Milton Pividori, PhD

Professional Titles

• Assistant Professor

Research Interests

Our research is focused on developing novel machine-learning methods to advance key computational aspects of precision medicine. We have a particular focus on the integration of genetic studies with relevant molecular patterns extracted from multi-omics data. For this, we aim to develop the next generation of methodologies that will consolidate large and heterogeneous sources of biomedical information to extract biological insight to ultimately improve human health.

Publications

• Pividori M, Schoettler N, Nicolae DL, Ober C, Im HK. Shared and distinct genetic risk factors for childhood-onset and adult-onset asthma: genome-wide and transcriptome-wide studies. Lancet Respir Med. 2019 Jun;7(6):509-522. PubMed PMID: 31036433
• Truong VQ, Woerner JA, Cherlin TA, Bradford Y, Lucas AM, Okeh CC, Shivakumar MK, Hui DH, Kumar R, Pividori M, Jones SC, Bossa AC, Turner SD, Ritchie MD, Verma SS. Quality Control Procedures for Genome-Wide Association Studies. Curr Protoc. 2022 Nov;2(11):e603. PubMed PMID: 36441943
• Hukku A, Pividori M, Luca F, Pique-Regi R, Im HK, Wen X. Probabilistic colocalization of genetic variants from complex and molecular traits: promise and limitations. Am J Hum Genet. 2021 Jan 7;108(1):25-35. PubMed PMID: 33308443
• Cooley M, Greene CS, Issac D, Pividori M, Sullivan BD. Parameterized algorithms for identifying gene co-expression modules via weighted clique decomposition. Proc 2021 SIAM Conf Appl Comput Discret Algorithms (2021). 2021;2021:111-122. PubMed PMID: 35391741
• Pividori M, Lu S, Li B, Su C, Johnson ME, Wei WQ, Feng Q, Namjou B, Kiryluk K, Kullo IJ, Luo Y, Sullivan BD, Voight BF, Skarke C, Ritchie MD, Grant SFA, Greene CS. Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms. Nat Commun. 2023 Sep 9;14(1):5562. PubMed PMID: 37689782
• Pividori M, Greene CS. A publishing infrastructure for AI-assisted academic authoring. bioRxiv. 2023 Jan 23. PubMed PMID: 36747665
• Pividori M, Rajagopal PS, Barbeira A, Liang Y, Melia O, Bastarache L, Park Y, Consortium G, Wen X, Im HK. PhenomeXcan: Mapping the genome to the phenome through the transcriptome. Sci Adv. 2020 Sep;6(37). PubMed PMID: 32917697
• Bugnon LA, Yones C, Raad J, Gerard M, Rubiolo M, Merino G, Pividori M, Di Persia L, Milone DH, Stegmayer G. DL4papers: a deep learning approach for the automatic interpretation of scientific articles. Bioinformatics. 2020 Jun 1;36(11):3499-3506. PubMed PMID: 32091584
• Stegmayer G, Di Persia LE, Rubiolo M, Gerard M, Pividori M, Yones C, Bugnon LA, Rodriguez T, Raad J, Milone DH. Predicting novel microRNA: a comprehensive comparison of machine learning approaches. Brief Bioinform. 2019 Sep 27;20(5):1607-1620. PubMed PMID: 29800232
• Pividori M, Im HK. ukbREST: efficient and streamlined data access for reproducible research in large biobanks. Bioinformatics. 2019 Jun 1;35(11):1971-1973. PubMed PMID: 30395166
• Pividori M, Joo J, Himes BE. Integrative analysis of genetic studies and gene co-expression patterns highlights shared and distinct transcriptional mechanisms associated with asthma, COPD and asthma-COPD overlap (ACO) syndrome. American Society of Human Genetics (ASHG) Annual Meeting 2023.
• Pividori M, Cernadas A, de Haro LA, Carrari F, Stegmayer G, Milone DH. Clustermatch: discovering hidden relations in highly diverse kinds of qualitative and quantitative data without standardization. Bioinformatics. 2019 Jun 1;35(11):1931-1939. PubMed PMID: 30357313
• Jia G, Li Y, Zhong X, Wang K, Pividori M, Alomairy R, Esposito A, Ltaief H, Terao C, Akiyama M, Matsuda K, Keyes DE, Im HK, Gojobori T, Kamatani Y, Kubo M, Cox NJ, Evans J, Gao X, Rzhetsky A. The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci. Nat Comput Sci. 2023 May;3(5):403-417. PubMed PMID: 38177845
• Stegmayer G, Pividori M, Milone DH. A very simple and fast way to access and validate algorithms in reproducible research. Brief Bioinform. 2016 Jan;17(1):180-3. PubMed PMID: 26223526
• Liang Y, Pividori M, Manichaikul A, Palmer AA, Cox NJ, Wheeler HE, Im HK. Polygenic transcriptome risk scores (PTRS) can improve portability of polygenic risk scores across ancestries. Genome Biol. 2022 Jan 13;23(1):23. PubMed PMID: 35027082
• Barbeira AN, Bonazzola R, Gamazon ER, Liang Y, Park Y, Kim-Hellmuth S, Wang G, Jiang Z, Zhou D, Hormozdiari F, Liu B, Rao A, Hamel AR, Pividori MD, Aguet F, Bastarache L, Jordan DM, Verbanck M, Do R, Stephens M, Ardlie K, McCarthy M, Montgomery SB, Segrè AV, Brown CD, Lappalainen T, Wen X, Im HK. Exploiting the GTEx resources to decipher the mechanisms at GWAS loci. Genome Biol. 2021 Jan 26;22(1):49. PubMed PMID: 33499903
• Barbeira AN, Pividori M, Zheng J, Wheeler HE, Nicolae DL, Im HK. Integrating predicted transcriptome from multiple tissues improves association detection. PLoS Genet. 2019 Jan;15(1):e1007889. PubMed PMID: 30668570
• Milton Pividori, Casey S. Greene. A publishing infrastructure for AI-assisted academic authoring. bioRxiv 2023.01.21.525030; doi: https://doi.org/10.1101/2023.01.21.525030
• Milton Pividori, Marylyn D. Ritchie, Diego H. Milone, Casey S. Greene. An efficient not-only-linear correlation coefficient based on machine learning. bioRxiv 2022.06.15.496326; doi: https://doi.org/10.1101/2022.06.15.496326
• Milton Pividori, et al. Projecting genetic associations through gene expression patterns highlights disease etiology and drug mechanisms. Nat Commun 14, 5562. https://doi.org/10.1038/s41467-023-41057-4
• Multi-ancestry gene-trait connection landscape using electronic health record (EHR) linked biobank data Binglan Li, Yogasudha Veturi, Anastasia Lucas, Yuki Bradford, Shefali S. Verma, Anurag Verma, Joseph Park, Wei-Qi Wei, Qiping Feng, Bahram Namjou, Krzysztof Kiryluk, Iftikhar Kullo, Yuan Luo, Milton Pividori, Hae Kyung Im, Casey S. Greene, Marylyn D. Ritchie medRxiv 2021.10.21.21265225; doi: https://doi.org/10.1101/2021.10.21.21265225
• Jia, G., Li, Y., Zhong, X. et al. The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci. Nat Comput Sci 3, 403–417 (2023). https://doi.org/10.1038/s43588-023-00453-y
• Jia, G., Zhong, X., Im, H.K. et al. Discerning asthma endotypes through comorbidity mapping. Nat Commun 13, 6712 (2022). https://doi.org/10.1038/s41467-022-33628-8

Professional Memberships

• American Society of Human Genetics (ASHG), Member
• International Society for Computational Biology (ISCB), Member

Practice Locations

UCHealth Anschutz Outpatient Pavilion - Anschutz Medical Campus
1635 Aurora Ct
Aurora, CO 80045
720-848-0000

Center Affiliations

• Center for Health Artificial Intelligence