CCD Publications





  • Kummerfeld E, Ramsey J. Causal Clustering for 1-Factor Measurement Models. KDD : proceedings. International Conference on Knowledge Discovery & Data Mining. 2016;2016:1655-1664. PubMed PMID: 27766182; PubMed Central PMCID: PMC5066593.
  • Malinsky D, Sprites P. Estimating Causal Effects with Ancestral Graph Markov Models. JMLR: Workshop and Conference Proceedings; PGM 2016. 2016;52:299-309. PubMed Central PMCID: PMC5313053.
  • Sedgewick AJ, Shi I, Donovan RM, Benos PV. Learning mixed graphical models with separate sparsity parameters and stability-based model selection. BMC bioinformatics. 2016 June 6;17 Suppl 5:175. PubMed PMID: 27294886; PubMed Central PMCID: PMC4905606.
  • Hyttinen A, Plis S, Järvisalo M, Eberhardt F, Danks D. Causal Discovery from Subsampled Time Series Data by Constraint Optimization. JMLR workshop and conference proceedings. 2016 August;52:216-227. PubMed PMID: 28203316; PubMed Central PMCID: PMC5305170.
  • Huang T, Alvarez AA, Pangeni RP, M Horbinski C, Lu S, Kim SH, James CD, J Raizer J, A Kessler J, Brenann CW, Sulman EP, Finocchiaro G, Tan M, Nishikawa R, Lu X, Nakano I, Hu B, Cheng SY. A regulatory circuit of miR-125b/miR-20b and Wnt signalling controls glioblastoma phenotypes through FZD6-modulated pathways. Nature communications. 2016 October 4;7:12885. PubMed PMID: 27698350; PubMed Central PMCID: PMC5059456.
  • Spagnolo DM, Gyanchandani R, Al-Kofahi Y, Stern AM, Lezon TR, Gough A, Meyer DE, Ginty F, Sarachan B, Fine J, Lee AV, Taylor DL, Chennubhotla SC. Pointwise mutual information quantifies intratumor heterogeneity in tissue sections labeled with multiple fluorescent biomarkers. Journal of pathology informatics. 2016 November 29;7:47. PubMed PMID: 27994939; PubMed Central PMCID: PMC5139455.
  • Lu S, Cai C, Yan G, Zhou Z, Wan Y, Chen V, Chen L, Cooper GF, Obeid LM, Hannun YA, Lee AV, Lu X. Signal-Oriented Pathway Analyses Reveal a Signaling Complex as a Synthetic Lethal Target for p53 Mutations. Cancer research. 2016 December 1;76(23):6785-6794. PubMed PMID: 27758891; PubMed Central PMCID: PMC5165695.
  • Zhou Z, Luo A, Shrivastava I, He M, Huang Y, Bahar I, Liu Z, Wan Y. Regulation of XIAP Turnover Reveals a Role for USP11 in Promotion of Tumorigenesis. EBioMedicine. 2017 February;15:48-61. PubMed PMID: 28040451; PubMed Central PMCID: PMC5233825.
  • Gong M, Zhang Kun, Liu T, Tao D, Glymour C, Scholkopf B. Domain Adaptation with Conditional Transferable Components. Proceedings of The 33rd International Conference on Machine Learning, JMLR: W&CP. 2016;48. PMCID: 5321138
  • Chikina M, Robinson JD, Clark NL. Hundreds of Genes Experienced Convergent Shifts in Selective Pressure in Marine Mammals. Molecular biology and evolution. 2016 September;33(9):2182-92. PubMed PMID: 27329977.
  • Ramsey J, Glymour M, Sanchez-Romero R, et. al. A million variables and more: the Fast Greedy Equivalence Search algorithm for learning high-dimensional graphical causal models, with an application to functional magnetic resonance images. International Journal of Data Science and Analytics. 2016 December 01. PMID: 28393106
  • Chen V, Paisley J, Lu X. Revealing common disease mechanisms shared by tumors of different tissues of origin through semantic representation of genomic alterations and topic modeling. BMC Genomics.BMC Genomics. 2017 Mar 14;18(Suppl 2):105. doi: 10.1186/s12864-017-3494-z. PMCID: PMC5374647. PMID: 28361690
  • Naeini MP, Cooper GF. Binary Classifer Calibration Using an Ensemble of Linear Trend Estimation. Proc SIAM Int Conf Data Min. 2016. PMCID: PMC5367639
  • Naeini MP, Cooper GF. Binary Classifier Calibration using an Ensemble of Near Isotonic Regression Models. Proceedings of ICDM 2016, IEEE International Confrence on Data Mining. 2016.
  • Ogarrio J, Spirtes P, Ramsey J. A Hybrid Causal Search Algorithm for Latent Variable Models. IN: JMLR Workshop and Conference Proceedings; From: International Conference on Probabilistic Graphical Models (PGM). 2016;52:368-79. PMCID: PMC5325717
  • Rathnam C, Lee S, Jiang Xia. An algorithm for direct causal learning of influences on patient outcomes. Artificial intelligence in medicine. 2016 November 05;75:1-15. PMCID: PMC5415921
  • Nguyen L, Tosun AB, Fine JL, Taylor L, Chennubhotla SC. Architectural patterns for differential diagnosis of proliferative breast lesions from histopathological images. 2017 IEEE 14th International Symposium on Biomedical Imaging, (ISBI 2017), Melbourne, VIC, 2017, pp.152-.155. doi:10.1109/ISBI.2017.7950490. NIHMSID 852397.
  • Scheines R, Ramsey J. Measurement Error and Causal Discovery. Proceedings of the UAI 2016 Workshop on Causation: Foundation to Application co-located with the 32nd Conference on Uncertainty in Artificial Intelligence (UAI 2016) Jersey City, USA. 2017 February 08; Vol 1792. PMCID: PMC5340263
  • Hanson SJ, Mastrovito D, Hanson C, Ramsey J, Glymour C. Scale-Free Exponents of Resting State are Biomarkers of Neuro-Typical and Atypical Brain Activity. bioRxiv preprint. 2016 August 10.
  • Sanchez-Romero R, Ramsey J, Liang JC, Glymour C. Identification of Mechanisms of Functional Signaling Between Human Hippocampus Regions. bioRxiv preprint online. 2016 December.
  • Wang Q, Miskov-Zivanov N, Liu Bing, Faeder JR., Lotze M, Clarke EM. Formal Modeling and Analysis of Pancreatic Cancer Microenvironment. [Internet]. 16 pages. Available from:
  • Malinsky D, Spirtes P. Estimating Causal Effects with Ancestral Graph Markov Models. [Internet]. Pittsburgh PA: Technical Report No. CMU-PHIL-194; 2016 July 13. Available from:
  • Ramsey JD, Malinsky D. Comparing the Performance of Graphical Structure Learning Algorithms with TETRAD. [Internet]. Technical report: 22 pages. Available from:
  • Strobl Eric, Visweswaran S, Zhang Kun. Approximate Kernel-based Conditional Independence Tests for Fast Non-Parametric Causal Discovery. [Internet]. 25 pages. Available from:
  • 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)
  • Böhm S, Szakal B, Herken BW, Sullivan MR, Mihalevic MJ, Kabbinavar FF, Branzei D, Clark NL, Bernstein KA. The Budding Yeast Ubiquitin Protease Ubp7 Is a Novel Component Involved in S Phase Progression. J Biol Chem. 2016 Feb 26;291(9):4442-52. doi: 10.1074/jbc.M115.671057. Epub 2016 Jan 6. PMID: 26740628; PMCID:     PMC4813472.


  • 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 N, Lu 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