Nychas E^*, Marfil-Sánchez A^*, Chen X, Mirhakkak M, Li H, Jia Q, Xu A, Nielsen HB, Niewdorp M, Loomba R, Ni Y^#, Panagiotou G^# (2025) Discovery of robust and highly specific microbiome signatures of non-alcoholic fatty liver disease. Microbiome 13(1), 10.

Hedin KA, Mirhakkak MH, Vaaben TH, Sands C, Pedersen M, Baker A, Vazquez-Uribe R, Schäuble S, Panagiotou G^#, Wellejus A^#, Sommer MOA^# (2024) Saccharomyces boulardii enhances anti-inflammatory effectors and AhR activation via metabolic interactions in probiotic communities. ISME Journal 18(1), wrae212.

Brandt P^*, Mirhakkak MH^*, Wagner L, Driesch D, Möslinger A, Fänder P, Schäuble S, Panagiotou G, Vylkova S^# (2023) High-throughput profiling of Candida auris isolates reveals clade-specific metabolic differences. Microbiol Spectr 11(3), e0049823. (Review)

Mirhakkak MH^*, Chen X^*, Heinekamp T, Sae-Ong T, Xu LL, Ni Y, Kurzai O, Barber AE, Brakhage AA, Boutin S, Schäuble S^#, Panagiotou G^# (2023) Genome-scale Metabolic modeling of Aspergillus fumigatus strains reveals growth dependencies on the lung microbiome. Nat Commun 14(1), 4369.

Seelbinder B^#, Lohinai Z^*, Vazquez-Uribe R, Brunke S, Chen X, Mirhakkak M, Lopez-Escalera S, Dome B, Megyesfalvi Z, Berta J, Galffy G, Dulka E, Wellejus A, Weiss GJ, Bauer M, Hube B, Sommer MOA, Panagiotou G (2023) Candida expansion in the gut of lung cancer patients associates with an ecological signature that supports growth under dysbiotic conditions. Nat Commun 14(1), 2673.

Alonso-Roman R, Last A, Mirhakkak MH, Sprague JL, Möller L, Großmann P, Graf K, Gratz R, Mogavero S, Vylkova S, Panagiotou G, Schäuble S, Hube B, Gresnigt MS (2022) Lactobacillus rhamnosus colonisation antagonizes Candida albicans by forcing metabolic adaptations that compromise pathogenicity. Nat Commun 13(1), 3192.

Brandt P, Gerwien F, Wagner L, Krüger T, Ramírez-Zavala B, Mirhakkak MH, Schäuble S, Kniemeyer O, Panagiotou G, Brakhage AA, Morschhäuser J, Vylkova S (2022) Candida albicans SR-like protein kinases regulate different cellular processes: Sky1 is involved in control of ion homeostasis, while Sky2 is important for dipeptide utilization. Front Cell Infect Microbiol 12, 850531.

Marfil-Sánchez A^*, Zhang L^*, Alonso-Pernas P, Mirhakkak M, Mueller M, Seelbinder B, Ni Y, Santhanam R, Busch A, Beemelmanns C, Ermolaeva M, Bauer M^#, Panagiotou G^# (2021) An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness. Gut Microbes 13(1), 1993598.

Mirhakkak M, Schäuble S, Klassert T, Brunke S, Brandt P, Loos D, Uribe R, de Oliveira Lino FS, Ni Y, Vylkova S, Slevogt H, Hube B, Weiss G, Sommer M, Panagiotou G^# (2021) Metabolic modeling predicts specific gut bacteria as key determinants for Candida albicans colonization levels. ISME J 15(5), 1257-1270.

Dissanayake TK, Schäuble S, Mirhakkak MH, Wu WL, Ng CK, Yip C-Y, García-López A, Wolf T, Yeung ML, Chan KH, Yuen KY, Panagiotou G, To KKW (2020) Comparative transcriptomic analysis of rhinovirus and influenza virus infection. Front Microbiol 11(1580), 1-13.