1. Dhandapany PS, Sadayappan S, Xue Y, Powell GT, Rani DS, Nallari P, Rai TS, Khullar M, Soares P, Bahl A, Tharkan JM, Vaideeswar P, Rathinavel A, Narasimhan C, Ayapati DR, Ayub Q, Mehdi SQ, Oppenheimer S, Richards MB, Price AL, Patterson N, Reich D, Singh L, Tyler-Smith C, Thangaraj K

A common MYBPC3 (cardiac myosin binding protein C) variant associated with cardiomyopathies in South Asia. Nature genetics 41: 187-91, 2009.  [Article] 

 doi: 10.1038/ng.309 PMID: 19151713.

 

2. Soares P, Ermini L, Thomson N, Mormina M, Rito T, Röhl A, Salas A, Oppenheimer S, Macaulay V, Richards MB

Correcting for purifying selection: an improved human mitochondrial molecular clock. American journal of human genetics 84: 740-59, 2009.  [Review] 

 doi: 10.1016/j.ajhg.2009.05.001 PMID: 19500773.

 

3. Pala M, Olivieri A, Achilli A, Accetturo M, Metspalu E, Reidla M, Tamm E, Karmin M, Reisberg T, Hooshiar Kashani B, Perego UA, Carossa V, Gandini F, Pereira JB, Soares P, Angerhofer N, Rychkov 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

Mitochondrial DNA signals of late glacial recolonization of europe from near eastern refugia. American journal of human genetics 90: 915-24, 2012.  [Article] 

 doi: 10.1016/j.ajhg.2012.04.003 PMID: 22560092.

 

4. 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.

 

5. Hill C, Soares P, Mormina M, Macaulay V, Clarke D, Blumbach PB, Vizuete-Forster M, Forster P, Bulbeck D, Oppenheimer S, Richards M

A mitochondrial stratigraphy for island southeast Asia. American journal of human genetics 80: 29-43, 2007.  [Article] 

 doi: 10.1086/510412 PMID: 17160892.

 

6. Ermini L, Olivieri C, Rizzi E, Corti G, Bonnal R, Soares P, Luciani S, Marota I, De Bellis G, Richards MB, Rollo F

Complete mitochondrial genome sequence of the Tyrolean Iceman. Current biology : CB 18: 1687-93, 2008.  [Article] 

 doi: 10.1016/j.cub.2008.09.028 PMID: 18976917.

 

7. Costa MD, Pereira JB, Pala M, Fernandes V, Olivieri A, Achilli A, Perego UA, Rychkov S, Naumova O, Hatina J, Woodward SR, Eng KK, Macaulay V, Carr M, Soares P, Pereira L, Richards MB

A substantial prehistoric European ancestry amongst Ashkenazi maternal lineages. Nature communications 4: 2543, 2013.  [Article] 

 doi: 10.1038/ncomms3543 PMID: 24104924.

 

8. 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

Ancient voyaging and polynesian origins. American journal of human genetics 88: 239-47, 2011.  [Article] 

 doi: 10.1016/j.ajhg.2011.01.009 PMID: 21295281.

 

9. 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.

 

10. 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.

 

11. Soares P, Achilli A, Semino O, Davies W, Macaulay V, Bandelt HJ, Torroni A, Richards MB

The archaeogenetics of Europe. Current biology : CB 20: R174-83, 2010.  [Review] 

 doi: 10.1016/j.cub.2009.11.054 PMID: 20178764.

 

12. 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 MC, Verini-Supplizi A, Houshmand M, Woodward SR, Semino O, Silvestrelli M, Giulotto E, Pereira L, Bandelt HJ, Torroni A

Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication. Proceedings of the National Academy of Sciences of the United States of America 109: 2449-54, 2012.  [Article] 

 doi: 10.1073/pnas.1111637109 PMID: 22308342.

 

13. Soares P, Trejaut JA, Loo JH, Hill C, Mormina M, Lee CL, Chen YM, Hudjashov G, Forster P, Macaulay V, Bulbeck D, Oppenheimer S, Lin M, Richards MB

Climate change and postglacial human dispersals in southeast Asia. Molecular biology and evolution 25: 1209-18, 2008.  [Article] 

 doi: 10.1093/molbev/msn068 PMID: 18359946.

 

14. Pereira F, Soares P, Carneiro J, Pereira L, Richards MB, Samuels DC, Amorim A

Evidence for variable selective pressures at a large secondary structure of the human mitochondrial DNA control region. Molecular biology and evolution 25: 2759-70, 2008.  [Article] 

 doi: 10.1093/molbev/msn225 PMID: 18845547.

 

15. Hill C, Soares P, Mormina M, Macaulay V, Meehan W, Blackburn J, Clarke D, Raja JM, Ismail P, Bulbeck D, Oppenheimer S, Richards M

Phylogeography and ethnogenesis of aboriginal Southeast Asians. Molecular biology and evolution 23: 2480-91, 2006.  [Article] 

 doi: 10.1093/molbev/msl124 PMID: 16982817.

 

16. 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.

 

17. Chaubey G, Metspalu M, Choi Y, Mägi R, Romero IG, Soares P, van Oven M, Behar DM, Rootsi S, Hudjashov G, Mallick CB, Karmin M, Nelis M, Parik J, Reddy AG, Metspalu E, van Driem G, Xue Y, Tyler-Smith C, Thangaraj K, Singh L, Remm M, Richards MB, Lahr MM, Kayser M, Villems R, Kivisild T

Population genetic structure in Indian Austroasiatic speakers: the role of landscape barriers and sex-specific admixture. Molecular biology and evolution 28: 1013-24, 2011.  [Article] 

 doi: 10.1093/molbev/msq288 PMID: 20978040.

 

18. Cerny V, Pereira L, Musilová E, Kujanová M, Vasíková A, Blasi P, Garofalo L, Soares P, Diallo I, Brdicka R, Novelletto A

Genetic structure of pastoral and farmer populations in the african sahel. Molecular biology and evolution 28: 2491-500, 2011.  [Article] 

 doi: 10.1093/molbev/msr067 PMID: 21436121.

 

19. Silva M, Alshamali F, Silva P, Carrilho C, Mandlate F, Jesus Trovoada M, Cerný V, Pereira L, Soares P

60,000 years of interactions between Central and Eastern Africa documented by major African mitochondrial haplogroup L2. Scientific reports 5: 12526, 2015.  [Article] 

 doi: 10.1038/srep12526 PMID: 26211407.

 

20. 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.

 

21. 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

A founder SDHB mutation in Portuguese paraganglioma patients. Endocrine-related cancer 20: L23-6, 2013.  [Letter] 

 doi: 10.1530/ERC-12-0399 PMID: 24092654.

 

22. Pereira JB, Costa MD, Vieira D, Pala M, Bamford L, Harich N, Cherni L, Alshamali F, Hatina J, Rychkov S, Stefanescu G, King T, Torroni A, Soares P, Pereira L, Richards MB

Reconciling evidence from ancient and contemporary genomes: a major source for the European Neolithic within Mediterranean Europe. Proceedings. Biological sciences 284: ., 2017.  [Article] 

 doi: 10.1098/rspb.2016.1976 PMID: 28330913.

 

23. Soares PA, Trejaut JA, Rito T, Cavadas B, Hill C, Eng KK, Mormina M, Brandão A, Fraser RM, Wang TY, Loo JH, Snell C, Ko TM, Amorim A, Pala M, Macaulay V, Bulbeck D, Wilson JF, Gusmão L, Pereira L, Oppenheimer S, Lin M, Richards MB

Resolving the ancestry of Austronesian-speaking populations. Human genetics 135: 309-26, 2016.  [Article] 

 doi: 10.1007/s00439-015-1620-z PMID: 26781090.

 

24. Brandão A, Eng KK, Rito T, Cavadas B, Bulbeck D, Gandini F, Pala M, Mormina M, Hudson B, White J, Ko TM, Saidin M, Zafarina Z, Oppenheimer S, Richards MB, Pereira L, Soares P

Quantifying the legacy of the Chinese Neolithic on the maternal genetic heritage of Taiwan and Island Southeast Asia. Human genetics 135: 363-76, 2016.  [Article] 

 doi: 10.1007/s00439-016-1640-3 PMID: 26875094.

 

25. Sahakyan H, Hooshiar Kashani B, Tamang R, Kushniarevich A, Francis A, Costa MD, Pathak AK, Khachatryan Z, Sharma I, van Oven M, Parik J, Hovhannisyan H, Metspalu E, Pennarun E, Karmin M, Tamm E, Tambets K, Bahmanimehr A, Reisberg T, Reidla M, Achilli A, Olivieri A, Gandini F, Perego UA, Al-Zahery N, Houshmand M, Sanati MH, Soares P, Rai E, Šarac J, Šaric T, Sharma V, Pereira L, Fernandes V, Cerný V, Farjadian S, Singh DP, Azakli H, Üstek D, Ekomasova Trofimova N, Kutuev I, Litvinov S, Bermisheva M, Khusnutdinova EK, Rai N, Singh M, Singh VK, Reddy AG, Tolk HV, Cvjetan S, Lauc LB, Rudan P, Michalodimitrakis EN, Anagnou NP, Pappa KI, Golubenko MV, Orekhov V, Borinskaya SA, Kaldma K, Schauer MA, Simionescu M, Gusar V, Grechanina E, Govindaraj P, Voevoda M, Damba L, Sharma S, Singh L, Semino O, Behar DM, Yepiskoposyan L, Richards MB, Metspalu M, Kivisild T, Thangaraj K, Endicott P, Chaubey G, Torroni A, Villems R

Origin and spread of human mitochondrial DNA haplogroup U7. Scientific reports 7: 46044, 2017.  [Article] 

 doi: 10.1038/srep46044 PMID: 28387361.

 

26. 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.

 

27. Pereira F, Carneiro J, Soares P, Maciel S, Nejmeddine F, Lenstra JA, Gusmão L, Amorim A

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: 663-8, 2008.  [Article] 

 doi: 10.1016/j.ympev.2008.08.026 PMID: 18809503.

 

28. Brucato N, Fernandes V, Kusuma P, Cerný V, Mulligan CJ, Soares P, Rito T, Besse C, Boland A, Deleuze JF, Cox MP, Sudoyo H, Stoneking M, Pereira L, Ricaut FX

Evidence of Austronesian Genetic Lineages in East Africa and South Arabia: Complex Dispersal from Madagascar and Southeast Asia. Genome biology and evolution 11: 748-758, 2019.  [Article] 

 doi: 10.1093/gbe/evz028 PMID: 30715341.

 

29. 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.

 

30. Rito T, Richards MB, Fernandes V, Alshamali F, Cerny V, Pereira L, Soares P

The First Modern Human Dispersals across Africa. PloS one 8: e80031, 2013.  [Article] 

 doi: 10.1371/journal.pone.0080031 PMID: 24236171.

 

31. 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.

 

32. 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.

 

33. 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.

 

34. Hernández CL, Soares P, Dugoujon JM, Novelletto A, Rodríguez JN, Rito T, Oliveira M, Melhaoui M, Baali A, Pereira L, Calderón R

Early Holocenic and Historic mtDNA African Signatures in the Iberian Peninsula: The Andalusian Region as a Paradigm. PloS one 10: e0139784, 2015.  [Article] 

 doi: 10.1371/journal.pone.0139784 PMID: 26509580.

 

35. Silva M, Oliveira M, Vieira D, Brandão A, Rito T, Pereira JB, Fraser RM, Hudson B, Gandini F, Edwards C, Pala M, Koch J, Wilson JF, Pereira L, Richards MB, Soares P

A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals. BMC evolutionary biology 17: 88, 2017.  [Article] 

 doi: 10.1186/s12862-017-0936-9 PMID: 28335724.

 

36. Macaulay V, Soares P, Richards MB

Rectifying long-standing misconceptions about the ¿ statistic for molecular dating. PloS one 14: e0212311, 2019.  [Article] 

 doi: 10.1371/journal.pone.0212311 PMID: 30779770.

 

37. Azevedo L, Soares PA, Quental R, Vilarinho L, Teles EL, Martins E, Diogo L, Garcia P, Cenni B, Wermuth B, Amorim A

Mutational spectrum and linkage disequilibrium patterns at the ornithine transcarbamylase gene (OTC). Annals of human genetics 70: 797-801, 2006.  [Article] 

 doi: 10.1111/j.1469-1809.2006.00283.x PMID: 17044854.

 

38. Musilová E, Fernandes V, Silva NM, Soares P, Alshamali F, Harich N, Cherni L, Gaaied AB, Al-Meeri A, Pereira L, Cerný V

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: 592-8, 2011.  [Article] 

 doi: 10.1002/ajpa.21522 PMID: 21660931.

 

39. Al-Abri A, Podgorná E, Rose JI, Pereira L, Mulligan CJ, Silva NM, Bayoumi R, Soares P, Cerný V

Pleistocene-Holocene boundary in Southern Arabia from the perspective of human mtDNA variation. American journal of physical anthropology 149: 291-8, 2012.  [Article] 

 doi: 10.1002/ajpa.22131 PMID: 22927010.

 

40. Podgorna E, Soares P, Pereira L, Cerny V

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  513-523, 2013.  [Article] 

 doi: 10.1111/ahg.12040.

 

41. Soares PA, Pereira F, Brion M, Alves C, Richards M, Carracedo A, Amorim A, Gusmão L

Relative Y-STR mutation rates estimated from the variance inside SNP defined lineages International Congress Series 1288: 82-84, 2006.  [] 

 doi: 10.1016/j.ics.2005.09.173.