Publications

  • C. Azencott, DREAM Idea Challenge Consortium, T. Norman, S. Friend, G. Stolovitzky, A. Goldenberg (2017) The inconvenience of data of convenience: computational research beyond post-mortem analyses. Nature Methods, 14, pp. 937–938.
  • Y. Mamatjan, S. Agnihotri, A. Goldenberg, P. Tonge, G. Zadeh, K. Aldape. (2017) Molecular signatures for tumor classification: an analysis of TCGA data. Journal of Molecular Diagnostics. In Press.
  • A. Mezlini, A. Goldenberg (2017) Incorporating Networks in a Probabilistic Graphical Model to Find Drivers for Complex Human Diseases. PloS Computational Biology, Oct 12;13(10):e1005580.
  • B. Wang, L. Huang, Y. Zhu, A. Kundaje, S. Batzoglou, A. Goldenberg (2017) Vicus: Exploiting Local Structures to Improve Biological Network Analysis. PloS Computational Biology, Oct 12;13(10):e1005621
  • H. Hou, L. Uuskula-Reimand, M. Makarem, S. Saleh, C. Corre, A. Metcalf, A. Goldenberg*, M. Palmert*, M. Wilson* (2017) Gene expression profiling of puberty-associated genes reveals abundant itssue and sex-specific changes across postnatal development. Human Molecular Genetics. Sep 15;26(18):3585-3599
  • TCGA Consortium (2017). Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma. Cancer Cell, 32(2), pp.185-203
  • F.MG. Cavalli, M. Remke, L. Rampasek, D.JH Shih, ..., A.Goldenberg*, V. Ramaswamy*, M.D. Taylor* (2017) Intertumoral heterogeneity within medulloblastoma subgroups. Cancer Cell, 31(6): 737-754
  • M. Leung, D. G. Bassani, A. Racine-Poon, A. Goldenberg, S. A. Ali, Gagandeep Kang, P. S. Premkumar and D E. Roth. (2017) Conditional Random Slope: A new approach for estimating individual child growth velocity in epidemiological research. American Journal of Human Biology, accepted. DOI: 10.1002/ajhb.23009
  • N. El-Hachem, D.Gendoo, L.Ghoraie, Z.Safikhani, P.Smirnov, C.Chung, K.Deng, A.Fang, E.Birkwood, C.Ho, R.Isserlin, G.Bader, A.Goldenberg, and B.Haibe-Kains (2017). Integrative cancer pharmacogenomics to infer large-scale drug taxonomy. Cancer Research, 77(11):3057-3069
  • Z. Safikhani, N. El-Hachem, P. Smirnov, M. Freeman, A. Goldenberg, N.J. Birkbak, A.H. Beck, H.J.W.L. Aerts, J. Quackenbush & B. Haibe-Kains (2016). Safikhani et al. reply. Nature, 540, E2–E4
  • Z. Safikhani, N. El Hachem, R. Quevedo, P. Smirnov, A. Goldenberg, N.J. Birkbak, C. Mason, C. Hatzis, L. Shi, H.J. Aerts, J. Quackenbush and B. Haibe-Kains. (2016) Assessment of pharmacogenomic agreement. F1000Research, 5, pp 825
  • SK Sieberts, F Zhu, J Garcia, E Stahl, A. Pratap, G. Pandey, D. Pappas, D. Aguilar, B. Anton, J. Bonet, R. Eksi, O. Fornes, E. Guney, G. Li, M.A Marin, B. Panwar, J. PlanasIglesias, D. Poglayen, J. Cui, AO. Flcao, C. Suver, B. Hoff, VSK. Blagurusamy, D. Dillenberger, EC. Neto, T. Norman, T. Aittokallio, M. Ammad-ud-din, C. Azencott, V. Bellon, V. Boeva, K. Bunte…, A. Goldenberg,…, M Hajiloo, D. Hidru, …, B. Wang, …, L. Mangravite(2016) Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nature Communications, 7(1), p. 12460
  • P Smirnov, Z Safikhani, N El-Hachem, D Wang, A She, C Olsen, M Freeman, H Selby, D Gendoo, P Grossman, A Beck, H Aerts, M Lupien, A Goldenberg, B Haibe-Kains. (2015) PharmacoGx: an R package for analysis of large pharmacogenomics datasets. In submission to Bioinformatics.
  • C Corre, G Shinoda, H Zhu, DL Cousminer, C Crossman, C Bellissimo, A Goldenberg, GQ Daley, MR Palmart. (2015) Sex specific regulation of weight and puberty by Lin28/let-7 axis. In submission to the Journal of Endocrinology.
  • R. Colak, T. Kim, H Kazan, Y Oh, M Cruz, A Valladares, J Peralta, J Escobedo, E Parra, P.M. Kim and A. Goldenberg (2015) JBASE: Joint Bayesian Analysis of Sub-phenotypes and Epistasis. Bioinformatics.
  • Saria, S., A. Goldenberg (2015). Subtyping: What it is and its role in precision medicine. IEEE Intelligent Systems Magazine. 30(4). pp 70-75. D Hidru and A Goldenberg (2014) EquiNMF: Graph Regularized Multiview Nonnegative Matrix Factorization. Workshop on Machine Learning in Computational Biology co-located with NIPS.
  • A.M. Mezlini, C. Baciu, S. Morrissy, M. Taylor, D. Malkin, A. Goldenberg (2014) Quantity or quality that is the question: integrative genome-wide association. In Proceedings of the ASHG Conference.
  • B Wang, A Mezlini, F Demir, M Fiume, T Zu, M Brudno, B Haibe-Kains and A Goldenberg (2014) Similarity network fusion for aggregating data types on a genomic scale. Nature Methods. Online Jan 26.
  • A Mezlini, B Wang, A Deshwar, Q Morris and A Goldenberg (2013) Identifying cancer specific functionally relevant miRNAs from gene expression and miRNA-to-gene networks using regularized regression. PloS One, 8(10).
  • Y Li, A Goldenberg, K Wong, Z Zhang (2013) A probabilistic approach to explore human microRNA targetome by integrating microRNA-overexpression data and sequence information. Bioinformatics
  • A M Mezlini, E JM Smith, M Fiume, O Buske, G Savich, S Shah, S Aparicion, D Chiang, A Goldenberg and M Brudno (2013) iReckon: Simultaneous isoform discovery and abundance estimation from RNA-seq data. Genome Research.
  • B Wang and A Goldenberg (2012) Local Diffusion and Cluster Score (LDCS) for Disease Subtyping. Electronic proceeds of the workshop on Machine Learning in Computational Biology, collocated w/ NIPS
  • Mostafavi S, Goldenberg A, Morris Q (2012) Labeling Nodes Using Three Degrees of Propagation. PLoS ONE 7(12): e51947. doi:10.1371/journal.pone.0051947
  • M.Alshalalfa, G. Bader, A. Goldenberg, Q. Morris, R. Alhajj (2012) Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study. BMC Systems Biology 6(1): 112
  • B.Wang, A. Mezlini and A. Goldenberg (2012) Combining multiple biological domains using patient network fusion. In Proceedings of the Machine Learning in Genetics and Genomics Workshop co-located with ICML
  • D.Warde-Farley, M. Brudno, Q. Morris, A Goldenberg (2012) Sub-phenotype Modeling in GWAS. In Proceedings of the Pacific Symposium on Biocomputing
  • A Goldenberg, S Mostafavi, G Quon, P Boutros, and Q Morris. (2011) Unsupervised detection of genes of influence in lung cancer using biological networks. Bioinformatics.
  • A Goldenberg and A Zheng (2006) Exploratory Study of a New Model for Evolving Networks, Lecture Notes in Computer Science, Vol 4503.
  • A Goldenberg, D Warde-Farley, M. Brudno, Q. Morris (2010) Mixture model for sub-phenotyping. Electronic proceedings of the workshop on Machine Learning in Computational Biology, collocated with NIPS
  • S Mostafavi, A Goldenberg, and Q Morris. (2010) Predicting Node Labels in Large Networks. Electronic Proceedings of the Workshop on Networks Across Disciplines: Theory and Applications
  • S Mostafavi, A Goldenberg and Q Morris. (2010) Predicting Node Characteristics from Molecular Networks. Chapter in Network Biology: Methods and Protocols, Springer
  • A Goldenberg, A Zheng, S Fienberg and E Airoldi (2009) A Survey of Statistical Network Models, Foundations and Trends in Machine Learning, Vol 2 (2): pp 129-233
  • A Goldenberg (2007) Scalable Graphical Models for Social Networks. PhD Thesis.
  • A Goldenberg and A Zheng (2006) Exploratory Study of a New Model for Evolving Networks, Lecture Notes in Computer Science, Vol 4503.
  • A Goldenberg and A Moore (2005) Bayes Net Graphs to Understand Coauthorship Networks, KDD Workshop on Link Discovery: Issues, Approaches and Applications.
  • A Goldenberg and A Moore (2004) Tractable Learning of Large Bayes Net Structures from Sparse Data, Proceedings of the Twenty First International Conference on Machine Learning.
  • A Goldenberg, J Kubica, P Komarek, A Moore and J Schneider (2003) A Comparison of Statistical and Machine Learning Algorithms on the Task of Link Completion, KDD Workshop on Link Analysis for Detecting Complex Behavior.
  • A Goldenberg and A Moore (2003) Empirical Bayes Screening for Link Analysis, Workshop on Text Analysis and Link Detection, International Joint Conference on Artificial Intelligence
  • A Goldenberg, G Shmueli, R Caruana and S Fienberg (2002) Early statistical detection of anthrax outbreaks by tracking over-the-counter medication sales, PNAS, 99, 5237 - 5240.
  • P Yu, A Goldenberg and Z Bi (2001) Time Series Forecasting Using Wavelets with Predictor-Corrector Boundary Treatment, KDD Workshop on Temporal Data Mining.
  • M Kantardzic, A Goldenberg, T Howe and P Fagey (2001) Artificial Neural Network Approach to Data Analysis and Parameter Estimation in Experimental Spectroscopy, Informatica, Vol 25, 1926.
Abstracts
  • A.Goldenberg and B. Wang. Optimizing risk stratification to discover novel neuroblastoma genes, American Society for Human Genetics (ASHG), San Francisco, 2012
  • B.Wang, A. Mezlini and A. Goldenberg. Combining multiple biological domains using patient network fusion. Oral Presentation. International Conference on Systems Biology (ICSB), Toronto,2012
  • R.Colak, H., Kazan, A. Hussin, Y. Oh, P.M. Kim, A. Goldenberg JBASE: Joint Bayesian Analyis of Sub-phenotypes and Epistasis, Poster, Genome Informatics, Cold Spring Harbour, NY, USA, 2011
  • A.Goldenberg, S. Mostafavi, G. Quon, A. Deshwar, P.C, Boutros and Q. Morris. Identifying miRNAs regulatory networks using mRNA expression data, Oral presentation, Systems Biology: Networks, Cold Spring Harbour, NY 2011
  • A.Goldenberg, S. Mostafavi, G. Quon, P.C. Boutros and Q. Morris. Identifying genes important at the onset of lung cancer, Poster, AACR-NCI Conference on Systems Biology: Confronting the Complexity of Cancer, San Diego, 2011
  • D.Foster, A. Goldenberg, L. Ungar Maximal Subset Feature Selection for BioInformatics Ungar Snowbird Learning Workshop, 2008