Bioinformatics and computational biology laboratory

GUIMARÃES, GABRIELA RAPOZO ; MAKLOUF, GIOVANNA RESK ; TEIXEIRA, CRISTIANE ESTEVES ; DE OLIVEIRA SANTOS, LEANDRO ; TESSAROLLO, NAYARA GUSMÃO ; DE TOLEDO, NAYARA EVELIN ; SERAIN, ALESSANDRA FREITAS ; de Lanna, Cristóvão Antunes ; PRETTI, MARCO ANTÔNIO ; DA CRUZ, JÉSSICA GONÇALVES VIEIRA ; FALCHETTI, MARCELO ; DIMAS, MYLLA M. ; FILGUEIRAS, IGOR SALERNO ; CABRAL-MARQUES, OTAVIO ; RAMOS, RODRIGO NALIO ; DE MACEDO, FABIANE CARVALHO ; RODRIGUES, FABIANA RESENDE ; BASTOS, NINA CARROSSINI ; DA SILVA, JESSE LOPES ; MARTINS, M. L. B. ; et.al . Single-cell resolution characterization of myeloid-derived cell states with implication in cancer outcome. Nature Communications, v. 15, p. e1, 2024. https://doi.org/10.1038/s41467-024-49916-4 

STAHNKE, Caroline; MOLINA DE ARMAS, Elvismary; BESSA PEREIRA CHAVES, Claudia; SCHERER, Nicole de Miranda; PALMA MATTA, Bruna; CARVALHO DE BARROS MOREIRA, Fábio; BERGMANN, Anke; BORONI, Mariana; EVANGELISTA DOS SANTOS, Anna Claudia; MARTINS MOREIRA, Miguel Angelo. BRCA1, BRCA2, and TP53 germline and somatic variants and clinicopathological characteristics of Brazilian patients with epithelial ovarian cancer. CANCER MEDICINE, WILEY, v. 1, p. 105236, 2023. DOI: 10.1002/cam4.6729 

PRETTI, MARCO ANTONIO M. ; GALVANI, RÔMULO G. ; SCHERER, NICOLE M. ; FARIAS, ALESSANDRO S. ; BORONI, MARIANA . In silico analysis of mutant epitopes in new SARS-CoV-2 lineages suggest global enhanced CD8+ T cell reactivity and also signs of immune response escape. INFECTION GENETICS AND EVOLUTION, v. 1, p. 105236, 2022. https://doi.org/10.1016/j.meegid.2022.105236 

LOPES, BRUNO A. ; POUBEL, CAROLINE PIRES ; TEIXEIRA, CRISTIANE ESTEVES ; CAYE-EUDE, AURÉLIE ; CAVÉ, HÉLÈNE ; MEYER, CLAUS ; MARSCHALEK, ROLF ; BORONI, MARIANA ; EMERENCIANO, MARIANA . Novel Diagnostic and Therapeutic Options for KMT2A-Rearranged Acute Leukemias. Frontiers in Pharmacology, v. 13, p. 2022.749472, 2022. http://dx.doi.org/10.3389/fphar.2022.749472 

FERRAZ-BANNITZ, RAFAEL ; BERALDO, REBECA A. ; PELUSO, AUGUSTO ; DALL, MORTEN ; BABAEI, PARIZAD ; FOGLIETTI, RAYANA CARDOSO ; MARTINS, LARISSA MARFORI ; GOMES, PATRICIA MOREIRA ; MARCHINI, JULIO SERGIO ; SUEN, VIVIAN MARQUES MIGUEL ; DE FREITAS, LUIZ C. CONTI ; NAVEGANTES, LUIZ CARLOS ; PRETTI, MARCO ANTÔNIO M. ; BORONI, MARIANA ; TREEBAK, JONAS T. ; MORI, MARCELO A. ; FOSS, MILTON CESAR ; FOSS-FREITAS, MARIA CRISTINA . Dietary Protein Restriction Improves Metabolic Dysfunction in Patients with Metabolic Syndrome in a Randomized, Controlled Trial. Nutrients, v. 14, p. 2670, 2022. http://dx.doi.org/10.3390/nu14132670 

SCANDOLARA, THALITA BASSO ; VALLE, SARA FERREIRA ; TEIXEIRA, CRISTIANE ESTEVES ; SCHERER, NICOLE DE MIRANDA ; DE ARMAS, ELVISMARY MOLINA ; FURTADO, CAROLINA ; BORONI, MARIANA ; JAQUES, HELLEN DOS SANTOS ; ALVES, FERNANDA MARA ; RECH, DANIEL ; PANIS, CAROLINA ; BONVICINO, CIBELE RODRIGUES . Somatic DNA Damage Response and Homologous Repair Gene Alterations and Its Association With Tumor Variant Burden in Breast Cancer Patients With Occupational Exposure to Pesticides. FRONTIERS IN ONCOLOGY, v. 12, p. 1, 2022. http://dx.doi.org/10.3389/fonc.2022.904813 

CAETANO, MÔNICA MARIA MAGALHÃES ; MOREIRA, GABRIELA ALVES ; SILVA, MARIA ROMÉRIA DA ; GUIMARÃES, GABRIELA RAPOZO ; SANTOS, LEANDRO DE OLIVEIRA ; PACHECO, AMANDA DE AMBRÓSIO ; SIQUEIRA, RAONI PAIS ; MENDES, FLÁVIA CARNEIRO ; MARQUES DA SILVA, EDUARDO DE ALMEIDA ; JUNIOR, ABELARDO SILVA ; RANGEL FIETTO, JULIANA LOPES ; SAITO, ÂNGELA ; BORONI, MARIANA ; BRESSAN, GUSTAVO COSTA . Impaired expression of serine/arginine protein kinase 2 (SRPK2) affects melanoma progression. Frontiers in Genetics, v. 13, p. 1, 2022. http://dx.doi.org/10.3389/fgene.2022.979735 

MATTA, BRUNA PALMA ; GOMES, RENAN ; MATTOS, DANIEL ; OLICIO, RENATA ; NASCIMENTO, CAROLINE MACEDO ; FERREIRA, GERSON MOURA ; BRANT, AYSLAN CASTRO ; BORONI, MARIANA ; FURTADO, CAROLINA ; LIMA, VALDIRENE ; MOREIRA, MIGUEL ÂNGELO MARTINS ; DOS SANTOS, ANNA CLÁUDIA EVANGELISTA . Familial history and prevalence of BRCA1, BRCA2 and TP53 pathogenic variants in HBOC Brazilian patients from a public healthcare service. Scientific Reports, v. 12, p. e1, 2022. http://dx.doi.org/10.1038/s41598-022-23012-3 

BUSSO-LOPES, ARIANE F. NEVES, LEANDRO X. CÂMARA, GUILHERME A. GRANATO, DANIELA C. PRETTI, MARCO ANTÔNIO M. HEBERLE, HENRY PATRONI, FÁBIO M. S. SÁ, JAMILE YOKOO, SAMI RIVERA, CÉSAR DOMINGUES, ROMÊNIA R. NORMANDO, ANA GABRIELA C. DE ROSSI, TATIANE MELLO, BARBARA P. GALDINO, NAYANE A. L. PAULETTI, BIANCA A. LACERDA, PAMMELA A. RODRIGUES, ANDRÉ AFONSO N. CASARIM, ANDRÉ LUIS M. DE LIMA-SOUZA, REYDSON A. DAMAS, INGRID I. MARIANO, FERNANDA V. GOLLOB, KENNETH J. MEDINA, TIAGO S. CERVIGNE, NILVA K. , et al. ; Connecting multiple microenvironment proteomes uncovers the biology in head and neck cancer. Nature Communications, v. 13, p. e1, 2022. http://dx.doi.org/10.1038/s41467-022-34407-1 

de Lanna, Cristóvão Antunes ; DA SILVA, BEATRIZ NASCIMENTO MONTEIRO ; DE MELO, ANDREIA CRISTINA ; BONAMINO, MARTÍN H. ; ALVES, LÍSIA DALTRO BORGES ; PINTO, LUIS FELIPE RIBEIRO ; CARDOSO, ABEL SILVEIRA ; ANTUNES, HÉLITON SPÍNDOLA ; BORONI, MARIANA ; COHEN GOLDEMBERG, DANIEL . Oral Lichen Planus and Oral Squamous Cell Carcinoma share key oncogenic signatures. Scientific Reports, v. 12, p. e1, 2022. http://dx.doi.org/10.1038/s41598-022-24801-6 

ALVES MOREIRA, GABRIELA ; MARIA MAGALHÃES CAETANO, MÔNICA ; ALVES DO VALE, JULIANA ; CERQUEIRA DE PAIVA, JANINE ; HUGO SOUSA GONÇALVES, VICTOR ; ANDRADE ALMEIDA, ALISSON ; VIANA GOMES SILVA, LUCAS ; REBELLATO GIORDANO MARTIM, FERNANDA ; VINÍCIUS DE ANDRADE BARROS, MARCUS ; RAPOZO GUIMARÃES, GABRIELA ; DE OLIVEIRA SANTOS, LEANDRO ; PAULA MARTINS DE SOUZA, ANA ; MACHADO-NEVES, MARIANA ; RICARDO TEIXEIRA, RÓBSON ; SILVA-JÚNIOR, ABELARDO ; LOPES RANGEL FIETTO, JULIANA ; BORONI, MARIANA ; LICURSI DE OLIVEIRA, LEANDRO ; COSTA BRESSAN, GUSTAVO . The SRPK inhibitor N-(2-(piperidin-1-yl)-5-(trifluoromethyl)phenyl) isonicotinamide (SRPIN340) increases the immune response against metastatic melanoma in mice. BIOCHEMICAL PHARMACOLOGY, v. 00, p. 115161, 2022. http://dx.doi.org/10.1016/j.bcp.2022.115161 

SOUSA-SQUIAVINATO, ANNIE CRISTHINE MORAES ; VASCONCELOS, RENATA IVO ; GEHREN, ADRIANA SARTORIO ; FERNANDES, PRISCILA VALVERDE ; DE OLIVEIRA, IVANIR MARTINS ; BORONI, MARIANA ; MORGADO-DÍAZ, JOSE ANDRÉS . Cofilin-1, LIMK1 and SSH1 are differentially expressed in locally advanced colorectal cancer and according to consensus molecular subtypes. Cancer Cell International, v. 21, p. s12935, 2021. http://dx.doi.org/10.1186/s12935-021-01770-w 

ANDRADE, RAISSA COELHO ; BORONI, MARIANA ; AMAZONAS, MARION KIELMANOWICZ ; VARGAS, FERNANDO REGLA . New drug candidates for osteosarcoma: Drug repurposing based on gene expression signature. COMPUTERS IN BIOLOGY AND MEDICINE, v. 122, p. 104470, 2021. http://dx.doi.org/10.1016/j.compbiomed.2021.104470 

GUIMARAES, G. R. ; ALMEIDA, P. P. ; SANTOS, L. O. ; RODRIGUES, L. P. ; CARVALHO, J. L. ; BORONI, M. . Hallmarks of Aging in Macrophages: Consequences to Skin Inflammaging. Cells, v. 10, p. 1323, 2021. http://dx.doi.org/10.3390/cells10061323 

POUBEL, CAROLINE PIRES ; BORONI, MARIANA ; EMERENCIANO, MARIANA . 13q12.2 deletions and FLT3 overexpression in acute leukemias. Blood Advances, v. 5, p. 2075-2078, 2021. http://dx.doi.org/10.1182/bloodadvances.2020003643 

SOARES-LIMA, SHEILA COELHO ; MEHANNA, HISHAM ; CAMUZI, DIEGO ; DE SOUZA-SANTOS, PAULO THIAGO ; SIMÃO, TATIANA DE ALMEIDA ; NICOLAU-NETO, PEDRO ; ALMEIDA LOPES, MONIQUE DE SOUZA ; CUENIN, CYRILLE ; TALUKDAR, FAZLUR RAHMAN ; BATIS, NIKOLAOS ; COSTA, IZABELLA ; DIAS, FERNANDO ; DEGLI ESPOSTI, DAVIDE ; BORONI, MARIANA ; HERCEG, ZDENKO ; RIBEIRO PINTO, LUIS FELIPE . Upper Aerodigestive Tract Squamous Cell Carcinomas Show Distinct Overall DNA Methylation Profiles and Different Molecular Mechanisms behind WNT Signaling Disruption. Cancers, v. 13, p. 3014, 2021. http://dx.doi.org/10.3390/cancers13123014 

JORGE, NATASHA ANDRESSA NOGUEIRA ; CRUZ, JÉSSICA GONÇALVES VIEIRA DA ; PRETTI, M. A. M. ; BONAMINO, MARTÍN HERNÁN ; POSSIK, P. A. ; BORONI, MARIANA . Poor clinical outcome in metastatic melanoma is associated with a microRNA-modulated immunosuppressive tumor microenvironment. Journal of Translational Medicine, v. 18, p. 1, 2020. http://dx.doi.org/10.1186/s12967-020-02235-w 

Barros, L. R. C. ; Souza-Santos, P. T. ; Pretti, M. A. M. ; Vieira, G. F. ; Bragatte, M. A. S. ; Mendes, M. F. A. ; De Freitas, M. V. ; Scherer, N. M. ; De Oliveira, I. M. ; Rapozo, D. C. M. ; Fernandes, P. V. ; Simão, T. A. ; Soares-Lima, S. C. ; Boroni, M. ; Ribeiro Pinto, L. F. ; Bonamino, M. H. High infiltration of B cells in tertiary lymphoid structures, TCR oligoclonality, and neoantigens are part of esophageal squamous cell carcinoma microenvironment. Journal of Leukocyte Biology, v. 12, p. 1e, 2020. http://dx.doi.org/10.1002/jlb.5ma0720-710rrr

Pérez, A. G. ; Andrade‑Da‑Costa, J. ; De Souza, W. F. ; De Souza Ferreira, M. ; Boroni, M. ; De Oliveira, I. M. ; Freire‑Neto, C. A.;  Fernandes, P. V. ; De Lanna, C. A. ; Souza‑Santos, P. T. ; Morgado‑Díaz, J. A. ; De-Freitas‑Junior, J. M. N‑glycosylation and receptor tyrosine kinase signaling affect claudin‑3 levels in colorectal cancer cells. Oncology Reports. 44, no. 4: 1649-1661, 2020. https://doi.org/10.3892/or.2020.7727

Boroni, M. ; Zonari, A. ; Oliveira, C. R. ; Alkatib, K. ; Cruz, E. ; Brace, L. E. ; Carvalho, J. L. Highly accurate Skin-Specific methylome analysis algorithm as a platform to screen and validate therapeutics for healthy aging. Clinical Epigenetics, 12(1):105, 2020. https://doi.org/10.1186/s13148-020-00899-1 

Jorge, N.A.N., Cruz, J.G.V., Pretti, M.A.M., Bonamino, H.M., Possik, A.P., Boroni, M. Poor clinical outcome in metastatic melanoma is associated with a microRNA-modulated immunosuppressive tumor microenvironment. J Transl Med 18, 56, 2020. https://doi.org/10.1186/s12967-020-02235-w