All original images / photographs in this website are copyrighted and may not be reproduced, transmitted, altered or used in any way without prior written permission from Wayne State University.


Wayne State University/Perinatology Research Branch - Single Cell Genomics, Roger Pique-Regi, Ph.D.Title

  • Associate Professor, Center for Molecular Medicine and Genetics,
    Department of Obstetrics and Gynecology, Wayne State University School of Medicine

Education and Training

  • B.S-M.S. in Telecomunications Engineering, Universitat Politecnica de Catalunya,
    Barcelona, Catalonia
  • Ph.D. in Electrical Engineering, University of Southern California, Los Angeles, CA
  • Postdoctoral training, University of Chicago, Human Genetics Department (JK Pritchard lab)

Research Accomplishments

  • Gene by environment interactions are enriched for association with complex traits. To demonstrate this, high-throughput functional genomic assays were combined with novel computational tools to detect differences in allele specific expression across environments.
  • Identification of gene regulatory sequences using functional genomics data.  A novel probabilistic framework, CENTIPEDE, was developed to predict tissue-specific regulatory sites for DNA-binding proteins using DNase-seq footprinting.
  • Identification of genetic variants that affect transcription factor binding which is a major mechanism by which non-coding variants affect gene expression and affect highly polygenic complex phenotypes. We developed tools to analyze and integrate DNase-QTLs, eQTLs and GWAS.
  • Development of machine learning and signal processing methods to analyze genomic datasets. Developed GADA, a method that combines a maximally sparse representation for copy number signal and sparse Bayesian learning (SBL) to reconstruct the signal from noisy observations.

Awards and Recognitions

  • "La Caixa" Fellowship for doctoral studies in United States , Fundacio La Caixa
  • "Chicago Fellows" postdoctoral scholarship, The University of Chicago
  • Young Investigator Award for attending the International Congress of Human Genetics in Montreal , ASHG
  • Top Ten Papers in Regulatory and Systems Genomics 2011, ISCB/RECOMB
  • Top Ten Papers in Regulatory and Systems Genomics 2012, ISCB/RECOMB
  • Outstanding Graduate Mentor Award in the Health Sciences, Wayne State University
  • Research Excellence Award, Wayne State University School of Medicine
  • R01- GM109215 "Functional Characterization of the Genetic and Environmental Determinants of Complex Traits" NIH-NIGMS (2014 - Present)

Research Interests

  • Analysis of functional genomics data (ATAC-seq, RNA-seq) both bulk and at single cell resolution
  • Development of computational tools and statistical genetics models
  • Molecular mechanisms regulating gene transcription, chromatin accessibility and transcription factor binding
  • Genetics of molecular traits, and gene by environment interactions
  • Precision medicine for cardiovascular disease, preterm birth and pregnancy complications.

Selected Publications

  • Pique-Regi R*, Monso-Varona J, Ortega A, Seeger RC, Triche TJ, Asgharzadeh S. Sparse representation and Bayesian detection of genome copy number alterations from microarray data. Bioinformatics. 2008 Feb 1;24(3):309-18. PubMed PMID: 18203770; PubMed Central PMCID: PMC2704547.
  • Pique-Regi R*, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res. 2011 Mar;21(3):447-55. PubMed PMID: 21106904; PubMed Central PMCID: PMC3044858.
  • Degner JF, Pai AA, Pique-Regi R*, Veyrieras JB, Gaffney DJ, Pickrell JK, De Leon S, Michelini K, Lewellen N, Crawford GE, Stephens M, Gilad Y, Pritchard JK. DNase I sensitivity QTLs are a major determinant of human expression variation. Nature. 2012 Feb 5;482(7385):390-4. PubMed PMID: 22307276; PubMed Central PMCID: PMC3501342.
  • Wen X, Luca F, Pique-Regi R*. Cross-population joint analysis of eQTLs: fine mapping and functional annotation. PLoS Genet. 2015 Apr 23;11(4):e1005176. PubMed PMID: 25906321; PubMed Central PMCID: PMC4408026.
  • 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 22;12(2):e1005875. PubMed PMID: 26901046; PubMed Central PMCID: PMC4764260.
  • 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 Dec;26(12):1627-1638. PubMed PMID: 27934696; PubMed Central PMCID: PMC5131815.
  • 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. 2017 Sep 22. PubMed PMID: 29028988
  • Burl RB, Ramseyer VD, Rondini EA, Pique-Regi R, Lee YH, Granneman JG. Deconstructing Adipogenesis Induced by β3-Adrenergic Receptor Activation with Single-Cell Expression Profiling. Cell Metab. 2018 Aug 7;28(2):300-309.e4. PubMed PMID: 29937373; PubMed Central PMCID: PMC6082711.
  • 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 Sep 25;PubMed PMID: 30254052.

(*) Indicates corresponding author.




  • Director of the Perinatal Immunobiology Unit, Wayne State University Perinatal Initiative in support of the Perinatology Research Branch, NICHD/NIH/DHHS
  • Associate Professor, Department of Obstetrics and Gynecology, C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine


  • Ph.D. – Chemical-Biological sciences with an emphasis on Reproductive Immunology, National Polytechnic Institute, National School of Biological Sciences/National Institute of Perinatology, Mexico City, Mexico
  • M.Sc. – Chemical-Biological sciences with an emphasis on Reproductive Biology, National Polytechnic Institute, National School of Biological Sciences/National Institute of Perinatology, Mexico City, Mexico
  • Chemist, Bacteriologist, Parasitologist – National School of Biological Sciences, National Polytechnic Institute, Mexico City, Mexico

Postdoctoral Training

  • University of Adelaide, Departments of Obstetrics & Gynecology, Adelaide, SA, Australia. Postdoctoral Fellow in Reproductive Immunology.
  • University of Alberta, Departments of Obstetrics & Gynecology. Edmonton, AB, Canada. Postdoctoral Fellow in Physiology of Pregnancy.

Research Accomplishments

Our unit has:

  • Provided a mechanism whereby alarmins induce sterile intra-amniotic inflammation and preterm labor and birth, known as the activation of the inflammasome.
  • Discovered the role of the inflammasome, a large protein complex in the cell cytoplasm that activates a pro-inflammatory response, in spontaneous term and preterm labor.
  • Discovered therapeutic strategies to prevent spontaneous preterm labor: Inhibition of the NLRP3 inflammasome complex, and activation of the PPARgamma pathway
  • Provided evidence that there is a unique cellular microenvironment at the human maternal-fetal interface in spontaneous term and preterm labor.
  • Described of the immune cellular response in the amniotic cavity of women with normal and complicated pregnancies
  • Determined the origin of amniotic neutrophils in the setting of intra-amniotic inflammation. Neutrophils are of fetal origin in spontaneous preterm labor, as compared to mostly maternal origin in term labor.
  • Discovery of Neutrophil Extracellular Traps (NETs) in the amniotic cavity and chorioamniotic membranes in the setting of intra-amniotic infection.
  • Described the immune mechanisms whereby vaginal progesterone prevents preterm labor and birth

Research Interests

  • The mechanisms whereby damage-associated molecular patterns (DAMPs) induce sterile intra-amniotic inflammation and spontaneous preterm labor and birth
  • The function of leukocytes in the amniotic cavity of women with intra-amniotic infection/inflammation
  • The homeostatic role of innate immune cells in late gestation in order to develop strategies to prevent inflammation-induced preterm labor
  • The roles of effector and regulatory T cells in spontaneous preterm labor

Select Publications

  • Garcia-Flores V, Romero R, Miller D, Xu Y, Done B, Veerapaneni C, Leng Y, Arenas-Hernandez M, Khan N, Panaitescu B, Hassan SS, Alvarez-Salas LM, Gomez-Lopez N. Inflammation-Induced Adverse Pregnancy and Neonatal Outcomes Can Be Improved by the Immunomodulatory Peptide Exendin-4. Front Immunol. 2018 Jun 18;9:1291. doi: 10.3389/fimmu.2018.01291. eCollection 2018. PMID: 29967606.
  • Frascoli M, Coniglio L, Witt R, Jeanty C, Fleck-Derderian S, Myers DE, Lee TH, Keating S, Busch MP, Norris PJ, Tang Q, Cruz G, Barcellos LF, Gomez-Lopez N, Romero R, MacKenzie TC. Alloreactive fetal T cells promote uterine contractility in preterm labor via IFN-γ and TNF-α. Sci Transl Med. 2018 Apr 25;10(438). pii: eaan2263. doi: 10.1126/scitranslmed.aan2263. PMID: 29695455.
  • Gomez-Lopez N, Romero R, Xu Y, Miller D, Leng Y, Panaitescu B, Silva P, Faro J, Alhousseini A, Gill N, Hassan SS, Hsu CD. The immunophenotype of amniotic fluid leukocytes in normal and complicated pregnancies. Am J Reprod Immunol. 2018 Apr;79(4):e12827. doi: 10.1111/aji.12827. Epub 2018 Mar 3. PMID: 29500850.
  • Miller D, Romero R, Unkel R, Xu Y, Vadillo-Ortega F, Hassan SS, Gomez-Lopez N. CD71+ erythroid cells from neonates born to women with preterm labor regulate cytokine and cellular responses. J Leukoc Biol. 2018 Apr;103(4):761-775. doi: 10.1002/JLB.5A0717-291RRR. Epub 2018 Feb 1. PMID: 29389020.
  • Gomez-Lopez N, Romero R, Xu Y, Leng Y, Garcia-Flores V, Miller D, Jacques SM, Hassan SS, Faro J, Alsamsam A, Alhousseini A, Gomez-Roberts H, Panaitescu B, Yeo L, Maymon E. Are amniotic fluid neutrophils in women with intraamniotic infection and/or inflammation of fetal or maternal origin? Am J Obstet Gynecol. 2017 Sep 28. pii: S0002-9378(17)31128-6. doi: 10.1016/j.ajog.2017.09.013. [Epub ahead of print] PubMed PMID: 28964823.
  • Gomez-Lopez N, Romero R, Plazyo O, Schwenkel G, Garcia-Flores V, Unkel R, Xu Y, Leng Y, Hassan SS, Panaitescu B, Cha J, Dey SK. Preterm labor in the absence of acute histologic chorioamnionitis is characterized by cellular senescence of the chorioamniotic membranes. Am J Obstet Gynecol. 2017 Nov;217(5):592.e1-592.e17. doi: 10.1016/j.ajog.2017.08.008. Epub 2017 Aug 25. PubMed PMID: 28847437.
  • Gomez-Lopez N, Romero R, Garcia-Flores V, Xu Y, Leng Y, Alhousseini A, Hassan SS, Panaitescu B. Amniotic fluid neutrophils can phagocytize bacteria: A mechanism for microbial killing in the amniotic cavity. Am J Reprod Immunol. 2017 Oct;78(4). doi: 10.1111/aji.12723. Epub 2017 Jul 13. PubMed PMID: 28703488; PubMed Central PMCID: PMC5623137.
  • Gomez-Lopez N, Romero R, Arenas-Hernandez M, Schwenkel G, St Louis D, Hassan SS, Mial TN. In vivo activation of invariant natural killer T cells induces systemic and local alterations in T-cell subsets prior to preterm birth. Clin Exp Immunol. 2017 Aug;189(2):211-225. doi: 10.1111/cei.12968. Epub 2017 May 10. PubMed PMID: 28369855; PubMed Central PMCID: PMC5508324.
  • Gomez-Lopez N, Romero R, Xu Y, Garcia-Flores V, Leng Y, Panaitescu B, Miller D, Abrahams VM, Hassan SS. Inflammasome assembly in the chorioamniotic membranes during spontaneous labor at term. Am J Reprod Immunol. 2017 May;77(5). doi: 10.1111/aji.12648. Epub 2017 Feb 24. PubMed PMID: 28233423; PubMed Central PMCID: PMC5429868.
  • Plazyo O, Romero R, Unkel R, Balancio A, Mial TN, Xu Y, Dong Z, Hassan SS, Gomez-Lopez N. HMGB1 Induces an Inflammatory Response in the Chorioamniotic Membranes That Is Partially Mediated by the Inflammasome. Biol Reprod. 2016 Dec;95(6):130. doi: 10.1095/biolreprod.116.144139. Epub 2016 Nov 2. PubMed PMID: 27806943; PubMed Central PMCID: PMC5315428.
  • Xu Y, Romero R, Miller D, Kadam L, Mial TN, Plazyo O, Garcia-Flores V, Hassan SS, Xu Z, Tarca AL, Drewlo S, Gomez-Lopez N. An M1-like Macrophage Polarization in Decidual Tissue during Spontaneous Preterm Labor That Is Attenuated by Rosiglitazone Treatment. J Immunol. 2016 Mar 15;196(6):2476-2491. doi: 10.4049/jimmunol.1502055. Epub 2016 Feb 17. PubMed PMID: 26889045; PubMed Central PMCID: PMC4779725.
  • St Louis D, Romero R, Plazyo O, Arenas-Hernandez M, Panaitescu B, Xu Y, Milovic T, Xu Z, Bhatti G, Mi QS, Drewlo S, Tarca AL, Hassan SS, Gomez-Lopez N. Invariant NKT Cell Activation Induces Late Preterm Birth That Is Attenuated by Rosiglitazone. J Immunol. 2016 Feb 1;196(3):1044-59. doi: 10.4049/jimmunol.1501962. Epub 2016 Jan 6. PubMed PMID: 26740111; PubMed Central PMCID: PMC4724534.
  • Gomez-Lopez N, Romero R, Plazyo O, Panaitescu B, Furcron AE, Miller D, Roumayah T, Flom E, Hassan SS. Intra-Amniotic Administration of HMGB1 Induces Spontaneous Preterm Labor and Birth. Am J Reprod Immunol. 2016 Jan;75(1):3-7. doi: 10.1111/aji.12443. PubMed PMID: 26781934; PubMed Central PMCID: PMC5029853.
  • Gomez-Lopez N, Olson DM, Robertson SA. Interleukin-6 controls uterine Th9 cells and CD8(+) T regulatory cells to accelerate parturition in mice. Immunol Cell Biol. 2016 Jan;94(1):79-89. doi: 10.1038/icb.2015.63. Epub 2015 Jun 15. PubMed PMID: 26073576.
  • Furcron AE, Romero R, Plazyo O, Unkel R, Xu Y, Hassan SS, Chaemsaithong P, Mahajan A, Gomez-Lopez N. Vaginal progesterone, but not 17α-hydroxyprogesterone caproate, has antiinflammatory effects at the murine maternal-fetal interface. Am J Obstet Gynecol. 2015 Dec;213(6):846.e1-846.e19. doi: 10.1016/j.ajog.2015.08.010. Epub 2015 Aug 8. PubMed PMID: 26264823; PubMed Central PMCID: PMC4729364.
  • Arenas-Hernandez M, Romero R, St Louis D, Hassan SS, Kaye EB, Gomez-Lopez N. An imbalance between innate and adaptive immune cells at the maternal-fetal interface occurs prior to endotoxin-induced preterm birth. Cell Mol Immunol. 2016 Jul;13(4):462-73. doi: 10.1038/cmi.2015.22. Epub 2015 Apr 6. PubMed PMID: 25849119; PubMed Central PMCID: PMC4947814.
  • Gomez-Lopez N, StLouis D, Lehr MA, Sanchez-Rodriguez EN, Arenas-Hernandez M. Immune cells in term and preterm labor. Cell Mol Immunol. 2014 Nov;11(6):571-81. doi: 10.1038/cmi.2014.46. Epub 2014 Jun 23. Review. PubMed PMID: 24954221; PubMed Central PMCID: PMC4220837.
  • Gomez-Lopez N, Vega-Sanchez R, Castillo-Castrejon M, Romero R, Cubeiro-Arreola K, Vadillo-Ortega F. Evidence for a role for the adaptive immune response in human term parturition. Am J Reprod Immunol. 2013 Mar;69(3):212-30. doi: 10.1111/aji.12074. Epub 2013 Jan 24. PubMed PMID: 23347265; PubMed Central PMCID: PMC3600361.
  • Gomez-Lopez N, Laresgoiti-Servitje E. T regulatory cells: regulating both term and preterm labor? Immunol Cell Biol. 2012 Nov;90(10):919-20. doi: 10.1038/icb.2012.48. Epub 2012 Oct 2. PubMed PMID: 23032368.
  • Gomez-Lopez N, Guilbert LJ, Olson DM. Invasion of the leukocytes into the fetal-maternal interface during pregnancy. J Leukoc Biol. 2010 Oct;88(4):625-33. doi: 10.1189/jlb.1209796. Epub 2010 Jun 2. Review. PubMed PMID: 20519637.
  • Gomez-Lopez N, Laresgoiti-Servitje E, Olson DM, Estrada-Gutiérrez G, Vadillo-Ortega F. The role of chemokines in term and premature rupture of the fetal membranes: a review. Biol Reprod. 2010 May;82(5):809-14. doi: 10.1095/biolreprod.109.080432. Epub 2010 Jan 20. Review. PubMed PMID: 20089887.
  • Laresgoiti-Servitje E, Gómez-López N, Olson DM. An immunological insight into the origins of pre-eclampsia. Hum Reprod Update. 2010 Sep-Oct;16(5):510-24. doi: 10.1093/humupd/dmq007. Epub 2010 Apr 12. Review. Erratum in: Hum Reprod Update. 2011 Mar-Apr;17(2):291. PubMed PMID: 20388637.
  • Gomez-Lopez N, Estrada-Gutierrez G, Jimenez-Zamudio L, Vega-Sanchez R, Vadillo-Ortega F. Fetal membranes exhibit selective leukocyte chemotaxic activity during human labor. J Reprod Immunol. 2009 Jun;80(1-2):122-31. doi: 10.1016/j.jri.2009.01.002. Epub 2009 Apr 29. PubMed PMID: 19406481.


Wayne State University/Perinatology Research Branch - Bioinformatics Director, Adi LaurentiuTarca, Ph.D.Title

  • Professor, Department of Obstetrics and Gynecology, Wayne State School of Medicine;
    Adjunct Professor, Department of Computer Science, Wayne State College of Engineering;

Education and Training

  • B.Sc. - Chemical Engineering, "Politehnica" University, Bucharest, Romania
  • M.Sc. - Electrochemistry, National Polytechnic Institute of Grenoble, France
  • Ph.D. - Chemical Engineering, Laval University, Quebec, Canada
  • Postdoctoral training - Bioinformatics, Laval University, Quebec, Canada

Research Accomplishments

  • Developed and applied neural network modeling and genetic algorithm optimization to engineering problems
  • Developed genomics data analysis methods and software packages available in Bioconductor including for:
    -normalization of microarray data (nnNorm)
    -analysis of signaling pathways (SPIA)
    -analysis of gene sets (PADOG)
    -predictive modeling (maPredictDSC)
  • Developed a customized standard for fetal growth assessment
  • Received multiple top awards in international systems biology/machine learning competitions sbv IMPROVER challenges and DREAM challenges
  • Developed the DREAM Preterm Birth Prediction Challenge to identify transcriptional markers for pregnancy dating and assessment of the risk of preterm birth

Awards and Recognitions

  • Funding NSERC (Canada) for Ph.D., Laval University, 2001 - 2003
  • Scholarship CNRS (France) for M.Sc., I.N.P. Grenoble, 2000
  • Scholarship TEMPUS (European Community) for M.Sc., I.N.P. Grenoble, 1999 - 2000
  • Scholarship TEMPUS for internship, U.S.T. Lille, 1997
  • Scholarship for Performance, U.P. Bucharest, 1998 - 1999

Research Interests

  • Methods for genomics data analysis and interpretation
  • Machine learning
  • Biomarkers in obstetrics
  • Personalized medicine

Selected Publications

  • Tarca AL, Romero R, Xu Z, Gomez-Lopez N, Erez O, Hsu CD, Hassan SS, Carey VJ. Targeted expression profiling by RNA-Seq improves detection of cellular dynamics during pregnancy and identifies a role for T cells in term parturition. Sci Rep; Sci Rep. 2019 Jan 29;9(1):848.
  • Tarca AL, Romero R, Gudicha DW, Erez O, Hernandez-Andrade E, Yeo L, Bhatti G, Pacora P, Maymon E, Hassan SS. A new customized fetal growth standard for African American women: the PRB/NICHD Detroit study. Am J Obstet Gynecol; 218(2S):S679-S91 e4, 2018.
  • Tarca AL, Fitzgerald W, Chaemsaithong P, Xu Z, Hassan SS, Grivel JC, Gomez-Lopez N, Panaitescu B, Pacora P, Maymon E, Erez O, Margolis L, Romero R. The cytokine network in women with an asymptomatic short cervix and the risk of preterm delivery. Am J Reprod Immunol, 2017.
  • Romero R, Erez O, Maymon E, Chaemsaithong P, Xu Z, Pacora P, Chaiworapongsa T, Done B, Hassan SS, Tarca AL. The maternal plasma proteome changes as a function of gestational age in normal pregnancy: a longitudinal study. Am J Obstet Gynecol, 217(1):67.e1-67.e21, 2017.
  • Erez O, Romero R, Maymon E, Chaemsaithong P, Done B, Pacora P, Panaitescu B, Chaiworapongsa T, Hassan SS, Tarca AL. The prediction of late-onset preeclampsia: Results from a longitudinal proteomics study. PLoS One;12(7):e0181468, 2017.
  • Tarca AL, Lauria M, Unger M, Bilal E, Boue S, Kumar Dey K, Hoeng J, Koeppl H, Martin F, Meyer P, Nandy P, Norel R, Peitsch M, Rice JJ, Romero R, Stolovitzky G, Talikka M, Xiang Y, Zechner C, Collaborators ID. Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge. Bioinformatics;29(22):2892-9, 2013.
  • Tarca AL, Draghici S, Bhatti G, Romero R. Down-weighting overlapping genes improves gene set analysis. BMC Bioinformatics;13:136, 2012.
  • Tarca AL, Draghici S, Khatri P, Hassan SS, Mittal P, Kim JS, Kim CJ, Kusanovic JP, Romero R. A novel signaling pathway impact analysis. Bioinformatics;25(1):75-82, 2009.
  • Tarca AL, Carey VJ, Chen XW, Romero R, Draghici S. Machine learning and its applications to biology. PLoS Comput Biol;3(6):e116, 2007.