Key publications using Genomic Services

Sequencing services

• HPV, HBV, and HIV-1 viral integration site mapping: A streamlined workflow from NGS to genomic insights of carcinogenesis.
  Shen-Gunther, J., ORCID and Easley, A. (2024)

• Regnase-2 inhibits glioblastoma cell proliferation
  Sowinska, W., Wawro, M., Kochan, J., Solecka, A., Polak, J., Kwinta, B. and Kasza, A., (2024)

• Plasma Levels of mir-34a-5p Correlate with Systemic Inflammation and Low Naïve CD4 T Cells in Common Variable Immunodeficiency
  Nyström, S., Hultberg, J., Blixt, E., Nilsdotter-Augustinsson, Å. and Larsson, M. (2024)

• Assessment of wood smoke induced pulmonary toxicity in normal- and chronic bronchitis-like bronchial and alveolar lung mucosa models at air–liquid interface
  Upadhyay, S., Rahman, M., Rinaldi, S., Koelmel, J., Lin, E.Z., Mahesh, P.A., Beckers, J., Johanson, G., Pollitt, K.J.G., Palmberg, L. and Irmler, M. (2024)

• Exploring the miRNAs Profile in Dark-Cutting Beef
  González-Blanco, L., Royo, L.J., Diñeiro, Y., García-Torres, S., Coto-Montes, A., Sierra, V. and Oliván, M. (2024)

• Mitigation of aeolian erosion of loess soil by Bio-Stimulated microbial induced calcite precipitation
  Raveh-Amit H, Gruber A, Abramov K, Tsesarsky M. (2024)

• Human placental microRNAs dysregulated by cadmium exposure predict neurobehavioral outcomes at birth
  Tehrani, J.M., Kennedy, E., Tung, P.W., Burt, A., Hermetz, K., Punshon, T., Jackson, B.P., Hao, K., Chen, J., Karagas, M.R. and Koestler, D.C. (2023)

• Novel mediator in anaphylaxis: decreased levels of miR-375-3p in serum and within extracellular vesicles of patients
  Nuñez-Borque, E., Fernandez-Bravo, S., Rodríguez Del Rio, P., Palacio-García, L., Di Giannatale, A., Di Paolo, V., Galardi, A., Colletti, M., Pascucci, L., Tome-Amat, J. and Cuesta-Herranz, J. (2023)

• Drug Resistance in Medulloblastoma Is Driven by YB-1, ABCB1 and a Seven-Gene Drug Signature
  Taylor, L., Wade, P.K., Johnson, J.E., Aldighieri, M., Morlando, S., Di Leva, G., Kerr, I.D. and Coyle, B. (2023)

• Placental microRNAs relate to early childhood growth trajectories
  Kennedy, E.M., Hermetz, K., Burt, A., Pei, D., Koestler, D.C., Hao, K., Chen, J., Gilbert-Diamond, D., Ramakrishnan, U., Karagas, M.R. and Marsit, C.J. (2023)

• Dysregulation of MicroRNAs in Adult Osteogenesis Imperfecta: The miROI Study
  Mercier‐Guery, A., Millet, M., Merle, B., Collet, C., Bagouet, F., Borel, O., Sornay‐Rendu, E., Szulc, P., Vignot, E., Gensburger, D. and Fontanges, E., (2023)

• Controlling Loess Erosion by Bio-Stimulated Microbial Induced Calcite Precipitation
  Tsesarsky, M., Gruber, A., Abramov, K. and Raveh-Amit, H. (2023)

• Glimepiride Compared to Liraglutide Increases Plasma Levels of miR-206, miR-182-5p, and miR-766-3p in Type 2 Diabetes Mellitus: A Randomized Controlled Trial
  Scherbak, N.N., Kruse, R., Nyström, T. and Jendle, J. (2023)

• Circulating miRNAs signature on breast cancer: the MCC-Spain project
  Gómez-Acebo, I., Llorca, J., Alonso-Molero, J., Díaz-Martínez, M., Pérez-Gómez, B., Amiano, P., Belmonte, T., Molina, A.J., Burgui, R., Castaño-Vinyals, G. and Moreno, V. (2023)

• Dendrimer-2PMPA Delays Muscle Function Loss and Denervation in a Murine Model of Amyotrophic Lateral Sclerosis
  Tallon, C., Sharma, A., Zhang, Z., Thomas, A.G., Ng, J., Zhu, X., Donoghue, A., Schulte, M., Joe, T.R., Kambhampati, S.P. and Sharma, R., (2022)

• Circulating MicroRNA Profiles as Potential Biomarkers for Differentiated Thyroid Cancer Recurrence
  Jankovic Miljus, J., Guillén-Sacoto, M.A., Makiadi-Alvarado, J., Wert-Lamas, L., Ramirez-Moya, J., Robledo, M., Santisteban, P. and Riesco-Eizaguirre, G. (2022)

• An Isogenic Collection of Pluripotent Stem Cell Lines With Elevated α-Synuclein Expression Validated for Neural Induction and Cortical Neuron Differentiation
  Natalwala, A., Behbehani, R., Yapom, R. and Kunath, T. (2022)

• Insight into the pulmonary molecular toxicity of heated tobacco products using human bronchial and alveolar mucosa models at air–liquid interface
  Rahman, M., Irmler, M., Introna, M., Beckers, J., Palmberg, L., Johanson, G., Upadhyay, S. and Ganguly, K. (2022)

• Small RNA-Seq Reveals Similar miRNA Transcriptome in Children and Young Adults with T-ALL and Indicates miR-143-3p as Novel Candidate Tumor Suppressor in This Leukemia
  Dawidowska, M., Maćkowska-Maślak, N., Drobna-Śledzińska, M., Kosmalska, M., Jaksik, R., Szymczak, D., Jarmuż-Szymczak, M., Sadowska-Klasa, A., Wojtaszewska, M., Sędek, Ł. and Wróbel, T. (2022)

• Extracellular circulating miRNAs as stress-related signature to search and rescue dogs
  Guelfi, G., Iaboni, M., Sansone, A., Capaccia, C., Santoro, M.M. and Diverio, S. (2022)

• Exploration of extracellular vesicle miRNAs, targeted mRNAs and pathways in prostate cancer: relation to disease status and progression
  Puhka, M., Thierens, L., Nicorici, D., Forsman, T., Mirtti, T., af Hällström, T., Serkkola, E. and Rannikko, A., (2022)

• Systemic delivery of large-scale manufactured Wharton’s Jelly mesenchymal stem cell-derived extracellular vesicles improves cardiac function after myocardial infarction
  Bellio, M.A., Kanashiro-Takeuchi, R.M., Takeuchi, L., Kulandavelu, S., Lee, Y.S., Balkan, W., Young, K.C., Hare, J.M. and Khan, A. (2022)

• Characterization of Extracellular Vesicles in Osteoporotic Patients Compared to Osteopenic and Healthy Controls
  Pepe, J., Rossi, M., Battafarano, G., Vernocchi, P., Conte, F., Marzano, V., Mariani, E., Mortera, S.L., Cipriani, C., Rana, I., Buonuomo, P.S., Bartuli, A., De Martino, V., Pelle, S., Pascucci, L., Toniolo, R.M., Putignani, L., Minisola, S. and Del Fattore, A. (2022)

• Circulating thrifty microRNA is related to insulin sensitivity, adiposity, and energy metabolism in adults with overweight and obesity: the POUNDS Lost trial
  Yoriko Heianza, Qiaochu Xue, Jennifer Rood, George A Bray, Frank M Sacks, Lu Qi (2022)

• Cell-Free DNA Sequencing Reveals Gene Variants in DNA Damage Repair Genes Associated with Prognosis of Prostate Cancer Patients
  Lieb V, Abdulrahman A, Weigelt K, Hauch S, Gombert M, Guzman J, Bellut L, Goebell PJ, Stöhr R, Hartmann A, Wullich B, Taubert H, Wach S. (2022)

• Cell-Free DNA Variant Sequencing Using Plasma and AR-V7 Testing of Circulating Tumor Cells in Prostate Cancer Patients
  Lieb V, Abdulrahman A, Weigelt K, Hauch S, Gombert M, Guzman J, Bellut L, Goebell PJ, Stöhr R, Hartmann A, Wullich B, Taubert H, Wach S. (2021)

• The epitranscriptomic writer ALKBH8 drives tolerance and protects mouse lungs from the environmental pollutant naphthalene.
  Leonardi, A., Kovalchuk, N., Yin, L., Lauren Endres, L., Sara Evke, S., Nevins, S., Samuel Martin, S., Dedon, P. C., Melendez, J.A., Van Winkle, L., Zhang, Q.-Y., Xinxin Ding, X., and Begley, T.J. (2020)

• Effects of cardiac sympathetic neurodegeneration and PPARγ activation on Rhesus macaque whole blood miRNA and mRNA expression profiles.
  Metzger, J.M., Lopez, M.S., Schmidt, J.K., Murphy, M.E., Vemuganti, R., and Emborg M.E. (2020)

• Unraveling the molecular signature of extracellular vesicles from endometrial-derived mesenchymal stem cells: potential modulatory effects and therapeutic applications
  Marinaro, F., Gómez-Serrano, M., Jorge, I., Silla-Castro, J.C., Vázquez, J., Sánchez-Margallo, F.M., Blázquez, R., López, E., Álvarez. V., and Casado, J.G. (2019)

• Equine arteritis virus long-term persistence is orchestrated by CD8+ T lymphocyte transcription factors, inhibitory receptors, and the CXCL16/CXCR6 axis
  Carossino, M., Dini, P., Kalbfleisch, T.S., Loynachan, A.T., Canisso, I.F., Cook, R.F., Timoney, P.J., and Balasuriya, U.B.R. (2019)

Nucleic acid isolation services

• Snack quality and snack timing are associated with cardiometabolic blood markers: the ZOE PREDICT study
  Bermingham, K.M., May, A., Asnicar, F., Capdevila, J., Leeming, E.R., Franks, P.W., Valdes, A.M., Wolf, J., Hadjigeorgiou, G., Delahanty, L.M. and Segata, N. (2024)

• Effects of CTLA-4 Single Nucleotide Polymorphisms on Toxicity of Ipilimumab-Containing Regimens in Patients With Advanced Stage Melanoma
  de Joode K, Mora AR, van Schaik RHN, Zippelius A, van der Veldt A, Gerard CL, Läubli H, Michielin O, von Moos R, Joerger M, Levesque MP, Aeppli S, Mangana J, Mangas C, Trost N, Meyer S, Parvex SL, Mathijssen R, Metaxas Y. (2024)

• Exploring the relationship between social jetlag with gut microbial composition, diet and cardiometabolic health, in the ZOE PREDICT 1 cohort
  Bermingham, K.M., Stensrud, S., Asnicar, F., Valdes, A.M., Franks, P.W., Wolf, J., Hadjigeorgiou, G., Davies, R., Spector, T.D., Segata, N. and Berry, S.E. (2023)

• Genetic and gut microbiome determinants of SCFA circulating and fecal levels, postprandial responses and links to chronic and acute inflammation
  Nogal, A., Asnicar, F., Vijay, A., Kouraki, A., Visconti, A., Louca, P., Wong, K., Baleanu, A.F., Giordano, F., Wolf, J. and Hadjigeorgiou, G. (2023)

• L1CAM immunocapture generates a unique extracellular vesicle population with a reproducible miRNA fingerprint
  Dunlop, R.A., Banack, S.A. and Cox, P.A. (2023)

• Associations between circulating microRNAs and coronary plaque characteristics: potential impact from physical exercise
  Taraldsen, M.D., Wiseth, R., Videm, V., Bye, A. and Madssen, E. (2022)

• Microbiome connections with host metabolism and habitual diet. Nature Medicine 27:321. DOI: 10.1038/s41591-020-01183-8
  Francesco, A., et al. (2021)

• Microbiome connections with host metabolism and habitual diet
  Asnicar, F., et al. (2021)

• Clinical and biochemical function of polymorphic NR0B1 GGAA-microsatellites in Ewing sarcoma: a report from the Children's Oncology Group
  Monument, M.J., Johnson, K.M., McIlvaine, E., Abegglen, L., Watkins, W.S., Jorde, L.B., Womer, R.B., Beeler, N., Monovich, L., Lawlor, E.R., Bridge, J.A., Schiffman, J.D., Krailo, M.K., Randall, R.L., and Lessnick, S.L. (2014)

qPCR and dPCR services

• Associations between circulating microRNAs and lipid-rich coronary plaques measured with near-infrared spectroscopy
  Sæther, J.C., Vesterbekkmo, E.K., Taraldsen, M.D., Gigante, B., Follestad, T., Røsjø, H.R., Omland, T., Wiseth, R., Madssen, E. and Bye, A., (2023)

• Specific Plasma MicroRNA Signatures Underlying the Clinical Outcomes of Hepatitis E Virus Infection
  Costafreda, M.I., Sauleda, S., Riveiro-Barciela, M., Rico, A., Llorens-Revull, M., Guix, S., Pintó, R.M., Bosch, A., Rodríguez-Frías, F., Rando, A. and Piron, M., (2023)

• Extracellular vesicles and microRNAs are altered in response to exercise, insulin sensitivity and overweight
  Doncheva, A.I., Romero, S., Ramirez‐Garrastacho, M., Lee, S., Kolnes, K.J., Tangen, D.S., Olsen, T., Drevon, C.A., Llorente, A., Dalen, K.T. and Hjorth, M. (2022)

• A prophylactic subcutaneous dose of the anticoagulant tinzaparin does not influence qPCR-based assessment of circulating levels of miRNA in humans
  Nilsson, A., Nerhall, A.M., Vechetti, I., Fornander, L., Wiklund, S., Alkner, B., Schilcher, J. and von Walden, F. (2022)

• Challenges in Cancer Biomarker Discovery Exemplified by the Identification of Diagnostic MicroRNAs in Prostate Tissues
  Ambrozkiewicz, F., Karczmarski, J., Kulecka, M., Paziewska, A., Cybulska, M., Szymanski, M., Dobruch, J., Antoniewicz, A., Mikula, M. and Ostrowski, J. (2020)

• Targeting the highly abundant circular RNA circSlc8a1 in cardiomyocytes attenuates pressure overload induced hypertrophy.
  Lim, T.B., Aliwarga, E., Luu, T.D.A., Li, Y.P., Ng, S.L., Annadoray, L., Sian, S., Ackers-Johnson, M.A., Foo, R.S.-Y. (2019)