Javad Nadaf, PhD

Javad Nadaf, PhD

  • Computational Scientist

Departments

Divisions

Education

MSc - Ferdowsi University, Mashad, Iran.

PhD - AgroCampus Rennes, France

Postdoctoral training - The University of Edinburgh, UK; McGill University, Canada

Research Interests

My research has focused on the bioinformatics and statistical analyses of disease-related (Epi)genomic data. I am interested in discovering cancer-predisposing germline variations and deciphering the interplay between the genome, epigenome and transcriptome in formation and progression of cancer.

Selected Publications

For a more updated list of publications please see:
http://www.ncbi.nlm.nih.gov/pubmed/?term=javad+nadaf
http://www.researchgate.net/profile/Javad_Nadaf

Rivera B, Gayden T, Carrot-Zhang J, Nadaf J, Boshari T, Faury D, Zeinieh M, Blanc R, Burk DL, Fahiminiya S, Bareke E, Schüller U, Monoranu CM, Sträter R, Kerl K, Niederstadt T, Kurlemann G, Ellezam B, Michalak Z, Thom M, Lockhart PJ, Leventer RJ, Ohm M, MacGregor D, Jones D, Karamchandani J, Greenwood CM, Berghuis AM, Bens S, Siebert R, Zakrzewska M, Liberski PP, Zakrzewski K, Sisodiya SM, Paulus W, Albrecht S, Hasselblatt M, Jabado N, Foulkes WD, Majewski J. Germline and somatic FGFR1 abnormalities in dysembryoplastic neuroepithelial tumors. Acta Neuropathol 131(6):847-63, 2016.

Lu C, Jain SU, Hoelper D, Bechet D, Molden RC, Ran L, Murphy D, Venneti S, Hameed M, Pawel BR, Wunder JS, Dickson BC, Lundgren SM, Jani KS, De Jay N, Papillon-Cavanagh S, Andrulis IL, Sawyer SL, Grynspan D, Turcotte RE, Nadaf J, Fahiminiyah S, Muir TW, Majewski J, Thompson CB, Chi P, Garcia BA, Allis CD, Jabado N, Lewis PW. Histone H3K36 mutations promote sarcomagenesis through altered histone methylation landscape. Science 352(6287):844–849, 2016.

Fahiminiya S*, Witkowski L*, Nadaf J*, Carrot-Zhang J, Goudie C, Hasselblatt M, Johann P, Kool M, Lee RS, Gayden T, Roberts CW, Biegel JA, Jabado N, Majewski J, Foulkes WD. Molecular analyses reveal close similarities between small cell carcinoma of the ovary, hypercalcemic type and atypical teratoid/rhabdoid tumor. Oncotarget 7(2):1732-40, 2016. (*co-first author)

Ataei-Kachouei M, Nadaf J, Akbari MT, Atri M, Majewski J, Riazalhosseini Y, Garshasbi M. Double Heterozygosity of BRCA2 and STK11 in Familial Breast Cancer Detected by Exome Sequencing. Iran J Public Health 44(10):1348-52, 2015. 

Li X, Liu X, Nadaf J, Le Bihan-Duval E, Berri C, Dunn I, Talbot R, De Koning DJ. Using Targeted Resequencing for Identification of Candidate Genes and SNPs for a QTL Affecting the pH Value of Chicken Meat. G3 (Bethesda) 5(10):2085-9, 2015.

Mendoza-Londono R, Fahiminiya S, Majewski J, Care4Rare Canada Consortium, Tétreault M, Nadaf J, Kannu P, Sochett E, Howard A, Stimec J, Dupuis L, Roschger  P, Klaushofer K, Palomo T, Ouellet J, Al-Jallad H, Mort JS, Moffatt P, Boudko S, Bächinger HP, Rauch F. Recessive osteogenesis imperfecta caused by missense mutations in SPARC. Am J Hum Genet 96(6):979-85, 2015. 

Tetreault M, Bareke E, Nadaf J*, Alirezaie N, Majewski J. Whole-exome sequencing as a diagnostic tool: current challenges and future opportunities. Expert Rev Mol Diagn 15(6):749-60, 2015. (*co-first author)

Ben-Omran T, Fahiminiya S, Sorfazlian N, Almuriekhi M, Nawaz Z, Nadaf J, Khadija KA, Zaineddin S, Kamel H, Majewski J, Tropepe V. Nonsense mutation in the WDR73 gene is associated with Galloway-Mowat syndrome. J Med Genet 52(6):381-90, 2015.

Cybulski C, Carrot-Zhang J, Kluźniak W, Rivera B, Kashyap A, Wokołorczyk D, Giroux S, Nadaf J, Hamel N, Zhang S, Huzarski T, Gronwald J, Byrski T, Szwiec M,  Jakubowska A, Rudnicka H, Lener M, Masojć B, Tonin PN, Rousseau F, Górski B, Dębniak T, Majewski J, Lubiński J, Foulkes WD, Narod SA, Akbari MR. Germline RECQL mutations are associated with breast cancer susceptibility. Nat Genet 47(6):643-6, 2015. 

Almuriekhi M, Shintani T, Fahiminiya S, Fujikawa A, Kuboyama K, Takeuchi Y, Nawaz Z, Nadaf J, Kamel H, Kitam AK, Samiha Z, Mahmoud L, Ben-Omran T, Majewski J, Noda M. Loss-of-Function Mutation in APC2 Causes Sotos Syndrome Features. Cell Rep 2015 Mar 3. pii: S2211-1247(15)00139-4   

Nadaf J#, Majewski J, Fahiminiya S. ExomeAI: detection of recurrent allelic imbalance in tumors using whole-exome sequencing data. Bioinformatics 31(3):429-31, 2015. (# corresponding author)

Donadeu FX, Fahiminiya S, Esteves CL, Nadaf J, Miedzinska K, McNeilly AS, Waddington D, Gérard N. Transcriptome profiling of granulosa and theca cells during dominant follicle development in the horse. Biol Reprod 91(5):111, 2014. 

Witkowski L, Carrot-Zhang J, Albrecht S, Fahiminiya S, Hamel N, Tomiak E, Grynspan D, Saloustros E, Nadaf J, Rivera B, Gilpin C, Castellsagué E, Silva-Smith R, Plourde F, Wu M, Saskin A, Arseneault M, Karabakhtsian RG, Reilly  EA, Ueland FR, Margiolaki A, Pavlakis K, Castellino SM, Lamovec J, Mackay HJ, Roth LM, Ulbright TM, Bender TA, Georgoulias V, Longy M, Berchuck A, Tischkowitz  M, Nagel I, Siebert R, Stewart CJ, Arseneau J, McCluggage WG, Clarke BA, Riazalhosseini Y, Hasselblatt M, Majewski J, Foulkes WD. Germline and somatic SMARCA4 mutations characterize small cell carcinoma of the ovary, hypercalcemic type. Nat Genet 46(5):438-43, 2014.

Nadaf J, Berri C, Dunn I, Godet E, Le Bihan-Duval E, De Koning DJ. An expression QTL of closely linked candidate genes affects pH of meat in chickens. Genetics 196(3):867-74, 2014. 

Nadaf J, Riggio V, Yu TP, Pong-Wong R. Effect of the prior distribution of SNP effects on the estimation of total breeding value. BMC Proc 2012 May 21;6 Suppl 2:S6.

Nadaf J, Pong-Wong R. Applying different genomic evaluation approaches on QTLMAS2010 dataset. BMC Proc 2011 May 27;5 Suppl 3:S9. 

Le Bihan-Duval E, Nadaf J, Berri C, Pitel F, Graulet B, Godet E, Leroux SY, Demeure O, Lagarrigue S, Duby C, Cogburn LA, Beaumont CM, Duclos MJ. Detection of a Cis eQTL controlling BCMO1 gene expression leads to the identification of a QTG for chicken breast meat color. PLoS One 6(7):e14825, 2011. 

Hadjipavlou G, Hemani G, Leach R, Louro B, Nadaf J*, Rowe S, de Koning DJ. Extensive QTL and association analyses of the QTLMAS2009 Data. BMC Proc 2010 Mar 31;4 Suppl 1:S11. (*co-first author)

Nadaf J, Pitel F, Gilbert H, Duclos MJ, Vignoles F, Beaumont C, Vignal A, Porter TE, Cogburn LA, Aggrey SE, Simon J, Le Bihan-Duval E. QTL for several metabolic traits map to loci controlling growth and body composition in an F2 intercross between high- and low-growth chicken lines. Physiol Genomics 38(3):241-9, 2009. 

Nadaf J, Gilbert H, Pitel F, Berri CM, Feve K, Beaumont C, Duclos MJ, Vignal  A, Porter TE, Simon J, Aggrey SE, Cogburn LA, Le Bihan-Duval E. Identification of QTL controlling meat quality traits in an F2 cross between two chicken lines selected for either low or high growth rate. BMC Genomics 8:155, 2007. 

Last update: September 2016