Publications

Recent Publications and Commentaries by Sage Bionetworks Scientists and Collaborators.

• Evidence for type II cells as cells of origin of K-Ras-induced distal lung adenocarcinoma.
  Xu X, Rock JR, Lu Y, Futtner C, Schwab B, Guinney J, Hogan BLM, Onaitis MW.  Proceedings of the National Academy of Sciences of the United States of America 2012 Mar;109(13):4910-5

• Correlation Set Analysis: Detecting active regulators in disease populations using prior causal knowledge..
  Huang C-L, Lamb J, Chindelevitch L, Kostrowicki J, Guinney J, DeLisi C, Ziemek D. BMC Bioinformatics 2012 Mar;13(1):46.

• The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
  Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, et.al. Nature 2012 Mar; 483(7391):603-307.

• Developing predictive molecular maps of human disease through community-based modeling.
  Derry JMJ, Mangravite LM, Suver C, Furia MD, Henderson D, Schildwachter X, Bot B, Izant J, Sieberts SK, Kellen MR, Friend SH.  Nature Genetics 2012 Jan;44(2):127-130.

• Integrative genomics strategies to elucidate the complexity of drug response. 
  Kasarskis A, Yang X, Schadt E.  Pharmacogenomics 2011 Dec;12(12):1695-715.

• Construction of regulatory networks using expression time-series data of a genotyped population 
  Yeung KY, Dombek KM, Lo K, Mittler JE, Zhu J, Schadt EE, Bumgarner RE, Raftery AE. Proceedings of the National Academy of Sciences 2011 Nov;108(48):19436-41.

• Identification of Causal Genes, Networks, and Transcriptional Regulators of REM Sleep and Wake. 
  Millstein J, Winrow CJ, Kasarskis A, Owens JR, Zhou L, Summa KC, Fitzpatrick K, Zhang B, Vitaterna MH, Schadt EE, Renger JJ, Turek FW.  Sleep 2011 Nov;34(11):1469-77.

• Clinicopathologic and gene expression parameters predicts liver cancer prognosis.
  Hao K, Lamb J, Zhang C, Xie T, Wang K, Zhang B, Chudin E, Lee NP, Mao M, Zhong H, Greenawalt D, Ferguson MD, Ng IO, Sham PC, Poon RT, Molony C, Schadt EE, Dai H, Luk JM.  BMC cancer 2011 Nov;11(1):481.

• Changes in Atherogenic Dyslipidemia Induced by Carbohydrate Restriction in Men Are Dependent on Dietary Protein Source.
  Mangravite LM, Chiu S, Wojnoonski K, Rawlings RS, Bergeron N, Krauss RM.  The Journal of nutrition 2011 Oct;141(12):2180-5.

• Expression of endothelin 2 and localized clear cell renal cell carcinoma. 
  Bot BM, Eckel-Passow JE, Legrand SN, Hilton T, Cheville JC, Igel T, Parker AS.  Human pathology 2011 Oct

• Opinion- Thinking Outside the Genome.
  Friend S.  The Scientist 2011;(October):11-13.

• Estimating variable structure and dependence in multitask learning via gradients .
  Guinney J, Wu Q, Mukherjee S.   Machine Learning 2011 Oct;83(3):265-287.

• Inferring Causal Genomic Alterations in Breast Cancer Using Gene Expression Data. 
  Tran LM, Zhang B, Zhang Z, Zhang C, Xie T, Lamb JR, Dai H, Schadt EE, Zhu J.  BMC systems biology 2011 Aug;5(1):121.
• Integrating Factor Analysis and a Transgenic Mouse Model to Reveal a Peripheral Blood Predictor of Breast Tumors. 
  Labreche HG, Nevins JR, Huang ES.  BMC medical genomics 2011 Jul;4(1):61.

• A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort.
  Greenawalt DM, Dobrin R, Chudin E, Hatoum IJ, Suver C, Beaulaurier J, Zhang B, Castro V, Zhu J, Sieberts SK, Wang S, Molony C, Heymsfield SB, Kemp DM, Reitman ML, Lum PY, Schadt EE, Kaplan LM. Genome research 2011 Jul;21(7):1008-16.

• Predictive Genes in Adjacent Normal Tissue Are Preferentially Altered by sCNV during Tumorigenesis in Liver Cancer and May Rate Limiting. 
  Lamb JR, Zhang C, Xie T, Wang K, Zhang B, Hao K, Chudin E, Fraser HB, Millstein J, Ferguson M, Suver C, Ivanovska I, Scott M, Philippar U, Bansal D, Zhang Z, Burchard J, Smith R, Greenawalt D, Cleary M, Derry J, Loboda A, Watters J, Poon RTP, Fan ST, Yeung C, Lee NPY, Guinney J, Molony C, Emilsson V, Buser-Doepner C, Zhu J, Friend S, Mao M, Shaw PM, Dai H, Luk JM, Schadt EE.  PloS one 2011 Jul;6(7):e20090.

• Impact of Young Age on Treatment Efficacy and Safety in Advanced Colorectal Cancer: A Pooled Analysis of Patients From Nine First-Line Phase III Chemotherapy Trials.  
  Blanke CD, Bot BM, Thomas DM, Bleyer A, Kohne C-H, Seymour MT, de Gramont A, Goldberg RM, Sargent DJ.   Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2011 Jul;29(20):2781-6.

• Leveraging crowdsourcing to facilitate the discovery of new medicines.  
  Norman TC, Bountra C, Edwards AM, Yamamoto KR, Friend SH.  Science translational medicine 2011 Jun;3(88):88mr1.

• Evaluation of Guanylyl Cyclase C Lymph Node Status for Colon Cancer Staging and Prognosis. 
  Sargent DJ, Resnick MB, Meyers MO, Goldar-Najafi A, Clancy T, Gill S, Siemons GO, Shi Q, Bot BM, Wu T-T, Beaudry G, Haince J-F, Fradet Y.  Annals of surgical oncology 2011 May;1-10

• Two or three year disease-free survival (DFS) as a primary end-point in stage III adjuvant colon cancer trials with fluoropyrimidines with or without oxaliplatin or irinotecan: data from 12,676 patients from MOSAIC, X-ACT, PETACC-3, C-06, C-07 and C89803. 
   Sargent D, Shi Q, Yothers G, Van Cutsem E, Cassidy J, Saltz L, Wolmark N, Bot B, Grothey A, Buyse M, de Gramont A.  European journal of cancer (Oxford, England : 1990) 2011 May;47(7):990-6.

• Integrative Network-based Association Studies: Leveraging cell regulatory models in the post-GWAS era.
   Atul J. Butte, Andrea Califano, Stephen Friend, Trey Ideker ES. Nature Precedings 2011;

• Meta-analysis of Dense Genecentric Association Studies Reveals Common and Uncommon Variants Associated with Height. 
  Lanktree MB,  et al.  American journal of human genetics 2011 Jan;88(1):6-18.

• Impact of gene expression noise on organismal fitness and the efficacy of natural selection
  Wang Z. and Zhang J. Proc Natl Acad Sci U S A. 2011. Apr 19;108(16):E67-76.

• The precompetitive Space: Time to Move the Yardsticks
  Norman, T., Edwards A.., Bountra C.and Friend SH. Sci Transl Med 2011: Vol. 3, Issue 76, p. 76

• Biomedical technology and the clinic of the future- POINT: Are we prepared for the future doctor visit?
  Friend, SH. and Ideker T. Nat Biotechnol. 2011 Mar;29(3):215

• Predictive, personalized, preventative, participatory cancer medicine
  Hood L. and Friend SH. Nature Reviews Clinical Oncology 2011. 8, 184-187

• An accelerated pathway for targeted cancer therapies
  McClellan M., Benner J., Schilsky R., Epstein D., Woosley R., Friend SH., Sidransky D., Geoghegan C. and Kessler D. Nature Reviews Drug Discovery 2011 10:1-2

• Forkhead Transcription Factor Foxq1 Promotes Epithelial–Mesenchymal Transition and Breast Cancer Metastasis Zhang H., et al. Cancer Res. 2011 Feb 15;71(4):1292-301

• Tumor-derived Jagged1 Promotes Osteolytic Bone Metastasis of Breast Cancer by Engaging Notch Signaling in Bone Cells Sethi N., Dai X., Winter C. and Kang Y. Cancer Cell 2011. 19, 1–14

• Identification of Genes and Networks Driving Cardiovascular and Metabolic Phenotypes in a Mouse F2 Intercross Derry J., et al. PLoS One. 2010 Dec 14;5(12):e14319

• A 10-Gene Progenitor Cell Signature Predicts Poor Prognosis in Lung Adenocarcnioma
  Onaitis M., Rawlins E., D’Amico TA., Guinney J., Harpole D. and Hogan B. Ann Thorac Surg. 2011 Apr;91(4):1046-50

• Estimating variable structure and dependence in multitask learning via gradients
  Guinney J, Wu Q., Mukherjee, S. Machine Learning 2011. 83; 265-287

• Bayesian Models for Detecting Epistatic Interactions from Genetic Data.
  Zhang Y, Jiang B, Zhu J, Liu JS. Ann Hum Genet. 2010 Nov 22. doi: 10.1111

• Opening Up to Precompetitive Collaboration
  Altshuler, JS. et al. Sci Transl Med 2010 Vol. 2, Issue 52, p. 52

• An Integrative Multi-Network and Multi-Classifier Approach to Predict Genetic Interactions
  Pandey G., Zhang B., Aaron N., Chang N., Myers CL., Zhu J., Kumar V., and Schadt EE. PLoS Comput Biol. 2010 September; 6(9): e1000928.

• Learning Gradients: Predictive Models that Infer Geometry and Statistical Dependence
  Wu Q., Guinney J., Maggioni M., and Mukherjee S. J. Machine Learning Research 11(Aug):2175−2198, 2010.

• Identification and validation of genes affecting aortic lesions in mice
  Yang X. et al. J Clin Invest. 2010;120(7):2414–2422. doi:10.1172/JCI42742.

• Something in Common
  Friend, SH. Sci Transl Med 2010 2, Issue 40, p. 40

• Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver.
  Yang X. et al. Genome Res. 2010 Aug;20(8):1020-36. Epub 2010 Jun 10.

• Liver and adipose expression associated SNPs are enriched for association to type 2 diabetes.
  Zhong H. et al. PLoS Genet. 2010 May 6;6:e1000932.

• A Bayesian Partition Method for Detecting Pleiotropic and Epistatic eQTL Module.
  Zhang W., Zhu J., Schadt EE., Liu J. PLoS Computational Biology 2010. 6: 1-10.

• Simultaneous Clustering of Multiple Gene Expression and Physical Interaction Datasets.
  Narayanan M., Vetta A., Schadt EE., Zhu J. PLoS Comput Biol. 2010. 6(4): e1000742.

• The need for precompetitive integrative bionetwork disease model building.
  Friend SH. Clin Pharmacol Ther. 2010 May;87(5):536-9.

• Assessing the prospects of genome-wide association studies performed in inbred mice.
  Su WL., Sieberts SK., Kleinhanz RR., Lux K., Millstein J., Molony C., Schadt EE. Mamm. Genome. 2010. 21(3-4):143-52.

• Characterizing Dynamic Changes in the Human Blood Transcriptional Network.
  Zhu J., Chen Y., Leonardson A., Wang K., Lamb JR., Emilsson V. and Schadt EE. PLoS Computational Biology 2010. 6(2).

• Integrating Pathway Analysis and Genetics of Gene Expression for Genome-wide Association Studies.
  Zhong J., Yang X., Kaplan L., Molony C., Schadt, EE. Am. Journal. Hum. 2010. 86(4):581-91.

• Molecular Networks as sensors and drivers of common human diseases.
  Schadt EE. Nature 2009. 461: 218-223.

• A network view of disease and compound screening.
  Schadt EE., Friend S., Shaywitz D. Nat Rev Drug Discov. 2009. 8(4):286-95.

• Meta-analysis of Inter-species Liver Co-expression Networks Elucidates Traits Associated with Common Human Diseases. Wang K, Narayanan M, Zhong H, Tompa M, Schadt EE, Zhu J.. PLoS Comput Biol. 2008. 5(12): e1000616.

• Validation of Candidate Causal Genes for Obesity Which Affect Shared Metabolic Pathways and Networks.
  Yang X., et al., Nature Genetics 2009. 41, 415-423.

• Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks.
  Zhu J., et al., Nat Genet. 2008. 40(7):854-61.

• Mapping the genetic architecture of gene expression in human liver.
  Schadt EE., et al., PLoS Biol. 2008. 6(5):e107.

• Genetics of gene expression and its effect on disease.
  Emilsson V., et al., Nature. 2008. 452(7186):423-8.

• Variations in DNA elucidate molecular networks that cause disease.
  Chen Y., et al., Nature. 2008. 452(7186):429-35.

 

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