The University of Chicago Header Logo

Francesca Luca

TitleProfessor
InstitutionUniversity of Chicago
DepartmentHuman Genetics
AddressChicago IL 60637
vCardDownload vCard

    Collapse Research 
    Collapse research activities and funding
    R01ES033634     (LUCA, FRANCESCA)May 12, 2022 - Feb 28, 2027
    NIH
    Functional genomics of GxE in cardiovascular disease: BPA, phthalates and their interactions with gene regulation
    Role: Principal Investigator
    R01HL162574     (PIQUE-REGI, ROGER)Mar 15, 2022 - Dec 31, 2026
    NIH
    Psychosocial and Genetic Effects on Gene Expression and Asthma
    Role: Co-Principal Investigator
    R01GM109215     (LUCA, FRANCESCA)Jul 15, 2014 - Apr 30, 2029
    NIH
    Functional Characterization of the Genetic and Environmental Determinants of Complex Traits
    Role: Principal Investigator

    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.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Arnold NS, Resztak J, Witonsky D, Alazizi A, Noren Hooten N, Evans MK, Odero-Marah V, Dluzen DF, Pique-Regi R, Luca F. Living in poverty is associated with gene expression changes in immune cells. Genetics. 2025 Apr 11. PMID: 40211598.
      Citations: 1     Fields:    Translation:HumansCells
    2. Okamoto J, Yin X, Ryan B, Chiou J, Luca F, Pique-Regi R, Im HK, Morrison J, Burant C, Fauman EB, Laakso M, Boehnke M, Wen X. Multi-INTACT: integrative analysis of the genome, transcriptome, and proteome identifies causal mechanisms of complex traits. Genome Biol. 2025 Feb 03; 26(1):19. PMID: 39901160; PMCID: PMC11789355.
      Citations: 2     Fields:    Translation:HumansCells
    3. Wei J, Resztak JA, Ranjbaran A, Alazizi A, Mair-Meijers HE, Slatcher RB, Zilioli S, Wen X, Luca F, Pique-Regi R. Functional characterization of eQTLs and asthma risk loci with scATAC-seq across immune cell types and contexts. Am J Hum Genet. 2025 Feb 06; 112(2):301-317. PMID: 39814021; PMCID: PMC11866969.
      Citations: 1     Fields:    Translation:HumansCells
    4. McCarthy-Leo CE, Brush GS, Pique-Regi R, Luca F, Tainsky MA, Finley RL. Comprehensive analysis of the functional impact of single nucleotide variants of human CHEK2. PLoS Genet. 2024 Aug; 20(8):e1011375. PMID: 39146382; PMCID: PMC11349238.
      Citations: 4     Fields:    Translation:Humans
    5. Boye C, Nirmalan S, Ranjbaran A, Luca F. Genotype?×?environment interactions in gene regulation and complex traits. Nat Genet. 2024 Jun; 56(6):1057-1068. PMID: 38858456; PMCID: PMC11492161.
      Citations: 12     Fields:    Translation:Humans
    6. Boye C, Kalita CA, Findley AS, Alazizi A, Wei J, Wen X, Pique-Regi R, Luca F. Characterization of caffeine response regulatory variants in vascular endothelial cells. Elife. 2024 Feb 09; 13. PMID: 38334359; PMCID: PMC10901511.
      Citations: 2     Fields:    Translation:Cells
    7. Resztak JA, Wei J, Zilioli S, Sendler E, Alazizi A, Mair-Meijers HE, Wu P, Wen X, Slatcher RB, Zhou X, Luca F, Pique-Regi R. Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single-cell resolution. Genome Res. 2023 06; 33(6):839-856. PMID: 37442575; PMCID: PMC10519413.
      Citations: 11     Fields:    Translation:HumansCells
    8. Resztak JA, Choe J, Nirmalan S, Wei J, Bruinsma J, Houpt R, Alazizi A, Mair-Meijers HE, Wen X, Slatcher RB, Zilioli S, Pique-Regi R, Luca F. Analysis of transcriptional changes in the immune system associated with pubertal development in a longitudinal cohort of children with asthma. Nat Commun. 2023 01 16; 14(1):230. PMID: 36646693; PMCID: PMC9842661.
      Citations: 9     Fields:    Translation:HumansCells
    9. Okamoto J, Wang L, Yin X, Luca F, Pique-Regi R, Helms A, Im HK, Morrison J, Wen X. Probabilistic integration of transcriptome-wide association studies and colocalization analysis identifies key molecular pathways of complex traits. Am J Hum Genet. 2023 01 05; 110(1):44-57. PMID: 36608684; PMCID: PMC9892769.
      Citations: 11     Fields:    Translation:HumansCells
    10. Resztak JA, Wei J, Zilioli S, Sendler E, Alazizi A, Mair-Meijers HE, Wu P, Wen X, Slatcher RB, Zhou X, Luca F, Pique-Regi R. Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single cell resolution. bioRxiv. 2022 Oct 15. PMID: 35313584; PMCID: PMC8936121.
      Citations:    
    11. Hukku A, Sampson MG, Luca F, Pique-Regi R, Wen X. Analyzing and reconciling colocalization and transcriptome-wide association studies from the perspective of inferential reproducibility. Am J Hum Genet. 2022 05 05; 109(5):825-837. PMID: 35523146; PMCID: PMC9118134.
      Citations: 26     Fields:    Translation:HumansCells
    12. Muehlbauer AL, Richards AL, Alazizi A, Burns MB, Gomez A, Clayton JB, Petrzelkova K, Cascardo C, Resztak J, Wen X, Pique-Regi R, Luca F, Blekhman R. Interspecies variation in hominid gut microbiota controls host gene regulation. Cell Rep. 2021 11 23; 37(8):110057. PMID: 34818542; PMCID: PMC8647622.
      Citations: 6     Fields:    Translation:HumansAnimalsCells
    13. Findley AS, Zhang X, Boye C, Lin YL, Kalita CA, Barreiro L, Lohmueller KE, Pique-Regi R, Luca F. A signature of Neanderthal introgression on molecular mechanisms of environmental responses. PLoS Genet. 2021 09; 17(9):e1009493. PMID: 34570765; PMCID: PMC8509894.
      Citations: 7     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    14. Resztak JA, Farrell AK, Mair-Meijers H, Alazizi A, Wen X, Wildman DE, Zilioli S, Slatcher RB, Pique-Regi R, Luca F. Psychosocial experiences modulate asthma-associated genes through gene-environment interactions. Elife. 2021 06 18; 10. PMID: 34142656; PMCID: PMC8282343.
      Citations: 10     Fields:    Translation:HumansCells
    15. Findley AS, Monziani A, Richards AL, Rhodes K, Ward MC, Kalita CA, Alazizi A, Pazokitoroudi A, Sankararaman S, Wen X, Lanfear DE, Pique-Regi R, Gilad Y, Luca F. Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions. Elife. 2021 05 14; 10. PMID: 33988505; PMCID: PMC8248987.
      Citations: 33     Fields:    Translation:HumansCells
    16. 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 01 07; 108(1):25-35. PMID: 33308443; PMCID: PMC7820626.
      Citations: 66     Fields:    Translation:Humans
    17. Zhang Y, Quick C, Yu K, Barbeira A, GTEx Consortium, Luca F, Pique-Regi R, Kyung Im H, Wen X. PTWAS: investigating tissue-relevant causal molecular mechanisms of complex traits using probabilistic TWAS analysis. Genome Biol. 2020 09 11; 21(1):232. PMID: 32912253; PMCID: PMC7488550.
      Citations: 44     Fields:    Translation:Cells
    18. Hukku A, Quick C, Luca F, Pique-Regi R, Wen X. BAGSE: a Bayesian hierarchical model approach for gene set enrichment analysis. Bioinformatics. 2020 03 01; 36(6):1689-1695. PMID: 31702789; PMCID: PMC7523653.
      Citations: 3     Fields:    Translation:Cells
    19. Findley AS, Richards AL, Petrini C, Alazizi A, Doman E, Shanku AG, Davis GO, Hauff N, Sorokin Y, Wen X, Pique-Regi R, Luca F. Interpreting Coronary Artery Disease Risk Through Gene-Environment Interactions in Gene Regulation. Genetics. 2019 10; 213(2):651-663. PMID: 31492806; PMCID: PMC6781890.
      Citations: 17     Fields:    Translation:HumansCells
    20. Richards AL, Muehlbauer AL, Alazizi A, Burns MB, Findley A, Messina F, Gould TJ, Cascardo C, Pique-Regi R, Blekhman R, Luca F. Gut Microbiota Has a Widespread and Modifiable Effect on Host Gene Regulation. mSystems. 2019 Sep 03; 4(5). PMID: 31481602; PMCID: PMC6722422.
      Citations: 61     Fields:    
    21. Imami L, Stanton SCE, Zilioli S, Tobin ET, Farrell AK, Luca F, Slatcher RB. Self-Disclosure and Perceived Responsiveness Among Youth With Asthma: Links to Affect and Anti-Inflammatory Gene Expression. Pers Soc Psychol Bull. 2019 08; 45(8):1155-1169. PMID: 30486748; PMCID: PMC9889136.
      Citations: 1     Fields:    Translation:Humans
    22. Kalita CA, Brown CD, Freiman A, Isherwood J, Wen X, Pique-Regi R, Luca F. High-throughput characterization of genetic effects on DNA-protein binding and gene transcription. Genome Res. 2018 11; 28(11):1701-1708. PMID: 30254052; PMCID: PMC6211638.
      Citations: 22     Fields:    Translation:HumansCells
    23. Kalita CA, Moyerbrailean GA, Brown C, Wen X, Luca F, Pique-Regi R. QuASAR-MPRA: accurate allele-specific analysis for massively parallel reporter assays. Bioinformatics. 2018 03 01; 34(5):787-794. PMID: 29028988; PMCID: PMC6049023.
      Citations: 20     Fields:    Translation:HumansCells
    24. Farrell AK, Slatcher RB, Tobin ET, Imami L, Wildman DE, Luca F, Zilioli S. Socioeconomic status, family negative emotional climate, and anti-inflammatory gene expression among youth with asthma. Psychoneuroendocrinology. 2018 05; 91:62-67. PMID: 29529520; PMCID: PMC5903571.
      Citations: 16     Fields:    Translation:HumansCells
    25. Richards AL, Watza D, Findley A, Alazizi A, Wen X, Pai AA, Pique-Regi R, Luca F. Environmental perturbations lead to extensive directional shifts in RNA processing. PLoS Genet. 2017 Oct; 13(10):e1006995. PMID: 29023442; PMCID: PMC5667937.
      Citations: 20     Fields:    Translation:HumansCells
    26. Wen X, Pique-Regi R, Luca F. Integrating molecular QTL data into genome-wide genetic association analysis: Probabilistic assessment of enrichment and colocalization. PLoS Genet. 2017 Mar; 13(3):e1006646. PMID: 28278150; PMCID: PMC5363995.
      Citations: 142     Fields:    Translation:Humans
    27. Moyerbrailean GA, Richards AL, Kurtz D, Kalita CA, Davis GO, Harvey CT, Alazizi A, Watza D, Sorokin Y, Hauff N, Zhou X, Wen X, Pique-Regi R, Luca F. High-throughput allele-specific expression across 250 environmental conditions. Genome Res. 2016 12; 26(12):1627-1638. PMID: 27934696; PMCID: PMC5131815.
      Citations: 73     Fields:    Translation:HumansCells
    28. Richards AL, Burns MB, Alazizi A, Barreiro LB, Pique-Regi R, Blekhman R, Luca F. Genetic and transcriptional analysis of human host response to healthy gut microbiota. mSystems. 2016 Jul-Aug; 1(4). PMID: 27709125; PMCID: PMC5047527.
      Citations: 22     Fields:    
    29. Wen X, Lee Y, Luca F, Pique-Regi R. Efficient Integrative Multi-SNP Association Analysis via Deterministic Approximation of Posteriors. Am J Hum Genet. 2016 06 02; 98(6):1114-1129. PMID: 27236919; PMCID: PMC4908152.
      Citations: 103     Fields:    Translation:Humans
    30. Moyerbrailean GA, Kalita CA, Harvey CT, Wen X, Luca F, Pique-Regi R. Which Genetics Variants in DNase-Seq Footprints Are More Likely to Alter Binding? PLoS Genet. 2016 Feb; 12(2):e1005875. PMID: 26901046; PMCID: PMC4764260.
      Citations: 34     Fields:    Translation:HumansCells
    31. Pacis A, Tailleux L, Morin AM, MacIsaac JL, Yotova V, Dumaine A, Danckaert A, Luca F, Grenier JC, Hansen KD, Gicquel B, Yu M, Pai A, He C, Tung J, Kobor MS, Pique-Regi R, Gilad Y, Barreiro LB, Lambourne J, Pastinen T. Bacterial infection remodels the DNA methylation landscape of human dendritic cells. Genome Res. 2015 Dec; 25(12):1801-11. PMID: 26392366; PMCID: PMC4665002.
      Citations: 126     Fields:    Translation:HumansCells
    32. Wen X, Luca F, Pique-Regi R. Cross-population joint analysis of eQTLs: fine mapping and functional annotation. PLoS Genet. 2015 Apr; 11(4):e1005176. PMID: 25906321; PMCID: PMC4408026.
      Citations: 67     Fields:    Translation:Humans
    33. Harvey CT, Moyerbrailean GA, Davis GO, Wen X, Luca F, Pique-Regi R. QuASAR: quantitative allele-specific analysis of reads. Bioinformatics. 2015 Apr 15; 31(8):1235-42. PMID: 25480375; PMCID: PMC4393517.
      Citations: 52     Fields:    Translation:HumansCells
    34. Luca F, Maranville JC, Richards AL, Witonsky DB, Stephens M, Di Rienzo A. Genetic, functional and molecular features of glucocorticoid receptor binding. PLoS One. 2013; 8(4):e61654. PMID: 23637875; PMCID: PMC3640037.
      Citations: 12     Fields:    Translation:HumansCells
    35. Wall JD, Kim SK, Luca F, Carbone L, Mootnick AR, de Jong PJ, Di Rienzo A. Incomplete lineage sorting is common in extant gibbon genera. PLoS One. 2013; 8(1):e53682. PMID: 23341974; PMCID: PMC3544895.
      Citations: 5     Fields:    Translation:HumansAnimals
    36. Luca F, Di Rienzo A. Allelic imbalance assays to quantify allele-specific gene expression and transcription factor binding. Methods Mol Biol. 2013; 1015:201-11. PMID: 23824858.
      Citations:    Fields:    Translation:HumansCells
    37. Maranville JC, Luca F, Stephens M, Di Rienzo A. Mapping gene-environment interactions at regulatory polymorphisms: insights into mechanisms of phenotypic variation. Transcription. 2012 Mar-Apr; 3(2):56-62. PMID: 22414753.
      Citations: 7     Fields:    Translation:HumansAnimals
    38. Maranville JC, Luca F, Richards AL, Wen X, Witonsky DB, Baxter S, Stephens M, Di Rienzo A. Interactions between glucocorticoid treatment and cis-regulatory polymorphisms contribute to cellular response phenotypes. PLoS Genet. 2011 Jul; 7(7):e1002162. PMID: 21750684; PMCID: PMC3131293.
      Citations: 74     Fields:    Translation:HumansCells
    39. Luca F, Hudson RR, Witonsky DB, Di Rienzo A. A reduced representation approach to population genetic analyses and applications to human evolution. Genome Res. 2011 Jul; 21(7):1087-98. PMID: 21628451; PMCID: PMC3129251.
      Citations: 24     Fields:    Translation:Humans
    40. Luca F, Kashyap S, Southard C, Zou M, Witonsky D, Di Rienzo A, Conzen SD. Adaptive variation regulates the expression of the human SGK1 gene in response to stress. PLoS Genet. 2009 May; 5(5):e1000489. PMID: 19461886; PMCID: PMC2679193.
      Citations: 22     Fields:    Translation:HumansCells
    41. Luca F, Bubba G, Basile M, Brdicka R, Michalodimitrakis E, Rickards O, Vershubsky G, Quintana-Murci L, Kozlov AI, Novelletto A. Multiple advantageous amino acid variants in the NAT2 gene in human populations. PLoS One. 2008 Sep 05; 3(9):e3136. PMID: 18773084; PMCID: PMC2527519.
      Citations: 26     Fields:    Translation:Humans
    42. Coop G, Bullaughey K, Luca F, Przeworski M. The timing of selection at the human FOXP2 gene. Mol Biol Evol. 2008 Jul; 25(7):1257-9. PMID: 18413354; PMCID: PMC2429961.
      Citations: 30     Fields:    Translation:Humans
    43. Quintana-Murci L, Quach H, Harmant C, Luca F, Massonnet B, Patin E, Sica L, Mouguiama-Daouda P, Comas D, Tzur S, Balanovsky O, Kidd KK, Kidd JR, van der Veen L, Hombert JM, Gessain A, Verdu P, Froment A, Bahuchet S, Heyer E, Dausset J, Salas A, Behar DM. Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter-gatherers and Bantu-speaking farmers. Proc Natl Acad Sci U S A. 2008 Feb 05; 105(5):1596-601. PMID: 18216239; PMCID: PMC2234190.
      Citations: 59     Fields:    Translation:HumansCells
    44. Luca F, Basile M, Giacomo FD, Novelletto A. Independent methods for evolutionary genetic dating provide insights into Y-chromosomal STR mutation rates confirming data from direct father-son transmissions. Hum Genet. 2005 Nov; 118(2):153-65. PMID: 16136324.
      Citations: 1     Fields:    Translation:HumansCells
    Luca's Networks
    Click the
    Explore
    buttons for more information and interactive visualizations!
    Concepts (184)
    Explore
    _
    Co-Authors (10)
    Explore
    _
    Similar People (60)
    Explore
    _
    Same Department Expand Description
    Explore
    _
    Physical Neighbors
    _