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Luka Clarke is a contracted researcher (FCT-DL57) at University of Lisboa, and member of the Cystic Fibrosis Laboratory at the BioISI Research Centre. He is/has been involved in several lines of research, including: 1) Characterization of the effects of premature termination codon (PTC) mutations on CFTR mRNA expression; 2) Investigation of alternative therapeutic options for CFTR variants (ie, PTC/Class I and splicing/Class V variants) not treatable by new modulator drugs; 3) Cystic fibrosis (CF) related transcriptomics, and meta-analysis of transcriptome datasets relevant to respiratory disorders; 4) Development of bioinformatic resources for high throughput data analysis. He has (co-)authored around 50 scientific publications, the majority in international peer-reviewed journals including leading titles such as Cell, Journal of Cell Biology, Chest and Human Mutation. These publications are currently attributed with ~1360 citations on Scopus (H factor = 22) and ~2130 citations on Google Scholar (H factor = 25). Since 2009 he has taught theoretical and practical classes and seminars to undergraduate and MSc courses in Molecular Biology, Human Molecular Genetics and Biochemistry at invited assistant professor level in the Department of Biochemistry at the Faculty of Sciences in Lisboa, and as part of various PhD programmes. He has supervised or co-supervised 6 Doctoral students (2 ongoing) and 7 Masters Students. He studied Zoology at Bristol University, UK, published his undergraduate research project in the journal Animal Behaviour, and graduated with the prize for the top student in Biological Sciences for that year (1990). He then obtained his PhD from the Royal Veterinary College, University of London (1997), publishing five papers in the area of molecular endocrinology related to seasonal breeding in the red deer. Following postdoctoral work on alternative splicing of human mismatch repair genes in the oncobiology laboratory of the Portuguese National Institute of Health in Lisbon, he joined the cystic fibrosis group at the University of Lisbon (M.D. Amaral lab). Initially, he worked on two EU projects focusing on development of lab-on-a-chip systems for CF diagnosis, and this work (originally related to potential diagnostic CF gene signatures) led to studies of CF-related gene expression and transcriptomics. His most recent focus has been on: 1) the effect of premature termination codon (PTC) variants in CFTR on mRNA abundance, integrity and stability using allele-specific comparative real time quantitative PCR; and 2) the search for potential correctors and/or therapeutic targets for PTC or splicing variants using cellular models of CF. In 2024 he started two new projects focusing on the use of antisense oligonucleotide therapies in the correction of rare CFTR splicing variants in the context of personalized medicine. He is experienced in most practical areas of molecular and cellular biology.
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Identification

Personal identification

Full name
Luka Alexander Clarke

Citation names

  • Clarke, Luka
  • Clarke, Luka A
  • Clarke, LA

Author identifiers

Ciência ID
591E-5E28-94A0
ORCID iD
0000-0003-3254-9121
Google Scholar ID
https://scholar.google.pt/citations?user=14hRaK8AAAAJ&hl=en&oi=ao
Scopus Author Id
9248448600

Websites

Knowledge fields

  • Natural sciences - Biological Sciences - Molecular Biology

Languages

Language Speaking Reading Writing Listening Peer-review
English (Mother tongue)
Portuguese Advanced (C1) Proficiency (C2) Advanced (C1) Proficiency (C2) Upper intermediate (B2)
French Intermediate (B1) Upper intermediate (B2) Intermediate (B1) Intermediate (B1)
German Beginner (A1) Intermediate (B1) Beginner (A1) Beginner (A1)
Spanish; Castilian Beginner (A1) Intermediate (B1) Beginner (A1) Beginner (A1)
Japanese Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1)
Education
Degree Classification
1997
Concluded
 PhD Molecular Endocrinology (Doctor of Philosophy)
University of London (Royal Veterinary College), United Kingdom
"Physiological function of prolactin based on hormone receptor studies in the red deer (Cervus elaphus)." (THESIS/DISSERTATION)
 n/a
1990/07/30
Concluded
 BSc (Hons) Zoology (Bachelor)
University of Bristol, United Kingdom
"Functional studies of bill-wiping behaviour in the starling (Sturnus vulgaris L.)" (THESIS/DISSERTATION)
 First Class Honours
Affiliation

Science

Category
Host institution 		Employer
2019/07/01 - Current Contracted Researcher (Research) Faculdade de Ciencias, Universidade de Lisboa, Portugal
Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal

Teaching in Higher Education

Category
Host institution 		Employer
2015/09/01 - 2019/06/30 Invited Assistant Professor (University Teacher) Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
2016 - 2018 Invited Assistant Professor (University Teacher) Universidade de Lisboa, Portugal
2015 - 2016 Assistant Professor (University Teacher) Universidade de Lisboa Faculdade de Ciências, Portugal
2013 - 2015 Invited Assistant Professor (University Teacher) Universidade de Lisboa Faculdade de Ciências, Portugal

Others

Category
Host institution 		Employer
2015/06/15 - 2017/12/31 Investigador em Regime Especial Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
2009/06/15 - 2015/05/15 Investigador Ciência 2008 Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
Projects

Grant

Designation Funders
2024/04/01 - 2028/03/31 - ORGESTRA – HORIZON-MSCA-DN-2022
101120108 - ORGESTRA – HORIZON-MSCA-DN-2022
Co-Principal Investigator (Co-PI)
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
2024/01/01 - 2024/08/31 CF-Splice: an ASO based strategy to correct a population specific CFTR splicing variant.
CF-Splice
Principal investigator
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
 Emily's Entourage
Ongoing
2020/01/01 - 2020/12/31 PTsense - novel compounds as potential drugs for CFTR PTC mutations
AMARAL19G0
Co-Principal Investigator (Co-PI)
Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
 Cystic Fibrosis Foundation Therapeutics Inc
Ongoing
2006/09/01 - 2009/09/01 Development of a complete integrated SNP analysis system.
STRP016833
Research Fellow
Faculdade de Ciencias, Universidade de Lisboa, Portugal
Concluded
2005/06/01 - 2006/06/01 Novel magnetoresistive gene chips for Cystic Fibrosis diagnosis
SFRH/BPD/20730/2004
Post-doc Fellow
Faculdade de Ciencias, Universidade de Lisboa, Portugal
2002/06/01 - 2005/06/01 Use of novel magnetoresistive gene chip technology for development of diagnostic arrays: use of Cystic Fibrosis as a model
QLK3-CT-2001-01982
Research Fellow
Faculdade de Ciencias, Universidade de Lisboa, Portugal
2000/12/01 - 2002/06/01 Characterization of the mutagenic effects of poly (ADP-ribose) polymerase deficiency in transgenic mice
34270/99
Post-doc Fellow
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
 Fundação para a Ciência e a Tecnologia
1997/09/01 - 2000/09/01 Identification and characterization of mutations in genes critical for colorectal cancer.
2/2.1/SAL/1397/95
Post-doc Fellow
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
1993/09/01 - 1997/09/01 Physiological function of prolactin based on studies of receptor gene expression in the red deer
BBSRC
PhD Student Fellow
Institute of Zoology of the Zoological Society of London, United Kingdom
 Biotechnology and Biological Sciences Research Council
Concluded

Contract

Designation Funders
2016/04/15 - 2019/11/04 Novos Fatores de Tráfego da CFTR Relacionados com a Diferenciação Celular Epitelial: Potenciais Alvos Terapêuticos para a Fibrose Quística
PTDC/BIM-MEC/2131/2014
Invited Scientist Fellow
Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2018/01/01 - 2019/06/30 RNA Life - Novel RNA regulators as potential drug targets for CF
AMARAL15XX1
Research Fellow
Cystic Fibrosis Foundation Therapeutics Inc
Concluded
2015/06/01 - 2017/12/31 Evaluation of CFTR mutations bearing Premature Termination Codons: NMD susceptibility
7207534
Research Fellow
Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
 Cystic Fibrosis Foundation Therapeutics Inc
2011/01/01 - 2013/12/31 Strategic Project - UI 4046 - 2011-2012
PEst-OE/BIA/UI4046/2011
Integration into Research Grant Fellow
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal

Universidade do Minho, Portugal

Universidade do Algarve, Portugal

Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Concluded

Other

Designation Funders
2024/09/01 - Current PTSuppress – Novel lead compounds as potential suppressor drugs for CFTR PTC mutations
PT-Suppress
Co-Principal Investigator (Co-PI)
2014/01/01 - 2014/12/31 Explorando o controle de qualidade do retículo endoplasmático - interacções proteicas como novos alvos terapêuticos na Fibrose Quística
EXPL/BIM-MEC/1451/2013
Other
Faculdade de Ciencias, Universidade de Lisboa, Portugal
 Fundação para a Ciência e a Tecnologia
2008/01/01 - 2008/12/31 Development of new methodologies for low abundance proteomics: application to cystic fibrosis
FP6-2003-LIFESCIHEALTH-2512044
Researcher
Concluded
Outputs

Publications

Book chapter
  1. Amaral, Margarida D.; Clarke, Luka A; Farinha, Carlos M.; Botelho, Hugo M. "Systems Biology and the New Omics". In Hodson and Geddes' Cystic Fibrosis. Taylor & Francis, 2023.
    Published
  2. Margarida D. Amaral; Luka A. Clarke; Carlos M. Farinha; Hugo M. Botelho. "Systems Biology and the New Omics". 96-110. {CRC, 2023.
    10.1201/9781003262763-10
  3. Lamurias, Andre; Clarke, LukaA; Couto, FranciscoM. "IICE: Web Tool for Automatic Identification of Chemical Entities and Interactions". edited by Bifet, Albert; May, Michael; Zadrozny, Bianca; Gavalda, Ricard; Pedreschi, Dino; Bonchi, Francesco; Cardoso, Jaime; Spiliopoulou, Myra, 285-288. 2015.
    10.1007/978-3-319-23461-8_31
  4. Freitas, P.P.; Ferreira, H.A.; Graham, D.L.; Clarke, L.A.; Amaral, M.D.; Martins, V.; Fonseca, L.; Cabral, J.S.. "Magnetoresistive DNA chips". 331-373. 2004.
Conference paper
  1. Lamurias, Andre; Sousa, Diana; Pereira, Sofia; Clarke, Luka; Couto, Francisco M. "ULISBOA at SemEval-2017 Task 12: Extraction and classification of temporal expressions and events". 2017.
    Published • 10.18653/v1/s17-2179
  2. Lamurias, A.; Pedro, V.; Clarke, L.; Couto, F.M.. "Annotating biomedical ontology terms in electronic health records using crowd-sourcing". 2015.
  3. Amaral, Margarida; Clarke, Luka A; Roxo Rosa, Mónica; SOUSA, LISETE. "Genomic and Proteomics approaches to study the genetic disease Cystic Fibrosis.". Paper presented in Proceedings of the Workshop on Statistics in Genomics and Proteomics., Estoril, 2006.
    Published
  4. Freitas, P.P.; Ferreira, H.; Graham, D.; Feliciano, N.; Carias, C.; Ferreira, R.; Clarke, L.; et al. "Spintronic biosensors for gene or micro-organism detection". 2005.
  5. Lagae, L.; Wirix-Speetjens, R.; Liu, C.-X.; Laureyn, W.; Borghs, G.; Harvey, S.; Galvin, P.; et al. "Magnetic biosensors for genetic screening of cystic fibrosis". 2005.
    10.1049/ip-cds:20050022
  6. Ferreira, H.A.; Graham, D.L.; Feliciano, N.; Clarke, L.A.; Amaral, M.D.; Freitas, P.P.. "Detection of cystic fibrosis related DNA targets using AC field focusing of magnetic labels and spin-valve sensors". 2005.
    10.1109/TMAG.2005.855340
Conference poster
  1. Botelho, Hugo M; Lopes-Pacheco, Miquéias; Pinto, Madalena C.; Silva, Iris AL; Clarke, Luka; Cachatra, V; Neumann, B; et al. "New kinase therapeutic targets for Cystic Fibrosis from a global functional genomics screen". Paper presented in 17th ECFS Basic Science Conference, 2022.
  2. Botelho, Hugo M; Lopes-Pacheco, Miquéias; Pinto, Madalena C.; Silva, Iris AL; Clarke, Luka A; Cachatra, V; Neumann, B; et al. "New kinase therapeutic targets for Cystic Fibrosis identified through high-content functional genomics screens". Paper presented in 5ª Conferência Anual da redeSAÚDE, 2021.
  3. Awatade, NT; Botelho, Hugo M; Felício, V; Clarke, LA; Silva, Iris AL; Marques, Luis; Ramos, M; Amaral, Margarida. "CFTR modulators enhance function R334W-CFTR both in intestinal organoids and conditionally reprogrammed human nasal epithelial cells". Paper presented in 14th ECFS Basic Science Conference, 2017.
  4. Awatade, NT; Botelho, Hugo M; Felício, V; Clarke, LA; Ramos, M; Amaral, Margarida. "To assess the efficacy of CFTR modulators on rare Cystic Fibrosis mutations using forskolin-induced swelling assay in human intestinal organoids". Paper presented in 13th ECFS Basic Science Conference, 2016.
  5. Awatade, NT; Botelho, Hugo M; Felício, V; Clarke, LA; Ramos, M; Amaral, Margarida. "Assessment of CFTR activity ex vivo as a basis for personalised medicine". Paper presented in 5th Workshop Structure and Function of Ion Channels and Transporters, 2015.
Journal article
  1. Clarke, Luka A.; Amaral, Margarida D.. "What Can RNA-Based Therapy Do for Monogenic Diseases?". Pharmaceutics 15 1 (2023): 260. http://dx.doi.org/10.3390/pharmaceutics15010260.
    10.3390/pharmaceutics15010260
  2. "Integrity and Stability of PTC Bearing CFTR mRNA and Relevance to Future Modulator Therapies in Cystic Fibrosis". Genes 12 11 (2021): 1810-1810. http://dx.doi.org/10.3390/genes12111810.
    10.3390/genes12111810
  3. Bene, Zsolt; Fejes, Zsolt; Szanto, Tibor Gabor; Fenyvesi, Ferenc; Váradi, Judit; Clarke, Luka A.; Panyi, Gyorgy; et al. "Enhanced Expression of Human Epididymis Protein 4 (HE4) Reflecting Pro-Inflammatory Status Is Regulated by CFTR in Cystic Fibrosis Bronchial Epithelial Cells". Frontiers in Pharmacology 12 (2021): http://dx.doi.org/10.3389/fphar.2021.592184.
    10.3389/fphar.2021.592184
  4. Silva, Iris A.L.; Doušová, Tereza; Ramalho, Sofia; Centeio, Raquel; Clarke, Luka A.; Railean, Violeta; Botelho, Hugo M.; et al. "Organoids as a personalized medicine tool for ultra-rare mutations in cystic fibrosis: The case of S955P and 1717-2A>G". Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease 1866 11 (2020): 165905. http://dx.doi.org/10.1016/j.bbadis.2020.165905.
    10.1016/j.bbadis.2020.165905
  5. Clarke, Luka A. "Mutant CFTR Drives TWIST1 mediated epithelial–mesenchymal transition". Cell Death & Disease (2020): http://dx.doi.org/10.1038/s41419-020-03119-z.
    10.1038/s41419-020-03119-z
  6. Sousa, Luis; Pankonien, Ines; Clarke, Luka A; Silva, Iris; Kunzelmann, Karl; Amaral, Margarida D. "KLF4 Acts as a wt-CFTR Suppressor through an AKT-Mediated Pathway". Cells 9 7 (2020): 1607. http://dx.doi.org/10.3390/cells9071607.
    10.3390/cells9071607
  7. Lamurias, A.; Sousa, D.; Clarke, L.A.; Couto, F.M.. "BO-LSTM: Classifying relations via long short-term memory networks along biomedical ontologies". BMC Bioinformatics 20 1 (2019): http://www.scopus.com/inward/record.url?eid=2-s2.0-85059594576&partnerID=MN8TOARS.
    10.1186/s12859-018-2584-5
  8. Simões, F.B.; Quaresma, M.C.; Clarke, L.A.; Silva, I.A.L.; Pankonien, I.; Railean, V.; Kmit, A.; Amaral, M.D.; Clarke, Luka. "TMEM16A chloride channel does not drive mucus production". Life Science Alliance 2 6 (2019): http://www.scopus.com/inward/record.url?eid=2-s2.0-85075115008&partnerID=MN8TOARS.
    10.26508/LSA.201900462
  9. Luka A. Clarke; Nikhil T. Awatade; Veronica M. Felício; Iris A. Silva; Maite Calucho; Luisa Pereira; Pilar Azevedo; et al. "The effect of premature termination codon mutations on CFTR mRNA abundance in human nasal epithelium and intestinal organoids: a basis for read-through therapies in cystic fibrosis". Human Mutation (2018): https://doi.org/10.1002/humu.23692.
    10.1002/humu.23692
  10. Lamurias, Andre; Clarke, Luka A; Couto, Francisco M. "Extracting microRNA-gene relations from biomedical literature using distant supervision.". PloS one 12 3 (2017): e0171929-e0171929. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=MEDLINE&KeyUT=MEDLINE:28263989&KeyUID=MEDLINE:28263989.
    10.1371/journal.pone.0171929
  11. Clarke, Luka. "Generating a Tolerogenic Cell Therapy Knowledge Graph from Literature.". Frontiers in Immunology (2017): http://europepmc.org/abstract/med/29238346.
    10.3389/fimmu.2017.01656
  12. Nagy, B.; Fila, L.; Clarke, L. A.; Gönczy, F.; Bede, O.; Nagy, D.; Újhelyi, R.; et al. "Human Epididymis Protein 4: A Novel Serum Inflammatory Biomarker in Cystic Fibrosis". Chest 150 3 (2016): 661-72.
    10.1016/j.chest.2016.04.006
  13. Bastos, Hugo P.; Sousa, Lisete; Clarke, Luka A.; Couto, Francisco M.. "Functional coherence metrics in protein families". Journal of Biomedical Semantics 7 (2016): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000379112300001&KeyUID=WOS:000379112300001.
    10.1186/s13326-016-0076-y
  14. Awatade NT; Uliyakina I; Farinha CM; Clarke LA; Mendes K; Solé A; Pastor J; Ramos MM; Amaral MD. "Measurements of Functional Responses in Human Primary Lung Cells as a Basis for Personalized Therapy for Cystic Fibrosis.". (2015): http://europepmc.org/abstract/med/26137539.
    10.1016/j.ebiom.2014.12.005
  15. Ramalho, A. S.; Clarke, L. A.; Sousa, M.; Felicio, V.; Barreto, C.; Lopes, C.; Amaral, M. D.. "Comparative ex vivo, in vitro and in silico analyses of a CFTR splicing mutation: Importance of functional studies to establish disease liability of mutations". J Cyst Fibros (2015):
    10.1016/j.jcf.2015.02.002
  16. Igreja, S.; Clarke, L. A.; Botelho, H. M.; Marques, L.; Amaral, M. D.. "Correction of a Cystic Fibrosis Splicing Mutation by Antisense Oligonucleotides". Hum Mutat (2015):
    10.1002/humu.22931
  17. Bastos, H. P.; Sousa, L.; Clarke, L. A.; Couto, F. M.. "GRYFUN: A Web Application for GO Term Annotation Visualization and Analysis in Protein Sets". PLoS One 10 3 (2015): e0119631-e0119631.
    10.1371/journal.pone.0119631
  18. Clarke, L. A.; Botelho, H. M.; Sousa, L.; Falcao, A. O.; Amaral, M. D.. "Transcriptome meta-analysis reveals common differential and global gene expression profiles in cystic fibrosis and other respiratory disorders and identifies CFTR regulators". Genomics (2015):
    10.1016/j.ygeno.2015.07.005
  19. Bastos, H. P.; Clarke, L. A.; Couto, F. M.. "Annotation extension through protein family annotation coherence metrics". Front Genet 4 (2013): 201-201.
    10.3389/fgene.2013.00201
  20. Almaça, J.; Faria, D.; Sousa, M.; Uliyakina, I.; Conrad, C.; Sirianant, L.; Clarke, L.A.; et al. "XHigh-content siRNA screen reveals global ENaC regulators and potential cystic fibrosis therapy targets". Cell 154 6 (2013): 1390-1390. http://www.scopus.com/inward/record.url?eid=2-s2.0-84884266668&partnerID=MN8TOARS.
    10.1016/j.cell.2013.08.045
  21. Clarke, L.A.; Sousa, L.; Barreto, C.; Amaral, M.D.. "Changes in transcriptome of native nasal epithelium expressing F508del-CFTR and intersecting data from comparable studies". Respiratory Research (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84875327356&partnerID=MN8TOARS.
    10.1186/1465-9921-14-38
  22. Ramalho, A.S.; Clarke, L.A.; Amaral, M.D.. "Quantification of CFTR transcripts.". Methods in molecular biology (Clifton, N.J.) 741 (2011): 115-135. http://www.scopus.com/inward/record.url?eid=2-s2.0-80052341883&partnerID=MN8TOARS.
    10.1007/978-1-61779-117-8_9
  23. Martins, J.R.; Kongsuphol, P.; Sammels, E.; Dahimène, S.; AlDehni, F.; Clarke, L.A.; Schreiber, R.; et al. "F508del-CFTR increases intracellular Ca 2+ signaling that causes enhanced calcium-dependent Cl - conductance in cystic fibrosis". Biochimica et Biophysica Acta - Molecular Basis of Disease 1812 11 (2011): 1385-1392. http://www.scopus.com/inward/record.url?eid=2-s2.0-80052869614&partnerID=MN8TOARS.
    10.1016/j.bbadis.2011.08.008
  24. Ramachandran, S.; Clarke, L.A.; Scheetz, T.E.; Amaral, M.D.; McCray Jr., P.B.. "Microarray mRNA expression profiling to study cystic fibrosis.". Methods in molecular biology (Clifton, N.J.) 742 (2011): 193-212. http://www.scopus.com/inward/record.url?eid=2-s2.0-80052546232&partnerID=MN8TOARS.
    10.1007/978-1-61779-120-8_12
  25. Graham, D.L.; Ferreira, H.A.; Feliciano, N.; Freitas, P.P.; Clarke, L.A.; Amaral, M.D.. "Magnetic field-assisted DNA hybridisation and simultaneous detection using micron-sized spin-valve sensors and magnetic nanoparticles". Sensors and Actuators, B: Chemical 107 2 (2005): 936-944. http://www.scopus.com/inward/record.url?eid=2-s2.0-18544368501&partnerID=MN8TOARS.
    10.1016/j.snb.2004.12.071
  26. Englmann, A.; Clarke, L.A.; Christan, S.; Amaral, M.D.; Schindelhauer, D.; Zink, D.. "The replication timing of CFTR and adjacent genes". Chromosome Research 13 2 (2005): 183-194. http://www.scopus.com/inward/record.url?eid=2-s2.0-18744383356&partnerID=MN8TOARS.
    10.1007/s10577-005-0845-4
  27. Ferreira, H.A.; Feliciano, N.; Graham, D.L.; Clarke, L.A.; Amaral, M.D.; Freitas, P.P.. "Rapid DNA hybridization based on ac field focusing of magnetically labeled target DNA". Applied Physics Letters 87 1 (2005): http://www.scopus.com/inward/record.url?eid=2-s2.0-24144471217&partnerID=MN8TOARS.
    10.1063/1.1984090
  28. Galvin, P.; Clarke, L.A.; Harvey, S.; Amaral, M.D.. "Microarray analysis in cystic fibrosis". Journal of Cystic Fibrosis 3 SUPPL. 2 (2004): 29-33. http://www.scopus.com/inward/record.url?eid=2-s2.0-11044238806&partnerID=MN8TOARS.
    10.1016/j.jcf.2004.05.006
  29. Amaral, M.D.; Clarke, L.A.; Ramalho, A.S.; Beck, S.; Broackes-Carter, F.; Rowntree, R.; Mouchel, N.; et al. "Quantitative methods for the analysis of CFTR transcripts/splicing variants". Journal of Cystic Fibrosis 3 SUPPL. 2 (2004): 17-23. http://www.scopus.com/inward/record.url?eid=2-s2.0-19944384117&partnerID=MN8TOARS.
    10.1016/j.jcf.2004.05.047
  30. Zink, D.; Amaral, M.D.; Englmann, A.; Lang, S.; Clarke, L.A.; Rudolph, C.; Alt, F.; et al. "Transcription-dependent spatial arrangements of CFTR and adjacent genes in human cell nuclei". Journal of Cell Biology 166 6 (2004): 815-825. http://www.scopus.com/inward/record.url?eid=2-s2.0-4544255977&partnerID=MN8TOARS.
    10.1083/jcb.200404107
  31. Ramalho, A.S.; Beck, S.; Farinha, C.M.; Clarke, L.A.; Heda, G.D.; Steiner, B.; Sanz, J.; et al. "Methods for RNA extraction, cDNA preparation and analysis of CFTR transcripts". Journal of Cystic Fibrosis 3 SUPPL. 2 (2004): 11-15. http://www.scopus.com/inward/record.url?eid=2-s2.0-19944409297&partnerID=MN8TOARS.
    10.1016/j.jcf.2004.05.004
  32. Clarke, L.A.; Rebelo, C.S.; Gonçalves, J.; Boavida, M.G.; Jordan, P.. "PCR amplification introduces errors into mononucleotide and dinucleotide repeat sequences". Journal of Clinical Pathology - Molecular Pathology 54 5 (2001): 351-353. http://www.scopus.com/inward/record.url?eid=2-s2.0-0034817160&partnerID=MN8TOARS.
    10.1136/mp.54.5.351
  33. Clarke, L.A.; Jordan, P.; Boavida, M.G.. "Cell type specificity in alternative splicing of the human mismatch repair gene hMSH2". European Journal of Human Genetics 8 5 (2000): 347-352. http://www.scopus.com/inward/record.url?eid=2-s2.0-0034078917&partnerID=MN8TOARS.
    10.1038/sj.ejhg.5200472
  34. Clarke, L.A.; Veiga, I.; Isidro, G.; Jordan, P.; Ramos, J.S.; Castedo, S.; Boavida, M.G.. "Pathological exon skipping in an HNPCC proband with MLHI splice acceptor site mutation". Genes Chromosomes and Cancer 29 4 (2000): 367-370. http://www.scopus.com/inward/record.url?eid=2-s2.0-0033767549&partnerID=MN8TOARS.
  35. Jabbour, H.N.; Clarke, L.A.; Bramley, T.; Postel-Vinay, M.-C.; Kelly, P.A.; Edery, M.. "Alternative splicing of the prolactin receptor gene generates a 1.7 kb RNA transcript that is linked to prolactin function in the red deer testis". Journal of Molecular Endocrinology 21 1 (1998): 51-59. http://www.scopus.com/inward/record.url?eid=2-s2.0-0031831059&partnerID=MN8TOARS.
    10.1677/jme.0.0210051
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Activities

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2022/03/02 Optimising mRNA integrity and read-through of CFTR bearing PTC mutations.
Supervisor
 VANESSA CRISTINA DE CARVALHO LUZ (Master)
Faculdade de Ciencias, Universidade de Lisboa, Portugal
2019/09/20 Regulation of glucose uptake in mammalian cells by protein phosphorylation networks
Supervisor
 andreia filipa almeida henriques (PhD)
2019/06/01 Information Retrieval using Machine Learning for Database Curation
(Thesis) Main arguer
 sofia pinheiro rodrigues de jesus (Master)
Faculdade de Ciencias, Universidade de Lisboa, Portugal
2019/05/03 Regulation of epithelial chloride transport by phospho-tyrosine-initiated protein networks
Supervisor
 cláudia almeida loureiro (PhD)
2019/02/08 Development of a text mining approach to disease network discovery
Supervisor
 andré francisco martins lamúrias (PhD)
Faculdade de Ciencias, Universidade de Lisboa, Portugal
2018/06/01 Identifying the sequence complexity of miRNAs and their functional impact in small-RNA-seq data
(Thesis) Main arguer
 inês correia viegas (Master)
Faculdade de Ciencias, Universidade de Lisboa, Portugal
2017/06/01 Single domain antibodies association to lipid-guide drug delivery as an innovative therapeutic strategy against cancer stem cells
(Thesis) Main arguer
 ana carolina malho sousa (Master)
Faculdade de Ciencias, Universidade de Lisboa, Portugal
2017/03/01 Previsão da Localização Subcelular de Proteínas Humanas com base em Aprendizagem Automática
(Thesis) Main arguer
 pedro de almeida martins (Master)
Faculdade de Ciencias, Universidade de Lisboa, Portugal
2017/03/01 Lab on a chip for Cystic Fibrosis
Supervisor
 Anna Pedrola Gómez (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2017/02/15 Validação de genes alvo da via Rac1/PAK1-BCL6/STAT5 envolvidos na progressão tumoral
(Thesis) Main arguer
 leonor bárbara freire abrantes (Master)
Faculdade de Ciencias, Universidade de Lisboa, Portugal
2016/11/23 Development of a miniaturized chip for personalized therapy of cystic fibrosis
Supervisor
 Rafaela Furtado Pereira (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2015/11/27 Effect of TGFß signalling on CFTR protein: consequences for epithelial differentiation in CF
Supervisor
 Margarida Quaresma (Master)
Faculdade de Ciencias, Universidade de Lisboa, Portugal
2015/06/01 Estudos dos efeitos do tratamento com rhHGF de células epiteliais brônquicas derivadas de doentes com Fibrose Quística: avaliação das propriedades regenerativas versus oncogénicas
(Thesis) Main arguer
 Andreia Duarte (Master)
Faculdade de Ciencias, Universidade de Lisboa, Portugal
2015/05/05 Functional coherence and annotation agreement metrics for enzyme families
Supervisor
 Hugo Bastos (PhD)
Faculdade de Ciencias, Universidade de Lisboa, Portugal
2014/09/26 Identifying interactions between chemical entities in text
(Thesis) Main arguer
 André Lamurias (Master)
Faculdade de Ciencias, Universidade de Lisboa, Portugal
2012/04/05 Role of Ubiquitin Ligases in Pathophysiology of Cystic Fibrosis
Supervisor
 Sara Canato (Master)
Faculdade de Ciencias, Universidade de Lisboa, Portugal
2009/06/01 A Magnetoresistive Biochip Platform: detection of DNA hybridization and antibody/cell recognition
(Thesis) Main arguer
 verónica cristina baião martins romão (PhD)
Universidade de Lisboa Instituto Superior Técnico, Portugal

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2010/01/01 - 2024/08/01 Human Molecular Biology (Year 3 Biochemistry/ Masters in Health Sciences) Human Molecular Biology (Mestrado) Faculdade de Ciencias, Universidade de Lisboa, Portugal
2009/09/01 - 2024/02/15 Molecular Biology (Year 3, Biochemistry) Molecular Biology (Licenciatura) Faculdade de Ciencias, Universidade de Lisboa, Portugal
2016/07/01 - 2019/07/31 Workshop: Epithelial Systems: Physiology & Pathophysiology (Pós-doutoramento) Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
2013/01/01 - 2018/07/31 BioSYS PhD Programme (Curso de doutoramento (conclusão de unidades curriculares)) Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
2011/09/01 - 2014/07/01 Biochemistry I (Health Sciences) (Licenciatura) Faculdade de Ciencias, Universidade de Lisboa, Portugal
2011/09/01 - 2013/07/01 Experimental Biochemistry II (Licenciatura)
Distinctions

Award

2019 Thomé Villar/Boehringer Ingelheim Prize (Team member)
2013 2013 Pfizer Research Award (Team Member)
1990 Rose-Bracher Memorial Prize, awarded to best final year student in Biological Sciences
University of Bristol, United Kingdom