CBMA

Archaeogenetics and phylogeography

Genetic history of populations in Southeast Asia, Europe and Africa

Mitochondrial DNA variation in health and disease

Genome-wide analysis of African and Southeast Asian populations

Effect of purifying selection in the molecular clock and population variation

Response of Human Populations to past changes in climate

Ancient DNA

Development of population genetic analysis tools

Genetic susceptibility to diseases

Biodiversity

Richards MB, Soares P, Torroni A (2016.) Palaeogenomics: Mitogenomes and Migrations in Europe’s Past. Current Biology 26(6): R243-R246. (IF: 9.571; citations: 0, Q1 in Biochemistry, Genetics and Molecular Biology)

Soares P, Rito T, Pereira L, Richards MB. (2016). A Genetic Perspective on African Prehistory. “Africa from MIS 6-2: Population Dynamics and Paleoenvironments”, edited by Sacha C. Jones and Brian A. Stewart. Springer Netherlands p: 383-405

Brandão A, Eng KK, Rito T, Cavadas B, Bulbeck D, Gandini F, Pala M, Mormina M, Hudson B, White J, Ko T-M, Saidin M, Zafarina Z, Oppenheimer S, Richards MB, Pereira L, Soares P (2016). Quantifying the legacy of the Chinese Neolithic on the maternal genetic heritage of Taiwan and Island Southeast Asia. Human Genetics 135(4): 363-376 (IF: 4.824; citations: 0, Q1 in Genetics)

Soares PA, Trejaut JA, Rito T, Cavadas B, Hill C, Eng KK, Mormina M, Brandão A, Fraser RM, Wang T-Y, Loo J-H, Snell C, Ko T-M, Amorim A, Pala M, Macaulay V, Bulbeck D, Wilson JF, Gusmão L, Pereira L, Oppenheimer S, Lin M, Richards MB (2016). Resolving the ancestry of Austronesian-speaking populations. Human Genetics 135(3): 309-326 (IF: 4.824; citations: 1, Q1 in Genetics)

Triska P, Soares P, Patin E, Fernandes V, Cerny V, Pereira L. (2015). Extensive Admixture and Selective Pressure Across the Sahel Belt. Genome Biology and Evolution 7(12):evv236 (IF: 4.229, citations: 0, Q1 in Genetics)

Silva M, Alshamali F, Silva P, Carrilho C, Mandlate F, Trovoada MJ, ?erný V, Pereira L, Soares P (2015). 60,000 years of interactions between Central and Eastern Africa documented by major African mitochondrial haplogroup L2. Scientific Reports 5:12526 , (IF: 5.578, citations: 2, Q1 in Multidisciplinary)

Cavadas B, Soares P, Camacho R, Brandão A, Costa MD, Fernandes V, Pereira JB, Rito T, Samuels DC, Pereira L (2015). Fine time-scaling of purifying selection on human non-synonymous mtDNA mutations based on worldwide population tree and mother-child pairs. Human Mutation 36: 1100-1111 (IF: 5.144; citations: 1, Q1 in Genetics)

Fernandes V, Triska P, Pereira JB, Alshamali F, Rito T, Machado A, Fajkošová Z, Cavadas B, ?erný V, Soares P, Richards MB, Pereira L (2015). Genetic stratigraphy of key demographic events in Arabia. Plos One 10: e0118625 (IF: 3.234, citations: 6, Q1 in Multidisciplinary)

Rito T, Richards MB, Fernandes V, Alshamali F, Cerny V, Pereira L, Soares P (2013). The First Modern Human Dispersals Across Africa. Plos One 8:e80031 (IF: 3.534; citations: 19, Q1 in Multidisciplinary)

Costa MD, Pereira JB, Pala M, Fernandes V, Olivieri A, Achilli A, Perego UA, Rychkov S, Naumova O, Hatina J, Woodward SR, Eng S, Carr M, Macaulay V, Soares P, Pereira L, Richards MB (2013). A substantial prehistoric European ancestry amongst Ashkenazi maternal lineages. Nature Communications 4:2543 (IF: 10.742; citations: 16, Q1 in Multidisciplinary)

Mellars P, Gori KC, Carr M, Soares PA, Richards MB (2013). Genetic and archaeological perspectives on the initial modern human colonization of southern Asia. Proceedings of the National Academy of Sciences USA 110:10699-10704 (IF: 9.809; citations: 51, Q1 in Multidisciplinary)

Soares P, Abrantes D, Rito T, Thomson N, Radivojac P, Li B, Macaulay V, Samuels DC, Pereira L. (2013). Evaluating purifying selection in the mitochondrial DNA of various mammalian species. Plos One 8: e58993. (IF: 3.534; citations: 15, Q1 in Multidisciplinary)

Soares P, Alshamali F, Pereira JB, Fernandes V, Silva NM, Afonso C, Costa MD, Musilová E, Macaulay V, Richards MB, Cerny V, Pereira L. (2012). The Expansion of mtDNA Haplogroup L3 within and out of Africa. Molecular Biology and Evolution 29: 915-927 (IF: 10.353; citations: 58, Q1 in Genetics)

Fernandes V, Alshamali F, Alves M, Costa MD, Pereira JB, Silva NM, Cherni L, Harich N, Cerny V, Soares P, Richards MB, Pereira L. (2012). The Arabian Cradle: Mitochondrial Relicts of the First Steps along the Southern Route out of Africa. American Journal of Human Genetics 90: 347-355 (IF: 11.202; citations: 44, Q1 in Genetics)

Pereira L, Soares P, Máximo V, Samuels DC. (2012). 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 (IF: 3.333; citations: 26, Q1 in Oncology)

Achilli A, Olivieri A, Soares P, Lancioni H, Kashani BH, Perego UA, Nergadze SG, Carossa V, Santagostino M, Capomaccio S, Felicetti M, Al-Achkar W, Penedo MCT, Verini-Supplizi A, Houshmand M, Woodward SR, Semino O, Silvestrelli M, Giulotto E, Pereira L, Bandelt H-J, Torroni A. (2012). Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication. Proceedings of the National Academy of Sciences USA 109: 2449-2454 (IF: 9.737; citations: 44, Q1 in Multidisciplinary)

Pereira L, Soares P, Radivojac P, Li B, Samuels DC. (2011). 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 (IF: 10.603; citations: 34, Q1 in Genetics)

Soares P, Rito T, Trejaut J, Mormina M, Hill C, Tinkler-Hundal E, Braid M, Clarke DJ, Loo JH, Thomson N, Denham T, Donohue M, Macaulay V, Lin M, Oppenheimer S, Richards MB. (2011). Ancient Voyaging and Polynesian Origins. American Journal of Human Genetics 88: 239-247 (IF: 10.603; citations: 73, Q1 in Genetics)

Soares P, Achilli A, Semino O, Davies W, Macaulay V, Bandelt HJ, Torroni A, Richards MB. (2010). The Archaeogenetics of Europe. Current Biology 20: R174-R183 (IF: 10.025; citations: 135, Q1 in Biochemistry, Genetics and Molecular Biology)

Soares P, Ermini L, Mormina M, Rito T, Röhl A, Salas A, Oppenheimer S, Macaulay V, Richards M. (2009). Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock. American Journal of Human Genetics 84: 740-759 (IF: 12.303; citations: 322, Q1 in Genetics)

Pereira F, Soares P, Carneiro J, Pereira L, Richards MB, Samuels DC, Amorim A. (2008). Evidence for variable selective pressures at a large secondary structure of the human mitochondrial DNA control region. Molecular Biology and Evolution 25: 2759-2770 (IF: 7.28; citations: 21, Q1 in Genetics)

Soares P, Trejaut JA, Loo J.-H, Hill C, Mormina M, Lee C-L, Chen Y.-M, Hudjashov G, Forster P, Macaulay V, Bulbeck D, Oppenheimer S, Lin M, Richards MB. (2008). Climate change and post-glacial human dispersals in Southeast Asia. Molecular Biology and Evolution 25: 1209-1218 (IF: 7.28; citations: 90, Q1 in Genetics)

Hill C, Soares P, Mormina M, Macaulay V, Clarke D, Blumbach PB, Vizuete-Forster M, Forster P, Bulbeck D, Oppenheimer S, Richards M. (2007). A mitochondrial stratigraphy for Island Southeast Asia. American Journal of Human Genetics 80: 29–43 (IF: 11.092; citations: 138, Q1 in Genetics)

Hill C, Soares P, Mormina M, Macaulay V, Meehan W, Blackburn J, Clarke D, Raja JM, Ismail P, Bulbeck D, Oppenheimer S, Richards M. (2006). Phylogeography and ethnogenesis of aboriginal Southeast Asians.Molecular Biology and Evolution 23: 2480-2491 (IF: 6.726; citations: 83, Q1 in Genetics)

Publication list includes the impact factor (IF) of the journal in the year of publication according to ISI WOK and the number of citations in Scopus and the ranking of the journal in its field in Scimago. Paper list is in chronological order.

Principal Investigator

 - “Testing the hypothesis of late Neolithic dispersals from Iberia using both ancient and contemporary mitochondrial genomes” (PTDC/EPH-ARQ/4164/2014) sponsored by FCT – € 198.264. Evaluated as Exceptional (9 in 9) by the FCT evaluation panel.

Team-member

 - Leverhulme Doctoral Scholarship Centre for Evolutionary Genomics. PI: Martin Richards, University of Huddersfield, United Kingdom. Ongoing (October 2015–September 2020)

Principal Investigator

 - “Genetic history and population structure in Southeast Asia” (PTDC/IVC-ANT/4917/2012) sponsored by FCT – €152.304. Evaluated as Exceptional (9 in 9) by the FCT evaluation panel. Finished (01/06/2013-30/09/2015). Final report evaluated as “A” (highest mark).

Team-member

 - “Microenvironment, metabolism and cancer”sponsored by ON2 program (Programa Operacional Regional do Norte- Quadro de Referência Estratégica Nacional). PI: Paula Soares, IPATIMUP, Portugal. Ongoing (01/01/2013-30/06/2015)

- “A Marie Curie Initial Training Network on the History, Archaeology and New Genetics of the Transatlantic Slave Trade” (EUROTAST Project Number: 290344) sponsored by the European Union Marie Curie. PI: Thomas Gilbert, University of Copenhagen, Denmark. Ongoing (01/11/2011-01/11/2015).

- “Dengue research Framework for Resisting Epidemics in Europe” (DENFREE Project Number: 282378) sponsored by the European Union FP7 Projects. PI: Anavaj Sakuntabhai, Institute Pasteur, France. Ongoing (01/01/2012-01/01/2017).

- “Genetic and chronological characterisation of the European settlement by modern humans in the Upper Palaeolithic” (PTDC/CS-ANT/113832/2009) sponsored by FCT. PI: Luísa Pereira, IPATIMUP, Portugal. Concluded (01/03/2011-01/03/2014)

- “L and U6 mtDNA lineages in Southern and Western Iberia: migratory links between Africa and Europe” sponsored by CRUP (Conselho de Reitorias das Universidades Portuguesa) and CRUE (Conferencia de Rectores de Universidades Españolas). PI: Luísa Pereira, IPATIMUP and Rosario Calderon, Universitat Complutense de Madrid, Spain. Concluded (01/02/2012-31/12/2013).

- “Using mitochondrial DNA to investigate the prehistoric settlement of Myanmar Pyay (Burma)” (BARDA-48208) sponsored by the British Academy, UK. PI: Martin Richards, University of Leeds, UK. Concluded (01/05/2008-30/04/2009).

Publication list includes the impact factor (IF) of the journal in the year of publication according to ISI WOK and the number of citations in Scopus and the ranking of the journal in its field in Scimago.

Richards MB, Soares P, Torroni A (2016.) Palaeogenomics: Mitogenomes and Migrations in Europe’s Past. Current Biology 26(6): R243-R246. (IF: 9.571; citations: 0, Q1 in Biochemistry, Genetics and Molecular Biology)

Brandão A, Eng KK, Rito T, Cavadas B, Bulbeck D, Gandini F, Pala M, Mormina M, Hudson B, White J, Ko T-M, Saidin M, Zafarina Z, Oppenheimer S, Richards MB, Pereira L, Soares P (2016). Quantifying the legacy of the Chinese Neolithic on the maternal genetic heritage of Taiwan and Island Southeast Asia. Human Genetics 135(4): 363-376 (IF: 4.824; citations: 0, Q1 in Genetics)

Soares PA, Trejaut JA, Rito T, Cavadas B, Hill C, Eng KK, Mormina M, Brandão A, Fraser RM, Wang T-Y, Loo J-H, Snell C, Ko T-M, Amorim A, Pala M, Macaulay V, Bulbeck D, Wilson JF, Gusmão L, Pereira L, Oppenheimer S, Lin M, Richards MB (2016). Resolving the ancestry of Austronesian-speaking populations. Human Genetics 135(3): 309-326 (IF: 4.824; citations: 1, Q1 in Genetics)

Triska P, Soares P, Patin E, Fernandes V, Cerny V, Pereira L. (2015). Extensive Admixture and Selective Pressure Across the Sahel Belt. Genome Biology and Evolution 7(12):evv236 (IF: 4.229, citations: 0, Q1 in Genetics)

Hernández CL, Soares P, Dugoujon JM, Novelletto A, Rodríguez JN, Rito T, Oliveira M, Melhaoui M, Baali A, Pereira L; Calderón R. (2015). Early Holocenic and historic mtDNA African signatures in the Iberian Peninsula: the Andalusian region as a paradigm. Plos One 10: e0139784. (IF: 3.234, citations: 0, Q1 in Multidisciplinary)

Silva M, Alshamali F, Silva P, Carrilho C, Mandlate F, Trovoada MJ, ?erný V, Pereira L, Soares P (2015). 60,000 years of interactions between Central and Eastern Africa documented by major African mitochondrial haplogroup L2. Scientific Reports 5:12526 , (IF: 5.578, citations: 2, Q1 in Multidisciplinary)

Cavadas B, Soares P, Camacho R, Brandão A, Costa MD, Fernandes V, Pereira JB, Rito T, Samuels DC, Pereira L (2015). Fine time-scaling of purifying selection on human non-synonymous mtDNA mutations based on worldwide population tree and mother-child pairs. Human Mutation 36: 1100-1111 (IF: 5.144; citations: 1, Q1 in Genetics)

Gomes V, Pala M, Salas A, Álvarez-Iglesias V, Amorim A, Gómez-Carballa A, Carracedo A, Clarke DJ, Hill C, Mormina M, Shaw MA, Dunne DW, Pereira R, Pereira V, Prata MJ, Sánchez-Diz P, Rito T, Soares P, Gusmão L, Richards MB (2015). Mosaic maternal ancestry in the Great Lakes region of East Africa. Human Genetics 134(9): 1013-1027 (IF: 4.824; citations: 0, Q1 in Genetics)

Fernandes V, Triska P, Pereira JB, Alshamali F, Rito T, Machado A, Fajkošová Z, Cavadas B, ?erný V, Soares P, Richards MB, Pereira L (2015). Genetic stratigraphy of key demographic events in Arabia. Plos One 10: e0118625 (IF: 3.234, citations: 6, Q1 in Multidisciplinary)

Pereira L, Soares P, Triska P, Rito T, Li B, Radivojac P, Samuels DC (2014). Global human frequencies of predicted nuclear pathogenic variants conditioning mitochondrial diseases and the role played by protein hydrophobicity in the pathogenicity. Scientific Reports 4:7155 (IF: 5.578; citations: 2, Q1 in Multidisciplinary)

Martins RG, Nunes JB, Máximo V, Soares P, Peixoto J, Catarino T, Rito T, Soares P, Pereira L, Sobrinho-Simões M, Santos AP, Couto J, Henrique R, Matos-Loureiro J, Dias P, Torres I, Lima J (2013). A founder SDHB mutation in Portuguese paraganglioma patients. Endocrine-related cancer 20:L23-L26 (IF: 4.907; citations: 4, Q1 in Oncology)

Rito T, Richards MB, Fernandes V, Alshamali F, Cerny V, Pereira L, Soares P (2013). The First Modern Human Dispersals Across Africa. Plos One 8:e80031 (IF: 3.534; citations: 19, Q1 in Multidisciplinary)

Podgorna E, Soares P, Pereira L, Cerny V (2013). The Genetic Impact of the Lake Chad Basin Population in North Africa as Documented by Mitochondrial Diversity and Internal Variation of the L3e5 Haplogroup. Annals of Human Genetics 77:513-523 (IF: 1.926; citations: 3, Q3 in Genetics)

Costa MD, Pereira JB, Pala M, Fernandes V, Olivieri A, Achilli A, Perego UA, Rychkov S, Naumova O, Hatina J, Woodward SR, Eng S, Carr M, Macaulay V, Soares P, Pereira L, Richards MB (2013). A substantial prehistoric European ancestry amongst Ashkenazi maternal lineages. Nature Communications 4:2543 (IF: 10.742; citations: 16, Q1 in Multidisciplinary)

Mellars P, Gori KC, Carr M, Soares PA, Richards MB (2013). Genetic and archaeological perspectives on the initial modern human colonization of southern Asia. Proceedings of the National Academy of Sciences USA 110:10699-10704 (IF: 9.809; citations: 51, Q1 in Multidisciplinary)

Soares P, Abrantes D, Rito T, Thomson N, Radivojac P, Li B, Macaulay V, Samuels DC, Pereira L. (2013). Evaluating purifying selection in the mitochondrial DNA of various mammalian species. Plos One 8: e58993. (IF: 3.534; citations: 15, Q1 in Multidisciplinary)

Al-Abri A, Podgorná E, Rose JI, Pereira L, Mulligan CJ, Silva NM, Bayoumi R, Soares P, ?erný V. (2012). Pleistocene-Holocene boundary in Southern Arabia from the perspective of human mtDNA variation. American Journal of Physical Anthropology 149:291-8 (IF: 2.481, citations: 16, Q1 in Anthropology)

Pala M, Olivieri A, Achilli A, Accetturo M, Metspalu E, Reidla M, Tamm E, Karmin M, Reisberg T, Kashani BH, Perego UA, Carossa V, Gandini F, Pereira JB, Soares P, Angerhofer N, Rychov S, Al-Zahery N, Carelli V, Sanati MH, Houshmand M, Hatina J, Macaulay V, Pereira L, Woodward SR, Davies W, Gamble C, Baird D, Semino O, Villems R, Torroni A, Richards MB. (2012). Mitochondrial DNA signals of Late Glacial re-colonisation of Europe from Near Eastern refugia. American Journal of Human Genetics 90: 915-924 (IF: 11.202, citations: 54, Q1 in Genetics)

Soares P, Alshamali F, Pereira JB, Fernandes V, Silva NM, Afonso C, Costa MD, Musilová E, Macaulay V, Richards MB, Cerny V, Pereira L. (2012). The Expansion of mtDNA Haplogroup L3 within and out of Africa. Molecular Biology and Evolution 29: 915-927 (IF: 10.353; citations: 58, Q1 in Genetics)

Fernandes V, Alshamali F, Alves M, Costa MD, Pereira JB, Silva NM, Cherni L, Harich N, Cerny V, Soares P, Richards MB, Pereira L. (2012). The Arabian Cradle: Mitochondrial Relicts of the First Steps along the Southern Route out of Africa. American Journal of Human Genetics 90: 347-355 (IF: 11.202; citations: 44, Q1 in Genetics)

Pereira L, Soares P, Máximo V, Samuels DC. (2012). 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 (IF: 3.333; citations: 26, Q1 in Oncology)

Achilli A, Olivieri A, Soares P, Lancioni H, Kashani BH, Perego UA, Nergadze SG, Carossa V, Santagostino M, Capomaccio S, Felicetti M, Al-Achkar W, Penedo MCT, Verini-Supplizi A, Houshmand M, Woodward SR, Semino O, Silvestrelli M, Giulotto E, Pereira L, Bandelt H-J, Torroni A. (2012). Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication. Proceedings of the National Academy of Sciences USA 109: 2449-2454 (IF: 9.737; citations: 44, Q1 in Multidisciplinary)

Cerny V, Pereira L, Musilová E, Kujanová M, Vasíková A, Blasi P, Garofalo L, Soares P, Diallo I, Brdicka R, Novelletto A. (2011). Genetic structure of pastoral and farmer populations in the African Sahel. Molecular Biology and Evolution 28: 2491-2500 (IF: 5.51; citations: 14, Q1 in Genetics)

Musilová E, Fernandes, V, Silva, NM, Soares P, Alshamali, F, Harich, N, Cherni, L, Gaaied, ABAE, Al-Meeri, A, Pereira, L, Cerný, V. (2011). Population history of the Red Sea - genetic exchanges between the Arabian Peninsula and East Africa signaled in the mitochondrial DNA HV1 haplogroup. American Journal of Physical Anthropology 145: 592-598 (IF: 2.824; citations: 11, Q1 in Anthropology)

Pereira L, Soares P, Radivojac P, Li B, Samuels DC. (2011). 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 (IF: 10.603; citations: 34, Q1 in Genetics)

Soares P, Rito T, Trejaut J, Mormina M, Hill C, Tinkler-Hundal E, Braid M, Clarke DJ, Loo JH, Thomson N, Denham T, Donohue M, Macaulay V, Lin M, Oppenheimer S, Richards MB. (2011). Ancient Voyaging and Polynesian Origins. American Journal of Human Genetics 88: 239-247 (IF: 10.603; citations: 73, Q1 in Genetics)

Chaubey G, Metspalu M, Choi Y, Mägi R, Romero IG, Soares P, Oven M, Behar DM, Rootsi S, Hudjashov G, Mallick CB, Karmin M, Nelis M, Parik J, Reddy AG, Metspalu E, Driem G, Xue Y, Tyler-Smith C, Thangaraj K, Singh L, Remm M, Richards MB, Lahr MM, Kayser M, Villems R, Kivisild T. (2011). Population Genetic Structure in Indian Austroasiatic speakers: The Role of Landscape Barriers and Sex-specific Admixture. Molecular Biology and Evolution 28: 1013-1024 (IF: 5.51; citations: 40, Q1 in Genetics)

Pereira L, Silva NM, Franco-Duarte R, Fernandes V, Pereira JB, Costa MD, Martins H, Soares P, Behar DM, Richards MB, Macaulay V. (2010). Population expansion in the North African Late Pleistocene signalled by mitochondrial DNA haplogroup U6. BMC Evolutionary Biology 10: 390 (IF: 3.702; citations: 31, Q1 in Ecology, Evolution, Behavior and Systematics)

Soares P, Achilli A, Semino O, Davies W, Macaulay V, Bandelt HJ, Torroni A, Richards MB. (2010). The Archaeogenetics of Europe. Current Biology 20: R174-R183 (IF: 10.025; citations: 135, Q1 in Biochemistry, Genetics and Molecular Biology)

Soares P, Ermini L, Mormina M, Rito T, Röhl A, Salas A, Oppenheimer S, Macaulay V, Richards M. (2009). Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock. American Journal of Human Genetics 84: 740-759 (IF: 12.303; citations: 322, Q1 in Genetics)

Dhandapany PS, Sadayappan S, Xue Y, Powell GT, Nallari P, Rai TS, Khullar M, Soares P, Bahl A, Tharkan JM, Vaideeswar P, Rathinavel A, Rani DS, Narasimhan C, Ayapati DR, Qasim A, Mehdi S, Oppenheimer S, Richards M, Singh L,, Tyler-Smith C, Thangaraj K. (2009). A common MYBPC3 (cardiac myosin binding protein C) variant associated with cardiomyopathies in South Asia. Nature Genetics 41:187-191 (IF: 34.284; citations: 124, Q1 in Genetics)

Pereira F, Carneiro J, Soares P, Maciel S, Nejmeddine F, Lenstra J.A, Gusmão L, Amorim A. (2008). A multiplex primer extension assay for the rapid identification of paternal lineages in domestic goat (Capra hircus): Laying the foundations for a detailed caprine Y chromosome phylogeny. Molecular Phylogenetics and Evolution 49: 663-668 (IF: 3.871; citations: 2; Q1 in Genetics)

Pereira F, Soares P, Carneiro J, Pereira L, Richards MB, Samuels DC, Amorim A. (2008). Evidence for variable selective pressures at a large secondary structure of the human mitochondrial DNA control region. Molecular Biology and Evolution 25: 2759-2770 (IF: 7.28; citations: 21, Q1 in Genetics)

Ermini L, Olivieri C, Rizzi E, Corti G, Bonnal R, Soares P, Luciani S, Marota I, De Bellis G, Richards MB, Rollo F. (2008). Complete Mitochondrial Genome Sequence of the Tyrolean Iceman. Current Biology 18: 1687-1693 (IF: 10.777; citations: 54, Q1 in Biochemistry, Genetics and Molecular Biology)

Soares P, Trejaut JA, Loo J.-H, Hill C, Mormina M, Lee C-L, Chen Y.-M, Hudjashov G, Forster P, Macaulay V, Bulbeck D, Oppenheimer S, Lin M, Richards MB. (2008). Climate change and post-glacial human dispersals in Southeast Asia. Molecular Biology and Evolution 25: 1209-1218 (IF: 7.28; citations: 90, Q1 in Genetics)

Hill C, Soares P, Mormina M, Macaulay V, Clarke D, Blumbach PB, Vizuete-Forster M, Forster P, Bulbeck D, Oppenheimer S, Richards M. (2007). A mitochondrial stratigraphy for Island Southeast Asia. American Journal of Human Genetics 80: 29–43 (IF: 11.092; citations: 138, Q1 in Genetics)

Hill C, Soares P, Mormina M, Macaulay V, Meehan W, Blackburn J, Clarke D, Raja JM, Ismail P, Bulbeck D, Oppenheimer S, Richards M. (2006). Phylogeography and ethnogenesis of aboriginal Southeast Asians.Molecular Biology and Evolution 23: 2480-2491 (IF: 6.726; citations: 83, Q1 in Genetics)

Azevedo L, Soares PA, Quental R, Vilarinho L, Teles EL, Martins E, Diogo L, Garcia P, Cenni B, Wermuth B, Amorim A. (2006). Mutational spectrum and linkage disequilibrium patterns at the ornithine transcarbamylase gene (OTC). Annals of Human Genetics 70: 797-801 (IF: 2.727; citations: 5, Q2 in Genetics)

Soares PA, Pereira F, Brion M, Alves C, Richards M, Carracedo A, Amorim A, Gusmao L. (2006). Relative Y-STR mutation rates estimated from the variance inside SNP defined lineages. Progress in Forensic Genetics 11: 82-84

Alves M, Alves J, Camacho R, Soares P, Pereira L. (2012). From networks to trees. Advances in Intelligent and Soft Computing 154: 129-136

800x600

Soares P, Rito T, Pereira L, Richards MB. (2016). A Genetic Perspective on African Prehistory. “Africa from MIS 6-2: Population Dynamics and Paleoenvironments”, edited by Sacha C. Jones and Brian A. Stewart. Springer Netherlands  p: 383-405

Richards MB, Chaubey G, Soares P, Pala M. (2015). Chapter 2: Archaeogenetics. “The Cambridge History of the World Volume 2: A World with Agriculture” edited by Graeme Barker and Candice Goucher. Cambridge University Press. p:26-54

 Pala M, Chaubey G, Soares P, Richards MB. (2014). The Archaeogenetics of European Ancestry. Encyclopedia of Life Science (ELS). John Wiley and Sons, Chichester

Ongoing

Co-supervisor of PhD student Petr Triska (sponsored by Marie Curie EUROTAST network), with Dr. Luísa Pereira (main supervisor) in Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Porto. PhD project: “The genetic legacy of the Transatlantic Slave Trade in Europe” (ongoing).

Co-supervisor of PhD student Andreia Brandão (sponsored by FCT), with Dr. Luísa Pereira (main supervisor) and Professor Martin Richards (University of Huddersfield) in Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Porto. PhD project: “História Genética e estrutura populacional do Sudeste Asiático” (ongoing).

 Co-supervisor of PhD student Marina Silva (sponsored by Leverhulme Trust), with Professor Martin Richards, Dr Maria Pala and Dr Ceiridwen Edwards (University of Huddersfield) in The School of Applied Sciences, University of Huddersfield (Huddersfield, United Kingdom) (ongoing).

Supervisor of Master Student Simão Rodrigues (Master in Molecular Genetics) in the Department of Biology of the University of Minho. Master project: “Settlement and flooding of the ancient Sundaland continent” (ongoing)

Supervisor of Master Student Raquel Silva (Master in Bioinformatics) in the Informatics Department of the University of Minho. Master project: “Estimating recombination frequency throughout the human genome using a phylogenetic-based method” (ongoing)

Co-supervisor of Master Student Joana Ferreira (Master in Bioinformatics) in the Informatics Department of the University of Minho with Dr. Luísa Pereira (main supervisor - i3S-IPATIMUP). Master project: “Genomic and transcriptomic analyses in cancers related with viral infection” (ongoing)

Finished

Supervisor of Master student Marina Soares Silva (MSc in Biodiversity, Genetics and Evolution), with Dr. Luísa Pereira (co-supervisor) in Faculdade de Ciências da Universidade do Porto (FCUP), Porto, Portugal. Msc project: “Phylogeography of mtDNA haplogroup L2” (Finished – December 2014).

Supervisor of Master Student Daniel Vieira (Master in Bioinformatics) in the Informatics Department of the University of Minho. Master project: “Testing the reliability of the estimated ancestral populations in human genome-wide data using different admixture algorithms” (Finished – December 2015)

Co-supervisor of Master Student Luís Oliveira (Master in Ecology) in the Biology Department of the University of Minho with Dr. Filipe Costa (Biology, University of Minho). Master project: “DNA barcodes de peixes marinhos da Europa: compilação de uma biblioteca de referência validada e investigação de padrões de divergência genética” (Finished – December 2015)