My Bibliography

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Kanai M, Elzur R, Zhou W, Daly MJ, Finucane HK. Meta-analysis fine-mapping is often miscalibrated at single-variant resolution. Cell Genom. 2022 Dec 14;2(12). doi: 10.1016/j.xgen.2022.100210. Epub 2022 Nov 4. PubMed PMID: 36643910; PubMed Central PMCID: PMC9839193.

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Zhou W, Kanai M, Wu KH, Rasheed H, Tsuo K, Hirbo JB, Wang Y, Bhattacharya A, Zhao H, Namba S, Surakka I, Wolford BN, Lo Faro V, Lopera-Maya EA, Läll K, Favé MJ, Partanen JJ, Chapman SB, Karjalainen J, Kurki M, Maasha M, Brumpton BM, Chavan S, Chen TT, Daya M, Ding Y, Feng YA, Guare LA, Gignoux CR, Graham SE, Hornsby WE, Ingold N, Ismail SI, Johnson R, Laisk T, Lin K, Lv J, Millwood IY, Moreno-Grau S, Nam K, Palta P, Pandit A, Preuss MH, Saad C, Setia-Verma S, Thorsteinsdottir U, Uzunovic J, Verma A, Zawistowski M, Zhong X, Afifi N, Al-Dabhani KM, Al Thani A, Bradford Y, Campbell A, Crooks K, de Bock GH, Damrauer SM, Douville NJ, Finer S, Fritsche LG, Fthenou E, Gonzalez-Arroyo G, Griffiths CJ, Guo Y, Hunt KA, Ioannidis A, Jansonius NM, Konuma T, Lee MTM, Lopez-Pineda A, Matsuda Y, Marioni RE, Moatamed B, Nava-Aguilar MA, Numakura K, Patil S, Rafaels N, Richmond A, Rojas-Muñoz A, Shortt JA, Straub P, Tao R, Vanderwerff B, Vernekar M, Veturi Y, Barnes KC, Boezen M, Chen Z, Chen CY, Cho J, Smith GD, Finucane HK, Franke L, Gamazon ER, Ganna A, Gaunt TR, Ge T, Huang H, Huffman J, Katsanis N, Koskela JT, Lajonchere C, Law MH, Li L, Lindgren CM, Loos RJF, MacGregor S, Matsuda K, Olsen CM, Porteous DJ, Shavit JA, Snieder H, Takano T, Trembath RC, Vonk JM, Whiteman DC, Wicks SJ, Wijmenga C, Wright J, Zheng J, Zhou X, Awadalla P, Boehnke M, Bustamante CD, Cox NJ, Fatumo S, Geschwind DH, Hayward C, Hveem K, Kenny EE, Lee S, Lin YF, Mbarek H, Mägi R, Martin HC, Medland SE, Okada Y, Palotie AV, Pasaniuc B, Rader DJ, Ritchie MD, Sanna S, Smoller JW, Stefansson K, van Heel DA, Walters RG, Zöllner S, Martin AR, Willer CJ, Daly MJ, Neale BM. Global Biobank Meta-analysis Initiative: Powering genetic discovery across human disease. Cell Genom. 2022 Oct 12;2(10):100192. doi: 10.1016/j.xgen.2022.100192. eCollection 2022 Oct 12. PubMed PMID: 36777996; PubMed Central PMCID: PMC9903716.

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Lopez-Pineda A, Vernekar M, Moreno-Grau S, Rojas-Muñoz A, Moatamed B, Lee MTM, Nava-Aguilar MA, Gonzalez-Arroyo G, Numakura K, Matsuda Y, Ioannidis A, Katsanis N, Takano T, Bustamante CD. Validating and automating learning of cardiometabolic polygenic risk scores from direct-to-consumer genetic and phenotypic data: implications for scaling precision health research. Hum Genomics. 2022 Sep 8;16(1):37. doi: 10.1186/s40246-022-00406-y. PubMed PMID: 36076307; PubMed Central PMCID: PMC9452874.

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Preston CG, Wright MW, Madhavrao R, Harrison SM, Goldstein JL, Luo X, Wand H, Wulf B, Cheung G, Mandell ME, Tong H, Cheng S, Iacocca MA, Pineda AL, Popejoy AB, Dalton K, Zhen J, Dwight SS, Babb L, DiStefano M, O'Daniel JM, Lee K, Riggs ER, Zastrow DB, Mester JL, Ritter DI, Patel RY, Subramanian SL, Milosavljevic A, Berg JS, Rehm HL, Plon SE, Cherry JM, Bustamante CD, Costa HA. ClinGen Variant Curation Interface: a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines. Genome Med. 2022 Jan 18;14(1):6. doi: 10.1186/s13073-021-01004-8. PubMed PMID: 35039090; PubMed Central PMCID: PMC8764818.

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Liu R, Rizzo S, Whipple S, Pal N, Pineda AL, Lu M, Arnieri B, Lu Y, Capra W, Copping R, Zou J. Evaluating eligibility criteria of oncology trials using real-world data and AI. Nature. 2021 Apr;592(7855):629-633. doi: 10.1038/s41586-021-03430-5. Epub 2021 Apr 7. PubMed PMID: 33828294; PubMed Central PMCID: PMC9007176.

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Lopez Pineda A, Pourshafeie A, Ioannidis A, Leibold CM, Chan AL, Bustamante CD, Frankovich J, Wojcik GL. Discovering prescription patterns in pediatric acute-onset neuropsychiatric syndrome patients. J Biomed Inform. 2021 Jan;113:103664. doi: 10.1016/j.jbi.2020.103664. Epub 2020 Dec 28. PubMed PMID: 33359113.

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Venkataraman GR, Pineda AL, Bear Don't Walk Iv OJ, Zehnder AM, Ayyar S, Page RL, Bustamante CD, Rivas MA. FasTag: Automatic text classification of unstructured medical narratives. PLoS One. 2020;15(6):e0234647. doi: 10.1371/journal.pone.0234647. eCollection 2020. PubMed PMID: 32569327; PubMed Central PMCID: PMC7307763.

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Nie A, Pineda AL, Wright MW, Wand H, Wulf B, Costa HA, Patel RY, Bustamante CD, Zou J. LitGen: Genetic Literature Recommendation Guided by Human Explanations. Pac Symp Biocomput. 2020;25:67-78. PubMed PMID: 31797587; PubMed Central PMCID: PMC7478937.

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Bucio D, Ormond KE, Hernandez D, Bustamante CD, Lopez Pineda A. A genetic counseling needs assessment of Mexico. Mol Genet Genomic Med. 2019 May;7(5):e668. doi: 10.1002/mgg3.668. Epub 2019 Apr 1. PubMed PMID: 30938092; PubMed Central PMCID: PMC6503023.

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Nie A, Zehnder A, Page RL, Zhang Y, Pineda AL, Rivas MA, Bustamante CD, Zou J. DeepTag: inferring diagnoses from veterinary clinical notes. NPJ Digit Med. 2018;1:60. doi: 10.1038/s41746-018-0067-8. eCollection 2018. PubMed PMID: 31304339; PubMed Central PMCID: PMC6550285.

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López-Pineda A, Rodríguez-Moran MF, Álvarez-Aguilar C, Fuentes Valle SM, Acosta-Rosales R, Bhatt AS, Sheth SN, Bustamante CD. Data mining of digitized health records in a resource-constrained setting reveals that timely immunophenotyping is associated with improved breast cancer outcomes. BMC Cancer. 2018 Sep 27;18(1):933. doi: 10.1186/s12885-018-4833-4. PubMed PMID: 30261931; PubMed Central PMCID: PMC6161369.

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Ye Y, Wagner MM, Cooper GF, Ferraro JP, Su H, Gesteland PH, Haug PJ, Millett NE, Aronis JM, Nowalk AJ, Ruiz VM, López Pineda A, Shi L, Van Bree R, Ginter T, Tsui F. A study of the transferability of influenza case detection systems between two large healthcare systems. PLoS One. 2017;12(4):e0174970. doi: 10.1371/journal.pone.0174970. eCollection 2017. PubMed PMID: 28380048; PubMed Central PMCID: PMC5381795.

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Pineda AL, Ogoe HA, Balasubramanian JB, Rangel Escareño C, Visweswaran S, Herman JG, Gopalakrishnan V. On Predicting lung cancer subtypes using 'omic' data from tumor and tumor-adjacent histologically-normal tissue. BMC Cancer. 2016 Mar 4;16:184. doi: 10.1186/s12885-016-2223-3. PubMed PMID: 26944944; PubMed Central PMCID: PMC4778315.

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López Pineda A, Ye Y, Visweswaran S, Cooper GF, Wagner MM, Tsui FR. Comparison of machine learning classifiers for influenza detection from emergency department free-text reports. J Biomed Inform. 2015 Dec;58:60-69. doi: 10.1016/j.jbi.2015.08.019. Epub 2015 Sep 16. PubMed PMID: 26385375; PubMed Central PMCID: PMC4684714.

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Pineda AL, Gopalakrishnan V. Novel Application of Junction Trees to the Interpretation of Epigenetic Differences among Lung Cancer Subtypes. AMIA Jt Summits Transl Sci Proc. 2015;2015:31-5. eCollection 2015. PubMed PMID: 26306226; PubMed Central PMCID: PMC4525224.