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About Sickkids
About SickKids

Anna Goldenberg, PhD

Research Institute
Scientist
Genetics & Genome Biology

University of Toronto
Assistant Professor
Department of Computer Science

Chair Positions
Canada Research Chair
Computational Medicine


Phone: 416.813.1564
Email: anna.goldenberg@sickkids.ca

For more information, visit:

Goldenberg Lab

Research Interests

  • Computational biology
  • Machine learning
  • Sub-phenotyping
  • Association studies
  • Networks

Research Activities

  • Developing statistical and machine learning methodology for sub-phenotyping
  • Refining the landscape of the disease by combining heterogeneous data sources
  • Method development for very large-scale data
  • Inferring, refining and using network-type data to improve prediction and disease understanding

Publications

Azencott CA, Aittokallio T, Roy S; DREAM Idea Challenge Consortium, Norman T, Friend S, Stolovitzky G, Goldenberg A. (2017) The inconvenience of data of convenience: computational research beyond post-mortem analyses. Nature Methods, 14, pp. 937–938.

Mamatjan Y, Agnihotri S, Goldenberg A, Tonge P, Mansouri S, Zadeh G, Aldape K. (2017) Molecular signatures for tumor classification: an analysis of TCGA data. Journal of Molecular Diagnostics. J Mol Diagn. 2017 Nov;19(6):881-891. doi: 10.1016/j.jmoldx.2017.07.008. Epub 2017 Sep 1. PMID: 28867603

Mezlini A, Goldenberg A. (2017) Incorporating networks in a probabilistic graphical model to find drivers for complex human diseases. PloS Computational Biology, Oct 12;13(10):e1005580.

Wang B, Huang L, Zhu Y, Kundaje A, Batzoglou S, Goldenberg A. (2017) Vicus: Exploiting local structures to improve biological network analysis. PloS Computational Biology, Oct 12;13(10):e1005621.

Hou H, Uuskula-Reimand L, Makarem M, Saleh S, Corre C, Metcalf A, Goldenberg A*, Palmert M*, Wilson M*. (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.

Cavalli FMG, Remke M, Rampasek L, Peacock J, Shih DJH, Luu B, Garzia L, Torchia J, Nor C, Morrissy AS, Agnihotri S, Thompson YY, Kuzan-Fischer CM, Farooq H, Isaev K, Daniels C, Cho BK, Kim SK, Wang KC, Lee JY, Grajkowska WA, Perek-Polnik M, Vasiljevic A, Faure-Conter C, Jouvet A, Giannini C, Nageswara Rao AA, Li KKW, Ng HK, Eberhart CG, Pollack IF, Hamilton RL, Gillespie GY, Olson JM, Leary S, Weiss WA, Lach B, Chambless LB, Thompson RC, Cooper MK, Vibhakar R, Hauser P, van Veelen MC, Kros JM, French PJ, Ra YS, Kumabe T, López-Aguilar E, Zitterbart K, Sterba J, Finocchiaro G, Massimino M, Van Meir EG, Osuka S, Shofuda T, Klekner A, Zollo M, Leonard JR, Rubin JB, Jabado N, Albrecht S, Mora J, Van Meter TE, Jung S, Moore AS, Hallahan AR, Chan JA, Tirapelli DPC, Carlotti CG, Fouladi M, Pimentel J, Faria CC, Saad AG, Massimi L, Liau LM, Wheeler H, Nakamura H, Elbabaa SK, Perezpeña-Diazconti M, Chico Ponce de León F, Robinson S, Zapotocky M, Lassaletta A, Huang A, Hawkins CE, Tabori U, Bouffet E, Bartels U, Dirks PB, Rutka JT, Bader GD, Reimand J, Goldenberg A*, Ramaswamy V*, Taylor MD*. (2017) Intertumoral heterogeneity within medulloblastoma subgroups. Cancer Cell, 31(6): 737-754.

Leung M, Bassani DG, Racine-Poon A, Goldenberg A, Ali SA, Kang G, Premkumar PS, Roth DE. (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

El-Hachem N, Gendoo D, Ghoraie L, Safikhani Z, Smirnov P, Chung C, Deng K, Fang A, Birkwood E, Ho C, Isserlin R, Bader G, Goldenberg A, Haibe-Kains, B. (2017). Integrative cancer pharmacogenomics to infer large-scale drug taxonomy. Cancer Research, 77(11):3057-3069.

Safikhani Z, El-Hachem N, Smirnov P, Freeman M, Goldenberg A, Birkbak NJ, Beck AH, Aerts HJWL, Quackenbush J, Baibe-Kains B. (2016). Safikhani et al. reply. Nature, 540, E2–E4

Safikhani Z, El-Hachem N, Quevedo R, Smirnov P, Goldenberg A, Birkbak NJ, Mason C, Hatzis C, Shi L, Aerts HJ, Quackenbush J, Haibe-Kains B. (2016) Assessment of pharmacogenomic agreement. F1000Research, 5, pp 825.

Sieberts SK, Zhu F, García-García J, Stahl E, Pratap A, Pandey G, Pappas D, Aguilar D, Anton B, Bonet J, Eksi R, Fornés O, Guney E, Li H, Marín MA, Panwar B, Planas-Iglesias J, Poglayen D, Cui J, Falcao AO, Suver C, Hoff B, Balagurusamy VS, Dillenberger D, Neto EC, Norman T, Aittokallio T, Ammad-Ud-Din M, Azencott CA, Bellón V, Boeva V, Bunte K, Chheda H, Cheng L, Corander J, Dumontier M, Goldenberg A, Gopalacharyulu P, Hajiloo M, Hidru D, Jaiswal A, Kaski S, Khalfaoui B, Khan SA, Kramer ER, Marttinen P, Mezlini AM, Molparia B, Pirinen M, Saarela J, Samwald M, Stoven V, Tang H, Tang J, Torkamani A, Vert JP, Wang B, Wang T, Wennerberg K, Wineinger NE, Xiao G, Xie Y, Yeung R, Zhan X, Zhao C; Members of the Rheumatoid Arthritis Challenge Consortium, Greenberg J, Kremer J, Michaud K, Barton A, Coenen M, Mariette X, Miceli C, Shadick N, Weinblatt M, de Vries N, Tak PP, Gerlag D, Huizinga TW, Kurreeman F, Allaart CF, Bridges SL Jr, Criswell L, Moreland L, Klareskog L, Saevarsdottir S, Padyukov L, Gregersen PK, Friend S, Plenge R, Stolovitzky G, Oliva B, Guan Y, Mangravite LM. (2016) Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nature Communications, 7(1), p. 12460.

Corre C, Shinoda G, Zhu H, Cousminer DL, Crossman C, Bellissimo C, Goldenberg A, Daley GQ, Palmert MR.  (2016) Sex specific regulation of weight and puberty by Lin28/let-7 axis. Journal of Endocrinology.

Rampasek L, Goldenberg A. (2016). TensorFlow: biology’s gateway to deep learning? Cell systems, 2(1), 12-14.

Colak R, Kim T, Kazan H, Oh Y, Cruz M, Valladares A, Peralta J, Escobedo J, Parra E, Kim PM, Goldenberg A. JBASE: Joint Bayesian analysis of sub-phenotypes and epistasis, Bioinformatics 32 (2), pp 203–210.

Smirnov P, Safikhani Z, El-Hachem N, Wang D, She A, Olsen C, Freeman M, Selby H, Gendoo D, Grossman P, Beck A, Aerta H, Lupien M, Goldenberg A, Haibe-Kains B. (2016) PharmacoGx: an R package for analysis of large pharmacogenomics datasets. Bioinformatics. 32(8), 1244–1246

Saria S, Goldenberg A. (2015). Subtyping: what it is and its role in precision medicine. IEEE Intelligent Systems Magazine. 30(4). 70-75.

Wang B, Mezlini A, Demir F, Fiume M, Zu T, Brudno M, Haibe-Kains B, Goldenberg A. (2014) Similarity network fusion for aggregating data types on genomic scale. Nature Methods. 11(3).  pp 333-337.

Mezlini A, Wang B, Deshwar A, Morris Q, Goldenberg A. (2013) Identifying cancer specific functionally relevant miRNAs from gene expression and miRNA-to-gene networks using regularized regression. PloS One, 8(10). E73168.

Li Y, Goldenberg A, Wong K, Zhang Z. (2013) A probabilistic approach to explore human microRNA targetome by integrating microRNA-overexpression data and sequence information. Bioinformatics 30 (5) pp 621-8.

Mezlini A, Smith E, Flume M, Buske O, Shah S, Aparicio S, Goldenberg A, Brudno M. (2013) iReckon: simultaneous isoform discovery and abundance estimation from RNA-Seq data. Genome Research. 23(3) p. 519-29

Warde-Farley D, Brudno M, Morris Q,  Goldenberg A. (2012) Mixture model for sub-phenotyping in GWAS. Pacific Symposium on Biocomputing 2012

Goldenberg A, Mostafavi  S, Quon G, Boutros PD, Morris QD. (2011) Unsupervised detection of genes of influence in lung cancer using biological networks. Bioinformatics 2011; doi: 10.1093/bioinformatics/btr533

Mostafavi S, Goldenberg A, Morris Q. (2010) Predicting node labels in large networks. Electronic Proceedings of the Workshop on Networks Across Disciplines: Theory and Applications.

Goldenberg A, Zheng A, Fienberg S, Airoldi E. (2009) A survey of statistical network models. Foundations and Trends in Machine Learning, Vol 2 (2): pp 129-233.

Goldenberg A, Zheng A. (2006) Exploratory study of a new model for evolving networks, Lecture Notes in Computer Science, Vol 4503.

Goldenberg A, Moore A. (2004) Tractable Learning of large Bayes net structures from sparse data, Proceedings of the 21st International Conference on Machine Learning.

Goldenberg A, Kubica J, Komarek P, Moore A, Schneider J. (2003) A comparison of statistical and machine learning algorithms on the task of link completion, Proceedings of the KDD Workshop on Link Analysis for Detecting Complex Behavior.

Goldenberg A, Shmueli G, Caruana R, Fienberg S. (2002) Early statistical detection of anthrax outbreaks by tracking over-the-counter medication sales, PNAS, 99, 5237 -- 5240.

Kantardzic M, Goldenberg A, Howe T, Fagey P. (2001) Artificial neural network approach to data analysis and parameter estimation in experimental spectroscopy, Informatica, Vol 25, 1926.