Bioinformatics

The work carried out in this WP involves R&D activities in the field of health sciences in close collaboration with CICS-UBI, including multi-disciplinary projects with topics such as: analysis of biological, clinical and epidemiological data for the identification of disease biomarkers; identification of genomic risk variants in case-control genetic epidemiology studies; computational analysis of genomic variants to assess their potential functional impact; virtual drug screening and drug-molecule interaction modelling; and other computational biology applications.

Team & Collaborators

• Ana Paula Duarte | WP leader
• Ana Ramalhinho
• Cláudio Maia
• Manuel C. Lemos
• Sílvia Socorro
• Luiza Granadeiro
• Noel Lopes | Professor, IPG
• Paulo Almeida
• Samuel Silvestre
• Gilberto Alves
• Renato Boto
• Fani Sousa
• Ana Palmeira-Oliveira
• Jorge Gama
• Luísa Amaral
• Elsa Cardoso
• Eugénia Gallardo
• Isabel Tomás Oliveira | PostDoc, UBI (07/2019-06/2021)
• Tiago Rosado | Research fellow, UBI (06/2019-07/2021)

Publications

Journal articles

• Rocha S., Socorro S., Passarinha L., Maia C.. (2022). Comprehensive Landscape of STEAP Family Members Expression in Human Cancers: Unraveling the Potential Usefulness in Clinical Practice Using Integrated Bioinformatics Analysis. Data 7, no. 5: 64.
• Brinca A., Ramalhinho A., Sousa Â., Oliani A., Breitenfeld L., Passarinha L., Gallardo E.. (2022). Follicular Fluid: A Powerful Tool for the Understanding and Diagnosis of Polycystic Ovary Syndrome. Biomedicines 2022, 10, 1254.
• Gomes D., Yaduvanshi S., Silvestre S., Duarte A., Santos A., Soares C., Kumar V., Passarinha L., Sousa A.. (2022). Taxifolin and Lucidin as Potential E6 Protein Inhibitors: p53 Function Re-Establishment and Apoptosis Induction in Cervical Cancer Cells. Cancers 14: 2834 DOI: 10.3390/cancers14122834.
• Cruz-Vicente P., Gonçalves A., Ferreira O., Queiroz J., Silvestre S., Passarinha L., Gallardo E.. (2022). Discovery of Small Molecules as Membrane-Bound Catechol-O-methyltransferase Inhibitors with Interest in Parkinson’s Disease: Pharmacophore Modeling, Molecular Docking and In Vitro Experimental Validation Studies. Pharmaceuticals., 15(1), 51.
• Rocha S., Sousa I., Gomes I., Arinto P., Costa-Pinheiro P., Coutinho E., Santos C., Jerónimo C., Lemos M., Passarinha L., Socorro S., Maia C.. (2021). Promoter demethylation up-regulates STEAP1 gene expression in human prostate cancer: in vitro and in silico analysis. Life, 11(11), 1251.
• Carvalho J., Lopes-Nunes J., Vialet B., Rosado T., Gallardo E., Vale J., Eloy C., Ferreira S., Palmeira-de-Oliveira R., Campello M., Paulo A., Barthélémy P., Mergny J., Salgado G., Queiroz J., Ellington A., Cruz C.. (2021). Nanoaggregate-forming lipid-conjugated AS1411 aptamer as a promising tumor-targeted delivery system of anticancer agents in vitro. Nanomedicine. 36, 102429.
• Gomes D., Silvestre S., Duarte A., Venuti A., Soares C., Passarinha L., Sousa Â.. (2021). In Silico Approaches: A Way to Unveil Novel Therapeutic Drugs for Cervical Cancer Management. Pharmaceuticals (Basel), 14(8): 741.
• Lopes-Nunes J., Agonia A., Rosado T., Gallardo E., Palmeira-de-Oliveira R., Palmeira-de-Oliveira A., Martinez-de-Oliveira J., Fonseca-Moutinho J., Campello M., Paiva A., Paulo A., Vulgamott A., Ellignton A., Oliveira P., Cruz C.. (2021). Aptamer-Functionalized Gold Nanoparticles for Drug Delivery to Gynecological Carcinoma Cells. Cancers (Basel), 13(16), 4038.
• Cruz-Vicente P., Passarinha L., Silvestre S., Gallardo E.. (2021). Recent Developments in New Therapeutic Agents against Alzheimer and Parkinson Diseases: In-Silico Approaches. 26(8), 2193.
• Carvalho J., Lopes-Nunes J., Figueiredo J., Santos T., Miranda A., Riscado M., Sousa F., Duarte A., Socorro S., Tomaz C., Felgueiras M., Teixeira R., Faria C., Cruz C.. (2021), Molecular Beacon Assay Development for Severe Acute Respiratory Syndrome Coronavirus 2 Detection. ACS Sensors, 21, 7015. (***)
• Gomes D., Silvestre S., Duarte A., Venuti A., Soares C., Passarinha L., Sousa A.. (2021). In Silico Approaches: A Way to Unveil Novel Therapeutic Drugs for Cervical Cancer Management. Pharmaceuticals. 14(8), 741.
• Bonifácio M., Mateus C., Alves A., Maldonado E., Duarte A., Domingues F., Oleastro M., Ferreira, S.. (2021). Natural Transformation as a Mechanism of Horizontal Gene Transfer in Aliarcobacter butzleri. Pathogens, 10, 909.
• Rosado T., Barroso M., Vieira D., Gallardo E.. (2021). Trends in microextraction approaches for handling human hair extracts – A review. Analytica Chimica Acta.,1185, 338792. (***)
• Lorigo M., Quintaneiro C., Breitenfeld L., Cairrao E.. (2021). UV-B Filter Octylmethoxycinnamate Alters the Vascular Contractility Patterns in Pregnant Women with Hypothyroidism. Biomedicines, 9(2):115.
• Marques H., Cruz-Vicente P., Rosado T., Barroso M., Passarinha L., Gallardo E.. (2021). Recent Developments in the Determination of Biomarkers of Tobacco Smoke Exposure in Biological Specimens: A Review. Int J Environ Res Public Health, 18(4), 1768.
• Meirinho S., Campos G., Rodrigues M., Fortuna A., Falcão A., Alves G.. (2020). Salting-out assisted liquid-liquid extraction method optimized by design of experiments for the simultaneous HPLC analysis of perampanel and stiripentol in mouse matrices. J Sep Sci., 43, 4289.
• Simão A., Antunes M., Marques H., Rosado T., Soares S., Gonçalves J., Barroso M., Andraus M., Gallardo E.. (2020). Recent bioanalytical methods for the determination of new psychoactive substances in biological specimens. Bioanalysis, Vol. 12, No. 21, 1557–1595.
• Rosado T., Gallardo E., Vieira D., Barroso M.. (2020). New miniaturized clean-up procedure for hair samples by means of microextraction by packed sorbent: determination of cocaine and metabolites. Analytical and Bioanalytical Chemistry, 412, 7963–7976.
• Simão A., Gonçalves J., Caramelo D., Rosado T., Barroso M., Restolho J., Fernández N., Rodilla J., Duarte A., Cristóvão A., Gallardo E.. (2020). Determination of N,N-dimethyltryptamine and beta-carbolines in plants used to prepare ayahuasca beverages by means of solid-phase extraction and gas-chromatography–mass spectrometry. SN Appl. Sci. 2, 463.
• Santos E., Luís Â., Gonçalves J., Rosado T., Pereira L., Gallardo E., Duarte A.. (2020). Julbernardia paniculata and Pterocarpus angolensis: From Ethnobotanical Surveys to Phytochemical Characterization and Bioactivities Evaluation. Molecules, 25, 1828.
• Rosado T., Gallardo E., Vieira D., Barroso M.. (2020). Microextraction by Packed Sorbent as a Novel Strategy for Sample Clean-Up in the Determination of Methadone and Eddp in Hair. Journal of Analytical Toxicology, 44 (8), 840.
• Esgalhado A., Reste-Ferreira D., Albino S., Sousa A., Amaral A., Martinho A., Oliveira I., Verde I., Lourenço O., Fonseca A., Cardoso E., Arosa F.. (2020). CD45RA, CD8β, and IFNγ Are Potential Immune Biomarkers of Human Cognitive Function. Frontiers in immunology, 11, 2846. (***)
• Duarte A., Rosado T., Costa A., Santos J., Gallardo E., Quintela T., Ishikawa H., Schwerk C., Schroten H., Gonçalves I., Santos C.. (2020). The bitter taste receptor TAS2R14 regulates resveratrol transport across the human blood-cerebrospinal fluid barrier. Biochemical Pharmacology, 177, 113953.

(***) Articles published in a top 10% most cited journal of the respective field.

Posters in conferences

• Gomes D., Passarinha L., Sousa. A.. (2021). Screening de potenciais inibidores da proteína E6 do HPV para tratamento do cancro do colo do útero. 3º Encontro Nacional de Jovens Investigadores em Oncologia. (virtual conference)
• Gomes D., Silvestre S., Duarte A., Soares C., Passarinha L., Sousa A.. (2021). Screening of E6 potential inhibitors in cervical cancer. 34th International Papillomavirus Conference. (virtual conference)
• Gomes D., Passarinha L., Sousa. A.. (2021). In silico and in vitro studies to discover potential E6 inhibitors for cervical cancer. Workshop on Structural Biophysics (Centre National de la Recherche Scientifique), Bordeaux, France.

Oral communications

• Gomes D., Yaduvanshi S., Silvestre S., Duarte A., Santos A., Soares C., Kumar V., Passarinha L., Sousa A.. Compostos naturais como potenciais inibidores da proteína E6: restabelecem a função da p53 induzindo a apoptose em células do cancro do colo do útero. 4º Encontro Nacional de Jovens Investigadores em Oncologia, Porto, Portugal, 2022.

Book chapters

• Pissarra I., Marques H., Cruz-Vicente P., Rosado T., Passarinha L., Araujo A., Barroso M., Gallardo E.. (2021). Bioanalytical methods for the determination of antipsychotics and metabolites in biological samples. In Leon V. Berhardt (Eds.) Advances in Medicine and Biology, (pp1-76) Nova Science Publishers, Inc.
• Antunes M., Simão A., Fonseca S., Gonçalves J., Soares S., Almeida E., Gameiro C., Rosado T., Duarte A., Barroso M., Araújo A., Rodilla J., Gallardo E.. (2020). Liquid chromatography-mass spectrometry as a tool to identify adulteration in different food industries. In Galanakis, C. (Eds.) Food Toxicology and Forensics, (pp 123-180) Academic Press.
• Antunes M., Simão A., Fonseca S., Gonçalves J., Soares S., Almeida E., Gameiro C., Rosado T., Duarte A., Barroso M., Araújo A., Rodilla J., Gallardo E.. (2020). The Role of CYP2D6 in Opiates and Opioids Consumers and Its Implications in Clinical and Forensic Toxicology. In Leon V. Berhardt (Eds.) Advances in Medicine and Biology, (pp 1-53), Nova Science Publishers, Inc.
• Simão A., Antunes M., Gonçalves J., Soares S., Castro T., Rosado T., Caramelo D., Barroso M., Araújo A., Rodilla J., Gallardo E.. (2020). The Role of Gas Chromatography in Clinical and Forensic Toxicology. In Henrichon, P. (Eds) Gas Chromatography: History, Methods and Applications, (pp 1-104), Nova Science Publishers, Inc.
• Gonçalves J., Simão A., Soares S., Gameiro C., Almeida E., Rosado T., Luís Â., Gallardo E., Duarte A.. (2020). Prunus avium L.: Composition, Analysis and Health Benefits. In William Schneider (Eds.) Prunus: Classification, Cultivation and Toxicity, (pp pp1-104), Nova Science Publishers, Inc.
• Soares S., Gonçalves J., Simão A., Rosado T., Caramelo D., Fernández N., Araújo A., Barroso M., Gallardo E., Lepkowsky C.. (2020). Paroxetine in Human Biological Specimens: A Review of Current Sample Pretreatment and Bioanalytical Approaches. In C. M. Lepkowsky (Eds.) The Pharmacological Guide to Paroxetine, Nova Science Publishers, Inc.

Patents

• Carvalho J., Lopes-Nunes J., Figueiredo J., Santos T., Miranda A., Riscado M., Sousa F., Duarte A., Socorro S., Tomaz C., Felgueiras M., Teixeira R., Faria C., Cruz C.. Método de deteção molecular do ácido ribonucleico do coronavírus da síndrome respiratória aguda grave 2. Portuguese Patent, 2022. (submitted)

Last Update | Feb 13, 2023 (9:34 AM)