References

 Papers and References to GeneNetwork

Highlighted References | Key References | Background References |

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  3. 2020 hits on 2019/05/13)
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  1. 1030 hits on 2019/05/13
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Highlighted References
Please send us citations to articles that we may have missed.
  1. Mulligan MK, Mozhui K, Prins P, Williams RW (2017) 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.] PDF version

  2. Williams RW, Williams EG (2017) 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.] PDF version

  3. Williams RW (2009) 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.] PDF version

  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) An atlas of gene expression and gene co-regulation in the human retina.Nucleic Acids Res. 2016 Jul 8;44(12):5773-84 RETINA database, and see the PDF. These data are now in GeneNetwork (Species = Human, Group = Retina).

  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) Systems proteomics and trans-omic integration illuminate new mechanisms in mitochondrial function. Science 352(6291):aad0189 HTML version, PDF

  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) HTML version

  7. Alam G, Miller DB, O'Callaghan JP, Lu L, Williams RW, Jones BC (2016) MPTP neurotoxicity is highly concordant between the sexes among BXD recombinant inbred mouse strains. Neurotoxicology in press PDF version

  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) 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). 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.] PDF version and the Supplementary Tables in one Excel file

  10. Xue Y, Li J, Yan L, Lu L, Liao FF (2015) 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) 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) 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) Cell cycle gene expression networks discovered using systems biology: Significance in carcinogenesis. J Cell Physiol 230:2533-42

  14. Williams EG, Auwerx J (2015) 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) 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) 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) Mitonuclear protein imbalance as a conserved longevity mechanism. Nature 497:451-457 PDF version

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) 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.] PDF version
  2. Williams RW, Mulligan MK (2012) Genetic and molecular network analysis of behavior. Int Rev Neurobiol. 104:135-57. [Explains the use of GeneNetwork in behavioral neurogenetics] PDF version
  3. Williams EG, Auwerx J (2015) 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.] PDF version
  4. Wang J, Williams RW, Manly KF (2003) WebQTL: Web-based complex trait analysis. Neuroinformatics 1: 299-308 Full Text PDF Version. [A good technical reference to WebQTL and GeneNetwork]
  5. Williams RW, Gu J, Qi S, Lu L (2003) The genetic structure of recombinant inbred mice: high-resolution consensus maps for complex trait analysis. Genome Biology 2(11)Full Text Version. [A detailed analysis of the genetics of recombinant inbred strains]
  6. Chesler EJ, Wang J, Lu L, Qu Y, Manly KF, Williams RW (2003) 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. [Best reference regarding interpretation of genetic correlations.]
  7. Chesler EJ, Lu L, Wang J, Williams RW, Manly KF (2004) WebQTL: rapid exploratory analysis of gene expression and genetic networks for brain and behavior. Nature Neuroscience 7: 485-486. Full Text PDF Version [A short review]
  8. Chesler EJ, Williams RW (2004) 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]
  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) 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) 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) Quantitative trait loci underlying gene product variation: a novel perspective for analyzing regulation of genome expression. Genetics 137: 289-301 Full Text PDF Version [The first published paper on system genetics. Impressive; before its time.]
    [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.
  12. Grisham W, Schottler NA, Valli-Marill J, Beck L, Beatty J (2010) Teaching bioinformatics and neuroinformatics by using free web-based tools. CBE--Life Sciences Education 9: 98-107 Full Text PDF Version
    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.
    Youtube videos of Dr. William Grisham teaching neurogenetics at UCLA:
    Part 1
    Part 2
    Part 3
    Part 4
    Part 5


  13. Grisham W (2009) 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
    An excellent example of how resources such as GeneNetwork and the Mouse Brain Library can be used in class room labs.
  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) 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. [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) 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) 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. [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 CTC abstract]
  19. Taylor BA, Heiniger HJ, Meier H (1973) 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
  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) 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) 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) 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.]
GeneNetwork (2019) (not complete)
  1. Théberge ET, Baker JA, Dubose C, Boyle JK, Balce K, Goldowitz D, Hamre KM (2019) 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) Evaluation of Sirtuin-3 probe quality and co-expressed genes using literature cohesion. BMC Bioinformatics 20(Suppl 2):104
GeneNetwork (2018) (not complete)
  1. Ashbrook DG, Mulligan MK, Williams RW Post-genomic behavioral genetics: From revolution to routine (2018) 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) 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) 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) 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) 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) Genomic loci modulating retinal ganglion cell death following elevated IOP in the mouse. Exp Eye Res 169:61-67
GeneNetwork (2017) (not complete)
  1. Baker JA, Li J, Zhou D, Yang M, Cook MN, Jones BC, Mulligan MK, Hamre KM, Lu L (2017) 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) 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) 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) 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) 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 (2017) 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) 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) 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) 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) 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
GeneNetwork (2016)
  1. Alam G, Miller DB, O'Callaghan JP, Lu L, Williams RW, Jones BC (2016) 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) 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) 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) 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) Systems genetics identifies Hp1bp3 as a novel modulator of cognitive aging. Neurobiol Aging 46:58-67
  6. Shi X, Walter NA, Harkness JH, Neve KA, Williams RW, Lu L, Belknap JK, Eshleman AJ, Phillips TJ, Janowsky A (2016) Genetic polymorphisms affect mouse and human Trace Amine-Associated Receptor 1 function. PLoS One 11(3):e0152581
  7. Schultz NG, Ingels J, Hillhouse A, Wardwell K, Chang PL, Cheverud JM, Lutz C, Lu L, Williams RW, Dean MD (2016) The genetic basis of baculum size and shape variation in mice. G3 (Bethesda) 6(5):1141-1151
  8. 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)
  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) Joint mouse-human phenome-wide association to test gene function and disease risk. Nat Commun 7:10464
  10. Williams EG, Wu Y, Jha P, Dubuis S, Blattmann P, Argmann CA, Houten SM, Amariuta T, Wolski W, Zamboni N, Aebersold R, Auwerx J (2016) Systems proteomics of liver mitochondria function. Science 352(6291):aad0189
GeneNetwork (2015)
  1. Ashbrook DG, Gini B, Hager R (2015) Genetic variation in offspring indirectly influences the quality of maternal behaviour in mice. eLIFE 4:e11814
  2. Ashbrook DG, Williams RW, Lu L, Hager R (2015) 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) Genomic regulation of senescence and innate immunity signaling in the retinal pigment epithelium. Mammalian Genome 26:210-221 Full text
  4. Cheng Q, Seltzer Z, Sima C, Lakschevitz FS, Glogauer M (2015) 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) 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) 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) 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) 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) 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) 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) Cell cycle gene expression networks discovered using systems biology: Significance in carcinogenesis. J Cell Physiol 230:2533-42
  12. Shea CJ, Carhuatanta KA, Wagner J, Bechmann N, Moore R, Herman JP, Jankord R (2015) Variable impact of chronic stress on spatial learning and memory in BXD mice. Physiol Behav. 150:69-77 Full text
  13. Xue Y, Li J, Yan L, Lu L, Liao FF (2015) Genetic variability to diet-induced hippocampal dysfunction in BXD recombinant inbred (RI) mouse strains. Behav Brain Res 292:83-94
  14. Williams EG, Auwerx J (2015) The convergence of systems and reductionist approaches in complex trait analysis. Cell 162:23-32. PDF version
GeneNetwork (2014)
  1. Ashbrook GN, Delprato A, Grellmann C, Klein M, Wetzel R, Overall RW, Badea A (2014) Transcript co-variance with Nestin in two mouse genetic reference populations identifies Lef1 as a novel candidate regulator of neural precursor cell proliferation in the adult hippocampus. Frontiers in Neuroscience in press
  2. Ashbrook DG, Williams RW, Lu L, Stein JL, Hibar DP, Nichols TE, Medland SE, Thompson PM, Hager R. (2014) Joint genetic analysis of hippocampal size in mouse and human identifies a novel gene linked to neurodegenerative disease. BMC Genomics 15:850
  3. Carhuatanta KA, Shea CJ, Herman JP, Jankord R (2014) Unique genetic loci identified for emotional behavior in control and chronic stress conditions. Front Behav Neurosci 8:341
  4. Emery FD, Parvathareddy J, Pandey AK, Cui Y, Williams RW, Miller MA (2014) 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) 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) 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) 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) 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) 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) Genome wide analysis of sex difference in gene expression profiles of bone formations using sfx mice and BXD RI strains. ScientificWorldJournal 2014:584910
  11. Hasenfuss SC, Bakiri L, Thomsen MK, Williams EG, Auwerx J, Wagner EF (2014) Regulation of steatohepatitis and PPARγ signaling by distinct AP-1 dimers. Cell Metab. 2014 Jan 7;19(1):84-95.
  12. Jones BC, O'Callaghan JP, Lu L, Williams RW, Alam G, Miller DB (2014) Genetic correlational analysis reveals no association between MPP+ and the severity of striatal dopaminergic damage following MPTP treatment in BXD mouse strains. Neurotoxicol Teratol pii: S0892-0362(14)00159-7
  13. Keeley PW, Whitney IE, Madsen NR, St John AJ, Borhanian S, Leong SA, Williams RW, Reese BE (2014) Independent genomic control of neuronal number across retinal cell types. Dev Cell 30:103-109
  14. Keeley PW, Zhou C, Lu L, Williams RW, Melmed S, Reese BE (2014) Pituitary tumor-transforming gene 1 regulates the patterning of retinal mosaics. Proc Natl Acad Sci USA 111:9295-
  15. Kweon KH, Lee CR, Jung SJ, Ban EJ, Kang SW, Jeong JJ, Nam KH, Jo YS, Lee J, Chung WY (2014) Sirt1 induction confers resistance to etoposide-induced genotoxic apoptosis in thyroid cancers. Int J Oncol 45:2065-2075
  16. Loos M, Mueller T, Gouwenberg Y, Wijnands R, van der Loo RJ, Birchmeier C, Smit AB, Spijker S (2014) Neuregulin-3 in the mouse medial prefrontal cortex regulates impulsive action. Biol Psychiatry 76:648-655
  17. Lotan A, Fenckova M, Fralten J, Alttoa A, Dixson L, Williams RW, van der Voet M (2014) Neuroinformatic analyses of common and distinct genetic components associate with major neuropsychiatric disorders. Frontiers in Neuroscience 8:331
  18. McLachlan SM, Aliesky H, Banuelos B, Magana J, Williams RW, Rapoport B. (2014) Immunoglobulin heavy chain variable region and major histocompatibility region genes are linked to induced graves' disease in females from two very large families of recombinant inbred mice. Endocrinology 155:4094-4103
  19. McLachlan SM, Hamidi S, Aliesky H, Williams RW, Rapoport B (2014) Sex, genetics and the control of thyroxine and thyrotropin in mice. Thyroid 24:1080-1087
  20. Muldoon PP, Jackson KJ, Perez E, Harenza JL, Molas S, Rais B, Anwar H, Zaveri NT, Maldonado R, Maskos U, McIntosh JM, Dierssen M, Miles MF, Chen X, De Biasi M, Damaj MI (2014) The alpha3beta4* nicotinic ACh receptor subtype mediates physical dependence to morphine: mouse and human studies. Br J Pharmacol 171:3845-3857
  21. Nguyen C, Baten A, Morahan G (2014) Comparison of sequence variants in transcriptomic control regions across 17 mouse genomes. Database (Oxford): bau020. doi: 10.1093/database/bau020
  22. Pandey AK, Lu L, Wang X, Homayouni R, Williams RW (2014) Functionally enigmatic genes: a case study of the brain ignorome. PLoS One 9(2):e88889
  23. Pandey AK, Williams RW (2014) Genetics of gene expression in CNS. Int Rev Neurobiol 116:195-231
  24. Pietrzykowski A, Spijker S (2014) Impulsivity and comorbid traits: a multi-step approach for finding putative responsible microRNAs in the amygdala. Frontiers in Neuroscience in press
  25. Pirinen E, Cantó C, Jo YS, Morato L, Zhang H, Menzies KJ, Williams EG, Mouchiroud L, Moullan N, Hagberg C, Li W, Timmers S, Imhof R, Verbeek J, Pujol A, van Loon B, Viscomi C, Zeviani M, Schrauwen P, Sauve AA, Schoonjans K, Auwerx J (2014) Pharmacological inhibition of poly(ADP-ribose) polymerases improves fitness and mitochondrial function in skeletal muscle. Cell Metab 19:1034-1041
  26. Poon A, Goldowitz D (2014) Identification of genetic loci that modulate cell proliferation in the adult rostral migratory stream using the expanded panel of BXD mice. BMC Genomics 15:206
  27. Porcu P, Morrow AL (2014) Divergent neuroactive steroid responses to stress and ethanol in rat and mouse strains: Relevance for human studies. Psychopharmacology (Berl) 231:3257-3272
  28. Ram R, Mehta M, Balmer L, Gatti DM, Morahan G (2014) Rapid identification of major-effect genes using the collaborative cross. Genetics 198:75-86 PMID: 25236450
  29. Ryu D, Jo YS, Lo Sasso G, Stein S, Zhang H, Perino A, Lee JU, Zeviani M, Romand R, Hottiger MO, Schoonjans K, Auwerx J (2014) A SIRT7-dependent acetylation switch of GABPβ1 controls mitochondrial function. Cell Metab in press
  30. Thompson RL, Williams RW, Kotb M, Sawtell NM. (2014) A forward phenotypically driven unbiased genetic analysis of host genes that moderate herpes simplex virus virulence and stromal keratitis in mice. PLoS One 9(3):e92342
  31. Toth LA, Trammell RA, Williams RW (2014) Mapping complex traits using families of recombinant inbred strains: an overview and example of mapping susceptibility to Candida albicans induced illness phenotypes. Pathog Dis 71:234-248
  32. Unger EL, Jones BC, Bianco LE, Allen RP, Earley CJ (2014) Diurnal variations in brain iron concentrations in BXD RI mice. Neuroscience 263:54-59
  33. van de Lagemaat LN, Nijhof B, Bosch DG, Kohansal-Nodehi M, Keerthikumar S, Heimel JA (2014) Age-related decreased inhibitory versus excitatory gene expression in the adult autistic brain. Frontiers in Neuroscience in press
  34. Vied CM, Freudenberg F, Wang Y, Raposo AA, Feng D, Nowakowski RS (2014) A multi-resource data integration approach: identification of candidate genes regulating cell proliferation during neocortical development. Frontiers in Neuroscience 8:257
  35. Wang L, Lu W, Zhang L, Huang Y, Scheib R, Liu X, Myers L, Lu L, Farber CR, Liu G, Wang CY, Deng H, Williams RW, Wang Y, Gu W, Jiao (2014) Trps1 differentially modulates the bone mineral density between male and female mice and its polymorphism associates with BMD differently between women and men. PLoS One 9(1):e84485
  36. 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) Multilayered genetic and omics dissection of mitochondrial activity in a mouse reference population. Cell 158:1415-1430
  37. Williams EG, Mouchiroud L, Frochaux M, Pandey A, Andreux PA, Deplancke B, Auwerx J (2014) An evolutionarily conserved role for the aryl hydrocarbon receptor in the regulation of movement. PLoS Genet 10:e1004673
  38. Ye R, Carneiro AM, Airey D, Sanders-Bush E, Williams RW, Lu L, Wang J, Zhang B, Blakely RD (2014) Evaluation of heritable determinants of blood and brain serotonin homeostasis using recombinant inbred mice. Genes Brain Behav. 13:247-260
GeneNetwork (2013)
  1. Bhandari P, Hill JS, Farris SP, Costin B, Martin I, Chan CL, Alaimo JT, Bettinger JC, Davies AG, Miles MF, Grotewiel M (2013) Chloride intracellular channels modulate acute ethanol behaviors in Drosophila, Caenorhabditis elegans and mice. Genes, Brain & Behavior 11:387-97
  2. Cheng Y, Gaughan J, Midic U, Han Z, Liang CG, Patel BG, Latham KE (2013) Systems genetics implicates cytoskeletal genes in oocyte control of cloned embryo quality. Genetics 193:877-896 PDF version
  3. Dogan A, Lasch P, Neuschl C, Millrose MK, Alberts R, Schughart K, Naumann D, Brockmann GA. (2013) ATR-FTIR spectroscopy reveals genomic loci regulating the tissue response in high fat diet fed BXD recombinant inbred mouse strains. BMC Genomics 14:386
  4. DuBose CS, Chesler EJ, Goldowitz D, Hamre KM (2013) Use of the expanded panel of BXD mice narrow QTL regions in ethanol-induced locomotor activation and motor incoordination. Alcohol Clin Exp Res 37:170-83
  5. Farris SP, Miles MF (2013) Fyn-dependent gene networks in acute ethanol sensitivity. PLoS One 8:e82435
  6. Houtkooper RH, Mouchiroud L, Ryu D, Moullan N, Katsyuba E, Knott G, Williams RW, Auwerx J (2013) Mitonuclear protein imbalance as a conserved longevity mechanism. Nature 497:451-457 PDF version
  7. Huang Y, Wang L, Bennett B, Williams RW, Wang YJ, Gu WK, Jiao Y (2013) Potential role of Atp5g3 in epigenetic regulation of alcohol preference or obesity from a mouse genomic perspective. Genet Mol Res 12:3662-3674
  8. Jellen LC, Lu L, Wang X, Unger EL, Earley CJ, Allen RP, Williams RW, Jones BC (2013) Iron deficiency alters expression of dopamine-related genes in the ventral midbrain in mice. Neuroscience 252:13-23
  9. Jiao Y, Chen H, Yan J, Wang L, Huang Y, Liu X, Williams RW, Lu L, Wang Y, Gu W (2013) Genome-wide gene expression profiles in antioxidant pathways and their potential sex differences and connections to vitamin C in mice. Int J Mol Sci 14:10042-62
  10. Jones BC, Miller DB, O'Callaghan JP, Lu L, Unger EL, Alam G, Williams RW (2013) Systems analysis of genetic variation in MPTP neurotoxicity in mice. Neurotoxicology 37C:26-34
  11. Liebe R, Hall RA, Williams RW, Dooley S, Lammert F (2013) Systems genetics of hepatocellular damage in vivo and in vitro: identification of a critical network on chromosome 11 in mouse. Physiological Genomics 45:931-939
  12. Lindblom RP, Aeinehband S, Parso R, Strom M, Al Nimer F, Zhang XM, Domingues CA, Flytzani S, Siez M, Piehl F (2013) Genetic variability in the rat Aplec C-type lectin gene cluster regulates lymphocyte trafficking and motor neuron survival after traumatic nerve root injury. Journal of Neuroinflammation 10:60
  13. Mulligan MK, Dubose C, Yue J, Miles MF, Lu L, Hamre KM (2013) Expression, covariation, and genetic regulation of miRNA biogenesis genes in brain supports their role in addiction, psychiatric disorders, and disease. Frontiers in Genetics 4:126
  14. Swaminathan S, Lu H, Williams RW, Lu L, Jablonski MM (2013) Genetic modulation of the iris transillumination defect: a systems genetics analysis using the expanded family of BXD glaucoma strains. Pigment Cell Melanoma Research 26:487-98
  15. Templeton JP, Wang X, Freeman NE, Ma Z, Lu A, Hejtmancik F, Geisert EE (2013) A crystallin gene network in the mouse retina. Exp Eye Res. 116C:129-140
  16. Templeton JP, Freeman NE, Nickerson JM, Jablonski MM, Rex TS, Williams RW, Geisert EE (2013) Innate immune network in the retina activated by optic nerve crush. Invest Ophthalmol Vis Sci. 54:2599-606
  17. Vanderlinden LA, Saba LM, Kechris K, Miles MF, Hoffman PL, Tabakoff B (2013) Whole brain and brain regional coexpression network interactions associated with predisposition to alcohol consumption. PLoS One 8:e68878.
GeneNetwork (2012)
  1. Alberts R, Chen H, Pommerenke C, Smit AB, Spijker S, Williams RW, Geffers R, Bruder D, Schughart K (2011) Expression QTL mapping in regulatory and helper T cells from the BXD family of strains reveals novel cell-specific genes, gene-gene interactions and candidate genes for auto-immune disease. BMC Genomics 12:610 PDF version
  2. Andreux PA, Williams EG, Koutnikova H, Houtkooper RH, Champy MF, Henry H, Schoonjana K, Williams RW, Auwerx J (2012) Systems genetics of metabolism: the use of the BXD murine reference panel for multiscalar integration of traits. Cell 150:1287-1299
  3. Boughter JD Jr, Mulligan MK, St John SJ, Tokita K, Lu L, Heck DH, Williams RW (2012) Genetic control of a central pattern generator: Rhythmic oromotor movement in mice Is controlled by a major locus near Atp1a2. PLoS One 7:e38169. Full Text version
  4. Bubier JA, Chesler EJ (2012) Accelerating discovery for complex neurological and behavioral disorders through systems genetics and integrative genomics in the laboratory mouse. Neurotherapeutics 9:338-348 Full Text version
  5. Bryant CD, Kole LA, Guido MA, Sokoloff G, Palmer AA (2012) Congenic dissection of a major QTL for methamphetamine sensitivity implicates epistasis. Genes, Brain and Behavior 11:623-632 PDF version
  6. Downing C, Balderrama-Durbin C, Kimball A, Biers J, Wright H, Gilliam D, Johnson TE (2012) Quantitative trait locus mapping for ethanol teratogenesis in BXD recombinant inbred mice. Alcohol Clin Exp Res. 36:1340-1354
  7. Durrant C, Swertz MA, Alberts R, Arends D, Möller S, Mott R, Prins P, van der Velde KJ, Jansen RC, Schughart K.(2012) Bioinformatics tools and database resources for systems genetics analysis in mice--a short review and an evaluation of future needs. Brief Bioinform 13:135-142 HTML version
  8. Gini B, Hager R (2012) Recombinant inbred systems can advance research in behavioral ecology. Front. Gene. 3:198 Full Text version
  9. Hager R, Lu L, Rosen GD, Williams RW. (2012) Genetic architecture supports mosaic brain evolution and independent brain-body size regulation. Nature Communications 3:1079 PDF version Full Text version
  10. Jellen LC, Unger EL, Lu L, Williams RW, Rousseau S, Wang X, Earley CJ, Allen RP, Miles MF, Jones BC (2012) Systems genetic analysis of the effects of iron deficiency in mouse brain. Neurogenetics 13:147-157
  11. McKnite AM, Perez-Munoz ME, Lu L, Williams EG, Brewer S, Andreux PA, Bastiaansen JW, Wang X, Kachman SD, Auwerx J, Williams RW, Benson AK, Peterson DA, Ciobanu DC (2012) Murine gut microbiota is defined by host genetics and modulates variation of metabolic traits. PLoS One 7:e39191 Full Text version
  12. Mulligan MK, Wang X, Adler AL, Mozhui K, Lu L, Williams RW (2012) Complex control of GABA(A) receptor subunit mRNA expression: variation, covariation, and genetic regulation. PLoS One 7:e34586 Full Text version
  13. Newbury AJ, Rosen GD (2012) Genetic, morphometric, and behavioral factors linked to the midsagittal area of the corpus callosum. Frontiers in Genetics 3:91
    PDF versionFull Text version
  14. Parker CC, Cheng R, Sokoloff G, Palmer AA (2012) Genome-wide association for methamphetamine sensitivity in an advanced intercross mouse line. Genes, Brain & Behavior 11:52-61
  15. Reinius B, Johansson MM, Radomska KJ, Morrow EH, Pandey GK, Kanduri C, Sandberg R, Williams RW, Jazin E (2012) Abundance of female-biased and paucity of male-biased somatically expressed genes on the mouse X-chromosome. BMC Genomics 13:607
  16. Rietman ML, Sommeijer JP; Neuro-Bsik Mouse Phenomics Consortium, Levelt CN, Heimel JA (2012) Candidate genes in ocular dominance plasticity. Frontiers in Neuroscience 6:11 PDF version
  17. Talishinsky A, Rosen GD (2012) Systems genetics of the lateral septal nucleus in mouse: Heritability, genetic control, and covariation with behavioral and morphological traits. PLoS One 7: e44236 PDF versionFull Text version
  18. Williams RW, Mulligan MK (2012) Genetic and molecular network analysis of behavior. Int Rev Neurobiol. 104:135-57 PDF version
  19. Wolen AR, Phillips CA, Langston MA, Vorster PJ, Bruce NA, York TP, Williams RW, Miles MF (2012) Genetic dissection of acute ethanol responsive gene networks in prefrontal cortex: Functional and mechanistic implications. PLoS One 7:e33575
  20. Yin L, Unger EL, Jellen LC, Earley CJ, Allen RP, Tomaszewicz A, Fleet JC, Jones BC. (2012) Systems genetic analysis of multivariate response to iron deficiency in mice. Am J Physiol Regul Integr Comp Physiol 302:R1282-96 PDF version
  21. Ziebarth JD, Cook MN, Wang X, Williams RW, Lu L, Cui Y (2012) Treatment- and population-dependent activity patterns of behavioral and expression QTLs. PLoS One 7:e31805. PDF versionFull Text version
  22. Zumbrun EE, Abdeltawab NF, Bloomfield HA, Chance TB, Nichols DK, Harrison PE, Kotb M, Nalca A (2012) Development of a murine model for aerosolized ebolavirus infection using a panel of recombinant inbred mice. Viruses. 2012 Dec 3;4(12):3468-3493
GeneNetwork (2011)
  1. Alberts R, Lu L, Williams RW, Schughart K. (2011) Genome-wide analysis of the mouse lung transcriptome reveals novel molecular gene interaction networks and cell-specific expression signatures. Respir Res 12:61 Full Text version
  2. Alberts R, Chen H, Pommerenke C, Smit AB, Spijker S, Williams RW, Geffers R, Bruder D, Schughart K (

    Web services initiated January, 1994 as The Portable Dictionary of the Mouse Genome ; June 15, 2001 as WebQTL; and Jan 5, 2005 as GeneNetwork.

    This site is currently operated by Rob Williams, Pjotr Prins, Zachary Sloan, Arthur Centeno, and Christian Fischer.

    Design and code by Pjotr Prins, Zach Sloan, Arthur Centeno, Christan Fischer, Danny Arends, Sam Ockman, Lei Yan, Xiaodong Zhou, Christian Fernandez, Ning Liu, Rudi Alberts, Elissa Chesler, Sujoy Roy, Evan G. Williams, Alexander G. Williams, Kenneth Manly, Jintao Wang, and Robert W. Williams, colleagues.


    GeneNetwork support from:

    • The UT Center for Integrative and Translational Genomics
    • NIGMS Systems Genetics and Precision Medicine Project (R01 GM123489, 2017-2021)
    • NIDA NIDA Core Center of Excellence in Transcriptomics, Systems Genetics, and the Addictome (P30 DA044223, 2017-2022)
    • NIA Translational Systems Genetics of Mitochondria, Metabolism, and Aging (R01AG043930, 2013-2018)
    • NIAAA Integrative Neuroscience Initiative on Alcoholism (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425, 2006-2017)
    • NIDA, NIMH, and NIAAA (P20-DA 21131, 2001-2012)
    • NCI MMHCC (U01CA105417), NCRR, BIRN, (U24 RR021760)

    Published in JOSS

    Development and source code on github with issue tracker and documentation. Join the mailing list and find us on IRC (#genenetwork channel).