Publications

Pre-Prints

Muehlbauer AL,  Richards AL,  Alazizi A,  Burns M,  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 (2020) doi: https://doi.org/10.1101/2020.08.17.255059.

Shanku AG, Findley A, Kalita CA, Shim H, Luca F, Pique-Regi R. circuitSNPs: Predicting genetic effects using a Neural Network to model regulatory modules of DNase-seq footprints. (2018) doi: https://doi.org/10.1101/337774.

2021

Findley A, Zhang X, Boye C, Lin Y, Kalita C, Barreiro L, Lohmueller KE, Pique-Regi R, Luca F. A signature of Neanderthal introgression on molecular mechanisms of environmental responses (2021) PLOS Genetics. In Press. doi: https://doi.org/10.1101/2021.03.15.435179.

Resztak JA, Farrell AK, Mair-Meijers HE, 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 (2021) Elife. 2021;10:e63852. doi: 10.7554/eLife.63852.

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 (2021)  eLife 2021;10:e67077 DOI: 10.7554/eLife.67077

Jiang Y, Farrell AK, Tobin ET, Mair-Meijers H, Wildman DE, Luca F, Slatcher RB, Zilioli S. Socioeconomic status, financial stress, and glucocorticoid resistance among youth with asthma: Testing the moderation effects of maternal involvement and warmth (2021) Brain, Behavior and Immunity. In press.

Hukku A, Pividori M, Luca F, Pique-Regi R, Kyung Im H, Wen X, Probabilistic Colocalization of Genetic Variants from Complex and Molecular Traits: Promise and Limitations (2021) Am J Hum Genet 108(1):25-35. doi: 10.1016/j.ajhg.2020.11.012.

2020

Messina F, Giombini E, Agrati C, Vairo F, Ascoli Bartoli T, Al Moghazi S, Piacentini M, Locatelli F, Kobinger G, Maeurer M, Zumla A, Capobianchi MR, Lauria FN, Ippolito G & COVID 19 INMI Network Medicine for IDs Study Group. COVID-19: viral–host interactome analyzed by network based-approach model to study pathogenesis of SARS-CoV-2 infection. J Transl Med 18, 233 (2020). https://doi.org/10.1186/s12967-020-02405-w

Pique-Regi R, Romero R, Tarca AL, Luca F, Xu Y, Alazizi A, Leng Y, Hsu C, Gomez-Lopez N. Does the human placenta express the canonical cell entry mediators for SARS-CoV-2? (2020) Elife. 9:e58716. doi: 10.7554/eLife.58716.

Hukku A, Quick C, Luca F, Pique-Regi R, Wen X. BAGSE: a Bayesian hierarchical model approach for gene set enrichment analysis. Bioinformatics. 2020 Mar 1;36(6):1689-1695. doi: 10.1093/bioinformatics/btz831. PubMed PMID: 31702789.

Talreja Jaya, Bauerfeld Christian, Sendler Edward, Pique-Regi Roger, Luca Francesca, Samavati Lobelia (2020) Derangement of Metabolic and Lysosomal Gene Profiles in Response to Dexamethasone Treatment in Sarcoidosis. Frontiers in Immunology 11: 779. https://doi.org/10.3389/fimmu.2020.00779

2019

Pique-Regi R, Romero R, Tarca AL,  Sendler ED,  Xu Y,  Garcia-Flores V,  Leng Y, Luca F,  Hassan S, Gomez-Lopez N. (2019) Single Cell Transcriptional Signatures of the Human Placenta in Term and Preterm Parturition. eLife 2019;8:e52004 DOI: 10.7554/eLife.52004

Findley AS, Richards AL, Petrini C, Alazizi A, Doman E, Shanku AG, Davis GO, Hauff NJ, Sorokin Y, Wen X, Pique-Regi R, Luca F. Interpreting coronary artery disease risk through gene-environment interactions in gene regulation. Genetics October 2019 213: 651-663; https://doi.org/10.1534/genetics.119.302419

Richards AL,  Muehlbauer AL,  Alazizi A,  Burns MB,  Gould TJ,  Cascardo C,  Pique-Regi R,  Blekhman R,  Luca F. Gut microbiota has a widespread and modifiable effect on host gene regulation (2018) mSystems 4:e0032318. https://doi.org/10.1128/mSystems.00323-18.

Imami L, Stanton SCE, Farrell A, Tobin E, Luca F, Zilioli S, Slatcher R (2018) Self-Disclosure and Perceived Responsiveness among Youth with Asthma: Links to Affect and Anti-Inflammatory Gene Expression. Personality and Social Psychology Bulletin. Personality and Social Psychology Bulletin. 45(8): 1155-1169.

Saad MH, Rumschlag M, Guerra MH, Savonen CL, Jaster AM, Olson PD, Alazizi A, Luca F, Pique-Regi R, Schmidt CJ, Bannon MJ (2019) Differentially expressed gene networks, biomarkers, long noncoding RNAs, and shared responses with cocaine identified in the midbrains of human opioid abusers. Sci Rep. 2019 9(1):1534. doi: 10.1038/s41598-018-38209-8.

2018

Kalita CA,  Brown CD,  Freiman A,  Isherwood J,  Wen X,  Pique-Regi R,  Luca F (2018)  High throughput characterization of genetic effects on DNA:protein binding and gene transcription. Genome Res. 28(11):1701-1708. doi: 10.1101/gr.237354.118.

Pai AA, Luca F (2018) Environmental influences on RNA processing: Biochemical, molecular and genetic regulators of cellular response. Wiley Interdiscip Rev RNA. 14:e1503. doi: 10.1002/wrna.1503.

Farrell A, Slatcher R, Tobin E, Imami L, Wildman D, Luca F, Zilioli S (2018) Socioeconomic status, family negative emotional climate, and anti-inflammatory gene expression among youth with asthma. Psychoneuroendocrinology. 91:62-67.

2012-2017

Lacher SE, Alazizi A, Wang X, Bell DA, Pique-Regi R, Luca F, Slattery M (2017) A hypermorphic antioxidant response element is associated with increased MS4A6A expression and Alzheimer’s disease. Redox Biology. https://doi.org/10.1016/j.redox.2017.10.018.

Kalita CA, Moyerbrailean GA, Brown C, Wen X, Luca F, Pique-Regi R (2017) QuASAR-MPRA: Accurate allele-specific analysis for massively parallel reporter assays. Bioinformatics. https://doi.org/10.1093/bioinformatics/btx598

Richards AL, Watza D,  Findley A,  Alazizi A,  Wen X,  Pai A,  Pique-Regi R, Luca F (2017) Environmental Perturbations Lead To Extensive Directional Shifts In RNA Processing. PLOS Genetics. https://doi.org/10.1371/journal.pgen.1006995

Luca F, Kupfer SS, Knights D, Khoruts A, Blekhman R (2017) Functional Genomics of Host-Microbiome Interactions in Humans. Trends in Genetics. doi:10.1016/j.tig.2017.10.001

Talreja J, Farshi P, Alazizi A, Luca F, Pique-Regi R, Samavati L (2017) RNA-sequencing Identifies Novel Pathways in Sarcoidosis Monocytes. Sci Rep. 7(1):2720. doi: 10.1038/s41598-017-02941-4.

Wen X, Pique-Regi R, Luca F (2017) Integrating Molecular QTL Data into Genome-wide Genetic Association Analysis: Probabilistic Assessment of Enrichment and Colocalization. PLOS Genetics. 13(3):e1006646. doi: 10.1371/journal.pgen.1006646.

Stanton SCE, Zilioli S, Briskin JL, Imami L, Tobin ET, Wildman DE, Mair-Meijers H, Luca F, Kane HS, Slatcher RB (2017) Mothers’ Attachment is Linked to their Children’s Anti-Inflammatory Gene Expression via Maternal Warmth. Social Psychological and Personality Science. doi/10.1177/1948550616687125.

Moyerbrailean GA, Richards A, Kurtz D, Kalita C, Davis G, Harvey C, Alazizi A, Watza D, Sorokin Y, Hauff N, Zhou X, Wen X, Pique-Regi R, and Luca F (2016) High-throughput allele-specific expression across 250 environmental conditions. Genome Res. (12):1627-1638.

Richards AL, Burns MB, Alazizi A, Barreiro LB, Pique-Regi R, Blekhman R, Luca F (2016) Genetic and transcriptional analysis of human host response to healthy gut microbiome. mSystems. 1 (4) e00067-16; DOI: 10.1128/mSystems.00067-16.

Moyerbrailean G, Harvey C, Kalita C, Wen X, Luca F, Pique-Regi R (2016) Which genetics variants in dnase-seq footprints are more likely to alter binding? PLoS Genet. 12(2):e1005875.

Nédélec Y, Sanz J, Baharian G, Szpiech ZA, Pacis A, Dumaine A, Grenier JC, Freiman A, Sams AJ, Hebert S, Sabourin AP, Luca F, Blekhman R, Hernandez RD, Pique-Regi R, Tung J, Yotova V, Barreiro LB (2016) Genetic ancestry and natural selection drive population differences in immune responses to pathogens. Cell. 167(3):657-669.e21. doi: 10.1016/j.cell.2016.09.025.

Wen X, Lee Y, Luca F, Pique-Regi R (2016) Efficient Integrative Multi-SNP Association Analysis using Deterministic Approximation of Posteriors. AJHG, 98, 6: 1114-1129.

Moyerbrailean G, Davis O, Harvey C, Watza D, Wen X, Pique-Regi R, Luca F. (2015) A high-throughput RNA-seq approach to profile transcriptional responses. Sci Rep, 29;5:14976. doi: 10.1038/srep14976.

Pacis A, Tailleux L, LambourneJ, YotovaV, Dumaine A, Danckaert A, Luca F, Grenier JC, HansenK, YuM, TungJ, HeC, PastinenT, Pique-Regi R, Gilad Y, Barreiro LB. “Bacterial Infection Remodels the DNA Methylation Landscape of Human Dendritic Cells”. (2015) Genome Res. 25(12):1801-11. doi: 10.1101/gr.192005.

Wen X, Luca F, Pique-Regi R(2015)Cross-population Meta-analysis of eQTLs: Fine Mapping and Functional Study. PLoS Genet. Vol 11:e1005176. doi: 10.1371/journal.pgen.1005176.  

Harvey C, Moyerbrailean G, Davis O, Wen X, Luca F, Pique-Regi R (2014) QuASAR: Quantitative Allele Specific Analysis of Reads. Bioinformatics. doi: 10.1093/bioinformatics/btu802.

Luca F, Maranville JC, Richards A, Witonsky D, Stephens M and Di Rienzo A (2013) Genetic, functional and molecular features of glucocorticoid receptor binding. PLOS ONE. 8(4):e61654. doi: 10.1371/journal.pone.0061654.

Luca F, Di Rienzo A (2013) Allelic imbalance assays to quantify allele-specific gene expression and transcription factor binding. Methods Mol Biol. 2013; 1015:201-11.

Wall JD⁺, Kim SK⁺, Luca F, Carbone L, Mootnick AR, de Jong PJ, Di Rienzo A (2013) Incomplete Lineage Sorting Is Common in Extant Gibbon Genera. PloS one 8 (1), e53682.

Maranville JC, Luca F, Stephens M, Di Rienzo A (2012) Mapping gene-environment interactions at regulatory polymorphisms: insights into mechanisms of phenotypic variation. Transcription. Vol 3:56-62.

Luca, F. (2012) Diet, Changes in Gene Expression and Human Evolution. In: eLS 2012, John Wiley & Sons, Ltd: Chichester. http://www.els.net/ [DOI: 10.1002/9780470015902.a0023644

2007-2011

Maranville JC⁺, Luca F⁺, Richards A, Wen X, Witonsky D, Baxter S, Stephens M and Di Rienzo A (2011) Interactions between glucocorticoid treatment and cis-regulatory polymorphisms contribute to cellular response phenotypes. PLoS Genetics. Vol. 7: e1002162. doi:10.1371/journal.pgen.1002162.

Luca F, Hudson RR, Witonsky D, Di Rienzo A. (2011) A reduced representation approach to population genetic analyses and applications to human evolution. Genome Research. Vol. 21:1087-98.

Luca F, Perry GH, Di Rienzo A (2010) Evolutionary Adaptations to Dietary Changes. Ann. Rev. Nutrition. Vol. 30: 291-314.

Luca F, Kashyap S, Southard C, Zou M, Witonsky D, Di Rienzo A, Conzen SD (2009) Adaptive variation regulates the expression of the human SGK1 gene in response to stress. PLoS Genet. 5:e1000489.

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 (2008) Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter-gatherers and Bantu-speaking farmers. Proc Natl Acad Sci USA 105:1596-601.

Coop G, Bullaughey K, Luca F, Przeworski M (2008) The timing of selection at the human FOXP2 gene. Mol Biol Evol 25:1257-9.

Luca F, Bubba G, Basile M, Brdicka R, Michalodimitrakis E, Rickards O, Vershubsky G, Quintana-Murci L, Kozlov AI, Novelletto A (2008) Multiple Advantageous Amino Acid Variants in the NAT2 Gene in Human Populations. PLoS ONE 3(9): e3136. doi:10.1371/journal.pone.0003136.

Luca F, Di Giacomo F, Benincasa T, Popa LO, Banyko J, Kracmarova A, Malaspina P, Novelletto A, Brdicka R (2007) Y-chromosomal variation in the Czech Republic. Am J Phys Anthropol 132:132-9.

Luca F and Di Rienzo A (2007) An Evolutionary Framework for Common Disease. In: Encyclopedia of Life Sciences. John Wiley & Sons, Ltd: Chichester http://www.els.net/ [10.1002/9780470015902.a0020758]

2003-2006

Patin E, Barreiro LB, Sabeti PC, Austerlitz F, Luca F, Sajantila A, Behar DM, Semino O, Sakuntabhai A, Guiso N,  Gicquel B, McElreavey K, Harding RM, Heyer E, Quintana-Murci L (2006) Deciphering the Ancient and Complex Evolutionary History of Human Arylamine N-Acetyltransferase Genes. Am J Hum Genet 78:423-36.

Luca F, Basile M, Di Giacomo F, Novelletto A (2005) Independent methods for evolutionary genetic dating provide insights into Y-chromosomal STR mutation rates confirming data from direct father-son transmissions. Hum Genet 31:1-13.

Di Giacomo F, Luca F, Popa LO, Akar N, Anagnou N, Banyko J, Brdicka R, Barbujani G, Papola F, Ciavarella G, Cucci F, Di Stasi L, Gavrila L, Kerimova MG, Kovatchev D, Kozlov AI, Loutradis A, Mandarino V, Mammi C, Michalodimitrakis EN, Paoli G, Pappa KI, Pedicini G, Terrenato L, Tofanelli S, Malaspina  P, Novelletto A (2004) Y chromosomal haplogroup J as a signature of the post-neolithic colonization of Europe. Hum. Genet. 115: 357-371.

Di Giacomo F, Luca F, Anagnou N, Ciavarella G, Cresta M, Cucci F, Di Stasi L, Agostiano V, Giparaki M, Loutradis A, Mammi C, Michalodimitrakis EN, Papola F, Pedicini G, Plata E, Terrenato L, Tofanelli S, Malaspina P, Novelletto A (2003) Clinal patterns of human Y chromosomal diversity in continental Italy and Greece are dominated by drift and founder effects. Mol. Phyl. Evol. 28: 387-395.