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
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, 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
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
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
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
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
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
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
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
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
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
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
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
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
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, 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
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
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
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.