CCD Members

Maathuis MH, Nandy P (2016) A review of some recent advances in causal inference. In P. Bühlmann, P. Drineas, M. Kane and M.J. van der Laan (Eds.), Handbook of Big Data, pp 387-407. Chapman and Hall/CRC, Boca Raton, FL. (arXiv:1506.07669)

Bonifay W E, Reise SP, Scheines R, Meijer RR. When are multidimensional data unidimensional enough for structural equation modeling? An evaluation of the DETECT multidimensionality index. Structural Equation Modeling: A Multidisciplinary Journal 2015;22(4):504-516.

Chen L, Cai C, Chen V, Lu, X. Trans-species learning of cellular signaling systems with bimodal deep belief networks.  Bioinformatics 2015;31:3008-15. doi: 10.1093/bioinformatics/btv315. Epub 2015 May 20. PMID: 25995230

Chikina M, Zaslavsky E, Sealfon SC. CellCODE: a robust latent variable approach to differential expression analysis for heterogeneous cell populations. Bioinformatics 2015;31:1584-91; doi: 10.1093/bioinformatics/btv015. Epub 2015 Jan 11. PMCID: PMC4426841 [Available on 2016-05-15]

Cooper GF, Bahar I, Becich MJ, Benos PV, Berg J, Espino JU, Glymour C, Jacobson RC, Kienholz ML, Lee AV, Lu X, Scheines R. The Center for Causal Discovery of Biomedical Knowledge from Big Data. J Am Med Informatics Assoc 2015;1-6. doi: 10.1093/jamia/ocv059. PMID: 26138794

Glymour C, Hanson C. Reverse Inference in Neuropsychology. British Journal for the Philosophy of Science 2015;0:1-15. doi: 10.1093/bjps/axv019

Huang GT, Tsamardinos I, Raghu V, Kaminski N, Benos PV. T-ReCS: stable selection of dynamically formed groups of features with application to prediction of clinical outcomes. Pacific Symposium on Biocomputing 2015; 431-42. PMCID: PMC4299881 [Available on 2016-01-01]

Lu S, Lu KN Cheng S, Ma X, Nystrom NLu X. Identifying driver genomic alterations in cancers by searching minimum-weight, mutually exclusive sets.  PLoS Computational Biology 2015;11(8):e1004257. doi: 10.1371/journal.pcbi.1004257. eCollection 2015. PMCID: PMC4552843

Murray-Watters A, Glymour C. What’s going on inside the arrows? Discovering the hidden springs in causal models. Philosophy of Science 2014; doi 10.1086/682962.

Plis S, Danks D, Yang J. Mesochronal structure learning. In: Meila M, Heskes T (Eds.). Uncertainty in Artificial Intelligence 31 (UAI-2015) Corvallis, OR: AUAI Press, 2015;702-711. [first two authors contributed equally]

Ramsey J. Scaling Up Greedy Equivalent Search for Continuous Variables. Technical Report. arXiv:1507.07749 [cs.AI], 2015.

Strobl EV, Visweswaran S. Dependence versus conditional dependence in local causal discovery from gene expression data. arXiv:1407.7566, 2014

Strobl EV, Visweswaran S. Markov blanket ranking using kernel-based conditional dependence measures. arXiv:1402.0108, 2014

Strobl EV, Visweswaran S. Markov boundary discovery with ridge regularized linear models. Journal of Causal Inference 2015; doi 10.1515/jci-2015-0011.

Visweswaran S, Ferreira A, Cooper GF. Personalized modeling for prediction with decision-path models. PLoS One 2015 Jun 22;10(6):e0131022. PMID: 26098570 PMCID: PMC4476684

Lu S, Mandava G, Yan G, Lu X. An exact algorithm for finding cancer driver somatic genome alterations: the weighted mutually exclusive maximum set cover problem. Algorithms Mol Biol. 2016 May 4;11:11. doi: 10.1186/s13015-016-0073-9. eCollection 2016. PubMed PMID: 27148394; PubMed Central PMCID: PMC4855522.

Haliloglu T, Bahar I. Adaptability of protein structures to enable functional interactions and evolutionary implications. Curr Opin Struct Biol. 2015 Dec;35:17-23. PubMed PMID: 26254902; PubMed Central PMCID: PMC4688206.

Hu D, Gur M, Zhou Z, Gamper A, Hung MC, Fujita N, Lan L, Bahar I, Wan Y. Interplay between arginine methylation and ubiquitylation regulates KLF4-mediated genome stability and carcinogenesis. Nat Commun. 2015 Sep 30;6:8419. PubMed PMID: 26420673; PubMed Central PMCID: PMC4598737.

Priedigkeit N, Wolfe N, Clark NL. Evolutionary signatures amongst disease genes permit novel methods for gene prioritization and construction of informative gene-based networks. PLoS Genet. 2015 Feb;11(2):e1004967. PubMed PMID: 25679399; PubMed Central PMCID: PMC4334549.

Wolfe NW, Clark NL. ERC analysis: web-based inference of gene function via evolutionary rate covariation. Bioinformatics. 2015 Dec 1;31(23):3835-7. PubMed PMID: 26243019; PubMed Central PMCID: PMC4751245.

Naeini MP, Cooper GF, Hauskrecht M. Binary Classifier Calibration Using a Bayesian Non-Parametric Approach. Proc SIAM Int Conf Data Min. 2015;2015:208-216. PubMed PMID: 26613068; PubMed Central PMCID: PMC4657569.

Plis S, Danks D, Freeman C, Calhoun V. Rate-Agnostic (Causal) Structure Learning. In: Advances in Neural Information Processing Systems 2015 (pp. 3285-3293). PMCID: PMC4863709

Spirtes P, Zhang K. Causal Discovery and Inference: Concepts and Recent Methodological Advances. Applied Informatics.PMCID: PMC4841209