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Anna Goldenberg

TitleScientist
InstitutionThe Hospital for Sick Children
DepartmentGenetics and Genome Biology
Address555 University Avenue
Toronto ON M5G 1X8
Phone416-813-1500
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    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Shen SY, Singhania R, Fehringer G, Chakravarthy A, Roehrl MHA, Chadwick D, Zuzarte PC, Borgida A, Wang TT, Li T, Kis O, Zhao Z, Spreafico A, Medina TDS, Wang Y, Roulois D, Ettayebi I, Chen Z, Chow S, Murphy T, Arruda A, O'Kane GM, Liu J, Mansour M, McPherson JD, O'Brien C, Leighl N, Bedard PL, Fleshner N, Liu G, Minden MD, Gallinger S, Goldenberg A, Pugh TJ, Hoffman MM, Bratman SV, Hung RJ, De Carvalho DD. Sensitive tumour detection and classification using plasma cell-free DNA methylomes. Nature. 2018 Nov; 563(7732):579-583. PMID: 30429608.
      View in: PubMed
    2. de Vega WC, Erdman L, Vernon SD, Goldenberg A, McGowan PO. Integration of DNA methylation & health scores identifies subtypes in myalgic encephalomyelitis/chronic fatigue syndrome. Epigenomics. 2018 May; 10(5):539-557. PMID: 29692205.
      View in: PubMed
    3. Rampasek L, Goldenberg A. Learning from Everyday Images Enables Expert-like Diagnosis of Retinal Diseases. Cell. 2018 Feb 22; 172(5):893-895. PMID: 29474917.
      View in: PubMed
    4. Zizzo AN, Erdman L, Feldman BM, Goldenberg A. Similarity Network Fusion: A Novel Application to Making Clinical Diagnoses. Rheum Dis Clin North Am. 2018 May; 44(2):285-293. PMID: 29622295.
      View in: PubMed
    5. Frank B, Maher Z, Hazelton JP, Resnick S, Dauer E, Goldenberg A, Lubitz AL, Smith BP, Saillant NN, Reilly PM, Seamon MJ. Venous thromboembolism after major venous injuries: Competing priorities. J Trauma Acute Care Surg. 2017 Dec; 83(6):1095-1101. PMID: 28700413.
      View in: PubMed
    6. Stefanik L, Erdman L, Ameis SH, Foussias G, Mulsant BH, Behdinan T, Goldenberg A, O'Donnell LJ, Voineskos AN. Brain-Behavior Participant Similarity Networks Among Youth and Emerging Adults with Schizophrenia Spectrum, Autism Spectrum, or Bipolar Disorder and Matched Controls. Neuropsychopharmacology. 2018 Apr; 43(5):1180-1188. PMID: 29105664.
      View in: PubMed
    7. Mezlini AM, Goldenberg A. Incorporating networks in a probabilistic graphical model to find drivers for complex human diseases. PLoS Comput Biol. 2017 Oct; 13(10):e1005580. PMID: 29023450.
      View in: PubMed
    8. Wang B, Huang L, Zhu Y, Kundaje A, Batzoglou S, Goldenberg A. Vicus: Exploiting local structures to improve network-based analysis of biological data. PLoS Comput Biol. 2017 Oct; 13(10):e1005621. PMID: 29023470.
      View in: PubMed
    9. Azencott CA, Aittokallio T, Roy S, Norman T, Friend S, Stolovitzky G, Goldenberg A. The inconvenience of data of convenience: computational research beyond post-mortem analyses. Nat Methods. 2017 Sep 29; 14(10):937-938. PMID: 28960198.
      View in: PubMed
    10. Hou H, Uusküla-Reimand L, Makarem M, Corre C, Saleh S, Metcalf A, Goldenberg A, Palmert MR, Wilson MD. Gene expression profiling of puberty-associated genes reveals abundant tissue and sex-specific changes across postnatal development. Hum Mol Genet. 2017 09 15; 26(18):3585-3599. PMID: 28911201.
      View in: PubMed
    11. Mamatjan Y, Agnihotri S, Goldenberg A, Tonge P, Mansouri S, Zadeh G, Aldape K. Molecular Signatures for Tumor Classification: An Analysis of The Cancer Genome Atlas Data. J Mol Diagn. 2017 11; 19(6):881-891. PMID: 28867603.
      View in: PubMed
    12. 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. Intertumoral Heterogeneity within Medulloblastoma Subgroups. Cancer Cell. 2017 06 12; 31(6):737-754.e6. PMID: 28609654.
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    13. Leung M, Bassani DG, Racine-Poon A, Goldenberg A, Ali SA, Kang G, Premkumar PS, Roth DE. Conditional random slope: A new approach for estimating individual child growth velocity in epidemiological research. Am J Hum Biol. 2017 Sep 10; 29(5). PMID: 28429467.
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    14. El-Hachem N, Gendoo DMA, Ghoraie LS, Safikhani Z, Smirnov P, Chung C, Deng K, Fang A, Birkwood E, Ho C, Isserlin R, Bader GD, Goldenberg A, Haibe-Kains B. Integrative Cancer Pharmacogenomics to Infer Large-Scale Drug Taxonomy. Cancer Res. 2017 06 01; 77(11):3057-3069. PMID: 28314784.
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    15. Safikhani Z, El-Hachem N, Smirnov P, Freeman M, Goldenberg A, Birkbak NJ, Beck AH, Aerts HJ, Quackenbush J, Haibe-Kains B. Safikhani et al. reply. Nature. 2016 11 30; 540(7631):E6-E8. PMID: 27905416.
      View in: PubMed
    16. Safikhani Z, El-Hachem N, Smirnov P, Freeman M, Goldenberg A, Birkbak NJ, Beck AH, Aerts HJ, Quackenbush J, Haibe-Kains B. Safikhani et al. reply. Nature. 2016 11 30; 540(7631):E11-E12. PMID: 27905423.
      View in: PubMed
    17. Safikhani Z, El-Hachem N, Smirnov P, Freeman M, Goldenberg A, Birkbak NJ, Beck AH, Aerts HJ, Quackenbush J, Haibe-Kains B. Safikhani et al. reply. Nature. 2016 11 30; 540(7631):E2-E4. PMID: 27905430.
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    18. 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, 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, Criswell L, Moreland L, Klareskog L, Saevarsdottir S, Padyukov L, Gregersen PK, Friend S, Plenge R, Stolovitzky G, Oliva B, Guan Y, Mangravite LM. Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nat Commun. 2016 10 10; 7:13205. PMID: 27721464.
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    19. Safikhani Z, Smirnov P, Freeman M, El-Hachem N, She A, Rene Q, Goldenberg A, Birkbak NJ, Hatzis C, Shi L, Beck AH, Aerts HJWL, Quackenbush J, Haibe-Kains B. Revisiting inconsistency in large pharmacogenomic studies. F1000Res. 2016; 5:2333. PMID: 28928933.
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    20. 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, 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, Louis Bridges S, Bridges SL, Criswell L, Moreland L, Klareskog L, Saevarsdottir S, Padyukov L, Gregersen PK, Friend S, Plenge R, Stolovitzky G, Oliva B, Guan Y, Mangravite LM. Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nat Commun. 2016 08 23; 7:12460. PMID: 27549343.
      View in: PubMed
    21. Safikhani Z, El-Hachem N, Quevedo R, Smirnov P, Goldenberg A, Juul Birkbak N, Mason C, Hatzis C, Shi L, Aerts HJ, Quackenbush J, Haibe-Kains B. Assessment of pharmacogenomic agreement. F1000Res. 2016; 5:825. PMID: 27408686; PMCID: PMC4926729.
    22. Rampasek L, Goldenberg A. TensorFlow: Biology's Gateway to Deep Learning? Cell Syst. 2016 01 27; 2(1):12-4. PMID: 27136685.
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    23. Corre C, Shinoda G, Zhu H, Cousminer DL, Crossman C, Bellissimo C, Goldenberg A, Daley GQ, Palmert MR. Sex-specific regulation of weight and puberty by the Lin28/let-7 axis. J Endocrinol. 2016 Mar; 228(3):179-91. PMID: 26698568; PMCID: PMC4772724 [Available on 03/01/17].
    24. Smirnov P, Safikhani Z, El-Hachem N, Wang D, She A, Olsen C, Freeman M, Selby H, Gendoo DM, Grossmann P, Beck AH, Aerts HJ, Lupien M, Goldenberg A, Haibe-Kains B. PharmacoGx: an R package for analysis of large pharmacogenomic datasets. Bioinformatics. 2016 04 15; 32(8):1244-6. PMID: 26656004.
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    25. Colak R, Kim T, Kazan H, Oh Y, Cruz M, Valladares-Salgado A, Peralta J, Escobedo J, Parra EJ, Kim PM, Goldenberg A. JBASE: Joint Bayesian Analysis of Subphenotypes and Epistasis. Bioinformatics. 2016 Jan 15; 32(2):203-10. PMID: 26411870; PMCID: PMC4708100.
    26. Wang B, Mezlini AM, Demir F, Fiume M, Tu Z, Brudno M, Haibe-Kains B, Goldenberg A. Similarity network fusion for aggregating data types on a genomic scale. Nat Methods. 2014 Mar; 11(3):333-7. PMID: 24464287.
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    27. Li Y, Goldenberg A, Wong KC, Zhang Z. A probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information. Bioinformatics. 2014 Mar 01; 30(5):621-8. PMID: 24135265.
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    28. Mezlini AM, Wang B, Deshwar A, Morris Q, Goldenberg A. Identifying cancer specific functionally relevant miRNAs from gene expression and miRNA-to-gene networks using regularized regression. PLoS One. 2013; 8(10):e73168. PMID: 24098326; PMCID: PMC3788788.
    29. Mostafavi S, Goldenberg A, Morris Q. Labeling nodes using three degrees of propagation. PLoS One. 2012; 7(12):e51947. PMID: 23284828; PMCID: PMC3532359.
    30. Mezlini AM, Smith EJ, Fiume M, Buske O, Savich GL, Shah S, Aparicio S, Chiang DY, Goldenberg A, Brudno M. iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data. Genome Res. 2013 Mar; 23(3):519-29. PMID: 23204306; PMCID: PMC3589540.
    31. Alshalalfa M, Bader GD, Goldenberg A, Morris Q, Alhajj R. Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study. BMC Syst Biol. 2012 Aug 28; 6:112. PMID: 22929553; PMCID: PMC3490713.
    32. Warde-Farley D, Brudno M, Morris Q, Goldenberg A. Mixture model for sub-phenotyping in GWAS. Pac Symp Biocomput. 2012; 363-74. PMID: 22174291.
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    33. Goldenberg A, Mostafavi S, Quon G, Boutros PC, Morris QD. Unsupervised detection of genes of influence in lung cancer using biological networks. Bioinformatics. 2011 Nov 15; 27(22):3166-72. PMID: 21965819.
      View in: PubMed
    34. Mostafavi S, Goldenberg A, Morris Q. Predicting node characteristics from molecular networks. Methods Mol Biol. 2011; 781:399-414. PMID: 21877293.
      View in: PubMed
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