Shadi Shokralla, Ph.D.
Dr. Shokralla’s graduate training, in conjunction with the Stanford Genome Technology Centre, was in molecular techniques for detection of microbial resistance amongst clinical isolates of bacteria. His main research interest is in technology development within next-generation sequencing platforms including Roche 454 GS FLX and Illumina MiSeq systems. He is currently developing new molecular approaches to total biodiversity assessment using environmental samples. As a part of the Biomonitoring 2.0 project, Dr. Shokralla is responsible for developing and optimizing protocols for DNA extraction, amplification, and sequencing.
Selected Peer-Reviewed Publications
1. Shokralla, S., Porter T. M., Gibson, J. F., Dobosz, R., Janzen, D. H., Hallwachs, W., Golding, G. B., & Hajibabaei, M. (2015). Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform. Scientific Reports 5: 9687 DOI: 10.1038/srep09687
2.Bertrand, C., Janzen, D. H., Hallwachs, W., Burns, J. M., Gibson, J. F., Shokralla, S., & Hajibabaei, M. (2014). Mitochondrial and nuclear phylogenetic analysis with Sanger and next-generation sequencing shows that, in Área de Conservación Guanacaste, NW Costa Rica, the skipper butterfly Urbanus belli (Hesperiidae) comprises three morphologically cryptic species. BMC Evolutionary Biology. 14: 153 DOI: 10.1186/1471-2148-14-153
3.Gibson, J. F., Shokralla, S., Porter, T. M., King, I., van Konynenburg, S., Janzen, D.H, Hallwachs, W., & Hajibabaei, M. (2014). Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics. Proceedings of the National Academy of Sciences of the United States of America.
4.Shokralla S, Gibson JF, Nikbakht H, Janzen DH, Hallwachs W, Hajibabaei M (2014) Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens. Molecular Ecology Resources. DOI: 10.1111/1755-0998.12236
5.Porter TM, Gibson JM, Shokralla S, Baird DJ, Golding GB, Hajibabaei M (2014) Rapid and accurate taxonomic classification of insect (Class Insecta) cytochrome c oxidase subunit 1 (COI) DNA barcode sequences using a naïve Bayesian classifier. Molecular Ecology Resources. DOI: 10.1111/1755-0998.12240
6.Hajibabaei, M, Spall, JL, Shokralla, S and van Konynenburg, S. (2012) Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol. BMC Ecology 12:28 DOI: 10.1186/1472-6785-12-28
7.Wallace LJ, Boilard SMAL, Eagle SHC, Spall JL, Shokralla S, Hajibabaei M. (2012) DNA barcodes for everyday life: Routine authentication of Natural Health Products. Food Research International 49: 446-452. DOI: 10.1016/j.foodres.2012.07.048
8.Shokralla S, Spall J, Gibson JF, Hajibabaei M (2012) Next-generation DNA sequencing technologies for environmental DNA research. Molecular Ecology 21: 1794-1805. DOI: 10.1111/j.1365-294X.2012.05538.x
9.Shokralla S, Zhou X, Janzen D, Hallwachs W, Landry JF, Jacobus L, Hajibabaei M. (2011) Pyrosequencing for mini-barcoding of fresh and old museum specimens. PLoS ONE, July 2011, Volume 6, Issue 7- e21252.
10.Hajibabaei M, Shokralla S, Zhou X, Singer GA, Baird D (2011) Environmental Barcoding: A next-generation sequencing approach for biomonitoring applications using river benthos. PLoS ONE, April 2011, Volume 6 , Issue 4 – e17497.
11.Hajibabaei M, Spall J, Shokralla S and van Konynenburg, S. (2012) Assessing biodiversity of a freshwater benthic macroinvertebrate community through non-destructive environmental barcoding of DNA from preservative ethanol. BMC Ecology 12:28 DOI: 10.1186/1472-6785-12-28
12.Parameswaran P, Jalili R, Tao L, Shokralla S, Gharizadeh B, Ronaghi M, Fire AZ (2007):”A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing.” Nucleic Acids Res 2007; 35: 19: e130.
13.Ronaghi M, Shokralla S, Gharizadeh B (2007): Pyrosequencing for discovery and analysis of DNA sequence variations. Pharmacogenomics, Volume 8, Number 10, October 2007, pp. 1437-1441(5).
14.Doostzadeh J*, Shokralla S*, Absalan F, Jalili R, Mohandessi S, Langston J, Davis R, Ronaghi M, Gharizadeh B (2008): High Throughput Automated Allele Frequency Estimation by Pyrosequencing. PLoS ONE. July 2008, Volume 3 , Issue 7 , e2693.
15.Wallace LJ, Boilard S, Eagle S, Spall J, Shokralla S, Hajibabaei M. (2012) DNA barcodes for everyday life: Routine authentication of Natural Health Products. Food Research International 49: 446-452. DOI: 10.1016/j.foodres.2012.07.048
16.Shokralla S, Singer GA, Hajibabaei M (2010) Direct PCR amplification and sequencing of specimens’ DNA from preservative ethanol. Biotechniques, Vol. 48, No. 3.
17.El-Naggar W, Hassan R, Barwa R, Shokralla S. and Elgaml A. (2010): Molecular Diagnosis of Gram Negative Bacteria in Urinary Tract Infections. Egyptian J. Medical Microbiology 19 (7), 115- 121.
18.El-Naggar W, Hassan R, Habib E, Shokralla S, and Abd-Elmagid E. (2010): A comparative study on Gram negative infections in Mansoura University Hospitals, Egypt. Egyptian J. Medical Microbiology 19 (3), 135- 146.
19.Habib E, Hassan. R, Abd El Galil, Shokralla S, and EL-Naggar F (2010): Molecular characterization of Metalo b-lacrtamase producing Clinical Pseudomonas aeruginosa isolates from Mansoura University Hospitals, Egypt. Egyptian J. Medical Microbiology 19 (4), 131- 141, 2010.
20.El-Naggar W, Habib E, Shokralla S, Barwa R, Abd El Galil K. and Abd-Elmagid E. (2010): Phenotypic and Genotypic charachterization of extended spectrum B-lactamase produced by enterobacteriaceae. Egyptian J. Medical Microbiology 19 (2), 59- 66.
Office: University of Guelph, Centre for Biodiversity Genomics, Rm. 108
Lab: University of Guelph, Centre for Biodiversity Genomics, Rms. 015-016
Biodiversity Institute of Ontario
University of Guelph
579 Gordon Street
Guelph, ON N1G 2W1
Tel 1: 519-824-4120 Ext 56007
Tel 2: 226-971-0169