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Publications

2021

  • Dick K, Pattang A, Hooker J, Nissan N, Sadowski M, Barnes B, Tan LH, Burnside D, Phanse S, Aoki H, Babu M, Dehne F, Golshani A, Cober R, Green J, and : Human-Soybean Allergies: Elucidation of the Seed Proteome & Comprehensive PPI Prediction. Journal of Proteome Research (JPR), 2021, 20(11):4925-4947 (doi: 10.1021/acs.jproteome.1c00138).

  • Nissan N, Cober ER, Sadowski M, Charette M, Golshani A, and : Identifying New Variation at the J locus, Previously Identified as e6, in Long Juvenile ‘Paranagoiana’ Soybean. Theoretical and Applied Genomics (TAAG), 2021, 134:1007-1014 (doi: 10.1007/s00122-020-03746-2).

  • Kato S, Morrison MJ, Bekele WA, Torkamaned D, Rajcan I, O'Donoughue L, Belzile F, and Cober ER: Genome-wide association study (GWAS) to identify soybean stem pushing resistance and lodging resistance loci. Canadian Journal of Plant Science, 2021, 101: 663–670 (dx.doi.org/10.1139/cjps-2020-0187).

 

2020

  • Dick K, Samanfar B, Barnes B, Cober E, Mimee B, Tan LT, Molnar SJ, Biggar K, Golshani A, Dehne F, and Green JR: PIPE4: Ultra-Fast PPI Predictor for Comprehensive Inter- and Cross-Species Interactomes. Scientific Report, 2020, 10(1):1390.

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2019

  • Samanfar B, Cober E, Charette M, Tan LH, Bekele WA, Morrison M, Kilian A, Belzile F, and Molnar SJ: Genetic Analysis of High Protein Content in ‘AC Proteus’ Related Soybean Populations Using SSR, SNP, DArT and DArTseq Markers, Scientific Report, 2019, 9(1):19657.

  • Burnside D, Schoenrock A, Moteshareie H, Hooshyar M, Basra P, Hajikarimloo M, Dick K, Barnes B, Kazmirchuk T, Jessulat M,Pitre S, Samanfar B, Babu M, Green JR, Wong A, Dehne F, Biggar KK, andGolshani A: In silco engineering of synthetic proteins from random amino acid sequences. 2019, 11:375-387.

  • Le Hoa Tan, Bahram Samanfar, Elroy Cober: Consolidation, GMO and food security: what’s the connection? Germination, 2019, March edition (non peer-reviewed).

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2018

  • Galvan I, Ghiyasvand M, Massatsky A, Babu M, Samanfar B, Omidi K, Moon T, Smith M, and Golshani A: Zinc oxide and silver nanoparticles toxicity in the baker's yeast, Saccharomyces cerevisiae. PLOS ONE, 2018, 13(3):e0193111.

  • Omidi K, Jessulat M, Hooshyar M, Burnside DJ, Schoenrock A, Kazmirchuk T, Hajikarimlou M, Daniel M, Moteshareie H, Ramotar D, Dehne F, Samanfar B, Babu M, and Golshani A: Uncharacterized ORF HUR1 influences the efficiency of non-homologous end-joining repair in Saccharomyces cerevisiae. GENE, 2018, 639:128-136.

 

2017

  • Samanfar B, Molnar SJ, Charette M, Schoenrock A, Belzile F, Dehne F, Golshani A, and Cober ER: Mapping and identification of a candidate gene for a novel maturity locus, E10, in soybean. Theoretical and Applied Genomics (TAG), 2017, 130(2):377-390.

  • Samanfar B, Shostak K, Moteshareie H, Hajikarimlou M, Shaikho S,  Omid K, Hooshyar M, Burnside D, Galván Márquez I, Kazmirchuk T,  Naing T, Ludovico P, York-Lyon A, Szereszewski K, Leung C, Yixin Jin J, Megarbane R, Smith ML, Babu M, Holcik M, and Golshani, A: The sensitivity of the yeast, Saccharomyces cerevisiae, to acetic acid is influenced by DOM34 and RPL36A. PeerJ, 2017 (Accepted).

  • Kazmirchuk T,Dick K, Burnside D, Barnes B, Moteshareie H, Hajikarimlou M, Hooshyar M,Omidi K, Ahmed D,Low A,Lettl C,Schoenrock A, Pitre S, Babu M, Cassol E, Samanfar B, WongA, Dehne F, Green J, andGolshani A: Designing Anti-Zika Virus Peptides Derived from Predicted Human-Zika Virus Protein-Protein Interactions. Computational biology and Chemistry, 2017, 71: 180-187.

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2016

  • Gagarinova A, Stewart G, Samanfar B, Phanse S, White CA, Aoki H, Deineko V, Beloglazova N, Yakunin AF, Golshani A, Brown EC, Babu M, Emili A: Systematic genetic screens reveal the dynamic global functional organization of the bacterial translation machinery. Cell Reports, 2016, 17(3):904-916.

  • Shaikho S, Dobson CC, Naing T, Samanfar B, Moteshareie H, Golshani A, and Holcik M: Elevated levels of ribosomal proteins L36 and L36A control expression of HSP90 in rhabdomyosarcoma. Translation, 2016, 4(2):e1244395.

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2015

  • Jessulat M, Malty RH, Nguyen-Tran DH, Deineko V, Aoki H, Vlasblom J, Omidi K, Jin K, Minic Z, Hooshyar M, Burnside D, Samanfar B, Phanse S, Freywald T, Prasad B, Zhang Z, Vizeacoumar F, Krogan NJ, Freywald A,GolshaniA ,and Babu M: Spindle checkpoint factors Bub1 and Bub2 promote DNA double strand break repair by Non-Homologous End Joining. MCB, Molecular and Cell Biology, 2015, 35 (14): 2448-2463.
     

2014

  • Schoenrock A, Samanfar B, Pitre S, Hooshyar M, Jin K,Philips C, Wang H, Phanse S, Omidi K, Gui Y, Alamgir Md, Wong A, Barrenas F, Babu M, Benson M, Langston M, Green JR, Dehne F, andGolshani A: Efficient prediction of human protein-protein interactions at a global scale. BMC Bioinformatics, 2014,15(1): 383-404.

  • Samanfar B, Tan LH, Shostak K, Chalabian F, Wu z, Alamgir MD, Sunba N, Burnside D, Omidi K, Hooshyar M, Galván Márquez I, Jessulat M, Smith M, Babu M, Azizi A, and Golshani A: A global investigation of gene deletion strains that affect premature stop codon bypass in yeast, Saccharomyces cerevisiae. Mol Biosyst., 2014, 10 (4): 916-924.

  • Vlasblom J, Zuberi K, Rodriguez H, Arnold R, Gagarinova A, Deineko V, Leung E, Samanfar B, Chang L, Phanse S, Golshani A, Greenblatt J, Houry W,Emili A, Morris Q, Bader G, and Babu M: Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli. Bioinformatics, 2014, pii:btu671.

  • Babu M, Arnold R, Bundalovic-Torma C, Gagarinova A, Wong KS, Phanse S, Kumar A, Wagih O, Lad K, Samanfar B, Stewart G, Graham C, Aoki H, Brown E, Golshani A, Kim P, Moreno-Hagelsieb G, Greenblatt J, Houry WA, Parkinson J, and Emili A: Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli. PLOS Genetics, 2014, 10(2):e1004120.

  • Omidi K, Hooshyar M, Jessulat M, Samanfar B, Sanders M, Burnside D, Pitre S, Schoenrock A, Xu J, Babu M, and Golshani A: Phosphatase complex Pph3/Psy2 is involved in regulation of efficient Non-Homologous End-Joining pathway in the Yeast. PLoS ONE, 2014, 9(1): e87248.

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2013

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2012

  • Pitre S, Hooshyar M, Schoenrock A, Samanfar B, Jessulat M, Green JR, Dehne F, and Golshani A: Short co-occurring polypeptide regions can predict global protein interaction maps. Nature Scientific Reports, 2012, 2:239.

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2011

  • Jessulat M,Pitre S, Gui Y, Hooshyar M, Omidi K, Samanfar B, Tan LH, Alamgir MD, Green J, Dehne F, and Golshani A: Recent advances in protein-protein interaction prediction: experimental and computational methods. Opin Drug Discov., 2011, 6(9): 921-935.

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2008

  • Omidi M, Asadi S, Samanfar B, and Nosraty SZ:The effect of thermal treatment and meristem size factor on virus free potato plantlet production.Iranian Journal of Agriculture, 2008, 39-1.

 

Books and Chapters

  • Burnside D, Moteshareie M, Galvan-Marquez I, Hooshyar M, Samanfar B, Shostak K, Omidi K, Peery H, Smith ML, and Golshani A:Use of chemical genomics to investigate the mechanism of action for inhibitory bioactive natural compounds. In G. Brahmachari (Ed.), Bioactive Natural Compounds: Biology and Chemistry. , 2015, 544 pages. ISBN: 978-3-527-33794-1.

  • Omidi M, Alishah O, and Samanfar B: Plant cytogenetics, 2009, 565 pages.ISBN: 978-964-03-5905-1.

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