creating a
healthier future

Genomics

The genomics scientific platform (GenCore) initiated in 2006 operating only two capillary sequencers: an ABI Prism 310 and a 3100 Genetic Analyzer (Applied BioSystems). Since then, the facility has been growing continuously, both in human resources and equipment. Today it is a full service facility dedicated to provide investigators state of the art technological solutions in the field of genomics and high throughput analysis. We offer technical expertise and support with experimental design, protocol development, and data analysis guidance. Training is another crucial aspect of our work.

The laboratory is proficient in providing: Sanger/NGS sequencing, cell line genotyping, exome sequencing, targeted DNA and RNA sequencing (panels), small genome sequencing, metagenome sequencing, whole transcriptome sequencing, single-cell sequencing, microarrays, quality control of nucleic acids. Other methodologies, probably yes, just ask! Additionally, due to the very dynamic and rapidly evolving field of genomics, we actively collaborate with different companies in developing NGS related products both for sample preparation and for bioinformatics data analysis. The facility is an Ion Torrent certified service provider.

Platform Head

Team

Applications

Sanger sequencing and fragment analysis

  • Sanger sequencing of plasmids and PCR products
    • Up to 800bp LOR (length of read)

Figure 1: Eletropherogram of plasmid Sanger sequencing

 

  • Fragment analysis
    • Capillary electrophoresis of various products.
    • Human cell line identification - analysis of 15 STRs and Amelogenin (Penta E, D18S51, D21S11, TH01, D3S1358, FGA, TPOX, D8S1179, vWA, Penta D, CSF1PO, D16S539, D7S820, D13S317 and D5S818) from cell pellet or genomic DNA, including a signed STR profile report.
    • Mouse cell line identification - Coming soon

Figure 2: Human cell line identification example report

 

Next-Generation Sequencing (NGS)

Image source: https://www.lubio.ch/blog/ngs-adapters

Some examples of available applications:

  • Targeted RNA-Seq
    • Ion AmpliSeq Transcriptome Human Gene Expression Kit and Ion AmpliSeq Transcriptome Mouse Gene Expression Kit for gene-level expression analysis; targets >20,000 human or mouse RefSeq transcripts; FFPE-compatible workflow.
    • Different panels for variant and fusion detection in many RNA sample types.
  • Targeted DNA-Seq
    • Exome sequencing
    • Gene panels
    • 16S rRNA sequencing
  • Whole genome sequencing (WGS)
    • Small genomes
    • Shallow WGS
    • ddRAD-Seq
    • Metagenomics
  • Whole transcriptome sequencing (WTS)

 

Microarrays

  • Genome-wide association studies (GWAS), SNP genotyping

    • Agrigenomics, microbiome, precision medicine, pharmacogenomics

https://www.thermofisher.com/pt/en/home/life-science/microarray-analysis.html

  • Array-based methylation measurement

https://www.illumina.com/techniques/microarrays/methylation-arrays.html

 

Quality control and quantification

  • Total RNA integrity assessment

 

  • Genomic DNA integrity assessment

 

  • miRNA and small RNA quantification

 

  • cell-free DNA quantification

 

  • Accurate measure of DNA and RNA concentration
    • Fluorimetric quantification
    • Initial DNA sample concentrations of 0.005 to 120 ng/μL (detection range of 0.1−120 ng)
    • Initial RNA sample concentrations of 0.2 to 200 ng/μL (detection range of 4−200 ng)

 

Single-cell sequencing

 

  • Single Cell Gene Expression
  • Single Cell Immune Profiling
  • Single Cell Multiome ATAC + Gene Expression

https://www.10xgenomics.com/platforms/chromium#products

Resources

Sanger sequencing and fragment analysis

3500xL Dx Genetic Analyzer, Applied Biosystems™

 

  • 24-capillary for Sanger sequencing and fragment analysis, 50 cm
  • POP-7™ Polymer
  • Calibrated for the following matrix/sequencing standards:
    • BigDye™ Terminator v3.1 (ROX, TAMRA™, Rhodamine 110, Rhodamine 6G)
    • DS-33 Matrix Standard Kit (Dye Set G5 - 6- FAM™ , VIC™ , NED™ , PET™ and LIZ™)
    • DS-30 Matrix Standard Kit (Dye Set D - 6-FAM™ , HEX™ , NED™ and ROX™)

 

3500 Genetic Analyzer, Applied Biosystems™

  • 8-capillary for Sanger sequencing and fragment analysis, 50 cm
  • POP-7™ Polymer
  • Calibrated for the following matrix/sequencing standards:
    • BigDye™ Terminator v3.1 (ROX, TAMRA™, Rhodamine 110, Rhodamine 6G)
    • DS-33 Matrix Standard Kit (Dye Set G5 - 6- FAM™ , VIC™ , NED™ , PET™ and LIZ™)
    • DS-30 Matrix Standard Kit (Dye Set D - 6-FAM™ , HEX™ , NED™ and ROX™)
    • BT5 matrix standard (6-FAM, BTG, BTY, BTR and BTO)
    • 4C Matrix Standards (Fluorescein, JOE, TMR and CXR)
    • 5C Matrix Standards (JOE, TMR-ET, CXR-ET and WEN)

 

Next-Generation Sequencing (NGS)

Ion Chef™ Instrument, Ion Torrent™

  • Provides automated library preparation, template preparation, and chip loading
  • The platform is equipped with two units.

https://www.thermofisher.com/order/catalog/product/4484177

 

Ion S5™ and Ion S5™ XL Systems, Ion Torrent™

 

  • The platform is equipped with one Ion S5™ and one Ion S5™ XL.
  • The Ion S5™XL has extra computing power, analyzing data 3-4x faster than the Ion S5™

 

 

Ion S5 series specifications

 

NextSeq™ 550 System, illumina

  • Combines next-generation sequencing (NGS) and array capabilities.
  • Two flow cell configurations (high and mid-output)
  • Integrated support for paired-end sequencing (read lengths up to 2×150 bp)

 

 

NextSeq 550 System sequencing performance

 

https://www.illumina.com/systems/sequencing-platforms/nextseq.html

 

Genexus™ Integrated Sequencer, Ion Torrent™

  • Single-day turnaround time from nucleic acid to report.
  • Hands-off, set-up-and-go workflow.
  • Oncology, reproductive health, inherited disease and infectious disease research solutions.

https://www.thermofisher.com/pt/en/home/life-science/sequencing/next-generation-sequencing/instruments/genexus-system.html

 

Microarrays

GeneTitan™ MC Fast Scan Instrument, Applied Biosystems™

 

  •  Hands-free, automated solution for genome-wide SNP genotyping and copy number variation analysis in human and agrigenomics.

https://www.thermofisher.com/order/catalog/product/00-0373

 

nCounter® Analysis System, NanoString Technologies

 

  • Direct digital detection system, which enables gene quantification without amplification: fluorescent bind directly to mRNA, miRNA or DNA
  • Measures up to 800 genes in a single reaction
  • Various panels available

 

https://nanostring.com/products/ncounter-analysis-system/ncounter-systems-overview/

 

Quality control and quantification

2100 Bioanalyzer Instrument, Agilent Technologies

 

  • Automated electrophoresis platform for sample quality control (QC) of nucleic acids and protein
  • QC assessment of sample size, integrity, purity and quantity

https://www.agilent.com/en/product/automated-electrophoresis/bioanalyzer-systems/bioanalyzer-instrument/2100-bioanalyzer-instrument-228250#features

 

Agilent 2200 TapeStation system, Agilent Technologies

  • Automated RNA, DNA and protein sample quality control

 

7500 Fast Real-Time PCR System, Applied Biosystems

  • Enables standard 96-well format high speed thermal cycling, delivering results in about 35 minutes
  • Calibrated for FAM™/SYBR® Green I, VIC®/JOE™, NED™/ TAMRA™/Cy3™, ROX™/Texas Red®  and Cy5™ dyes

 

Qubit™ 3 Fluorometer

  • Detects fluorescent dyes specifically bound to the target molecule
  • Accurate, precise, and sensitive measurements of nucleic acids

 

Single-cell sequencing

Chromium Controller, 10X Genomics

  • Advanced microfluidics to perform single cell partitioning and barcoding powered by Next GEM technology.

https://www.10xgenomics.com/instruments/chromium-controller

 

Publications

Publications

Tavares de Sousa H, Ferreira M, Gullo I, Rocha AM, Pedro A, Leitão D, Oliveira C, Carneiro F, Magro F. Fibrosis-related transcriptome unveils a distinctive remodeling matrix pattern in penetrating ileal Crohn's disease. J Crohns Colitis. 2024 May 3:jjae064. doi: 10.1093/ecco-jcc/jjae064. Epub ahead of print. PMID: 38700484.

 

Pereira J, Melo S, Ferreira RM, Carneiro P, Yang V, Maia AF, Carvalho J, Figueiredo C, Machado JC, Morais-de-Sá E, Seruca R, Figueiredo J. E-cadherin variants associated with oral facial clefts trigger aberrant cell motility in a REG1A-dependent manner. Cell Commun Signal. 2024 Feb 27;22(1):152. doi: 10.1186/s12964-024-01532-x. PMID: 38414029; PMCID: PMC10898076.

 

Adem B, Bastos N, Ruivo CF, Sousa-Alves S, Dias C, Vieira PF, Batista IA, Cavadas B, Saur D, Machado JC, Cai D, Melo SA. Exosomes define a local and systemic communication network in healthy pancreas and pancreatic ductal adenocarcinoma. Nat Commun. 2024 Feb 21;15(1):1496. doi: 10.1038/s41467-024-45753-7. PMID: 38383468; PMCID: PMC10881969.

 

Melo J, Cavadas B, Pereira L, Figueiredo C, Leite M. Transcriptomic remodeling of gastric cells by Helicobacter pylori outer membrane vesicles. Helicobacter. 2024 Jan-Feb;29(1):e13031. doi: 10.1111/hel.13031. Epub 2023 Nov 23. PMID: 37997013.

 

Socodato R, Almeida TO, Portugal CC, Santos ECS, Tedim-Moreira J, Galvão-Ferreira J, Canedo T, Baptista FI, Magalhães A, Ambrósio AF, Brakebusch C, Rubinstein B, Moreira IS, Summavielle T, Pinto IM, Relvas JB. Microglial Rac1 is essential for experience-dependent brain plasticity and cognitive performance. Cell Rep. 2023 Dec 26;42(12):113447. doi: 10.1016/j.celrep.2023.113447. Epub 2023 Nov 18. PMID: 37980559.

 

Normanno N, Machado JC, Pescarmona E, Buglioni S, Navarro L, Esposito Abate R, Ferro A, Mensink R, Lambiase M, Lespinet-Fabre V, Calgua B, Jermann PM, Ilié M, Hofman P. European Real-World Assessment of the Clinical Validity of a CE-IVD Panel for Ultra-Fast Next-Generation Sequencing in Solid Tumors. Int J Mol Sci. 2023 Sep 7;24(18):13788. doi: 10.3390/ijms241813788. PMID: 37762091; PMCID: PMC10531166.

 

Maqueda,J.J.,Giovanazzi,A.Rocha,A.M., Rocha, S., Silva, I., Saraiva, N., Bonito, N., Carvalho, J., Maia, L., Wauben, M. H. M., & Oliveira, C. Adapter dimer contamination in sRNA-sequencing datasets predicts sequencing failure and batch effects and hampers extracellular vesicle-sRNA analysis. J Ex Bio, 2023 Sep 7; 2, e91. https://doi.org/10.1002/jex2.91

 

Peixoto J, Príncipe C, Pestana A, Osório H, Pinto MT, Prazeres H, Soares P, Lima RT. Using a Dual CRISPR/Cas9 Approach to Gain Insight into the Role of LRP1B in Glioblastoma. Int J Mol Sci. 2023 Jul 10;24(14):11285. doi: 10.3390/ijms241411285. PMID: 37511044; PMCID: PMC10379115.

 

Maqueda JJ, Santos M, Ferreira M, Marinho S, Rocha S, Rocha M, Saraiva N, Bonito N, Carvalho J, Oliveira C. NGS Data Repurposing Allows Detection of tRNA Fragments as Gastric Cancer Biomarkers in Patient-Derived Extracellular Vesicles. Int J Mol Sci. 2023 May 18;24(10):8961. doi: 10.3390/ijms24108961. PMID: 37240307; PMCID: PMC10219402.

 

Pedro N, Brucato N, Cavadas B, Lisant V, Camacho R, Kinipi C, Leavesley M, Pereira L, Ricaut FX. First insight into oral microbiome diversity in Papua New Guineans reveals a specific regional signature. Mol Ecol. 2023 May;32(10):2551-2564. doi: 10.1111/mec.16702. Epub 2022 Oct 10. PMID: 36151926.

 

Gomes AC, Sousa DM, Oliveira TC, Fonseca Ó, Pinto RJ, Silvério D, Fernandes AI, Moreira AC, Silva T, Teles MJ, Pereira L, Saraiva M, Lamghari M, Gomes MS. Serum amyloid A proteins reduce bone mass during mycobacterial infections. Front Immunol. 2023 Apr 21;14:1168607. doi: 10.3389/fimmu.2023.1168607. PMID: 37153579; PMCID: PMC10161249.

 

Faria L, Canato S, Jesus TT, Gonçalves M, Guerreiro PS, Lopes CS, Meireles I, Morais-de-Sá E, Paredes J, Janody F. Activation of an actin signaling pathway in pre-malignant mammary epithelial cells by P-cadherin is essential for transformation. Dis Model Mech. 2023 Feb 1;16(2):dmm049652. doi: 10.1242/dmm.049652. Epub 2023 Feb 21. PMID: 36808468; PMCID: PMC9983776.

 

Catarino TA, Pacheco-Leyva I, Al-Dalali F, Ghezzo MN, Fernandes MT, Costa T, Dos Santos NR. Cdkn2a inactivation promotes malignant transformation of mouse immature thymocytes before the β-selection checkpoint. Exp Hematol. 2022 Dec;116:30-36. doi: 10.1016/j.exphem.2022.10.001. Epub 2022 Oct 12. PMID: 36240953.

 

Ribeiro R, Macedo JC, Costa M, Ustiyan V, Shindyapina AV, Tyshkovskiy A, Gomes RN, Castro JP, Kalin TV, Vasques-Nóvoa F, Nascimento DS, Dmitriev SE, Gladyshev VN, Kalinichenko VV, Logarinho E. In vivo cyclic induction of the FOXM1 transcription factor delays natural and progeroid aging phenotypes and extends healthspan. Nat Aging. 2022 May;2(5):397-411. doi: 10.1038/s43587-022-00209-9. Epub 2022 May 5. PMID: 37118067.

 

Campos AB, Duarte-Silva S, Fernandes B, das Neves SP, Marques F, Teixeira-Castro A, Neves-Carvalho A, Monteiro-Fernandes D, Portugal CC, Socodato R, Summavielle T, Ambrósio AF, Relvas JB, Maciel P. Profiling Microglia in a Mouse Model of Machado-Joseph Disease. Biomedicines. 2022 Jan 23;10(2):237. doi: 10.3390/biomedicines10020237. PMID: 35203447; PMCID: PMC8869404.

 

Raimundo L, Paterna A, Calheiros J, Ribeiro J, Cardoso DSP, Piga I, Neto SJ, Hegan D, Glazer PM, Indraccolo S, Mulhovo S, Costa JL, Ferreira MU, Saraiva L. BBIT20 inhibits homologous DNA repair with disruption of the BRCA1-BARD1 interaction in breast and ovarian cancer. Br J Pharmacol. 2021 Sep;178(18):3627-3647. doi: 10.1111/bph.15506. Epub 2021 Jun 11. Erratum in: Br J Pharmacol. 2022 Apr;179(7):1470-1472. PMID: 33899955; PMCID: PMC9124438.

 

Pedro N, Fernandes V, Cavadas B, Guimarães JT, Barros H, Tavares M, Pereira L. Field and Molecular Epidemiology: How Viral Sequencing Changed Transmission Inferences in the First Portuguese SARS-CoV-2 Infection Cluster. Viruses. 2021 Jun 10;13(6):1116. doi: 10.3390/v13061116. PMID: 34200621; PMCID: PMC8226748.

 

Canedo T, Portugal CC, Socodato R, Almeida TO, Terceiro AF, Bravo J, Silva AI, Magalhães JD, Guerra-Gomes S, Oliveira JF, Sousa N, Magalhães A, Relvas JB, Summavielle T.Astrocyte-derived TNF and glutamate critically modulate microglia activation by methamphetamine. Neuropsychopharmacology. 2021 Dec;46(13):2358-2370. doi: 10.1038/s41386-021-01139-7. Epub 2021 Aug 16. PMID: 34400780; PMCID: PMC8581027.

 

Albuquerque P, Ribeiro I, Correia S, Mucha AP, Tamagnini P, Braga-Henriques A, Carvalho MF, Mendes MV. Complete Genome Sequence of Two Deep-Sea Streptomyces Isolates from Madeira Archipelago and Evaluation of Their Biosynthetic Potential. Mar Drugs. 2021 Nov 1;19(11):621. doi: 10.3390/md19110621. PMID: 34822492; PMCID: PMC8622039.

 

Cortes-Figueiredo F, Carvalho FS, Fonseca AC, Paul F, Ferro JM, Schönherr S, Weissensteiner H, Morais VA. From Forensics to Clinical Research: Expanding the Variant Calling Pipeline for the Precision ID mtDNA Whole Genome Panel. Int J Mol Sci. 2021 Nov 6;22(21):12031. doi: 10.3390/ijms222112031.

 

Paço A, Leitão-Castro J, Freitas R. Epigenetic Regulation of CDH1 Is Altered after HOXB7-Silencing in MDA-MB-468 Triple-Negative Breast Cancer Cells. Genes (Basel). 2021 Oct 3;12(10):1575. doi: 10.3390/genes12101575. PMID: 34680970; PMCID: PMC8535730.

 

Sierra B, Magalhães AC, Soares D, Cavadas B, Perez AB, Alvarez M, Aguirre E, Bracho C, Pereira L, Guzman MG. Multi-Tissue Transcriptomic-Informed In Silico Investigation of Drugs for the Treatment of Dengue Fever Disease. Viruses. 2021 Aug 4;13(8):1540. doi: 10.3390/v13081540. PMID: 34452405; PMCID: PMC8402662.

 

Monteiro J, Pratas D, Videira A, Pereira F. Revisiting the Neurospora crassa mitochondrial genome. Lett Appl Microbiol. 2021 Oct;73(4):495-505. doi: 10.1111/lam.13538. Epub 2021 Jul 31. PMID: 34265094.

 

Cardoso A, Martins AC, Maceiras AR, Liu W, Castro I, Castro AG, Bandeira A, Di Santo JP, Cumano A, Li Y, Vieira P, Saraiva M. Interleukin-10 induces interferon-γ-dependent emergency myelopoiesis. Cell Rep. 2021 Oct 26;37(4):109887. doi: 10.1016/j.celrep.2021.109887. PMID: 34706233.

 

Cardoso RMS, Rodrigues SC, Gomes CF, Duarte FV, Romao M, Leal EC, Freire PC, Neves R, Simões-Correia J. Development of an optimized and scalable method for isolation of umbilical cord blood-derived small extracellular vesicles for future clinical use. Stem Cells Transl Med. 2021 Jun;10(6):910-921. doi: 10.1002/sctm.20-0376. Epub 2021 Feb 12. PMID: 33577723; PMCID: PMC8133342.

 

Pedro N, Silva CN, Magalhães AC, Cavadas B, Rocha AM, Moreira AC, Gomes MS, Silva D, Sobrinho-Simões J, Ramos A, Cardoso MJ, Filipe R, Palma P, Ceia F, Silva S, Guimarães JT, Sarmento A, Fernandes V, Pereira L, Tavares M. Dynamics of a Dual SARS-CoV-2 Lineage Co-Infection on a Prolonged Viral Shedding COVID-19 Case: Insights into Clinical Severity and Disease Duration. Microorganisms. 2021 Feb 2;9(2):300. doi: 10.3390/microorganisms9020300. PMID: 33540596; PMCID: PMC7912897.

 

Zerrifi SEA, Redouane EM, Mugani R, Ribeiro I, de Fátima Carvalho M, Campos A, Barakate M, Vasconcelos V, Oudra B, El Khalloufi F. Moroccan actinobacteria with promising activity against toxic cyanobacteria Microcystis aeruginosa. Environ Sci Pollut Res Int. 2021 Jan;28(1):235-245. doi: 10.1007/s11356-020-10439-2. Epub 2020 Aug 17. PMID: 32808126.

 

Laundos TL, Vasques-Nóvoa F, Gomes RN, Sampaio-Pinto V, Cruz P, Cruz H, Santos JM, Barcia RN, Pinto-do-Ó P, Nascimento DS. Corrigendum: Consistent long-term therapeutic efficacy of human umbilical cord matrix-derived mesenchymal stromal cells after myocardial infarction despite individual differences and transient engraftment. Front Cell Dev Biol. 2023 Aug 18;11:1265005. doi: 10.3389/fcell.2023.1265005. Erratum for: Front Cell Dev Biol. 2021 Feb 04;9:624601. PMID: 37664464; PMCID: PMC10471974.

 

Cavadas B, Leite M, Pedro N, Magalhães AC, Melo J, Correia M, Máximo V, Camacho R, Fonseca NA, Figueiredo C, Pereira L. Shedding Light on the African Enigma: In Vitro Testing of Homo sapiens-Helicobacter pylori Coevolution. Microorganisms. 2021 Jan 25;9(2):240. doi: 10.3390/microorganisms9020240. PMID: 33503840; PMCID: PMC7912213.

 

Eufrásio A, Perrod C, Ferreira FJ, Duque M, Galhardo M, Bessa J. In Vivo Reporter Assays Uncover Changes in Enhancer Activity Caused by Type 2 Diabetes-Associated Single Nucleotide Polymorphisms. Diabetes. 2020 Dec;69(12):2794-2805. doi: 10.2337/db19-1049. Epub 2020 Sep 10. PMID: 32912862; PMCID: PMC7679775.

 

Lobo S, Pereira C, Oliveira C, Almeida GM. Skipping Exon-v6 from CD44v6-Containing Isoforms Influences Chemotherapy Response and Self-Renewal Capacity of Gastric Cancer Cells. Cancers (Basel). 2020 Aug 22;12(9):2378. doi: 10.3390/cancers12092378. PMID: 32842638; PMCID: PMC7564355.

 

Brito Â, Vieira J, Vieira CP, Zhu T, Leão PN, Ramos V, Lu X, Vasconcelos VM, Gugger M, Tamagnini P. Comparative Genomics Discloses the Uniqueness and the Biosynthetic Potential of the Marine Cyanobacterium Hyella patelloides. Front Microbiol. 2020 Jul 7;11:1527. doi: 10.3389/fmicb.2020.01527. PMID: 32774329; PMCID: PMC7381351.

 

Barroso-Vilares M, Macedo JC, Reis M, Warren JD, Compton D, Logarinho E. Small-molecule inhibition of aging-associated chromosomal instability delays cellular senescence. EMBO Rep. 2020 May 6;21(5):e49248. doi: 10.15252/embr.201949248. Epub 2020 Mar 5. PMID: 32134180; PMCID: PMC7202060.

 

Pereira MS, Durães C, Catarino TA, Costa JL, Cleynen I, Novokmet M, Krišti? J, Štambuk J, Conceição-Neto N, Machado JC, Marcos-Pinto R, Magro F, Vermeire S, Lauc G, Lago P, Pinho SS. Genetic Variants of the MGAT5 Gene Are Functionally Implicated in the Modulation of T Cells Glycosylation and Plasma IgG Glycome Composition in Ulcerative Colitis. Clin Transl Gastroenterol. 2020 Apr;11(4):e00166. doi: 10.14309/ctg.0000000000000166. PMID: 32352685; PMCID: PMC7263653.

 

Sousa J, Cá B, Maceiras AR, Simões-Costa L, Fonseca KL, Fernandes AI, Ramos A, Carvalho T, Barros L, Magalhães C, Chiner-Oms Á, Machado H, Veiga MI, Singh A, Pereira R, Amorim A, Vieira J, Vieira CP, Bhatt A, Rodrigues F, Rodrigues PNS, Gagneux S, Castro AG, Guimarães JT, Bastos HN, Osório NS, Comas I, Saraiva M. Mycobacterium tuberculosis associated with severe tuberculosis evades cytosolic surveillance systems and modulates IL-1β production. Nat Commun. 2020 Apr 23;11(1):1949. doi: 10.1038/s41467-020-15832-6. PMID: 32327653; PMCID: PMC7181847.

 

Garcia SAB, Araújo M, Freitas R. Dataset of HOXB7, HOXB8 and HOXB9 expression profiles in cell lines representative of the breast cancer molecular subtypes Luminal a (MCF7), Luminal b (BT474), HER2+ (SKBR3) and triple-negative (MDA231, MDA468), compared to a model of normal cells (MCF10A). Data Brief. 2020 Apr 18;30:105572. doi: 10.1016/j.dib.2020.105572. PMID: 32346580; PMCID: PMC7182708.

 

Oliveira BM, Pinto A, Correia A, Ferreira PG, Vilanova M, Teixeira L. Characterization of Myeloid Cellular Populations in Mesenteric and Subcutaneous Adipose Tissue of Holstein-Friesian Cows. Sci Rep. 2020 Feb 4;10(1):1771. doi: 10.1038/s41598-020-58678-0. PMID: 32019985; PMCID: PMC7000716.

 

Sousa D, Matthiesen R, Lima RT, Vasconcelos MH. Deep Sequencing Analysis Reveals Distinctive Non-Coding RNAs When Comparing Tumor Multidrug-Resistant Cells and Extracellular Vesicles with Drug-Sensitive Counterparts.Cancers (Basel). 2020 Jan 14;12(1). pii: E200. doi: 10.3390/cancers12010200.

 

Torres AL, Bidarra SJ, Vasconcelos DP, Barbosa JN, Silva EA, Nascimento DS, Barrias CC. Microvascular engineering: Dynamic changes in microgel-entrapped vascular cells correlates with higher vasculogenic/angiogenic potential. Biomaterials. 2020 Jan;228:119554. doi: 10.1016/j.biomaterials.2019.119554. Epub 2019 Oct 18. PMID: 31677395.

 

Barroso-Vilares M, Macedo JC, Reis M, Warren JD, Compton D, Logarinho E. Small-molecule inhibition of aging-associated chromosomal instability delays cellular senescence. EMBO Rep. 2020 May 6;21(5):e49248. doi: 10.15252/embr.201949248. Epub 2020 Mar 5. PMID: 32134180; PMCID: PMC7202060.

 

Teles SP, Oliveira P, Ferreira M, Carvalho J, Ferreira P, Oliveira C. Integrated Analysis of Structural Variation and RNA Expression of FGFR2 and Its Splicing Modulator ESRP1 Highlight the ESRP1amp-FGFR2norm-FGFR2-IIIchigh Axis in Diffuse Gastric Cancer. Cancers (Basel). 2019 Dec 25;12(1):70. doi: 10.3390/cancers12010070. PMID: 31881796; PMCID: PMC7017189.

 

Gomes S, Cavadas B, Ferreira JC, Marques PI, Monteiro C, Sucena M, Sousa C, Vaz Rodrigues L, Teixeira G, Pinto P, Tavares de Abreu T, Bárbara C, Semedo J, Mota L, Carvalho AS, Matthiesen R, Pereira L, Seixas S. Profiling of lung microbiota discloses differences in adenocarcinoma and squamous cell carcinoma.Sci Rep. 2019 Sep 6;9(1):12838. doi: 10.1038/s41598-019-49195-w.

 

Gomes S, Cavadas B, Ferreira JC, Marques PI, Monteiro C, Sucena M, Sousa C, Vaz Rodrigues L, Teixeira G, Pinto P, Tavares de Abreu T, Bárbara C, Semedo J, Mota L, Carvalho AS, Matthiesen R, Pereira L, Seixas S. Profiling of lung microbiota discloses differences in adenocarcinoma and squamous cell carcinoma. Sci Rep. 2019 Sep 6;9(1):12838. doi: 10.1038/s41598-019-49195-w. PMID: 31492894; PMCID: PMC6731246.

 

Mereiter S, Martins ÁM, Gomes C, Balmaña M, Macedo JA, Polom K, Roviello F, Magalhães A, Reis CA. O-glycan truncation enhances cancer-related functions of CD44 in gastric cancer. FEBS Lett. 2019 Jul;593(13):1675-1689. doi: 10.1002/1873-3468.13432. Epub 2019 May 27. PMID: 31077346.

 

Rocha S, Carvalho J, Oliveira P, Voglstaetter M, Schvartz D, Thomsen AR, Walter N, Khanduri R, Sanchez JC, Keller A, Oliveira C, Nazarenko I. 3D Cellular Architecture Affects MicroRNA and Protein Cargo of Extracellular Vesicles. Adv Sci (Weinh). 2018 Dec 20;6(4):1800948. doi: 10.1002/advs.201800948. PMID: 30828519; PMCID: PMC6382357.

 

Pinheiro J, Lisboa J, Pombinho R, Carvalho F, Carreaux A, Brito C, Pöntinen A, Korkeala H, Dos Santos NMS, Morais-Cabral JH, Sousa S, Cabanes D. MouR controls the expression of the Listeria monocytogenes Agr system and mediates virulence. Nucleic Acids Res. 2018 Oct 12;46(18):9338-9352. doi: 10.1093/nar/gky624. PMID: 30011022; PMCID: PMC6182135.

 

Monteiro C, Marques PI, Cavadas B, Damião I, Almeida V, Barros N, Barros A, Carvalho F, Gomes S, Seixas S. Characterization of microbiota in male infertility cases uncovers differences in seminal hyperviscosity and oligoasthenoteratozoospermia possibly correlated with increased prevalence of infectious bacteria. Am J Reprod Immunol. 2018 Jun;79(6):e12838. doi: 10.1111/aji.12838.

 

Oliveira M, Lert-Itthiporn W, Cavadas B, Fernandes V, Chuansumrit A, Anunciação O, Casademont I, Koeth F, Penova M, Tangnararatchakit K, Khor CC, Paul R, Malasit P, Matsuda F, Simon-Lorière E, Suriyaphol P, Pereira L, Sakuntabhai A. Joint ancestry and association test indicate two distinct pathogenic pathways involved in classical dengue fever and dengue shock syndrome. PLoS Negl Trop Dis. 2018 Feb 15;12(2):e0006202. doi: 10.1371/journal.pntd.0006202. PMID: 29447178; PMCID: PMC5813895.

 

Da Cruz Paula A, Leitão C, Marques O, Rosa AM, Santos AH, Rêma A, de Fátima Faria M, Rocha A, Costa JL, Lima M, Lopes C. Molecular characterization of CD44+/CD24-/Ck+/CD45- cells in benign and malignant breast lesions. Virchows Arch. 2017 Mar;470(3):311-322. doi: 10.1007/s00428-017-2068-4. Epub 2017 Jan 23. PMID: 28116522.