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Anna Goldenberg

TitleSenior Scientist
InstitutionThe Hospital for Sick Children
DepartmentGenetics and Genome Biology
Address555 University Avenue
Toronto ON M5G 1X8
Phone416-813-1500
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    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. Mezlini AM, Das S, Goldenberg A. Finding associations in a heterogeneous setting: statistical test for aberration enrichment. Genome Med. 2021 Apr 23; 13(1):68. PMID: 33892787.
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    2. Sokolowski DJ, Faykoo-Martinez M, Erdman L, Hou H, Chan C, Zhu H, Holmes MM, Goldenberg A, Wilson MD. Single-cell mapper (scMappR): using scRNA-seq to infer the cell-type specificities of differentially expressed genes. NAR Genom Bioinform. 2021 Mar; 3(1):lqab011. PMID: 33655208.
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    3. Yasodhara A, Dong V, Azhie A, Goldenberg A, Bhat M. Identifying Modifiable Predictors of Long-Term Survival in Liver Transplant Recipients With Diabetes Mellitus Using Machine Learning. Liver Transpl. 2021 Apr; 27(4):536-547. PMID: 33113221.
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    4. McCradden MD, Joshi S, Anderson JA, Mazwi M, Goldenberg A, Zlotnik Shaul R. Patient safety and quality improvement: Ethical principles for a regulatory approach to bias in healthcare machine learning. J Am Med Inform Assoc. 2020 12 09; 27(12):2024-2027. PMID: 32585698.
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    5. Jacobs GR, Voineskos AN, Hawco C, Stefanik L, Forde NJ, Dickie EW, Lai MC, Szatmari P, Schachar R, Crosbie J, Arnold PD, Goldenberg A, Erdman L, Ameis SH. Integration of brain and behavior measures for identification of data-driven groups cutting across children with ASD, ADHD, or OCD. Neuropsychopharmacology. 2021 02; 46(3):643-653. PMID: 33168947.
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    6. Haibe-Kains B, Adam GA, Hosny A, Khodakarami F, Waldron L, Wang B, McIntosh C, Goldenberg A, Kundaje A, Greene CS, Broderick T, Hoffman MM, Leek JT, Korthauer K, Huber W, Brazma A, Pineau J, Tibshirani R, Hastie T, Ioannidis JPA, Quackenbush J, Aerts HJWL. Transparency and reproducibility in artificial intelligence. Nature. 2020 Oct; 586(7829):E14-E16. PMID: 33057217.
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    7. Adam G, Rampášek L, Safikhani Z, Smirnov P, Haibe-Kains B, Goldenberg A. Machine learning approaches to drug response prediction: challenges and recent progress. NPJ Precis Oncol. 2020; 4:19. PMID: 32566759.
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    8. Liu Z, Nguyen QPH, Guan Q, Albulescu A, Erdman L, Mahdaviyeh Y, Kang J, Ouyang H, Hegele RG, Moraes T, Goldenberg A, Dell SD, Mennella V. A quantitative super-resolution imaging toolbox for diagnosis of motile ciliopathies. Sci Transl Med. 2020 03 18; 12(535). PMID: 32188719.
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    9. Spann A, Yasodhara A, Kang J, Watt K, Wang B, Goldenberg A, Bhat M. Applying Machine Learning in Liver Disease and Transplantation: A Comprehensive Review. Hepatology. 2020 03; 71(3):1093-1105. PMID: 31907954.
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    10. Eng SWM, Olazagasti JM, Goldenberg A, Crowson CS, Oddis CV, Niewold TB, Yeung RSM, Reed AM. A Clinically and Biologically Based Subclassification of the Idiopathic Inflammatory Myopathies Using Machine Learning. ACR Open Rheumatol. 2020 Mar; 2(3):158-166. PMID: 32039563.
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    11. Aristizabal MJ, Anreiter I, Halldorsdottir T, Odgers CL, McDade TW, Goldenberg A, Mostafavi S, Kobor MS, Binder EB, Sokolowski MB, O'Donnell KJ. Biological embedding of experience: A primer on epigenetics. Proc Natl Acad Sci U S A. 2020 09 22; 117(38):23261-23269. PMID: 31624126.
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    12. Suzuki H, Kumar SA, Shuai S, Diaz-Navarro A, Gutierrez-Fernandez A, De Antonellis P, Cavalli FMG, Juraschka K, Farooq H, Shibahara I, Vladoiu MC, Zhang J, Abeysundara N, Przelicki D, Skowron P, Gauer N, Luu B, Daniels C, Wu X, Forget A, Momin A, Wang J, Dong W, Kim SK, Grajkowska WA, Jouvet A, Fèvre-Montange M, Garrè ML, Nageswara Rao AA, Giannini C, Kros JM, French PJ, Jabado N, Ng HK, Poon WS, Eberhart CG, Pollack IF, Olson JM, Weiss WA, Kumabe T, López-Aguilar E, Lach B, Massimino M, Van Meir EG, Rubin JB, Vibhakar R, Chambless LB, Kijima N, Klekner A, Bognár L, Chan JA, Faria CC, Ragoussis J, Pfister SM, Goldenberg A, Wechsler-Reya RJ, Bailey SD, Garzia L, Morrissy AS, Marra MA, Huang X, Malkin D, Ayrault O, Ramaswamy V, Puente XS, Calarco JA, Stein L, Taylor MD. Recurrent noncoding U1 snRNA mutations drive cryptic splicing in SHH medulloblastoma. Nature. 2019 10; 574(7780):707-711. PMID: 31664194.
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    13. Rampášek L, Hidru D, Smirnov P, Haibe-Kains B, Goldenberg A. Dr.VAE: improving drug response prediction via modeling of drug perturbation effects. Bioinformatics. 2019 10 01; 35(19):3743-3751. PMID: 30850846.
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    14. Harmon LA, Haase DJ, Kufera JA, Adnan S, Cabral D, Lottenberg L, Cunningham KW, Bonne S, Burgess J, Etheridge J, Rehbein JL, Semon G, Noorbakhsh MR, Cragun BN, Agrawal V, Truitt M, Marcotte J, Goldenberg A, Behbahaninia M, Keric N, Hammer PM, Nahmias J, Grigorian A, Turay D, Chakravarthy V, Lalchandani P, Kim D, Chapin T, Dunn J, Portillo V, Schroeppel T, Stein DM. Infection after penetrating brain injury-An Eastern Association for the Surgery of Trauma multicenter study oral presentation at the 32nd annual meeting of the Eastern Association for the Surgery of Trauma, January 15-19, 2019, in Austin, Texas. J Trauma Acute Care Surg. 2019 07; 87(1):61-67. PMID: 31033883.
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    15. Mer AS, Ba-Alawi W, Smirnov P, Wang YX, Brew B, Ortmann J, Tsao MS, Cescon DW, Goldenberg A, Haibe-Kains B. Integrative Pharmacogenomics Analysis of Patient-Derived Xenografts. Cancer Res. 2019 Sep 01; 79(17):4539-4550. PMID: 31142512.
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    16. Nelson W, Zitnik M, Wang B, Leskovec J, Goldenberg A, Sharan R. To Embed or Not: Network Embedding as a Paradigm in Computational Biology. Front Genet. 2019; 10:381. PMID: 31118945.
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    17. Oyefiade A, Erdman L, Goldenberg A, Malkin D, Bouffet E, Taylor MD, Ramaswamy V, Scantlebury N, Law N, Mabbott DJ. PPAR and GST polymorphisms may predict changes in intellectual functioning in medulloblastoma survivors. J Neurooncol. 2019 Mar; 142(1):39-48. PMID: 30607709.
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    18. 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 11; 563(7732):579-583. PMID: 30429608.
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    19. Zitnik M, Nguyen F, Wang B, Leskovec J, Goldenberg A, Hoffman MM. Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities. Inf Fusion. 2019 Oct; 50:71-91. PMID: 30467459.
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    20. 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 05; 10(5):539-557. PMID: 29692205.
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    21. Rampasek L, Goldenberg A. Learning from Everyday Images Enables Expert-like Diagnosis of Retinal Diseases. Cell. 2018 02 22; 172(5):893-895. PMID: 29474917.
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    22. 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.
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    23. 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 12; 83(6):1095-1101. PMID: 28700413.
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    24. 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 04; 43(5):1180-1188. PMID: 29105664.
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    25. 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.
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    26. 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.
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    27. 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 09 29; 14(10):937-938. PMID: 28960198.
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    28. 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.
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    29. 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.
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    30. 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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    31. 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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    32. 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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    33. 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.
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    34. 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.
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    35. 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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    36. 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 VSK, 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 TWJ, 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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    37. 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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    38. 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 VSK, 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 TWJ, Kurreeman F, Allaart CF, Louis Bridges S, 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.
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    39. 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.
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    40. 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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    41. 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.
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    42. 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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    43. 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.
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    44. 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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    45. 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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    46. 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.
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    47. Mostafavi S, Goldenberg A, Morris Q. Labeling nodes using three degrees of propagation. PLoS One. 2012; 7(12):e51947. PMID: 23284828.
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    48. 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.
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    49. 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.
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    50. 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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    51. 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.
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    52. Mostafavi S, Goldenberg A, Morris Q. Predicting node characteristics from molecular networks. Methods Mol Biol. 2011; 781:399-414. PMID: 21877293.
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    53. Krinsky GA, Lee VS, Theise ND, Weinreb JC, Morgan GR, Diflo T, John D, Teperman LW, Goldenberg AS. Transplantation for hepatocellular carcinoma and cirrhosis: sensitivity of magnetic resonance imaging. Liver Transpl. 2002 Dec; 8(12):1156-64. PMID: 12474156.
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