Philip Awadalla Laboratory
Philip Awadalla - Malaria

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Our latest papers and research materials

Publications - Philip Awadalla Laboratory

 

Below is a list of our most recent publications, they involve genomic data processing and statistical population genomics.

 

2016
Relaxed selection during a recent human expansion.
Stephan Peischl, Isabelle Dupanloup, Adrien Foucal, Michèle Jomphe, Vanessa Bruat, Jean-Cristophe Grenier, Alexandre Gouy, Elias Gbeha, Lars Bosshard, Elodie Hip-Ki, Mawussé Agbessi, Alan Hodgkinson, Hélène Vézina, Philip Awadalla, Laurent Excoffier
bioRxiv.
2016.
bioRxiv

Depression and risk of type 2 diabetes: the potential role of metabolic factors.
N Schmitz, SS Deschênes, RJ Burns, KJ Smith, A Lesage, I Strychar, R Rabasa-Lhoret, C Freitas, Awadalla P, Graham E, JL. Wang
Molecular Psychiatry.
2016.
doi: 10.1038/mp.2016.7

Family Based Whole Exome Sequencing Reveals the Multifaceted Role of Notch Signaling in Congenital Heart Disease.
Christoph Preuss , Melanie Capredon , Florian Wünnemann , Philippe Chetaille, Andrea Prince, Beatrice Godard, Severine Leclerc, Nara Sobreira, Hua Ling, Philip Awadalla, Maryse Thibeault, Paul Khairy, MIBAVA Leducq consortium, Mark E. Samuels, Gregor Andelfinger
PLOS Genetics.
2016.
doi: 10.1371/journal.pgen.1006335

Rationale, design, and methods for Canadian alliance for healthy hearts and minds cohort study (CAHHM)–a Pan Canadian cohort study.
Sonia S Anand, Jack V Tu, Philip Awadalla, Sandra Black, Catherine Boileau, David Busseuil, Dipika Desai, Jean-Pierre Després, Russell J de Souza, Trevor Dummer, Sébastien Jacquemont, Bartha Knoppers, Eric Larose, Scott A Lear, Francois Marcotte, Alan R Moody, Louise Parker, Paul Poirier, Paula J Robson, Eric E Smith, John J Spinelli, Jean-Claude Tardif, Koon K Teo, Natasa Tusevljak, Matthias G Friedrich.
BMC Public Health.
2016.
doi: 10.1186/s12889-016-3310-8

A haplotype-based normalization technique for the analysis and detection of allele specific expression.
A Hodgkinson, JC Grenier, E Gbeha, P Awadalla
BMC bioinformatics.
2016.
doi: 10.1186/s12859-016-1238-8

Impact of the X chromosome and sex on regulatory variation
Kimberly R Kukurba, Princy Parsana, Brunilda Balliu, Kevin S Smith, Zachary Zappala, David A Knowles, Marie-Julie Favé, Joe R Davis, Xin Li, Xiaowei Zhu, James B Potash, Myrna M Weissman, Jianxin Shi, Anshul Kundaje, Douglas F Levinson, Philip Awadalla, Sara Mostafavi, Alexis Battle, Stephen B Montgomery
Genome Research.
2016.
doi: 10.1101/gr.197897.115

Gain-of-function missense variant in SLC12A2, encoding the bumetanide-sensitive NKCC1 cotransporter, identified in human schizophrenia.
Nancy D Merner, Adriana Mercado, Arjun R Khanna, Alan Hodgkinson, Vanessa Bruat, Philip Awadalla, Gerardo Gamba, Guy A Rouleau, Kristopher T Kahle
Journal of psychiatric research.
2016.
doi: 10.1016/j.jpsychires.2016.02.016

Comparative Analysis of Iron Homeostasis in Sub-Saharan African Children with Sickle Cell Disease and Their Unaffected Siblings.
Gomez S, Diawara A, Gbeha E, Awadalla P, Sanni A, Idaghdour Y, Rahimy MC
Frontiers in Pediatrics.
2016.
doi: 10.3389/fped.2016.00008

Aortic dilation associated with a de novo mutation in the SOX18 gene. Expanding the clinical spectrum of Hypotrichosis-Lymphedema-Telangiectasia Syndrom
Florian Wünnemann, Victor Kokta, Séverine Leclerc, Maryse Thibeault, Catherine McCuaig, Afshin Hatami, Chantal Stheneur, Jean-Christophe Grenier, Philip Awadalla, Grant A. Mitchell, Gregor Andelfinger, Christoph Preuss
Canadian Journal of Cardiology.
2016.
doi: 10.1016/j.cjca.2015.04.004

Replication study of MATR3 in familial and sporadic amyotrophic lateral sclerosis.
Leblond CS, Gan-Or Z, Spiegelman D, Laurent SB, Szuto A, Hodgkinson A, Dionne-Laporte A, Provencher P, de Carvalho M, Orrù S, Brunet D, Bouchard JP, Awadalla P, Dupré N, Dion PA, Rouleau GA
Neurobiol Aging.
2016.
doi: 10.1016/j.neurobiolaging.2015.09.013

ARMC5 mutations in a large French-Canadian family with cortisol-secreting β-adrenergic/vasopressin responsive bilateral macronodular adrenal hyperplasia.
Isabelle Bourdeau, Sylvie Oble, Fabien Magne, Isabelle Lévesque, Katia Caceres, Serge Nolet, Philip Awadalla, Johanne Tremblay, Pavel Hamet, Maria Candida Barisson Villares Fragoso, André Lacroix.
Eur. J. Endocrinol.
2016.
doi: 10.1530/EJE-15-0642

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences.
GD Poznik, Y Xue, FL Mendez, 1000 Genomes Project Consortium, CD Bustamante, Tyler-Smith C
Nature Genetics.
2016.
doi: 10.1038/ng.3559

Clinical, Genetic, and Urinary Factors Associated with Uromodulin Excretion.
Stéphan Troyanov, Catherine Delmas-Frenette, Guillaume Bollée, Sonia Youhanna, Vanessa Bruat, Philip Awadalla, Olivier Devuyst, François Madore.
Clin J Am Soc Nephrol.
2016.
doi: 10.2215/CJN.04770415

2015
DNA Methylation and Its Relation to Immunological Phenotypes in Peripheral Blood: A Study of Anti-CCP Antibody Positivity from a Population-Based Pool.
Sasha Bernatsky, Xiaojian Shao, Marie-Michelle Simon, Marvin J Fritzler, Philip Awadalla, Marie Hudson, Ines Colmegna, Tony Kwan, Tomi Pastinen
Arthritis & Rheumatology.
2015.

A global reference for human genetic variation.
1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR
Nature.
2015.
doi: 10.1038/nature15393

Recombination affects accumulation of damaging and disease-associated mutations in human populations.
J Hussin; A Hodgkinson; Y Idaghdour; J Grenier; J Goulet; E Gbeha; E Hip-Ki; P Awadalla
Nature Genetics.
2015.
doi: 10.1101/006064, Download Paper

An integrated map of structural variation in 2,504 human genomes.
PH Sudmant, T Rausch, EJ Gardner, RE Handsaker, A Abyzov, J Huddleston, Y Zhang, K Ye, G Jun, M Hsi-Yang Fritz, MK Konkel, A Malhotra, AM Stütz, X Shi, F Paolo Casale, J Chen, F Hormozdiari, G Dayama, K Chen, M Malig, MJ Chaisson, K Walter, S Meiers, S Kashin, E Garrison, A Auton, HY Lam, X Jasmine Mu, C Alkan, D Antaki, T Bae, E Cerveira, P Chines, Z Chong, L Clarke, E Dal, L Ding, S Emery, X Fan, M Gujral, F Kahveci, JM Kidd, Y Kong, EW Lameijer, S McCarthy, P Flicek, RA Gibbs, G Marth, CE Mason, A Menelaou, DM Muzny, BJ Nelson, A Noor, NF Parrish, M Pendleton, A Quitadamo, B Raeder, EE Schadt, M Romanovitch, A Schlattl, R Sebra, AA Shabalin, A Untergasser, JA Walker, M Wang, F Yu, C Zhang, J Zhang, X Zheng-Bradley, W Zhou, T Zichner, J Sebat, MA Batzer, SA McCarroll, 1000 Genomes Project Consortium, RE Mills, MB Gerstein, A Bashir, O Stegle, SE Devine, C Lee, EE Eichler, JO Korbel./div>
Nature.
2015.
doi: 10.1038/nature15394

Industrial Pollution Emissions are associated with Anti-CCP Antibodies.
Sasha Bernatsky, Marvin Fritzler, Marie Hudson, Ines Colmegna, Paul Fortin, Allan Brand, Louis Bessette, Philip Awadalla, Audrey Smargiassi
JOURNAL OF RHEUMATOLOGY.
2015.

A computational framework for prioritizing noncoding regulatory variants in cancer.
Yao Fu, Zhu Liu, Shaoke Lou, Vincenza Colonna, Jason Bedford, Xinmeng Mu, Kevin Y Yip, Hyun Min Kang, Tuuli Lappalainen, Andrea Sboner, Haiyuan Yu, Mark Rubin, Chris Tyler-Smith, Ekta Khurana, Mark Gerstein, 1000 Genomes Project Consortium
Cancer Research
2015.
doi: 10.1158/1538-7445.AM2015-4854

Association of age-dependent height and bone mineral density decline with increased arterial stiffness and rate of fractures in hypertensive subjects.
R EL-BIKAI, R TAHIR, J TREMBLAY, M JOFFRES, O ŠEDA, L ŠEDOVÁ, P AWADALLA, C LABERGE, B KNOPPERS, P DUMAS, D GAUDET, L STE-MARIE, P HAMET
Journal of Hypertension
2015.
doi: 10.1097/HJH.0000000000000475

2014
Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel.
Delaneau O, Marchini J; 1000 Genomes Project Consortium.
Nature Communications

The landscape of human STR variation.
Willems T, Gymrek M, Highnam G; 1000 Genomes Project Consortium, Mittelman D, Erlich Y.
Genome Res.
2014.
doi: 10.1101/gr.177774.114

Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.
Colonna, V and Consortium, The 1000 Genomes Project
Genome Biology
2014.
doi: 10.1186/gb-2014-15-6-r88

Genetically encoded impairment of neuronal KCC2 cotransporter function in human idiopathic generalized epilepsy.
K Kahle, N Merner, P Friedel, L Silayeva, B Liang, A Khanna, Y Shang, P Lachance-Touchette, C Bourassa, A Levert, PA Dion, B Walcott, D Spiegelman, A Dionne-Laporte, A Hodgkinson, P Awadalla, H Nikbakht, J Majewski, P Cossette, TZ Deeb, SJ Moss, I Medina, GA Rouleau
EMBO Reports.
2014.
doi: 10.15252/embr.201438840

CKD pathophysiology and clinical studies: Associations between a umod gene variant, uromodulin excretion and renal function in a large canadian survey: the CARTeGENE study
C Delmas-Frenette, S Troyanov, P Awadalla, O Devuyst, F Madore
NEPHROLOGY DIALYSIS TRANSPLANTATION.
2014.
doi: 10.1093/ndt/gfu148

High-Resolution Genomic Analysis of Human Mitochondrial RNA Sequence Variation.
Hodgkinson A, Idaghdour Y, Gbeha E, Grenier J, Hip-Ki E, Bruat V, Goulet J, de Malliard T, Awadalla P
Science.
2014.
doi: 10.1126/science.1251110

Genomic Architecture of Sickle Cell Disease in West African Children
Quinlan J, Idaghdour Y, Goulet J, Gbeha E, de Malliard T, Bruat V, Grenier J, Gomez S, Sanni A, Rahimy M, Awadalla P
Frontiers in Genetics.
2014.
doi: 10.3389/fgene.2014.00026

Prevalence, Awareness, and Management of CKD and Cardiovascular Risk Factors in Publicly Funded Health Care.
Verhave J, Troyanov S, Mongeau F, Fradette L, Bouchard J, Awadalla P, Madore F
Clin J Am Soc Nephrol.
2014.
doi: 10.2215/CJN.06550613

2013
Reconstructing Native American migrations from whole-genome and whole-exome data.
Reconstructing Native American migrations from whole-genome and whole-exome data.
Gravel S, Zakharia F, Moreno-Estrada A, Byrnes JK, Muzzio M, Rodriguez-Flores JL, Kenny EE, Gignoux CR, Maples BK, Guiblet W, Dutil J, Via M, Sandoval K, Bedoya G; 1000 Genomes Project, Oleksyk TK, Ruiz-Linares A, Burchard EG, Martinez-Cruzado JC, Bustamante CD.
PLoS Genet.
2013.
doi: 10.1371/journal.pgen.1004023

Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division.
Abyzov A, Iskow R, Gokcumen O, Radke D, Balasubramanian S, Pei B, Habegger L, 1000 Genomes Project Consortium, Lee C, Gerstein M
Genome Res.
2013.
doi: 10.1101/gr.154625.113

Cohort profile of the CARTaGENE study: Quebec's population-based biobank for public health and personalized genomics.
Awadalla P, Boileau C, Payette Y, Idaghdour Y, Goulet J, Knoppers B, Hamet P, Laberge C, Project C
Int J Epidemiol.
2013.
doi: 10.1093/ije/dys160

Whole-exome sequencing reveals a rapid change in the frequency of rare functional variants in a founding population of humans.
Casals F, Hodgkinson A, Hussin J, Idaghdour Y, Bruat V, de Maillard T, Grenier J, Gbeha E, Hamdan F, Girard S, Spinella J, Larivière M, Saillour V, Healy J, Fernández I, Sinnett D, Michaud J, Rouleau G, Haddad E, Deist F, Awadalla P
PLoS Genet.
2013.
doi: 10.1371/journal.pgen.1003815

Identifying recent adaptations in large-scale genomic data.
Grossman S, Andersen K, Shlyakhter I, Tabrizi S, Winnicki S, Yen A, Park D, Griesemer D, Karlsson E, Wong S, Cabili M, Adegbola R, Bamezai R, Hill A, Vannberg F, Rinn J, 1000 Genomes Project, Lander E, Schaffner S, Sabeti P
Cell.
2013.
doi: 10.1016/j.cell.2013.01.035

Selective constraint, background selection, and mutation accumulation variability within and between human populations.
Hodgkinson A, Casals F, Idaghdour Y, Grenier J, Hernandez R, Awadalla P
BMC Genomics.
2013.
doi: 10.1186/1471-2164-14-495

Rare allelic forms of PRDM9 associated with childhood leukemogenesis.
Hussin J, Sinnett D, Casals F, Idaghdour Y, Bruat V, Saillour V, Healy J, Grenier J, de Malliard T, Busche S, Spinella J, Larivière M, Gibson G, Andersson A, Holmfeldt L, Ma J, Wei L, Zhang J, Andelfinger G, Downing J, Mullighan C, Awadalla P
Genome Res.
2013.
doi: 10.1101/gr.144188.112

Integrative annotation of variants from 1092 humans: application to cancer genomics.
Khurana E, Fu Y, Colonna V, Mu X, Kang H, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani U, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüs Z, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin S, MacArthur D, Marth G, Muzny D, Pers T, Ritchie G, Rosenfeld J, Sisu C, Wei X, Wilson M, Xue Y, Yu F, 1000 Genomes Project Consortium, Dermitzakis E, Yu H, Rubin M, Tyler-Smith C, Gerstein M
Science.
2013.
doi: 10.1126/science.1235587

Genome Diversity and Applications in Genetic Studies of the Human Malaria Parasites Plasmodium falciparum and Plasmodium vivax
Pattaradilokrat S, Mu J, Awadalla P, Su X
Book. Malaria Parasites: Comparative Genomics, Evolution and Molecular Biology.
2013.

Exome sequencing identifies mutations in the gene TTC7A in French-Canadian cases with hereditary multiple intestinal atresia.
Samuels M, Majewski J, Alirezaie N, Fernandez I, Casals F, Patey N, Decaluwe H, Gosselin I, Haddad E, Hodgkinson A, Idaghdour Y, Marchand V, Michaud J, Rodrigue M, Desjardins S, Dubois S, Deist F, Awadalla P, Raymond V, Maranda B
J Med Genet.
2013.
doi: 10.1136/jmedgenet-2012-101483

Harnessing genomics to identify environmental determinants of heritable disease.
Yauk C, Argueso J, Auerbach S, Awadalla P, Davis S, Demarini D, Douglas G, Dubrova Y, Elespuru R, Glover T, Hales B, Hurles M, Klein C, Lupski J, Manchester D, Marchetti F, Montpetit A, Mulvihill J, Robaire B, Robbins W, Rouleau G, Shaughnessy D, Somers C, Taylor J, Trasler J, Waters M, Wilson T, Witt K, Bishop J
Mutat Res.
2013.
doi: 10.1016/j.mrrev.2012.08.002

Hypervariable antigen genes in malaria have ancient roots.
Zilversmit M, Chase E, Chen D, Awadalla P, Day K, McVean G
BMC Evol Biol.
2013.
doi: 10.1186/1471-2148-13-110

2012
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, Awadalla P
Stat Appl Genet Mol Biol.
2012.
doi: 10.2202/1544-6115.1713

Next-generation sequencing approaches for genetic mapping of complex diseases.
Casals F, Idaghdour Y, Hussin J, Awadalla P
J Neuroimmunol.
2012.
doi: 10.1016/j.jneuroim.2011.12.017

The 1000 Genomes Project: data management and community access.
Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P, 1000 Genomes Project Consortium
Nat Methods.
2012.
doi: 10.1038/nmeth.1974

An integrated map of genetic variation from 1,092 human genomes.
1000 Genomes Project Consortium, Abecasis G, Auton A, Brooks L, DePristo M, Durbin R, Handsaker R, Kang H, Marth G, McVean G
Nature.
2012.
doi: 10.1038/nature11632

P35 Évidence de risque accru d’ostéoporose dans le diabète et l’hypertension: importance de la masse musculaire.
El Bikai R, Dumas P, Awadalla P, Temblay J, Laberge C, Ste-Marie L, Hamet P
Diabetes & Metabolism.
2012.
doi: 10.1016/S1262-3636(12)71137-0

Rare copy number variants contribute to congenital left-sided heart disease.
Hitz M, Lemieux-Perreault L, Marshall C, Feroz-Zada Y, Davies R, Yang S, Lionel A, D'Amours G, Lemyre E, Cullum R, Bigras J, Thibeault M, Chetaille P, Montpetit A, Khairy P, Overduin B, Klaassen S, Hoodless P, Awadalla P, Hussin J, Idaghdour Y, Nemer M, Stewart A, Boerkoel C, Scherer S, Richter A, Dubé M, Andelfinger G
PLoS Genet.
2012.
doi: 10.1371/journal.pgen.1002903

Exploiting gene expression variation to capture gene-environment interactions for disease.
Idaghdour Y, Awadalla P
Front Genet.
2012.
doi: 10.3389/fgene.2012.00228

Evidence for additive and interaction effects of host genotype and infection in malaria.
Idaghdour Y, Quinlan J, Goulet J, Berghout J, Gbeha E, Bruat V, de Malliard T, Grenier J, Gomez S, Gros P, Rahimy M, Sanni A, Awadalla P
Proc Natl Acad Sci U S A.
2012.
doi: 10.1073/pnas.1204945109

70 17q21.31 CNV DOSE DEPENDENT EFFECT ON THE PREVALENCE OF HYPERTENSION AND DYSLIPIDEMIA COMORBIDITY
Ivanga M, Sandoval J, Idaghdour Y, Corbeil G, Awadalla P, Seda O, Chalmers J, Harrap S, McMahon S, Marre M, et al.
Journal of Hypertension.
2012.
doi: 10.1097/01.hjh.0000419895.80861.ec

CASE REPORT: INFLAMMATORY BOWEL DISEASE CROHN'S-LIKE, LIVER CIRRHOSIS, RECURRENT BLEPHARITIS AND NAIL HYPOPLASIA IN AN 6 YEAR OLD BOY
Piquer M, Alsina L, Alvaro M, Martin-Mateos M, Casals F, Awadalla P, Plaza A, Martin de Carpi J, Juan M, Arostegui J
Journal of Clinical immunology.
2012.

2011
Plasmodium falciparum genetic diversity maintained and amplified over 5 years of a low transmission endemic in the Peruvian Amazon.
Branch O, Sutton P, Barnes C, Castro J, Hussin J, Awadalla P, Hijar G
Mol Biol Evol.
2011.
doi: 10.1093/molbev/msq311

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 M, Bertranpetit J
BMC Evol Biol.
2011.
doi: 10.1186/1471-2148-11-202

Variation in genome-wide mutation rates within and between human families.
Conrad D, Keebler J, DePristo M, Lindsay S, Zhang Y, Casals F, Idaghdour Y, Hartl C, Torroja C, Garimella K, Zilversmit M, Cartwright R, Rouleau G, Daly M, Stone E, Hurles M, Awadalla P, 1000 Genomes Project
Nat Genet.
2011.
doi: 10.1038/ng.862

The variant call format and VCFtools.
Danecek P, Auton A, Abecasis G, Albers C, Banks E, DePristo M, Handsaker R, Lunter G, Marth G, Sherry S, McVean G, Durbin R, 1000 Genomes Project Analysis Group
Bioinformatics.
2011.
doi: 10.1093/bioinformatics/btr330

Demographic history and rare allele sharing among human populations.
Gravel S, Henn B, Gutenkunst R, Indap A, Marth G, Clark A, Yu F, Gibbs R, 1000 Genomes Project, Bustamante C
Proc Natl Acad Sci U S A.
2011.
doi: 10.1073/pnas.1019276108

Age-dependent recombination rates in human pedigrees.
Hussin J, Roy-Gagnon M, Gendron R, Andelfinger G, Awadalla P
PLoS Genet.
2011.
doi: 10.1371/journal.pgen.1002251

High recombination rates and hotspots in a Plasmodium falciparum genetic cross.
Jiang H, Li N, Gopalan V, Zilversmit M, Varma S, Nagarajan V, Li J, Mu J, Hayton K, Henschen B, Yi M, Stephens R, McVean G, Awadalla P, Wellems T, zhuan Su X
Genome Biol.
2011.
doi: 10.1186/gb-2011-12-4-r33

Similarity in recombination rate estimates highly correlates with genetic differentiation in humans.
Laayouni H, Montanucci L, Sikora M, Melé M, Dall'Olio G, Lorente-Galdos B, McGee K, Graffelman J, Awadalla P, Bosch E, Comas D, Navarro A, Calafell F, Casals F, Bertranpetit J
PLoS One.
2011.
doi: 10.1371/journal.pone.0017913

Mapping copy number variation by population-scale genome sequencing.
Mills R, Walter K, Stewart C, Handsaker R, Chen K, Alkan C, Abyzov A, Yoon S, Ye K, Cheetham R, Chinwalla A, Conrad D, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva L, Iqbal Z, Kang S, Kidd J, Konkel M, Korn J, Khurana E, Kural D, Lam H, Leng J, Li R, Li Y, Lin C, Luo R, Mu X, Nemesh J, Peckham H, Rausch T, Scally A, Shi X, Stromberg M, Stütz A, Urban A, Walker J, Wu J, Zhang Y, Zhang Z, Batzer M, Ding L, Marth G, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler E, Gerstein M, Hurles M, Lee C, McCarroll S, Korbel J, 1000 Genomes Project
Nature.
2011.
doi: 10.1038/nature09708

A population genetic approach to mapping neurological disorder genes using deep resequencing.
Myers R, Casals F, Gauthier J, Hamdan F, Keebler J, Boyko A, Bustamante C, Piton A, Spiegelman D, Henrion E, Zilversmit M, Hussin J, Quinlan J, Yang Y, Lafrenière R, Griffing A, Stone E, Rouleau G, Awadalla P
PLoS Genet.
2011.
doi: 10.1371/journal.pgen.1001318

The Importance of the Natural History of Malaria.
Zilversmit M, Awadalla P
E-Letter, Science.
2011.

2010
Direct measure of the de novo mutation rate in autism and schizophrenia cohorts.
Awadalla P, Gauthier J, Myers R, Casals F, Hamdan F, Griffing A, Côté M, Henrion E, Spiegelman D, Tarabeux J, Piton A, Yang Y, Boyko A, Bustamante C, Xiong L, Rapoport J, Addington A, DeLisi J, Krebs M, Joober R, Millet B, Fombonne E, Mottron L, Zilversmit M, Keebler J, Daoud H, Marineau C, Roy-Gagnon M, Dubé M, Eyre-Walker A, Drapeau P, Stone E, Lafrenière R, Rouleau G
Am J Hum Genet.
2010.
doi: 10.1016/j.ajhg.2010.07.019

A map of human genome variation from population-scale sequencing.
1000 Genomes Project Consortium, Abecasis G, Altshuler D, Auton A, Brooks L, Durbin R, Gibbs R, Hurles M, McVean G
Nature.
2010.
doi: 10.1038/nature09534

De novo mutations in the gene encoding the synaptic scaffolding protein SHANK3 in patients ascertained for schizophrenia.
Gauthier J, Champagne N, Lafrenière R, Xiong L, Spiegelman D, Brustein E, Lapointe M, Peng H, Côté M, Noreau A, Hamdan F, Addington A, Rapoport J, Delisi L, Krebs M, Joober R, Fathalli F, Mouaffak F, Haghighi A, Néri C, Dubé M, Samuels M, Marineau C, Stone E, Awadalla P, Barker P, Carbonetto S, Drapeau P, Rouleau G, Team S
Proc Natl Acad Sci U S A.
2010.
doi: 10.1073/pnas.0906232107

Mutations in centrosomal protein CEP152 in primary microcephaly families linked to MCPH4.
Guernsey D, Jiang H, Hussin J, Arnold M, Bouyakdan K, Perry S, Babineau-Sturk T, Beis J, Dumas N, Evans S, Ferguson M, Matsuoka M, Macgillivray C, Nightingale M, Patry L, Rideout A, Thomas A, Orr A, Hoffmann I, Michaud J, Awadalla P, Meek D, Ludman M, Samuels M
Am J Hum Genet.
2010.
doi: 10.1016/j.ajhg.2010.06.003

Plasmodium falciparum genome-wide scans for positive selection, recombination hot spots and resistance to antimalarial drugs.
Mu J, Myers R, Jiang H, Liu S, Ricklefs S, Waisberg M, Chotivanich K, Wilairatana P, Krudsood S, White N, Udomsangpetch R, Cui L, Ho M, Ou F, Li H, Song J, Li G, Wang X, Seila S, Sokunthea S, Socheat D, Sturdevant D, Porcella S, Fairhurst R, Wellems T, Awadalla P, zhuan Su X
Nat Genet.
2010.
doi: 10.1038/ng.528

Diversity of human copy number variation and multicopy genes.
Sudmant P, Kitzman J, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, 1000 Genomes Project, Eichler E
Science.
2010.
doi: 10.1126/science.1197005

Low-complexity regions in Plasmodium falciparum: missing links in the evolution of an extreme genome.
Zilversmit M, Volkman S, DePristo M, Wirth D, Awadalla P, Hartl D
Mol Biol Evol.
2010.
doi: 10.1093/molbev/msq108

2009
Genomewide association studies: history, rationale, and prospects for psychiatric disorders.
Committee P, Cichon S, Craddock N, Daly M, Faraone S, Gejman P, Kelsoe J, Lehner T, Levinson D, Moran A, Sklar P, Sullivan P
Am J Psychiatry.
2009.
doi: 10.1176/appi.ajp.2008.08091354

2008
Selection shapes malaria genomes and drives divergence between pathogens infecting hominids versus rodents.
Prugnolle F, McGee K, Keebler J, Awadalla P
BMC Evol Biol.
2008.
doi: 10.1186/1471-2148-8-223

2007
Structural polymorphism and diversifying selection on the pregnancy malaria vaccine candidate VAR2CSA.
Bockhorst J, Lu F, Janes J, Keebler J, Gamain B, Awadalla P, Su X, Samudrala R, Jojic N, Smith J
Mol Biochem Parasitol.
2007.
doi: 10.1016/j.molbiopara.2007.06.007

Genome-wide variation and identification of vaccine targets in the Plasmodium falciparum genome.
Mu J, Awadalla P, Duan J, McGee K, Keebler J, Seydel K, McVean G, zhuan Su X
Nat Genet.
2007.
doi: 10.1038/ng1924

2006
Phenotypic variation and natural selection at catsup, a pleiotropic quantitative trait gene in Drosophila.
Carbone M, Jordan K, Lyman R, Harbison S, Leips J, Morgan T, DeLuca M, Awadalla P, Mackay T
Curr Biol.
2006.
doi: 10.1016/j.cub.2006.03.051

A murine specific expansion of the Rhox cluster involved in embryonic stem cell biology is under natural selection.
Jackson M, Watt A, Gautier P, Gilchrist D, Driehaus J, Graham G, Keebler J, Prugnolle F, Awadalla P, Forrester L
BMC Genomics.
2006.
doi: 10.1186/1471-2164-7-212

Global genetic diversity and evolution of var genes associated with placental and severe childhood malaria.
Trimnell A, Kraemer S, Mukherjee S, Phippard D, Janes J, Flamoe E, zhuan Su X, Awadalla P, Smith J
Mol Biochem Parasitol.
2006.
doi: 10.1016/j.molbiopara.2006.03.012

2005
Recombination hotspots and population structure in Plasmodium falciparum.
Mu J, Awadalla P, Duan J, McGee K, Joy D, McVean G, zhuan Su X
PLoS Biol.
2005.
doi: 10.1371/journal.pbio.0030335

2004
Functional divergence caused by ancient positive selection of a Drosophila hybrid incompatibility locus.
Barbash D, Awadalla P, Tarone A
PLoS Biol.
2004.
doi: 10.1371/journal.pbio.0020142

Low linkage disequilibrium indicative of recombination in foot-and-mouth disease virus gene sequence alignments.
Haydon D, Bastos A, Awadalla P
J Gen Virol.
2004.

2003
Local differentiation in Plasmodium falciparum drug resistance genes in Sudan.
Abdel-Muhsin A, Mackinnon M, Awadalla P, Ali E, Suleiman S, Ahmed S, Walliker D, Babiker H
Parasitology.
2003.
doi: 10.1017/S0031182003003020

The evolutionary genomics of pathogen recombination.
Awadalla P
Nat Rev Genet.
2003.
doi: 10.1038/nrg964

Diversity and linkage of genes in the self-incompatibility gene family in Arabidopsis lyrata.
Charlesworth D, Mable B, Schierup M, Bartolomé C, Awadalla P
Genetics.
2003.

2002
A coalescent-based method for detecting and estimating recombination from gene sequences.
McVean G, Awadalla P, Fearnhead P
Genetics.
2002.

2001
The question of Plasmodium falciparum population structure.
Awadalla P, Walliker D, Babiker H, Mackinnon M
Trends Parasitol.
2001.

Does human mtDNA recombine?
Eyre-Walker A, Awadalla P
J Mol Evol.
2001.
doi: 10.1007/s002390010232

Identification and characterization of a polymorphic receptor kinase gene linked to the self-incompatibility locus of Arabidopsis lyrata.
Schierup M, Mable B, Awadalla P, Charlesworth D
Genetics.
2001.

1999
Linkage disequilibrium and recombination in hominid mitochondrial DNA.
Awadalla P, Eyre-Walker A, Smith J
Science.
1999.

Recombination and selection at Brassica self-incompatibility loci.
Awadalla P, Charlesworth D
Genetics.
1999.