1. Pereira L, Mutesa L, Tindana P, Ramsay M

African genetic diversity and adaptation inform a precision medicine agenda. Nature reviews. Genetics 22: 284-306, 2021. [Review] 

 doi: 10.1038/s41576-020-00306-8 PMID: 33432191.

 

2. Pereira L, Soares P, Triska P, Rito T, van der Waerden A, Li B, Radivojac P, Samuels DC

Global human frequencies of predicted nuclear pathogenic variants and the role played by protein hydrophobicity in pathogenicity potential. Scientific reports 4: 7155, 2014. [Article] 

 doi: 10.1038/srep07155 PMID: 25412673.

 

3. Pereira L, Soares P, Máximo V, Samuels DC

Somatic mitochondrial DNA mutations in cancer escape purifying selection and high pathogenicity mutations lead to the oncocytic phenotype: pathogenicity analysis of reported somatic mtDNA mutations in tumors. BMC cancer 12: 53, 2012. [Article] 

 doi: 10.1186/1471-2407-12-53 PMID: 22299657.

 

4. Pereira L, Soares P, Radivojac P, Li B, Samuels DC

Comparing Phylogeny and the Predicted Pathogenicity of Protein Variations Reveals Equal Purifying Selection across the Global Human mtDNA Diversity. American journal of human genetics 88: 433-9, 2011. [Article] 

 doi: 10.1016/j.ajhg.2011.03.006 PMID: 21457906.

 

5. Pereira L, Alshamali F, Andreassen R, Ballard R, Chantratita W, Cho NS, Coudray C, Dugoujon JM, Espinoza M, González-Andrade F, Hadi S, Immel UD, Marian C, Gonzalez-Martin A, Mertens G, Parson W, Perone C, Prieto L, Takeshita H, Rangel Villalobos H, Zeng Z, Zhivotovsky L, Camacho R, Fonseca NA

PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile. International journal of legal medicine 125: 629-36, 2011. [Article] 

 doi: 10.1007/s00414-010-0472-2 PMID: 20552217.

 

6. Pereira L, Silva NM, Franco-Duarte R, Fernandes V, Pereira JB, Costa MD, Martins H, Soares P, Behar DM, Richards MB, Macaulay V

Population expansion in the North African late Pleistocene signalled by mitochondrial DNA haplogroup U6. BMC evolutionary biology 10: 390, 2010. [Article] 

 doi: 10.1186/1471-2148-10-390 PMID: 21176127.

 

7. Pereira L, Cerný V, Cerezo M, Silva NM, Hájek M, Vasíková A, Kujanová M, Brdicka R, Salas A

Linking the sub-Saharan and West Eurasian gene pools: maternal and paternal heritage of the Tuareg nomads from the African Sahel. European journal of human genetics : EJHG 18: 915-23, 2010. [Article] 

 doi: 10.1038/ejhg.2010.21 PMID: 20234393.

 

8. Pereira L, Freitas F, Fernandes V, Pereira JB, Costa MD, Costa S, Máximo V, Macaulay V, Rocha R, Samuels DC

The diversity present in 5140 human mitochondrial genomes. American journal of human genetics 84: 628-40, 2009. [Article] 

 doi: 10.1016/j.ajhg.2009.04.013 PMID: 19426953.

 

9. Pereira L, Gonçalves J, Bandelt HJ

Mutation C11994T in the mitochondrial ND4 gene is not a cause of low sperm motility in Portugal. Fertility and sterility 89: 738-41, 2008. [Editorial Material] 

 doi: 10.1016/j.fertnstert.2007.03.048 PMID: 17517394.

 

10. Pereira L, Gonçalves J, Franco-Duarte R, Silva J, Rocha T, Arnold C, Richards M, Macaulay V

No evidence for an mtDNA role in sperm motility: data from complete sequencing of asthenozoospermic males. Molecular biology and evolution 24: 868-74, 2007. [Article] 

 doi: 10.1093/molbev/msm004 PMID: 17218641.

 

11. Pereira L, Richards M, Goios A, Alonso A, Albarrán C, Garcia O, Behar DM, Gölge M, Hatina J, Al-Gazali L, Bradley DG, Macaulay V, Amorim A

Evaluating the forensic informativeness of mtDNA haplogroup H sub-typing on a Eurasian scale. Forensic science international 159: 43-50, 2006. [Article] 

 doi: 10.1016/j.forsciint.2005.06.008 PMID: 16076538.

 

12. Pereira L, Richards M, Goios A, Alonso A, Albarrán C, Garcia O, Behar DM, Gölge M, Hatina J, Al-Gazali L, Bradley DG, Macaulay V, Amorim A

High-resolution mtDNA evidence for the late-glacial resettlement of Europe from an Iberian refugium. Genome research 15: 19-24, 2005. [Article] 

 doi: 10.1101/gr.3182305 PMID: 15632086.

 

13. Pereira L, Cunha C, Alves C, Amorim A

African female heritage in Iberia: a reassessment of mtDNA lineage distribution in present times. Human biology; an international record of research 77: 213-29, 2005. [Article] 

 PMID: 16201138.

 

14. Pereira L, Gonçalves J, Goios A, Rocha T, Amorim A

Human mtDNA haplogroups and reduced male fertility: real association or hidden population substructuring. International journal of andrology 28: 241-7, 2005. [Article] 

 doi: 10.1111/j.1365-2605.2005.00539.x PMID: 16048637.

 

15. Pereira L, Van Asch B, Amorim A

Standardisation of nomenclature for dog mtDNA D-loop: a prerequisite for launching a Canis familiaris database. Forensic science international 141: 99-108, 2004. [Article] 

 doi: 10.1016/j.forsciint.2003.12.014 PMID: 15062947.

 

16. Pereira L, Cunha C, Amorim A

Predicting sampling saturation of mtDNA haplotypes: an application to an enlarged Portuguese database. International journal of legal medicine 118: 132-6, 2004. [Article] 

 doi: 10.1007/s00414-003-0424-1 PMID: 14872253.

 

17. Pereira L, Gusmão L, Alves C, Amorim A, Prata MJ

Bantu and European Y-lineages in Sub-Saharan Africa. Annals of human genetics 66: 369-78, 2002. [Article] 

 doi: doi:10.1017/S0003480002001306 PMID: 12485470.

 

18. Pereira L, Prata MJ, Amorim A

Mismatch distribution analysis of Y-STR haplotypes as a tool for the evaluation of identity-by-state proportions and significance of matches--the European picture. Forensic science international 130: 147-55, 2002. [Article] 

 PMID: 12477636.

 

19. Pereira L, Macaulay V, Torroni A, Scozzari R, Prata MJ, Amorim A

Prehistoric and historic traces in the mtDNA of Mozambique: insights into the Bantu expansions and the slave trade. Annals of human genetics 65: 439-58, 2001. [Article] 

 doi: doi:10.1017/S0003480001008855 PMID: 11806853.

 

20. Pereira L, Dupanloup I, Rosser ZH, Jobling MA, Barbujani G

Y-chromosome mismatch distributions in Europe. Molecular biology and evolution 18: 1259-71, 2001. [Article] 

 PMID: 11420365.

 

21. Pereira L, Prata MJ, Amorim A

Diversity of mtDNA lineages in Portugal: not a genetic edge of European variation. Annals of human genetics 64: 491-506, 2000. [Article] 

 PMID: 11281213.

 

22. Pereira L, Prata MJ, Brión M, Jobling MA, Carracedo A, Amorim A

Clinal variation of YAP+ Y-chromosome frequencies in Western Iberia. Human biology; an international record of research 72: 937-44, 2000. [Article] 

 PMID: 11236865.

 

23. Pereira L, Gusmão L, Prata MJ, Mota P, Trovoada MJ, Amorim A

Variation in STR loci of the human myelin basic protein gene: north Portugal and São Tomé e Príncipe. Human biology; an international record of research 72: 481-7, 2000. [Article] 

 PMID: 10885193.

 

24. Pereira L, Gusmão L, Prata MJ, Moto P, Trovoada MJ, Amorim A

Detection of additional structural variation at the FES/FPS system and population data from S. Tomé e Príncipe and North Portugal. International journal of legal medicine 112: 204-6, 1999. [Article] 

 PMID: 10335889.

 

1. Magalhães AC, Ricardo S, Moreira AC, Nunes M, Tavares M, Pinto RJ, Gomes MS, Pereira L

InfectionCMA: A Cell MicroArray Approach for Efficient Biomarker Screening in In Vitro Infection Assays. Pathogens (Basel, Switzerland) 11: ., 2022. [Article] 

 doi: 10.3390/pathogens11030313 PMID: 35335638.

 

2. 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 9: ., 2021. [Article] 

 doi: 10.3390/microorganisms9020240 PMID: 33503840.

 

3. 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 13: ., 2021. [Article] 

 doi: 10.3390/v13061116 PMID: 34200621.

 

4. Magalhães AC, Pedro N, Pereira L

Genomic Insights into the Human Susceptibility to SARS-CoV-2 Infection. Acta medica portuguesa 34: 407-409, 2021. [Editorial Material] 

 doi: 10.20344/amp.16168 PMID: 33821785.

 

5. Pedro N, Pinto RJ, Cavadas B, Pereira L

Sub-Saharan African information potential to unveil adaptations to infectious disease. Human molecular genetics 30: R138-R145, 2021. [Review] 

 doi: 10.1093/hmg/ddab001 PMID: 33461217.

 

6. Gomes MS, Pereira L

Special Issue: From Host-Pathogen Interaction to Host-Directed Therapies. Microorganisms 9: ., 2021. [Editorial Material] 

 doi: 10.3390/microorganisms9122606 PMID: 34946207.

 

7. Cavadas B, Camacho R, Ferreira JC, Ferreira RM, Figueiredo C, Brazma A, Fonseca NA, Pereira L

Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci. Microorganisms 8: ., 2020. [Article] 

 doi: 10.3390/microorganisms8081196 PMID: 32781641.

 

8. Fernandes V, Brucato N, Ferreira JC, Pedro N, Cavadas B, Ricaut FX, Alshamali F, Pereira L

Genome-Wide Characterization of Arabian Peninsula Populations: Shedding Light on the History of a Fundamental Bridge between Continents. Molecular biology and evolution 36: 575-586, 2019. [Article] 

 doi: 10.1093/molbev/msz005 PMID: 30649405.

 

9. Cavadas B, Pereira JB, Correia M, Fernandes V, Eloy C, Sobrinho-Simões M, Soares P, Samuels DC, Máximo V, Pereira L

Genomic and transcriptomic characterization of the mitochondrial-rich oncocytic phenotype on a thyroid carcinoma background. Mitochondrion 46: 123-133, 2019. [Article] 

 doi: 10.1016/j.mito.2018.04.001 PMID: 29631022.

 

10. Alshamali F, Kundu B, Pereira L

Investigating the resolution of ancestry testing in geographic regions characterized by high population admixture Forensic science international. Genetics Supplement Series 7: 12-13, 2019. [Article] 

 doi: 10.1016/j.fsigss.2019.09.005.

 

11. Oliveira M, Ferreira J, Fernandes V, Sakuntabhai A, Pereira L

Host ancestry and dengue fever: from mapping of candidate genes to prediction of worldwide genetic risk FUTURE VIROLOGY 13:  647-655, 2018. [Article] 

 doi: 10.2217/fvl-2018-0073.

 

12. Cavadas B, Ferreira J, Camacho R, Fonseca NA, Pereira L

QmihR: Pipeline for quantification of microbiome in human RNA-seq Advances in Intelligent Systems and Computing 616: 173-179, 2017. [Proceedings Paper] 

 doi: 10.1007/978-3-319-60816-7_21.

 

13. Triska P, Soares P, Patin E, Fernandes V, Cerny V, Pereira L

Extensive Admixture and Selective Pressure Across the Sahel Belt. Genome biology and evolution 7: 3484-95, 2015. [Article] 

 doi: 10.1093/gbe/evv236 PMID: 26614524.

 

14. Fernandes V, Triska P, Pereira JB, Alshamali F, Rito T, Machado A, Fajkošová Z, Cavadas B, Cerný V, Soares P, Richards MB, Pereira L

Genetic stratigraphy of key demographic events in arabia. PloS one 10: e0118625, 2015. [Article] 

 doi: 10.1371/journal.pone.0118625 PMID: 25738654.

 

15. Cavadas B, Soares P, Camacho R, Brandão A, Costa MD, Fernandes V, Pereira JB, Rito T, Samuels DC, Pereira L

Fine Time Scaling of Purifying Selection on Human Nonsynonymous mtDNA Mutations Based on the Worldwide Population Tree and Mother-Child Pairs. Human mutation 36: 1100-11, 2015. [Article] 

 doi: 10.1002/humu.22849 PMID: 26252938.

 

16. Soares P, Abrantes D, Rito T, Thomson N, Radivojac P, Li B, Macaulay V, Samuels DC, Pereira L

Evaluating purifying selection in the mitochondrial DNA of various mammalian species. PloS one 8: e58993, 2013. [Article] 

 doi: 10.1371/journal.pone.0058993 PMID: 23533597.

 

17. Soares P, Alshamali F, Pereira JB, Fernandes V, Silva NM, Afonso C, Costa MD, Musilová E, Macaulay V, Richards MB, Cerny V, Pereira L

The Expansion of mtDNA Haplogroup L3 within and out of Africa. Molecular biology and evolution 29: 915-27, 2012. [Article] 

 doi: 10.1093/molbev/msr245 PMID: 22096215.

 

18. Fernandes V, Alshamali F, Alves M, Costa MD, Pereira JB, Silva NM, Cherni L, Harich N, Cerny V, Soares P, Richards MB, Pereira L

The Arabian cradle: mitochondrial relicts of the first steps along the southern route out of Africa. American journal of human genetics 90: 347-55, 2012. [Article] 

 doi: 10.1016/j.ajhg.2011.12.010 PMID: 22284828.

 

19. Cerný V, Mulligan CJ, Fernandes V, Silva NM, Alshamali F, Non A, Harich N, Cherni L, El Gaaied AB, Al-Meeri A, Pereira L

Internal diversification of mitochondrial haplogroup R0a reveals post-last glacial maximum demographic expansions in South Arabia. Molecular biology and evolution 28: 71-8, 2011. [Article] 

 doi: 10.1093/molbev/msq178 PMID: 20643865.

 

20. Harich N, Costa MD, Fernandes V, Kandil M, Pereira JB, Silva NM, Pereira L

The trans-Saharan slave trade - clues from interpolation analyses and high-resolution characterization of mitochondrial DNA lineages. BMC evolutionary biology 10: 138, 2010. [Article] 

 doi: 10.1186/1471-2148-10-138 PMID: 20459715.

 

21. Cerný V, Fernandes V, Costa MD, Hájek M, Mulligan CJ, Pereira L

Migration of Chadic speaking pastoralists within Africa based on population structure of Chad Basin and phylogeography of mitochondrial L3f haplogroup. BMC evolutionary biology 9: 63, 2009. [Article] 

 doi: 10.1186/1471-2148-9-63 PMID: 19309521.

 

22. Costa MD, Cherni L, Fernandes V, Freitas F, Ammar El Gaaied AB, Pereira L

Data from complete mtDNA sequencing of Tunisian centenarians: Testing haplogroup association and the "golden mean" to longevity. Mechanisms of ageing and development 130: 222-6, 2009. [Article] 

 doi: 10.1016/j.mad.2008.12.001 PMID: 19133286.

 

23. Freitas F, Oliveira S, Rocha R, Pereira L

mtDNA GeneExtractor: A computer tool for mtDNA gene/region information extraction. Mitochondrion 9: 36-40, 2009. [Article] 

 doi: 10.1016/j.mito.2008.11.003 PMID: 19070686.

 

24. Cherni L, Fernandes V, Pereira JB, Costa MD, Goios A, Frigi S, Yacoubi-Loueslati B, Amor MB, Slama A, Amorim A, El Gaaied AB, Pereira L

Post-last glacial maximum expansion from Iberia to North Africa revealed by fine characterization of mtDNA H haplogroup in Tunisia American journal of physical anthropology 139: 253-260, 2008. [Article] 

 doi: 10.1002/ajpa.20979 PMID: 19090581.

 

25. Cerný V, Mulligan CJ, Rídl J, Zaloudková M, Edens CM, Hájek M, Pereira L

Regional differences in the distribution of the sub-Saharan, West Eurasian, and South Asian mtDNA lineages in Yemen. American journal of physical anthropology 136: 128-37, 2008. [Article] 

 doi: 10.1002/ajpa.20784 PMID: 18257024.

 

26. Goios A, Prieto L, Amorim A, Pereira L

Specificity of mtDNA-directed PCR-influence of NUclear MTDNA insertion (NUMT) contamination in routine samples and techniques. International journal of legal medicine 122: 341-5, 2008. [Article] 

 doi: 10.1007/s00414-007-0191-5 PMID: 17874117.

 

27. Goios A, Meirinhos J, Rocha R, Lopes R, Amorim A, Pereira L

RepeatAround: A software tool for finding and visualizing repeats in circular genomes and its application to a human mtDNA database. Mitochondrion 6: 218-24, 2006. [Article] 

 doi: 10.1016/j.mito.2006.06.001 PMID: 16854633.

 

28. Amorim A, Pereira L

Pros and cons in the use of SNPs in forensic kinship investigation: a comparative analysis with STRs. Forensic science international 150: 17-21, 2005. [Article] 

 doi: 10.1016/j.forsciint.2004.06.018 PMID: 15837005.

 

29. Goios A, Nogueira C, Pereira C, Vilarinho L, Amorim A, Pereira L

mtDNA single macrodeletions associated with myopathies: absence of haplogroup-related increased risk. Journal of inherited metabolic disease 28: 769-78, 2005. [Article] 

 doi: 10.1007/s10545-005-0023-z PMID: 16151908.

 

30. Alves C, Amorim A, Gusmão L, Pereira L

VWA STR genotyping: further inconsistencies between Perkin-Elmer and Promega kits. International journal of legal medicine 115: 97-9, 2001. [Article] 

 PMID: 11724440.