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Boolean implication networks derived from large scale, whole genome microarray datasets
Debashis Sahoo, David L Dill, Andrew J Gentles, Robert Tibshirani, Sylvia K Plevritis
Genome Biol. 2008; 9(10): R157. Published online 2008 October 30. doi: 10.1186/gb-2008-9-10-r157
PMCID:
PMC2760884
Abstract Full Text PDF–5.0M Supplementary Material

Is Cited by the Following 13 Articles in this Archive:

Pathway-based identification of a smoking associated 6-gene signature predictive of lung cancer risk and survival
Nancy Lan Guo, Ying-Wooi Wan
Artif Intell Med. Author manuscript; available in PMC 2013 August 10.
Published in final edited form as: Artif Intell Med. 2012 February 10: doi: 10.1016/j.artmed.2012.01.001
PMCID:
PMC3351561
Free in PMC on 2013/08/10
Pathway-based identification of a smoking associated 6-gene signature predictive of lung cancer risk and survival
Nancy Lan Guo, Ying-Wooi Wan
Artif Intell Med. Author manuscript; available in PMC 2013 August 10.
Published in final edited form as: Artif Intell Med. 2012 February 10: doi: 10.1016/j.artmed.2012.01.001
PMCID:
PMC3351561
Free in PMC on 2013/08/10
Three differentiation states risk-stratify bladder cancer into distinct subtypes
Jens-Peter Volkmer, Debashis Sahoo, Robert K. Chin, Philip Levy Ho, Chad Tang, Antonina V. Kurtova, Stephen B. Willingham, Senthil K. Pazhanisamy, Humberto Contreras-Trujillo, Theresa A. Storm, Yair Lotan, Andrew H. Beck, Benjamin I. Chung, Ash A. Alizadeh, Guilherme Godoy, Seth P. Lerner, Matt van de Rijn, Linda D. Shortliffe, Irving L. Weissman, Keith S. Chan
Proc Natl Acad Sci U S A. 2012 February 7; 109(6): 2078–2083. Published online 2012 January 19. doi: 10.1073/pnas.1120605109
Correction in:
Proc Natl Acad Sci U S A. 2012 February 28; 109(9): 3600.
PMCID:
PMC3277552
Abstract Full Text PDF–1.3M Supplementary Material Correction
Human bone marrow hematopoietic stem cells are increased in frequency and myeloid-biased with age
Wendy W. Pang, Elizabeth A. Price, Debashis Sahoo, Isabel Beerman, William J. Maloney, Derrick J. Rossi, Stanley L. Schrier, Irving L. Weissman
Proc Natl Acad Sci U S A. 2011 December 13; 108(50): 20012–20017. Published online 2011 November 28. doi: 10.1073/pnas.1116110108
PMCID:
PMC3250139
Abstract Full Text PDF–1.4M Supplementary Material
Single-cell dissection of transcriptional heterogeneity in human colon tumors
Piero Dalerba, Tomer Kalisky, Debashis Sahoo, Pradeep S. Rajendran, Michael E. Rothenberg, Anne A. Leyrat, Sopheak Sim, Jennifer Okamoto, Darius M. Johnston, Dalong Qian, Maider Zabala, Janet Bueno, Norma F. Neff, Jianbin Wang, Andrew A. Shelton, Brendan Visser, Shigeo Hisamori, Yohei Shimono, Marc van de Wetering, Hans Clevers, Michael F. Clarke, Stephen R. Quake
Nat Biotechnol. Author manuscript; available in PMC 2012 June 1.
Published in final edited form as: Nat Biotechnol. 2011 November 13; 29(12): 1120–1127. doi: 10.1038/nbt.2038
PMCID:
PMC3237928
Free in PMC on 2012/06/01
Predicting gene ontology from a global meta-analysis of 1-color microarray experiments
Mikhail G Dozmorov, Cory B Giles, Jonathan D Wren
BMC Bioinformatics. 2011; 12(Suppl 10): S14. Published online 2011 October 18. doi: 10.1186/1471-2105-12-S10-S14
PMCID:
PMC3236836
Abstract Full Text PDF–5.8M
Express Path Analysis Identifies a Tyrosine Kinase Src-centric Network Regulating Divergent Host Responses to Mycobacterium tuberculosis Infection
Ahmad Faisal Karim, Pallavi Chandra, Aanchal Chopra, Zaved Siddiqui, Ashima Bhaskar, Amit Singh, Dhiraj Kumar
J Biol Chem. 2011 November 18; 286(46): 40307–40319. Published online 2011 September 27. doi: 10.1074/jbc.M111.266239
PMCID:
PMC3220550
Abstract Full Text Supplementary Material
Constructing Biological Pathways by a Two-Step Counting Approach
Hsiuying Wang, Henry Horng-Shing Lu, Tung-Hung Chueh
PLoS One. 2011; 6(6): e20074. Published online 2011 June 1. doi: 10.1371/journal.pone.0020074
PMCID:
PMC3105984
Abstract Full Text PDF–225K Supplementary Material
A novel network model identified a 13-gene lung cancer prognostic signature
Nancy Lan Guo, Ying-Wooi Wan, Swetha Bose, James Denvir, Michael L. Kashon, Michael E. Andrew
Int J Comput Biol Drug Des. Author manuscript; available in PMC 2012 February 17.
Published in final edited form as: Int J Comput Biol Drug Des. 2011; 4(1): 19–39. Published online 2011 February 17. doi: 10.1504/IJCBDD.2011.038655
PMCID:
PMC3095973
Abstract Full Text PDF–1.1M Supplementary Material
MiDReG: A method of mining developmentally regulated genes using Boolean implications
Debashis Sahoo, Jun Seita, Deepta Bhattacharya, Matthew A. Inlay, Irving L. Weissman, Sylvia K. Plevritis, David L. Dill
Proc Natl Acad Sci U S A. 2010 March 30; 107(13): 5732–5737. Published online 2010 March 15. doi: 10.1073/pnas.0913635107
PMCID:
PMC2851930
Abstract Full Text PDF–2.1M Supplementary Material
Automatic Parameter Learning for Multiple Local Network Alignment
Jason Flannick, Antal Novak, Chuong B. Do, Balaji S. Srinivasan, Serafim Batzoglou
J Comput Biol. 2009 August; 16(8): 1001–1022. doi: 10.1089/cmb.2009.0099
PMCID:
PMC3154456
Abstract Full Text PDF–868K
Reconstruct gene regulatory network using slice pattern model
Yadong Wang, Guohua Wang, Bo Yang, Haijun Tao, Jack Y Yang, Youping Deng, Yunlong Liu
BMC Genomics. 2009; 10(Suppl 1): S2. Published online 2009 July 7. doi: 10.1186/1471-2164-10-S1-S2
PMCID:
PMC2709263
Abstract Full Text PDF–982K Supplementary Material
A Factor Graph Nested Effects Model To Identify Networks from Genetic Perturbations
Charles J. Vaske, Carrie House, Truong Luu, Bryan Frank, Chen-Hsiang Yeang, Norman H. Lee, Joshua M. Stuart
PLoS Comput Biol. 2009 January; 5(1): e1000274. Published online 2009 January 30. doi: 10.1371/journal.pcbi.1000274
PMCID:
PMC2613752
Abstract Full Text PDF–579K Supplementary Material
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