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Benchmark publications in integrative genomics and systems biology and links to research groups and companies engaged in genomics research and open access consortia.

Key integrative genomics papers published by Sage Bionetworks staff while at Rosetta Inpharmatics / Merck

  1.  An integrative genomics approach to infer causal associations between gene expression and disease. 
    Schadt EE, Lamb J, Yang X, Zhu J, Edwards S, Guhathakurta D, Sieberts SK, Monks S, Reitman M, Zhang C, Lum PY, Leonardson A, Thieringer R, Metzger JM, Yang L, Castle J, Zhu H, Kash SF, Drake TA, Sachs A, Lusis AJ.
    Nat Genet. 2005 Jul;37(7):710-7. Epub 2005 Jun 19.
  2. Genetics of gene expression and its effect on disease.
    Emilsson V, Thorleifsson G, Zhang B, Leonardson AS, Zink F, Zhu J, Carlson S, Helgason A, Walters GB, Gunnarsdottir S, Mouy M, Steinthorsdottir V, Eiriksdottir GH, Bjornsdottir G, Reynisdottir I, Gudbjartsson D, Helgadottir A, Jonasdottir A, Jonasdottir A, Styrkarsdottir U, Gretarsdottir S, Magnusson KP, Stefansson H, Fossdal R, Kristjansson K, Gislason HG, Stefansson T, Leifsson BG, Thorsteinsdottir U, Lamb JR, Gulcher JR, Reitman ML, Kong A, Schadt EE, Stefansson K.
    Nature. 2008 Mar 27;452(7186):423-8. Epub 2008 Mar 16.
  3. Variations in DNA elucidate molecular networks that cause disease.
    Chen Y, Zhu J, Lum PY, Yang X, Pinto S, MacNeil DJ, Zhang C, Lamb J, Edwards S, Sieberts SK, Leonardson A, Castellini LW, Wang S, Champy MF, Zhang B, Emilsson V, Doss S, Ghazalpour A, Horvath S, Drake TA, Lusis AJ, Schadt EE.
    Nature. 2008 Mar 27;452(7186):429-35. Epub 2008 Mar 16.
  4.  Mapping the genetic architecture of gene expression in human liver.
    Schadt EE, Molony C, Chudin E, Hao K, Yang X, Lum PY, Kasarskis A, Zhang B, Wang S, Suver C, Zhu J, Millstein J, Sieberts S, Lamb J, GuhaThakurta D, Derry J, Storey JD, Avila-Campillo I, Kruger MJ, Johnson JM, Rohl CA, van Nas A, Mehrabian M, Drake TA, Lusis AJ, Smith RC, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, Ulrich R.
    PLoS Biol. 2008 May 6;6(5):e107.
  5.  Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks.
    Zhu J, Zhang B, Smith EN, Drees B, Brem C Kruglyak L, Bumgarner RE, Schadt EE.
    Nat Genet. 2008 Jul;40(7):854-61. Epub 2008 Jun 15.

Key integrative genomics papers published by other groups

  1.  Integrated genomic and proteomic analyses of a systematically perturbed metabolic network.
    Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L.
    Science. 2001 May 4;292(5518):929-34.
  2. Genetic dissection of transcriptional regulation in budding yeast.
    Brem RB, Yvert G, Clinton R, Kruglyak L.
    Science. 2002 Apr 26;296(5568):752-5. Epub 2002 Mar 28.
  3. Causal protein-signaling networks derived from multiparameter single-cell data.
    Sachs K, Perez O, Pe'er D, Lauffenburger DA, Nolan GP.
    Science. 2005 Apr 22;308(5721):523-9. Erratum in: Science. 2005 Aug 19;309(5738):1187.
  4. Evidence for dynamically organized modularity in the yeast protein-protein interaction network.
    Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, Zhang LV, Dupuy D, Walhout AJ, Cusick ME, Roth FP, Vidal M.
    Nature. 2004 Jul 1;430(6995):88-93. Epub 2004 Jun 9. Erratum in: Nature. 2004 Jul 15;430(6997):380.
  5. The genetics of plant metabolism.
    Keurentjes JJ, Fu J, de Vos CH, Lommen A, Hall RD, Bino RJ, van der Plas LH, Jansen RC, Vreugdenhil D, Koornneef M.
    Nat Genet. 2006 Jul;38(7):842-9. Epub 2006 Jun 4.
  6. Quantitative trait loci underlying gene product variation: a novel perspective for analyzing regulation of genome expression.
    Damerval C, Maurice A, Josse JM, de Vienne D.
    Genetics (1994) 137:289-301

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Leading integrative genomics academic groups and resources  

Companies focused on integrative genomics and modeling 

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Benchmark open sharing efforts for clinical and genetics data

Centrally funded & managed projects 

Consortia projects

Benchmark non-biological open data sharing efforts

 

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