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Post by djoser-xyyman on Oct 27, 2014 20:24:38 GMT -5
www.ipatimup.pt/site/PersonView.aspx?PersonId=84Short CV I have a degree in Biology (1995), a master degree in Applied Human Genetics (1997) and a PhD in Biology – field of Human Population Genetics (2001), by Faculty of Sciences, University of Porto. I was post-doc at Ipatimup and Department of Statistics of University of Oxford. I am a researcher at Ipatimup since 2004 and group leader since 2006. I have been interested in using genetics to infer the past and evolution of human populations as well as on disentangling between neutral and pathological diversities. I have been working on the genetic diversity of European, African, Near Eastern and Arabian Peninsula human populations. I am co-author of 75 peer-reviewed papers in international journals and a popular science book. Highlights - Using high-resolution population genetic studies (complete mitochondrial genomes and genome-wide studies) for a fine characterisation of main human migrations, as: out-of-Africa; settlement of Southeast Asia and Europe; post-glacial expansions in several regions of the world; Neolithisation of Europe; and transatlantic slave trade. - Cross-talk between mitochondrial and nuclear genomes. Evaluation of selection effects and pathogenicity. - Genetic susceptibility to Dengue infection in Europe. Supervisor of Andreia Brandão, PhD Student Farida Alshamali, Research Consultant Joana Pereira, Post Doc Marisa Oliveira, PhD Student Orlando Anunciação, Post Doc Pedro Soares, External Researcher Petr Triska, PhD Student Susana Seixas, Project Manager Verónica Fernandes, Post Doc 
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Post by djoser-xyyman on Oct 27, 2014 20:26:41 GMT -5
First Author
C IF
1. 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.
11 3.3
2. 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.
24 10.6
3. 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.
3 2.6
4. 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.
20 3.7
5. 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.
16 4.4
6. 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.
53 12.3
7. 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.
9 4.2
8. 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.
36 6.4
9. 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.
11 1.4
10. 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.
82 10.1
11. 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.
20 1.0
12. 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.
18 2.3
13. 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.
36 2.1
14. 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.
25 1.4
15. Pereira L, Gusmão L, Alves C, Amorim
25 1.4
15. 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.
39 2.3
16. 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.
6 1.0
17. 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.
107 2.1
18. 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.
20 5.4
19. 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.
83 2.1
20. 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.
13 1.5
21. 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.
1 1.5
22. 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.
3 1.8
Senior Author
C IF
1. 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.
5 3.5
2. 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.
24 10.4
3. 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.
21 11.2
4. 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.
13 5.6
5. 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.
17 3.7
6. 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.
16 4.3
7. 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.
12 3.9 (*)
8. 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.
1 4.1
9. 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.
27 2.4
10. 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.
24 2.4
11. 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.
12 2.6
12. 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.
3 2.2
13. 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.
35 1.6
14. 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.
3 1.7
15. 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.
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