For a full list of publications click here.

Selected publications.

* equal contribution, # corresponding author

• Djeddi S*^, Fernandez-Salinas D*^, Huang GX, Mohanty C, Kendziorski C, Gazal S., Boyce J, Ober C., Gern J, Barrett N, Gutierrez-Arcelus M#. Rhinovirus infection of airway epithelial cells uncovers the non-ciliated subset as a likely driver of genetic risk to childhood-onset asthma. Cell Genom. 2024 Sep 11;4(9):100636. PMID: 39197446

• Chiñas M, Fernandez-Salinas M, Aguiar V, Nieto-Caballero V, Lefton M, Nigrovic P, Ermann J#, Gutierrez-Arcelus M#. Functional genomics implicates natural killer cells in the pathogenesis of ankylosing spondylitis. HGG Adv. 2024 Oct 28;6(1):100375. PMID: 39468794

• Nieto-Caballero VE*, Reijneveld J*, Asgari S, Lopez K, Iwany SK, Luo Y, Nathan A, Fernandez-Salinas S^, Chiñas M^, Huang C-C, Zhang Z, León SR, Calderon RI, Lecca L, Murray M, Van Rhijn I, Raychaudhuri S, Moody DB, Suliman S#, Gutierrez-Arcelus M#. History of tuberculosis disease is associated with genetic regulatory variation in Peruvians. PLoS Genet. 2024 Jun 13;20(6):e1011313. PMID: 38870230.

• Wang Q, Kim T, Martínez-Bonet M, Aguiar VRC^, Sim S, Cui J, Sparks JA, Chen X, Todd M, Wauford B, Marion MC, Langefeld CD, Weirauch MT, Gutierrez-Arcelus M, Nigrovic PA#. High-throughput identification of functional regulatory SNPs in systemic lupus erythematosus. Nat Commun. 2024 Aug 9;15(1):6804. PMID: 39122710

• Ermann J, Lefton M, Wei K, Gutierrez-Arcelus M. Understanding Spondyloarthritis Pathogenesis: The Promise of Single-Cell Profiling. Curr Rheumatol Rep. 2024 Apr;26(4):144-154. PMID: 38227172

• Kratchmarov R, Djeddi S, Dunlap G, He W, Jia X, Burk CM, Ryan T, McGill A, Allegretti JR, Kataru RP, Mehrara BJ, Taylor EM, Agarwal S, Bhattacharyya N, Bergmark RW, Maxfield AZ, Lee S, Roditi R, Dwyer DF, Boyce JA, Buchheit KM, Laidlaw TM, Shreffler WG, Rao DA, Gutierrez-Arcelus M, Brennan PJ. TCF1-LEF1 co-expression identifies a multipotent progenitor cell (TH2-MPP) across human allergic diseases. Nat Immunol. 2024 May;25(5):902-915. PMID: 38589618

• Kim T, Martínez-Bonet M, Wang Q, Hackert N, Sparks JA, Baglaenko Y, Koh B, Darbousset R, Laza-Briviesca R, Chen X, Aguiar VRC, Chiu DJ, Westra HJ, Gutierrez-Arcelus M, Weirauch MT, Raychaudhuri S, Rao DA, Nigrovic PA. Non-coding autoimmune risk variant defines role for ICOS in T peripheral helper cell development. Nat Commun. 2024 Mar 9;15(1):2150. doi: 10.1038/s41467-024-46457-8.PMID: 38459032

• Huang GX, Mandanas MV, Djeddi S, Fernandez-Salinas D, Gutierrez-Arcelus M, Barrett NA. Increased glycolysis and cellular crosstalk in eosinophilic chronic rhinosinusitis with nasal polyps. Front Immunol. 2024 Feb 20;15:1321560. PMID: 38444858

• Wang X, Hallen NR, Lee M, Samuchiwal S, Ye Q, Buchheit KM, Maxfield AZ, Roditi RE, Bergmark RW, Bhattacharyya N, Ryan T, Gakpo D, Raychaudhuri S, Dwyer D, Laidlaw TM, Boyce JA, Gutierrez-Arcelus M, Barrett NA#. Type 2 inflammation drives an airway basal stem cell program through insulin receptor substrate signaling. J Allergy Clin Immunol. 2023 Jun;151(6):1536-1549.

• Aguiar VRC, Castelli EC, Single RM, Bashirova A, Ramsuran V, Kulkarni S, Augusto DG, Martin MP, Gutierrez-Arcelus M, Carrington M, Meyer D. Comparison between qPCR and RNA-seq reveals challenges of quantifying HLA expression. Immunogenetics. 2023 Jun;75(3):249-262.

• Lam KP, Chiñas M, Julé AM, Taylor M, Ohashi M, Benamar M, Crestani E, Son MBF, Chou J, Gebhart C, Chatila T, Newburger J, Randolph A, Gutierrez-Arcelus M, Henderson LA. SARS-CoV-2-specific T cell responses in patients with multisystem inflammatory syndrome in children. Clin Immunol. 2022 Oct;243:109106.

• Robles-Espinoza CD, Mohammadi P, Bonilla X, Gutierrez-Arcelus M#. Allele-specific expression: applications in cancer and technical considerations. Current Opinion in Genetics & Development. 2020 Dec 28;66:10-19.

• Gutierrez-Arcelus M*, Baglaenko Y*, Arora J, Hannes S, Luo Y, Amariuta T, Teslovich N, Rao DA, Ermann J, Jonsson AH, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Navarrete C, Rich SS, Taylor KD, Rotter JI, Gregersen PK, Esko T, Brenner MB, Raychaudhuri S#. Allele-specific expression changes dynamically during T cell activation in HLA and other autoimmune loci. Nature Genetics, 2020 Mar;52(3):247-253.

• Gutierrez-Arcelus M, Teslovich N, Mola AR, Polidoro RB, Nathan A, Hannes S, Slowikowski K, Watts GFM, Korsunsky I, Brenner MB, Raychaudhuri S#, Brenner PJ#. Lymphocyte innateness defined by transcriptional states reflects a balance between proliferation and effector functions. Nature Communications, 2019 Feb 8;10(1):687.

• Davenport EE, Amariuta T, Gutierrez-Arcelus M, Slowikowski K, Westra HJ, Luo Y, Shen C, Rao DA, Zhang Y, Pearson S, von Schack D, Beebe JS, Bing N, John S, Vincent MS, Zhang B, Raychaudhuri S#. Discovering in vivo cytokine-eQTL interactions from a lupus clinical trial. Genome Biol. 2018 Oct 19;19(1):168.

• Donlin LT, Rao DA, Wei K, Slowikowski K, McGeachy MJ, Turner JD, Meednu N, Mizoguchi F, Gutierrez-Arcelus M, Lieb DJ, Keegan J, Muskat K, Hillman J, Rozo C, Ricker E, Eisenhaure TM, Li S, Browne EP, Chicoine A, Sutherby D, Noma A; Accelerating Medicines Partnership RA/SLE Network, Nusbaum C, Kelly S, Pernis AB, Ivashkiv LB, Goodman SM, Robinson WH, Utz PJ, Lederer JA, Gravallese EM, Boyce BF, Hacohen N, Pitzalis C, Gregersen PK, Firestein GS, Raychaudhuri S, Moreland LW, Holers VM, Bykerk VP, Filer A, Boyle DL, Brenner MB, Anolik JH#. Methods for high-dimensonal analysis of cells dissociated from cryopreserved synovial tissue. Arthritis Res Ther. 2018 Jul 11;20(1):139.

• Gutierrez-Arcelus M, Rich SS, Raychaudhuri S#. Autoimmune diseases - connecting risk alleles with molecular traits of the immune system. Nat Rev Genet. 2016 Mar;17(3):160-74.

• Gutierrez-Arcelus M*, Ongen H*, Lappalainen T*, Montgomery SB*, Buil A, Yurovsky A, Bryois J, Giger T , Romano L, Planchon A, Falconnet E, Bielser D, Gagnebin M, Padioleau I, Borel C, Letourneau A, Makrythanasis P, Guipponi M, Gehrig C, Antonarakis SE#, Dermitzakis ET#. Tissue-specific effects of genetic and epigenetic variation on gene regulation and splicing. Plos Genet. 2015 Jan 29;11(1):e1004958

• Panousis NI, Gutierrez-Arcelus M, Dermitzakis ET#, Lappalainen T#. Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies. Genome Biol. 2014 Sep 20;15(9):467.

• Popadin K*, Gutierrez-Arcelus M*, Dermitzakis ET#, Antonarakis SE#. Genetic and Epigenetic Regulation of Human lincRNA Gene Expression. Am J Hum Genet. 2013 Dec 5;93(6):1015-26.

• Kilpinen H*, Waszak SM*, Gschwind AR, Raghav SK, Witwicki RM, Orioli A, Migliavacca E, Wiederkehr M, Gutierrez-Arcelus M, Panousis NI, Yurovsky A, Lappalainen T, Romano-Palumbo L, Planchon A, Bielser D, Bryois J, Padioleau I, Udin G, Thurnheer S, Hacker D, Core LJ, Lis JT, Hernandez N#, Reymond A#, Deplancke B#, Dermitzakis ET#. Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science. 2013 Nov 8;342(6159):744-7.

• Gutierrez-Arcelus M, Lappalainen T, Montgomery SB, Buil A, Ongen H, Yurovsky A, Bryois J, Giger T , Romano L, Planchon A, Falconnet E, Bielser D, Gagnebin M, Padioleau I, Borel C, Letourneau A, Makrythanasis P, Guipponi M, Gehrig C, Antonarakis SE#, Dermitzakis ET#. Passive and active DNA methylation and the interplay with genetic variation in gene regulation. eLife 2013;2:e00523

  • Research Highlight in Nature Review Genetics

  • Research Highlight in Genome Biology

• Stranger BE, Montgomery SB, Dimas AS, Parts L, Stegle O, Ingle CE, Sekowska M, Smith GD, Evans D, Gutierrez-Arcelus M, Price A, Raj T, Nisbett J, Nica AC, Beazley C, Durbin R, Deloukas P, Dermitzakis ET#. Patterns of cis regulatory variation in diverse human populations. PLoS Genet. 2012 Apr;8(4):e1002639

• Montgomery SB, Lappalainen T, Gutierrez-Arcelus M, Dermitzakis ET#. Rare and common regulatory variation in population-scale sequenced human genomes. PLoS Genet. 2011 Jul;7(7):e1002144

• Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, Nisbett J, Guigo R, Dermitzakis ET#. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature. 2010 Apr 1;464(7289):773-7

• Lee AS, Gutierrez-Arcelus M, Perry GH, Vallender EJ, Johnson WE, Miller GM, Korbel JO, Lee C#. Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies. Hum Mol Genet. 2008 Apr 15;17(8):1127-36

• Flores M, Morales L, Gonzaga-Jauregui C, Domínguez-Vidaña R, Zepeda C, Yañez O, Gutierrez M, Lemus T, Valle D, Avila MC, Blanco D, Medina-Ruiz S, Meza K, Ayala E, García D, Bustos P, González V, Girard L, Tusie-Luna T, Dávila G, Palacios R#. Recurrent DNA inversion rearrangements in the human genome. Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6099-106