> PublicationsOur latest papers and research materials
Below is a list of our most recent publications, they involve genomic data processing and statistical population genomics.
2012 Next-generation sequencing approaches for genetic mapping of complex diseases. Casals F., Idaghdour Y., Hussin J. and Awadalla P J Neuroimmunol 2012 (in press)
A family-based probabilistic method for capturing de novo mutations from high-throughput short-read sequencing data. Cartwright R., Hussin J., Keebler J., Stone E., and Awadalla P Published in J Stat Appl Genet Mol Biol. 2012. Vol. 11 Iss. 2, Article 6.
2011 Age-dependent recombination rates in human pedigrees. Hussin J., Gendron R., Roy-Gagnon M-H., Andelfinger G. and Awadalla P. 2011. Published in PLoS Genet 2011 Sept; 7(9):e1002251.
Variation in genome-wide mutation rates within and between human families. Conrad DF, Keebler J, DePristo MA, Lindsay SJ, Zhang Y, Cassals F, Idaghdour Y, Torroja C, Garimella K, Zilversmit M, Rouleau GA, Daly M, Stone E, Hurles M, Awadalla P and the 1000 Genomes Project. Published in Nature Genetics 2011 Jun 12; 43(7):712-4
A Population Genetic Approach to Mapping Neurological Disorder Genes using Deep Resequencing. Myers RA., Casals F., Gauthier J., Keebler J., Boyko A., Bustamante C., Piton A. M., Spiegelman D., Henrion E., Zilversmit M., Hussin J., Idaghdour Y., Quinlan J., Yang Y., Lafreniere R., Griffing AR., Stone E. A., Rouleau G. A., and Awadalla P. Published in PLoS Genet. 2011;7(2):e1001318.
Mapping copy number variation by population-scale genome sequencing. Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Allan C, Abyzov A, Yoon SC, Ye K, Cheethman RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha L, Hormozdiari F, Lakoucheva LM, 1000 Genomes Project. Published in Nature. 2011 Feb 3; 470(7332):59-65.
Genetic adaptation of the antibacterial human innate immunity network. Casals F, Sikora M, Laayouni H, Montanucci L, Muntasell A, Lazarus R, Calafell F, Awadalla P, Netea MG, Bertranpetit J. Published in BMC Evol Biol. 2011 Jul11; 11:202.
Hongying J, Na Li, Gopalan Vivek, Sudhir Varma, Vijayaraj Nagarajan, Jian Li1,, Jianbing Mu, Zilversmit M., Hayton K, Henschen B, Yi Ming, Stephens R, McVean G, Awadalla P, Wellems TE., and Xin-zhuan Su. High chromosome recombination rates and hotspots in a Plasmodium falciparum genetic cross. Genome Biol. 2011 Apr 4; 12(4):R33
Branch OH, Sutton PL, Castro JC, Barnes C, Hussin J, Awadalla P, Guerra GH. Plasmodium Falciparum Genetic Diversity Maintained and Amplified Over Five Years of a Low Transmission Endemic in the Peruvian Amazon. Mol Biol Evol. 2011 Jul; 28(7):1973-86.
Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG, Yu F, Gibbs RA, 1000 Genomes Project, Bustamante CD. Demographic history and rare allele sharing among human populations. Proc Natl Acad Sci USA. 2011 Jul 19; 108(29):11983-8.
Laayouni H, Montanucci L, Sikora M, Melé M, Dall’Olio GM, Lorente-Galdos B, McGee KM, Graffelman J, Awadalla P, Bosch E, Comas D, Navarro A, Calafell F, Casals F, Bertranpetit J. Similarity in recombination rate estimates highly correlates with genetic differentiation in humans. PloS One. 2011 Mar 28; 6(3):e17913.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genomes Project Analysis Group. The variant call format and VCtools. Bioinformatics. 2011 Aug 1;27(15):2156-8
Cartwright, R., Hussin J., Keebler, J., Stone, EA., Awadalla, P. 2011. Statistical methods for detecting de novo mutations from next-generation sequencing data. Statistical Methods in Molecular Biology and Genetics (in press).
2010
Awadalla P., Gauthier J., Myers R., Casals F., Hamdan FF., Griffin A., Cote M., Henrion E., Spiegelman D., Tarabeux J., Piton A., Yang Y., Boyko A., Bustamante C., Xiong L., Rapoport J.L., Addington A.M., Lynn E., DeLisi J., Krebs M.-O., Joober R., Millet B., Fombonne E., Mottron L., Zilversmit M., Keebler J., H. Daoud, Marineau C., Roy-Gagnon M.-H., Dube M.-P., Lafrenière R.G., Drapeau P., Stone E.A., and Rouleau G.A. 2010. Direct Estimates of De novo Mutation Rates and Constraints in Autism and Schizophrenia. Amer. J Hum Genet. 87(3):316-24.
Mu J, Myers R, Jiang H, Liu S, Ricklefs S, Waisberg M, Chotivanich K, Wilairata P, Krudsood S, White N, Udomsangpetch R, Cui L, Ho M, Fengzheng O, Li H, Jiangping S, Li G, Wang X, Suon S, Sreng S, Socheat D, Sturdevant D, Porcella S, Fairhurst R, Wellems T, Awadalla P*, Xin‑zhuan S* (2010) Genome-wide positive selection, recombination hotspots, and loci associated with Plasmodium falciparum resistance to antimalarial drugs. Nat Genet. 2010 Mar; 42(3):268-71.*corresponding author.
Gauthier J, Champagne N, Lafrenière RG, Xiong L, Spiegelman D, Brustein E, Lapointe M, Peng H, Côté M, Noreau A, Hamdan FF, Addington AM, Rapoport JL, Delisi LE, Krebs MO, Joober R, Fathalli F, Mouaffak F, Haghighi AP, Néri C, Dubé MP, Samuels ME, Marineau C, Stone EA, Awadalla P, Barker PA, Carbonetto S, Drapeau P, Rouleau GA; the S2D Team. 2010. De novo mutations in the gene encoding the synaptic scaffolding protein SHANK3 in patients ascertained for schizophrenia. Proc Natl Acad Sci U S A. 2010 Apr 27; 107(17):7863-8.
Guernsey D.L., Jiang H., Hussin J., Arnold M., Bouyakdan K., Perry S., Babineau-Sturk T., Beis J., Dumas N., Evans S.C., Ferguson M., Matsuoka M., Macgillivray C., Nightingale M., Patry L., Rideout A.L. , Thomas A., Orr A., Hoffman I., Michaud J.L., Awadalla P., Meek D.C., Ludman M., Samuels M.E. Mutations in centrosomal protein CEP152 in primary microcephaly families linked to MCPH4. Am J Hum Genet. 2010 Jul 9;87(1):40-51.
Zilversmit MM, Volkman SK, Depristo MA, Wirth DF, Awadalla P, Hartl DL. 2010. Low-Complexity Regions in Plasmodium falciparum: Missing Links in the Evolution of an Extreme Genome. Mol Biol Evol. 2010 Sep; 27(9):2198-209.
1000 Genomes Consortium. 2010. A map of human genome variation from population scale sequencing. Nature Oct 28;467(7319):1061-73.
Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J; 1000 Genomes Project, Eichler EE. Diversity of human copy number variation and multicopy genes. Science. 2010 Oct 29; 330(6004):641-6.
S. Pattaradilokrat, R. Myers, J. Mu, P. Awadalla and X. Su. 2010. Plasmodium falciparum genetic diversity and the development of Single Nucleotide Polymorphism map. For Comparative Genomics of Plasmodium Parasites. Editors J. Carlton, K. Deitsch. Horizon Scientific Press.
2007-2009
Mu J., Awadalla P. *, Duan J., McGee K., Keebler J., Joy D., McVean G.A.T., and Su X. (2007) Genome‑wide variation and identification of vaccine targets in the Plasmodium falciparum genome. *corresponding author. Nature Genetics 39(1):126-130.
Bockhorst J, Lu F, Janes JH, Keebler J, Gamain B, Awadalla P., Su XZ., Samudrala R, Jojic N, Smith JD. (2007) Structural polymorphism and diversifying selection on the pregnancy malaria vaccine candidate VAR2CSA. Molecular Biochemistry and Parasitology.148:169
Prugnolle, F. McGee KM., Keebler J., and Awadalla P. * (2008) Selection shapes malaria genomes and drives divergence between pathogens infecting hominids versus rodents. BMC Evol Biol. 2008 Jul 30; 8:223.
Psychiatric GWAS Consortium Coordinating Committee, Cichon S, Craddock N, Daly M, Faraone SV, Gejman PV, Kelsoe J, Lehner T, Levinson DF, Moran A, Sklar P, Sullivan PF, and other 164 collaborators. (2009) Genomewide association studies: history, rationale, and prospects for psychiatric disorders. Am J Psychiatry. 2009 May; 166(5):540-56.
P. Awadalla, K. McGee and X. Su. 2007. The evolutionary importance of recombination in pathogens. for Encyclopedia of Infectious Disease. M. Tibareync editor. Wiley.
2004-2006
Barbash D.A. *, Awadalla P. *, Tarone A. (2004) Functional divergence casued by ancient positive selection of an X-linked Drosophila hybrid incompatibility locus. PLoS, Biology. 2(6):839-48. *joint first authors.
Haydon D., Bastos A., Awadalla P. (2004) Low linkage disequilibrium indicative of recombination in foot and mouth disease virus gene sequence alignments. Journal of General Virology 85:1095-1100.
Carbone M.A., Jordan K. W., Lyman R. F., Harbison S. T., Leips J.W., DeLuca M., Awadalla P. and Mackay T.F.C. Molecular and phenotypic evidence of diversifying selection for longevity in Drosophila. Current Biology, 16:912.
Mu J., Awadalla P.*, Duan J., McGee K., Joy D., McVean G.A.T., and Su X. *. (2005) Chromosome-wide population structure and recombination rate variation in Plasmodium falciparum. PLoS, Biology 3:335. *corresponding author.
Trimnell, Kraemer S., Mukherjee S., Phippard D., Janes J., Flamoe E., Su XZ., Awadalla P. *, Smith J. D. * (2006) Global genetic diversity of UpsA var genes and the placental malaria vaccine candidate var2csa: Implications for severe malaria. Molecular Biochemistry and Parasitology.148:169. *corresponding authors.
Jackson M., Watt A., Gautier P, Gilchrist D, Driehaus J, Graham GJ, Keebler J, Prugnolle F, Awadalla P., and Forrester L. (2006) Functional Divergence of the rHox Gene Cluster in Mice is driven by Positive Selection. BMC Genomics, 7:212.
1998-2003
Awadalla P. (2003) The evolutionary genomics of recombination in pathogens. Nature Reviews Genetics 4:50-60
Charlesworth D., Mable B., Bartolome C., Schierup M., Awadalla P. (2003) Polymorphism and Divergence at members of the Self-Incompatibility Gene Family in Arabidopsis lyrata. Genetics 164:1519-1535.
McVean G., Awadalla P. and Fearnhead P. (2002) A Coalescent-based Method for Detecting and Estimating Recombination from Gene Sequences. Genetics 160(3); 1231-41.
Abdel-Muhsin, Mackinnon M., Awadalla P., Suleiman S., Ahmed S., Walliker D., Babiker H. A. (2003) Local differentiation and selection in Plasmodium falciparum drug resistance genes in Sudan. Parasitology, 126:391-400 Awadalla P., Eyre-Walker A., and Maynard Smith J. (1999) Linkage Disequilibrium and Recombination in Hominid Mitochondrial DNA. Science 286:2524-2525.
Awadalla P. and Charlesworth D. (1999) Recombination and Selection at Brassica Self-Incompatibility Loci. Genetics 152: 413-425.
Awadalla P., Eyre-Walker A., and Maynard Smith J. (2000) Questioning evidence for recombination in human mitochondria. Science Technical comment 288:1931a-e.
Charlesworth D., Awadalla P., Mable B., and Schierup M. (2000) Population level studies of multiallelic self-incompatibility loci, with particular reference to Brassicaceae. Annals of Botany (Special Issue) 85(A):227-240.
Awadalla P., Walliker D., Babiker H., Mackinnon M. (2001) The Question of Plasmodium falciparum Population Structure. Trends in Parasitology 17(8):351-353.
Eyre-Walker A and Awadalla P. (2001) Do Human Mitochondria Recombine? Journal of Molecular Evolution 53(4-5):430-5.
Schierup M., Mable B., Awadalla P. and Charlesworth D. (2001) Identification and characterization of a polymorphic receptor kinase gene linked to the self-incompatibility locus of Arabidopsis lyrata. Genetics 158(1):387-99.
P. Awadalla. 2003. Mitochondrial Inheritance. P.42 for Human Evolutionary Genetics, M. Jobling, C. Tyler-Smith, M. Hurles editors. Taylor and Francis |
