysis of natural allelic variation controlling Arabidopsis thaliana seed germinability in response to cold and dark: identification of three major quantitative trait loci. Molecular Plant, doi:10.1093/mp/ssm014 + +30. Mouse Phenotype Database Integration Consortium ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17436037)) Integration of mouse phenome data resources. Mammalian Genome, 18:157-163. +[*PDF Preprint Version*]("http://www.har.mrc.ac.uk/research/bioinformatics/publications/Preprint1.pdf) + +31. Miyairi I, Tatireddigari VR, Mahdi OS, Rose LA, Belland RJ, Lu L, Williams RW, Byrne GI ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17641048)) The p47 GTPases Iigp2 and Irgb10 regulate innate immunity and inflammation to murine Chlamydia psittaci. J Immunol 179:1814-1824 + +32. Mozhui K, Hamre KM, Holmes A, Lu L, Williams RW ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17131200)) Genetic and structural analysis of the basolateral amygdala complex in BXD recombinant inbred mice. Behav Genet. 37:223-243 +[*Full Text MS Word Version (authors' copy)*](http://www.genenetwork.org/images/upload/Mozhui_et_al_2007.doc) + + + +33. Peirce JL, Broman KW, Lu L, Williams RW ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17400728)) A simple method for combining genetic mapping data from multiple crosses and experimental designs. PLoS ONE 2:e1036 +[*Full Text PDF Version*]("http://www.plosone.org/article/fetchObjectAttachment.action;jsessionid=009B2741B48AC1CB94E68107E714A1B0?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0001036&representation=PDF), +[*Full Text HTML Version*]("http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0001036") + + +34. Pérez-Enciso M, Quevedo JR, Bahamonde A ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17352813)) Genetical genomics: use all data. BMC Genomics 8:69. +[*Full Text PDF Version*](http://www.biomedcentral.com/content/pdf/1471-2164-8-69.pdf), +[*Full Text HTML Version*]("http://www.biomedcentral.com/1471-2164/8/69) + +35. Rosen GD, Bai J, Wang Y, Fiondella CG, Threlkeld SW, LoTurco JJ, Galaburda AM ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17218481)) Disruption of neuronal migration by RNAi of Dyx1c1 results in neocortical and hippocampal malformations. Cereb Cortex 17:2562-72. +[*Full Text PDF Version*](http://cercor.oxfordjournals.org/cgi/reprint/bhl162v1.pdf) + +36. Rosen GD, Chesler EJ, Manly KF, Williams RW (2007) An informatics approach to systems neurogenetics. Methods Mol Biol 401:287-303 + +37. Sunkin SM, Hohmann JG ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17911164)) Insights from spatially mapped gene expression in the mouse brain. Human Molecular Genetics 16: R209-219 +[*Full Text PDF Version*](http://hmg.oxfordjournals.org/cgi/reprint/16/R2/R209.pdf), +[*Full Text HTML Version*](http://hmg.oxfordjournals.org/cgi/content/full/16/R2/R209) + +38. Swertz MA, Jansen RC ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17297480)) Beyond standardization: dynamic software infrastructure for systems biology. Nature Reviews Genetics:235-243 + +39. Taylor M, Valdar W, Kumar A, Flint J, Mott R ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17400728)) Management, presentation and interpretation of genome scans using GSCANDB. Bioinformatics 23:1545-1549 +[*Full Text PDF Version*](http://bioinformatics.oxfordjournals.org/cgi/reprint/23/12/1545), +[*Full Text HTML Version*](http://bioinformatics.oxfordjournals.org/cgi/content/full/23/12/1545) + + +40. Vazquez-Chona F, Lu L, Williams RW, Geisert EE (2007) Genetic influences on retinal gene expression and wound healing. Gene Regulation and Systems Biology 1:327-348 +[*Full Text PDF Version*](/images/upload/Vazquez2007.pdf) + +41. von Rohr P, Friberg M, Kadarmideen HN ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17688316)) Prediction of transcription factor binding sites using results from genetical genomics investigations. Journal of Bioinformatics and Computational Biology 5:773-793 +[*Full Text PDF Version*](/images/upload/vonRohr_etal_2007.pdf) + + +42. Wan X, Pavlidis P ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17917127)) Sharing and reusing gene expression profiling data in neuroscience. Neuroinformatics 5:161-75. +[*HTML example of using GEMMA and GeneNetwork*](http://www.bioinformatics.ubc.ca/pavlidis/lab/reuse/walkthrough.pdf) + +43. Zou W, Aylor DL, Zeng ZB ([2007](http://www.biomedcentral.com/1471-2105/8/7)) eQTL Viewer: visualizing how sequence variation affects genome-wide transcription. BMC Bioinformatics 8:7. +[*Full Text PDF Version*]("http://www.biomedcentral.com/content/pdf/1471-2105-8-7.pdf), +[*Full Text HTML Version*](http://www.biomedcentral.com/1471-2105/8/7) + + + +<div id="2006"> </div> + +> ### GeneNetwork (2006) + +1. Aliesky HA, Pichurin PN, Chen CR, Williams RW, Rapoport B, McLachlan SM ([2006](http://www.ncbi.nlm.nih.gov/pubmed/16543368)) Probing the genetic basis for thyrotropin receptor antibodies and hyperthyroidism in immunized CXB recombinant inbred mice. Endocrinology 147:2789-800. +[*Full Text PDF Version*](http://endo.endojournals.org/cgi/reprint/147/6/2789.pdf), +[*Full Text HTML Version*](http://endo.endojournals.org/cgi/content/full/147/6/2789). + +2. Bao L, Wei L, Peirce JL, Homayouni R, Li H, Zhou M, Chen H, Lu L, Williams RW, Pfeffer LM, Goldowitz D, Cui Y ([2006](http://www.ncbi.nlm.nih.gov/pubmed/16783639)) Combining gene expression QTL mapping and phenotypic spectrum analysis to uncover gene regulatory relationships. Mammalian Genome 17:575-583 +[*Full Text PDF Version*](http://www.springerlink.com/content/v32720xj70343812/fulltext.pdf), +[*Full Text HTML Version*](http://www.springerlink.com/content/v32720xj70343812/fulltext.html). + +3. Beatty J, Laughlin RE ([2006](http://www.biomedcentral.com/1471-2202/7/16)) Genomic regulation of natural variation in cortical and noncortical brain volume. BMC Neuroscience 7:16 [This mapping study made use of both the <a HREF="www.mbl.org" target="_blank" >Mouse Brain Libray</a> online collection of sections of BXD brains and GeneNetwork/WebQTL.] + +4. Bennett B, Carosone-Link P, Zahniser NR, Johnson TE ([2006](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16803863&query_hl=2&itool=pubmed_docsum)) Confirmation and fine mapping of ethanol sensitivity quantitative trait loci, and candidate gene testing in the LXS recombinant inbred mice. J Pharmacol Exp Ther 319:299-307 (doi: 10.1038/ng1938) +[*Full Text PDF Version*](http://jpet.aspetjournals.org/cgi/reprint/319/1/299.pdf) + +5. Bennett B, Downing C, Parker C, Johnson TE ([2006](http://www.ncbi.nlm.nih.gov/pubmed/16730093)) Mouse genetic models in alcohol research. Trends Genet 22:367-74 + +6. Cervino ACL, Darvasi A, Fallahi M, Mader CC, Tsinoremas NF (2006) An integrated in silico gene mapping strategy in inbred mice ([2006](http://www.genetics.org/cgi/content/full/175/1/321)) Genetics 175:321-333 + +7. Chesler EJ, Langston MA ([2006](http://www.springerlink.com/content/ut638ph1845x1768/)) Combinatorial genetic regulatory network analysis tools for high throughput transcriptomic data. In: Lecture Notes in Computer Science. Springer, Heidelberg, Vol. 4023: 150-165. + +8. De Haro L, Panda S([2006](http://www.ncbi.nlm.nih.gov/pubmed/17107940)) Systems biology of circadian rhythms: an outlook. Journal of Biological Rhythms 21:507 +[*Full Text PDF Version*](http://jbr.sagepub.com/cgi/reprint/21/6/507.pdf) + +9. Jones LC, McCarthy KA, Beard JL, Keen CL, Jones BC ([2006](http://www.ncbi.nlm.nih.gov/pubmed/16910173)) Quantitative genetic analysis of brain copper and zinc in BXD recombinant inbred mice. Nutritional Neuroscience 9:81-92 [This paper includes a large data set consisting of 16 traits related to copper and zinc metabolism in the CNS that is part of the Mouse BXD Phenotype database in GeneNetwork. The entire data set can be found by entering the search term "Jones LC" in the ALL search field.] + +10. Kadarmideen HN, Janss LLG ([2006](http://www.ncbi.nlm.nih.gov//pubmed/17132818)) Population and systems genetics analyses of cortisol in pigs divergently selected for stress. Physiological Genomics 29:57-65 [*Full Text PDF Version*](http://physiolgenomics.physiology.org/cgi/reprint/29/1/57?ck=nck), [*Full Text HTML Version*](http://physiolgenomics.physiology.org/cgi/content/full/29/1/57?ck=nck). [One of several great papers in a freely available (open) Special Issue of Mammalian Genome devoted to QTLs, Expression and Complex Trait Analysis. This study makes great use of the BXD INIA Brain mRNA M430 PDNN data set and GeneNetwork/WebQTL.] + +11. Kadarmideen HN, von Rohr, P, Janss LLG ([2006](http://www.ncbi.nlm.nih.gov//pubmed/16783637)) From genetical genomics to systems genetics: potential applications in quantitative genomics and animal breeding. Mammalian Genome 17:548-564 [*Full Text PDF Version*](http://www.springerlink.com/media/788y661n1l5tvhac6eet/contributions/4/4/2/5/4425640024004428.pdf), [*Full Text HTML Version*](http://www.springerlink.com/media/12d237nvvh7krwan8q9x/contributions/4/4/2/5/4425640024004428_html/fulltext.html) .[One of several great papers in a freely available (open) Special Issue of Mammalian Genome devoted to QTLs, Expression and Complex Trait Analysis. This study makes great use of the BXD INIA Brain mRNA M430 PDNN data set and GeneNetwork/WebQTL.] + +12. Kamminga LM, Bystrykh LV, de Boer A, Houwer S, Douma J, Weersing E, Dontje B, de Haan G ([2006](http://www.ncbi.nlm.nih.gov//pubmed/16293602)) The Polycomb group gene Ezh2 prevents hematopoietic stem cell exhaustion. Blood 107:2170-2179 +[*Full Text PDF Version*](http://bloodjournal.hematologylibrary.org/cgi/reprint/2005-09-3585v1.pdf) + +13. Keeley MB, Wood MA, Isiegas C, Stein J, Hellman K, Hannenhalli S, Abel T ([2006](http://www.learnmem.org/cgi/reprint/13/2/135.pdf?ck=nck)) Differential transcriptional response to nonassociative and associative components of classical fear conditioning in the amygdala and hippocampus. Learning and Memory 13:135-142103:780-785. + +14. Kempermann G, Chesler EJ, Lu L, Williams RW, Gage FH (<a href="http://www.pnas.org/cgi/content/full/103/3/780" target="_blank">2006</a>) Natural variation and genetic covariance in adult hippocampal neurogenesis. Proceedings of the National Academy of Science 103:780-785. + +15. Korostynski M, Kaminska-Chowaniec D, Piechota M, Przewlocki R ([2006](http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1553451)) Gene expression profiling in the striatum of inbred mouse strains with distinct opioid-related phenotypes. BMC Genomics 7: 146 (doi: 10.1186/1471-2164-7-146). [*Full Text HTML Version*](http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1553451). [A combination of data sources including the Rosen HBP Striatum data set used to study opioid-related traits. Their [Fig 3C](http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1553451&rendertype=figure&id=F3) and [Fig 5](http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1553451&rendertype=figure&id=F5) take good advantage of GeneNetwork and WebQTL output graphs.] + +16. Lan H, Chen M, Flowers JB, Yandell BS, Stapleton DS, Mata CM, Mui ET, Flowers MT, Schueler KL, Manly KF, Williams RW, Kendziorski C, Attie A ([2006](http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pgen.0020006)) Combined expression trait correlations and expression quantitative trait locus mapping. PLoS Genetics 2:e6 [Please cite this work if you make use of the B6BTBRF2 liver transcriptome data.] + +17. Liu Y, Li J, Sam L, Goh CS, Gerstein M, Lussier YA ([2006](http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0020159)) An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits. PLoS Computional Biology 2:e159 + +18. Loney KD, Uddin RK, Singh SM ([2006]("http://www.ncbi.nlm.nih.gov/pubmed/16433728)) Analysis of metallothionein brain gene expression in relation to ethanol preference in mice using cosegregation and gene knockouts. Alcohol Clin Exp Res 30:15-25 + +19. Martin MV, Dong H, Vallera D, Lee D, Lu L, Williams RW, Rosen GD, Cheverud JM, Csernansky JG ([2006](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17081266&query_hl=1&itool=pubmed_docsum)) Independent quantitative trait loci influence ventral and dorsal hippocampal volume in recombinant inbred strains of mice. Gene, Brain and Behavior 5:614-623. + +20. van Os R, Ausema A, Noach EJ, van Pelt K, Dontje BJ, Vellenga E, de Haan G ([2006](http://www.ncbi.nlm.nih.gov/pubmed/16371023)) Identification of quantitative trait loci regulating haematopoietic parameters in B6AKRF2 mice. British Journal of Haematolology 132:80-90. + +21. Peirce JL, Li H, Wang J, Manly KF, Hitzemann RJ, Belknap JK, Rosen GD, Goodwin S, Sutter TR, Williams RW, Lu L [2006](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=Abstract&list_uids=16783644&query_hl=1&itool=pubmed_docsum)) How replicable are mRNA expression QTL? Mammalian Genome 17:643-656. [*Full Text PDF Version*](http://www.springerlink.com/content/a23g75163p624324/fulltext.pdf), [*Full Text HTML Version*](http://www.springerlink.com/content/a23g75163p624324/fulltext.html). [An important paper in which four matched expression data sets (whole brain and striatum) generated using both recombinant inbred and F2 intercrosses were directly compared.] + +22. Ponomarev I, Maiya R, Harnett MT, Schafer GL, Ryabinin AE, Blednov YA, Morikawa H, Boehm SL 2nd, Homanics GE, Berman AE, Lodowski KH, Bergeson SE, Harris RA [2006](http://www.ncbi.nlm.nih.gov/pubmed/16783644) Transcriptional signatures of cellular plasticity in mice lacking the alpha1 subunit of GABAA receptors. J Neurosci 26:5673-83 +[*Full Text PDF Version*](tp://www.jneurosci.org/cgi/reprint/26/21/5673.pdf), +[*Full Text HTML Version*](http://www.jneurosci.org/cgi/content/full/26/21/5673) + +23. Radcliffe RA, Lee MJ, Williams RW ([2006](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=Abstract&list_uids=16783639&query_hl=1&itool=pubmed_docsum)) Prediction of cis-QTLs in a pair of inbred mouse strains with the use of expression and haplotype data from public databases. Mammalian Genome 17:629-642 [*Full Text PDF Version*](http://www.springerlink.com/content/3u641hgk642221r6/fulltext.pdf), [*Full Text HTML Version*](http://www.springerlink.com/content/3u641hgk642221r6/fulltext.html) + + +24. Rulten SL, Ripley TL, Hunt CL, Stephens DN, Mayne LV ([2006](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16594979&query_hl=2&itool=pubmed_docsum)) Sp1 and NFkappaB pathways are regulated in brain in response to acute and chronic ethanol. Genes Brain Behav 5:257-273 [This study exploited the original GeneNetwork Affymetrix U74Av2 brain data set to validate a set of transcripts modulated by ethanol treatment.] + +25. Saba L, Bhave SV, Grahame N, Bice P, Lapadat R, Belknap J, Hoffman PL, Tabakoff B ([2006](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16783646&query_hl=8&itool=pubmed_docsum)) Candidate genes and their regulatory elements: alcohol preference and tolerance. Mammalian Genome 17:669-688 [*Full Text PDF Version*](http://www.springerlink.com/content/224237686jx80v61/fulltext.pdf), [*Full Text HTML Version*](http://www.springerlink.com/content/224237686jx80v61/fulltext.html) [A lovely paper describing results of a whole brain BXD study involving males from 30 strains (four individual arrays (not pooled) per strain). The data described in this study have been made accessible from GeneNetwork.] + +26. Shifman S, Bell JT, Copley BR, Taylor M, Williams RW, Mott R, Flint J ([2006](http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040395)) A high resolution single nucleotide polymorphism genetic map of the mouse genome. PLoS Biology 4:2227-2237 [*Full Text PDF Version*](http://biology.plosjournals.org/archive/1545-7885/4/12/pdf/10.1371_journal.pbio.0040395-L.pdf) [A comprehensive analysis of recombination rates using several populations of mice, including most major genetic reference populations.] + +27. van Os R, Ausema A, Noach EJ, van Pelt K, Dontje BJ, Vellenga E, de Haan G ([2006](http://www.blackwell-synergy.com/doi/abs/10.1111/j.1365-2141.2005.05835.x)) Identification of quantitative trait loci regulating haematopoietic parameters in B6AKRF2 mice. British Journal of Haematology 132:80-90 + +28. Veenstra-VanderWeele J, Qaadir A, Palmer AA, Cook EH Jr, de Wit H. ([2006](http://www.ncbi.nlm.nih.gov/pubmed/16237383)) Association between the casein kinase 1 epsilon gene region and subjective response to D-amphetamine. Neuropsychopharmacology 31:1056-1063 [*Full Text HTML Version*](http://www.nature.com/npp/journal/v31/n5/full/1300936a.html) [This mapping study made use of GeneNetwork/WebQTL to show that "the region that contains Csnk1e was also found to contain a QTL for MA sensitivity, and complementary data from WebQTL (Chesler et al, 2005) showed that this same region of mouse chromosome 15 influenced Csnk1e transcript abundance, indicating the presence of a cis-acting eQTL."] + +29. Voy BH, Scharff JA, Perkins AD, Saxton AM, Borate B, Chesler EJ, Branstetter LK, Langston MA ([2006](http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16854212)) Extracting gene networks for low-dose radiation using graph theoretical algorithms. PLoS Computational Biology 2:e89. [A paper that introduces the use of cliques in analyzing microarray data sets. One of the GeneNetwork databases (BXD Hematopoietic Stem Cells) was used to follow up on a strong candidate gene, Tubby-like protein 4 *Tulp4*) that may have a role in immune function. + +30. Williams RH, Cotsapas CJ, Cowley MJ, Chan E, Nott DJ, Little PF ([2006](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=Abstract&list_uids=16874319&query_hl=3&itool=pubmed_docsum)) Normalization procedures and detection of linkage signal in genetical-genomics experiments. Nature Genetics 38:855-856. [A set of letters to the editor by Rohan Williams and colleagues, Chesler and colleagues, and Petretto and colleagues. All three letters highlight some of the technical challenges of analyzing expression data in a genetic context and point to the need for great care and attention to normalization methods. Well worth reviewing. Normalization is still very much an art, and it is quite likely that no one normalization procedure will be optimal for all different research questions. The old adage: "different horses for different courses" is likley to apply.] + +31. Williams RW ([2006]("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=Abstract&list_uids=16783631&query_hl=1&itool=pubmed_docsum)) Expression genetics and the phenotype revolution. Mammalian Genome 17:496-502 [*Full Text PDF Version*](http://www.springerlink.com/content/921734n56j08400n/fulltext.pdf),[*Full Text HTML Version*](http://www.springerlink.com/content/921734n56j08400n/fulltext.html). [My take on where systems genetics may take us in the next few years.] + +<div id="2005"> </div> + +> ### GeneNetwork (2005) + + + +1. Alberts R, Terpstra P, Bystrykh LV, de Haan G, Jansen RC ([2005]("http://www.ncbi.nlm.nih.gov/pubmed&dopt=Abstract&list_uids=15711547&query_hl=10)) A statistical multiprobe model for analyzing cis and trans genes in genetical genomics experiments with short-oligonucleotide arrays Genetics 171:1437-1439 +2. Alberts R, Fu J, Swertz MA, Lubbers LA, Albers CJ, Jansen RC ([2005](http://www.ncbi.nlm.nih.gov/pubmed/15975223)) Combining microarrays and genetic analysis. Brief Bioinform. 6:135-145 +[*Full text PDF version*](http://bib.oxfordjournals.org/cgi/reprint/6/2/135.pdf) + +3. Bystrykh L, Weersing E, Dontje B, Sutton S, Pletcher MT, Wiltshire T, Su AI, Vellenga E, Wang J, Manly KF, Lu L, Chesler EJ, Alberts R, Jansen RC, Williams RW, Cooke M, de Haan G ([2005](http://www.ncbi.nlm.nih.gov/pubmed/15711547) Uncovering regulatory pathways affecting hematopoietic stem cell function using “genetical genomics." Nature Genetics, 37:225-232 + +4. Chesler EJ, Lu L, Shou S, Qu Y, Gu J, Wang J, Hsu HC, Mountz JD, Baldwin N, Langston MA, Threadgill DW, Manly KF, Williams RW ([2005](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15711545&query_hl=10)) Genetic dissection of gene expression reveals polygenic and pleiotropic networks modulating brain structure and function. Nature Genetics 37: 233-242 + + +5. Flaherty L, Herron B, Symula D ([2005](http://www.genome.org/cgi/content/abstract/15/12/1741)) Genome Research 15:1741-1745 [*Full text PDF version*](http://www.genome.org/cgi/reprint/15/12/1741.pdf) + +6. Garlow SJ, Boone E, Li W, Owens MJ, Nemeroff CB ([2005](http://endo.endojournals.org/cgi/content/abstract/146/5/2362)) Genetic analysis of hypothalamic corticotropin-releasing factor system. Endocrinology 146: 2362-2368 + +7. Gammie SC, Hasen NS, Awad TA, Auger AP, Jessen HM, Panksepp JB, Bronikowski AM ([2005](http://www.eeob.iastate.edu/faculty/BronikoA/annespdfs/MBres.pdf)) Gene array profiling of large hypothalamic CNS regions in lactating and randomly cycling virgin mice. Molecular Brain Research 139: 201-211 + +8. Kerns RT, Ravindranathan A, Hassan S, Cage MP, York T, Williams RW, Miles MF ([2005](http://www.jneurosci.org/cgi/content/full/25/9/2255)) Ethanol-responsive brain region expression networks: implications for behavioral responses to acute ethanol in DBA/2J versus C57BL/6J mice. Journal of Neuroscience 25: 2255-2266 [[www.brainchip.vcu.edu/kerns_apptable1.pdf](http://www.brainchip.vcu.edu/kerns_apptable1.pdf) for a complete table of modulated transcripts.] + +9. Li HQ, Lu L, Manly KF, Wang J, Zhou M, Williams RW, Cui Y ([2005](http://hmg.oupjournals.org/cgi/content/abstract/ddi124v1)) Inferring gene transcriptional modulatory relations: a genetical genomics approach. Human Molecular Genetics 14: 1119-1125 + +10. Li J, Burmeister M ([2005](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16244315&query_hl=5&itool=pubmed_docsum)) Genetical genomics: combining genetics with gene expression analysis. Human Molecular Genetics 14:163-169. + [[*Full text PDF version*](/images/upload/Li_Burmeister_2005.pdf)] + + +11. Lozier JN, Tayebi N, Zhang P ([2005](http://www.bloodjournal.org/cgi/content/abstract/)) Mapping of genes that control the antibody response to human factor IX in mice. Blood 105: 1029-1035 + +12. MacLaren EJ, Sikela JM ([2005](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16205357&query_hl=3&itool=pubmed_docsum)) Cerebellar gene expression profiling and eQTL analysis in inbred mouse strains selected for ethanol sensitivity. Alcoholism: Clinical and Experimental Research 29: 1568-1579. +[*HTML*](http://www.alcoholism-cer.com/pt/re/alcoholism/abstract.00000374-200509000-00002.htm;jsessionid=HBGNJpQldfCKvpYr6XLCzW3fF4YT1mzCVTXGcCMNYCL6N4WlDLlK!901085598!181195628!8091!-1) and +[*PDF* reprints.](http://www.alcoholism-cer.com/pt/re/alcoholism/pdfhandler.00000374-200509000-00002.pdf;jsessionid=HBGNJpQldfCKvpYr6XLCzW3fF4YT1mzCVTXGcCMNYCL6N4WlDLlK!901085598!181195628!8091!-1) + +13. Matthews B, Bhave SV, Belknap JK, Brittingham C, Chesler EJ, Hitzemann RJ, Hoffman PL, Lu L, McWeeney S, Miles MR, Tabakoff B, Williams RW ([2005](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16205371&query_hl=1&itool=pubmed_docsum)) Complex genetics of interactions of alcohol and CNS function and behavior. Alcoholism: Clinical and Experimental Research 29:1706-1719 + +14. Mountz JD, Yang P, Wu Q, Zhou J, Tousson A, Fitzgerald A, Allen J, Wang X, Cartner S, Grizzle WE, Yi N, Lu L, Williams RW, Hsu HC ([2005]("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15683449&query_hl=4)) Genetic segregation of spontaneous erosive arthritis and generalized autoimmune disease in BXD2 recombinant inbred strain of mice. Scadinavian Journal of Immunology 61:1-11 +[*Full Text PDF Version*](/images/upload/Mountz2005.pdf) + +15. Li CX, Wei X, Lu L, Peirce JL, Wiliams RW, Waters RS ([2005]("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16338823&query_hl=12&itool=pubmed_docsum)) Genetic analysis of barrel field size in the first somatosensory area (S1) in inbred and recombinant inbred strains of mice. Somatosensory and Motor Research 22:141-150 + +16. Palmer AA, Verbitsky M, Suresh R, Kamen HM, Reed CI, Li N, Burkhart-Kasch S, McKinnon CS, Belknap JK, Gilliam TC, Phillips TJ ([2005](http://www.ncbi.nlm.nih.gov/pubmed/16104378)) Gene expression differences in mice divergently selected for methamphetamine sensitivity. Mammalian Genome 16:291-305 + +17. Pravenec M, Kren V ([2005](ttp://www.ncbi.nlm.nih.gov/pubmed/15728137)) Genetic analysis of complex cardiovascular traits in the spontaneously hypertensive rat. Exp Physiol 90:273-276 +[*Full Text PDF Version*](http://ep.physoc.org/cgi/reprint/90/3/273.pdf), +[*Full Text HTML Version*](http://ep.physoc.org/cgi/content/full/90/3/273) + +18. Scott RE, White-Grindley E, Ruley HE, Chesler EJ, Williams RW ([2005]("http://www3.interscience.wiley.com/cgi-bin/fulltext/109860478/HTMLSTART)) P2P-R expression is genetically coregulated with components of the translation machinery and with PUM2, a translational repressor that associates with the P2P-R mRNA. Journal of Cellular Physiology 204:99-105 [ *Full text HTML version*](http://www3.interscience.wiley.com/cgi-bin/fulltext/109860478/HTMLSTART) + +19. Vazquez-Chona FR, Khan AN, Chan CK, Moore AN, Dash PK, Rosario Hernandez R, Lu L, Chesler EJ, Manly KF, Williams RW, Geisert Jr EE ([2005](http://www.molvis.org/molvis/v11/a115/)) Genetic networks controlling retinal injury. Molecular Vision 11:958-970 + +20. Yang H, Crawford N, Lukes L, Finney R, Lancaster M, Hunter KW ([2005](http://www.ncbi.nlm.nih.gov/pubmed/15728137)) Metastasis predictive signature profiles pre-exist in normal tissues. Clin Exp Metastasis 22:593-603 +[*Full Text HTML Version*]("http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16475030) + + + +<div id="2004"> </div> + +> ### GeneNetwork (2004) + +1. Baldwin NE, Chesler EJ, Kirov S, Langston MA, Snoddy JR, Williams RW, Zhang B (2004) Computational, integrative and comparative methods for the elucidation of genetic co-expression networks. Journal of Biomedicine and Biotechnology 2:172-180 +[*HTML*](ttp://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=16046823) and [*PDF* reprints.](http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1184052&blobtype=pdf) + + +2. Carlborg O, De Koning DJ, Chesler EJ, Manly KM, Williams RW, Haley CS ([2004](http://bioinformatics.oupjournals.org/cgi/content/abstract/bti241v1)) Methological aspects of the genetic dissection of gene expression. Bioinformatics 10:1093 + +3. Chesler EJ, Williams RW ([2004](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15474587&query_hl=10)) Brain gene expression: genomics and genetics. International Review of Neurobiology 60:59-95 + +4. Fernandes K, Paya-Cano JL, Sluyter F, D'Souza U, Plomin R, Schalkwyk LC ([2004](http://www.blackwell-synergy.com/links/doi)) Hippocampal gene expression profiling across eight mouse inbred strains: towards understanding the molecular basis for behaviour. European Journal of Neuroscience 19:2576-2582 +[*Full Text HTML Version*](http://www.bloodjournal.org/cgi/content/full/104/2/374) + +5. Henckaerts E, Langer JC, Hans-Willem Snoeck HW (2004) Quantitative genetic variation in the hematopoietic stem cell and progenitor cell compartment and in lifespan are closely linked at multiple loci in BXD recombinant inbred mice. Blood 104:374-379 [*Full Text HTML Version*](http://www.bloodjournal.org/cgi/content/full/104/2/374) + + +6. Hitzemann R, Reed C, Malmanger B, Lawler M, Hitzemann B, Cunningham B, McWeeney S, Belknap J, Harrington C, Buck K, Phillips T, Crabbe J ([2004](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15597075)) On the integration of alcohol-related quantitative trait loci and gene expression analyses. Alcoholism: Clinical and Experimental Research 28:1437-1448 [Please cite this paper is you plan to use the B6D2F2 OHSU data set.] + +7. Maiya RP ([2004](http://64.233.179.104/search?q=cache:3ajOyi3RpywJ:www.lib.utexas.edu/etd/d/2004/maiyar34683/maiyar34683.pdf+webqtl&hl=en)) Regulation of dopamine transporter: a role for ethanol and protein interactions. Dissertation, University of Texas, Austin + +8. Orth AP, Batalow S, Perrone M, Chanda SK ([2004](http://www.ashley-pub.com/doi/abs/10.1517/14728222.8.6.587)) The promise of genomics to identify novel therapeutic targets. Expert Opion of Therapeutic Targets 8:587-596 + +9. Pomp D, Allan MF, Wesolowski SR ([2004](http://www.animal-science.org/cgi/content/full/82/13_suppl/E300)) Quantitative genomics: Exploring the genetic architecture of complex trait predisposition. J Anim Sci 82:E300-E312 +[*Full Text HTML Version*](http://jas.fass.org/cgi/reprint/82/13_suppl/E300.pdf) + + + +10. Ponomarev I, Schafer GL, Blednov YA, Williams RW, Iver VR, Harris A ([2004](http://www.ncbi.nlm.nih.gov/pubmed/15544578)) Convergent analysis of cDNA and short oligomer microarrays, mouse null mutant, and bioinformatics resources to study complex traits. Genes, Brain and Behavior 3:360-368 + + +11. Simon P, Schott K, Williams RW, Schaeffel F ([2004](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15610169)) Post-translational regulation of the immediate early gene EGR1 by light in the mouse retina. European Journal of Neuroscience 20:3371-3377 + + +12. Zareparsi S, Hero A, Zack DJ, Williams RW, Swaroop A ([2004](http://www.iovs.org/cgi/content/full/45/8/2457)) Seeing the unseen: microarray-based gene expression profiling in vision. Investigative Ophthalmology and Visual Science 45:2457-2462 [*Full text HTML version*](http://www.iovs.org/cgi/content/full/45/8/2457) + + +<div id="2003"> </div> + +> ### GeneNetwork (2003) + + +1. Bolivar V, Flaherty L (2003) A region on chromosome 15 controls intersession habituation in mice. Journal of Neuroscience 23: 9435-9438 [*Full Text HTML and PDF Versions*](http://www.jneurosci.org/cgi/content/full/23/28/9435) + + +2. Jones BC, Reed CL, Hitzemann R, Wiesinger JA, McCarthy KA, Buwen JP, Beard JL [2003](http://www.ncbi.nlm.nih.gov/pubmed/14744041)) Quantitative genetic analysis of ventral midbrain and liver iron in BXD recombinant inbred mice. Nutr Neuroscience 6:369-77 +<a href="images/upload/Jones_2003_NN1203.pdf" target="_blank" >*Full Text PDF Version*</a> + +3. Hitzemann R, Hitzemann B, Rivera S, Gatley J, Thanos P, Shou S, Lu L, Williams RW ([2003](http://www.ncbi.nlm.nih.gov/pubmed/12543998)) Dopamine D2 receptor binding, Drd2 expression and the number of dopamine neurons in the BXD recombinant inbred series: genetic relationships to alcohol and other drug associated phenotypes. Alcoholism: Clinical and Experimental Research 27:1-11 + + +4. Hitzemann R, Malmanger B, Reed C, Lawler M, Hitzemann B, Coulombe S, Buck K, Rademacher B, Walter N, Polyakov Y, Sikela J, Williams RW, Flint J, Talbot C ([2003]("http://www.ncbi.nlm.nih.gov/pubmed/14722723)) A strategy for integration of QTL, gene expression, and sequence analyses. Mammalian Genome 14:733-747 + +5. Lionikas A, Blizard DA, Vandenbergh DJ, Glover MG, Stout JT, Vogler GP, McClearn GE, Larsson L ([2003](http://physiolgenomics.physiology.org/cgi/content/full/16/1/141)) Genetic architecture of fast- and slow-twitch skeletal muscle weight in 200-day-old mice of the C57BL/6J and DBA/2J lineage. Physiological Genomics 16:141-152 + +6. Peirce J, Chesler EJ, Williams RW, Lu L (2003) Genetic architecture of the mouse hippocampus: identification of gene loci with regional effects. Genes, Brain and Behavior 2:238–252 +[*Full Text PDF Version*](images/upload/Peirce_Lu_2003.pdf) +7. Rosen GD, La Porte NT, Diechtiareff B, Pung, CJ, Nissanov J, Gustafson C, Bertrand L, Gefen S, Fan Y, Tretiak OJ, Manly KF, Parks MR, Williams AG, Connolly MT, Capra JA, Williams RW (2003) Informatics center for mouse genomics: the dissection of complex traits of the nervous system. Neuroinformatics 1:327–342 +<a href="images/upload/Rosen_2003.pdf" target="_blank" >*Full Text PDF Version*</a> + +<div id="Background"> </div> + + + +> ### Background references on inbred strains and other key resources + + +> Williams RW, Gu J, Qi S, Lu L ([2001](https://ncbi.nlm.nih.gov/pubmed/11737945)) The genetic structure of recombinant inbred mice: high-resolution consensus maps for complex trait analysis. Genome Biology 2:46.1–46.18 [*Full Text HTML and PDF Version*](http://genomebiology.com/content/2/11/RESEARCH0046) . [General background on recombinant inbred strains.] + +> Williams RW, Bennett B, Lu L, Gu J, DeFries JC, Carosone-Link PJ, Rikke BA, Belknap JK, Johnson TE ([2004](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15457343)) Genetic structure of the LXS panel of recombinant inbred mouse strains: a powerful resource for complex trait analysis. Mammalian Genome 15:637-647 [Background on origins and the genetic structure large panel of LXS strains. Please cite this paper is you have used LXS data sets.] + +> Grubb SC, Churchill GA, Bogue MA ([2004](http://www.ncbi.nlm.nih.gov/pubmed/15130929)) A collaborative database of inbred mouse strain characteristics. Bioinformatics 20:2857-2859 [One of two key papers on the Mouse Phenome Project and database at The Jackson Laboratory. The mouse diversity panel (MDP) is a superset of strains that are part of the Phenome Project. [*Full Text PDF Version*](http://bioinformatics.oxfordjournals.org/cgi/reprint/20/16/2857)] + +> Bogue MA, Grubb SC ([2004](http://www.ncbi.nlm.nih.gov/pubmed/15619963)) The mouse phenome project. Genetica 122:71-74 [One of two key papers on the Mouse Phenome Project and database at The Jackson Laboratory. The mouse diversity panel (MDP) is a superset of strains that are part of the Phenome Project. Please contact Dr. Molly Bogue for information on the Phenome Project: mollyb@jax.org] + + +> Frazer KA, Eskin E, Kang HM, Bogue MA, Hinds DA, Beilharz EJ, Gupta RV, Montgomery J, Morenzoni MM, Nilsen GB, Pethiyagoda CL, Stuve LL, Johnson FM, Daly MJ, Wade CM, Cox DR ([2007](http://www.ncbi.nlm.nih.gov/pubmed/17660834)) A sequence-based variation map of 8.27 million SNPs in inbred mouse strains. Nature 448, 1050-3 + +> Loudet O, Chaillou S, Camilleri C, Bouchez D, Daniel-Vedele F ([2002](http://www.inra.fr/qtlat/BayxSha/Loudet2002.pdf)) Bay-0 x Shahdara recombinant inbred line population: a powerful tool for the genetic dissection of complex traits in Arabidopsis. Theoretical and Applied Genetics 104:1173-1184 [*Full Text PDF Version*](http://www.inra.fr/qtlat/BayxSha/Loudet2002.pdf). [Please cite this paper is you have used the BXS Arabidopsis data sets.] + + +> Jirout M, Krenova D, Kren V, Breen L, Pravenec M, Schork NJ, Printz MP ([2003](http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12925886&query_hl=3)) A new framework marker-based linkage map and SDPs for the rat HXB/BXH strain set. expression differences in mice diverently selected for methamphetamine sensitivity. Mammalian Genome 14: 537-546 + + +> Shifman S, Bell JT, Copley BR, Taylor M, Williams RW, Mott R, Flint J ([2006](http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0040395)) A high resolution single nucleotide polymorphism genetic map of the mouse genome. PLoS Biology 4:2227-2237 [*Full Text PDF Version*](http://biology.plosjournals.org/archive/1545-7885/4/12/pdf/10.1371_journal.pbio.0040395-L.pdf). [A comprehensive analysis of recombination rates using several populations of mice, including most major GRPs.] + + +> ### Information about this page: +> This text originally generated by RWW, April 2003. Updated by RWW, Oct 15, Dec 17, 2004; RWW Jan 19, 2005; EJC Mar 9; RWW Mar 29, Apr 15; RWW Jan 7, 2006, Jan 21, July 26, Aug 26, 2006s; May 2007; Feb 2008; March 19 2008 |