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Research Outputs 2009 2020

2020

Complement pathway in Alzheimer's pathology and retinal neurodegenerative disorders: the road ahead

Mirzaei, M., Deng, L., Gupta, V. B., Graham, S. & Gupta, V., 1 Feb 2020, In : Neural Regeneration Research. 15, 2, p. 257-258 2 p.

Research output: Contribution to journalReview articleResearchpeer-review

Open Access
File
2019

Abiotic stress responsive microRNome and proteome: how correlated are they?

Gharechahi, J., Sharifi, G., Mirzaei, M., Zeinalabedini, M. & Hosseini Salekdeh, G., Sep 2019, In : Environmental and Experimental Botany. 165, p. 150-160 11 p.

Research output: Contribution to journalReview articleResearchpeer-review

proteome
microRNA
abiotic stress
plant response
gene
Open Access
File
Vertebrate Photoreceptor Cells
Oxidative Phosphorylation
Amyloid
Photoreceptor Cells
Alzheimer Disease

Clinically relevant post-translational modification analyses: maturing workflows and bioinformatics tools

Pascovici, D., Wu, J. X., McKay, M. J., Joseph, C., Noor, Z., Kamath, K., Wu, Y., Ranganathan, S., Gupta, V. & Mirzaei, M., 1 Jan 2019, In : International Journal of Molecular Sciences. 20, 1, p. 1-30 30 p., 16.

Research output: Contribution to journalReview articleResearchpeer-review

Open Access
File
Workflow
Post Translational Protein Processing
Bioinformatics
Computational Biology
Proteins

Comparative proteomics investigation of central carbon metabolism in Euglena gracilis grown under predominantly phototrophic, mixotrophic and heterotrophic cultivations

Hasan, M. T., Sun, A., Khatiwada, B., McQuade, L., Mirzaei, M., Te'o, J., Hobba, G., Sunna, A. & Nevalainen, H., Nov 2019, In : Algal Research. 43, 11 p., 101638.

Research output: Contribution to journalArticleResearchpeer-review

Euglena gracilis
proteomics
metabolism
carbon
enzymes

Evidence from the proteome for local adaptation to extreme heat in a widespread tree species

Maher, T., Mirzaei, M., Pascovici, D., Wright, I. J., Haynes, P. A. & Gallagher, R. V., Mar 2019, In : Functional Ecology. 33, 3, p. 436-446 11 p.

Research output: Contribution to journalArticleResearchpeer-review

local adaptation
proteome
heat
protein
Eucalyptus grandis
Open Access
File
proteomics
water stress
drought
rice
cultivars

Loss of Shp2 rescues BDNF/TrkB signaling and contributes to improved retinal ganglion cell neuroprotection

Chitranshi, N., Dheer, Y., Mirzaei, M., Wu, Y., Salekdeh, G. H., Abbasi, M., Gupta, V., Vander Wall, R., You, Y., Graham, S. L. & Gupta, V., 6 Feb 2019, In : Molecular Therapy. 27, 2, p. 424-441 18 p.

Research output: Contribution to journalArticleResearchpeer-review

trkB Receptor
Retinal Ganglion Cells
Glaucoma
Endoplasmic Reticulum Stress
Apoptosis

Plant–microbe symbiosis: what has proteomics taught us?

Khatabi, B., Gharechahi, J., Ghaffari, M. R., Liu, D., Haynes, P. A., McKay, M. J., Mirzaei, M. & Salekdeh, G. H., Aug 2019, In : Proteomics. 19, 16, 20 p., 1800105.

Research output: Contribution to journalReview articleResearchpeer-review

Symbiosis
Proteomics
Functional analysis
Productivity
Food Supply

Proteomes of leaf-growing zones in rice genotypes with contrasting drought tolerance

Wu, Y., Mirzaei, M., Pascovici, D., Haynes, P. A. & Atwell, B. J., May 2019, In : Proteomics. 19, 9, 11 p., 1800310.

Research output: Contribution to journalArticleResearchpeer-review

Drought
Droughts
Proteome
Genotype
Drying

Retinoid x receptor modulation protects against ER stress response and rescues glaucoma phenotypes in adult mice

Dheer, Y., Chitranshi, N., Gupta, V., Sharma, S., Pushpitha, K., Abbasi, M., Mirzaei, M., You, Y., Graham, S. L. & Gupta, V., 1 Apr 2019, In : Experimental Neurology. 314, p. 111-125 15 p.

Research output: Contribution to journalArticleResearchpeer-review

Retinoid X Receptors
Retinoids
Glaucoma
Phenotype
Retina

Root endophytic fungus Piriformospora indica improves drought stress adaptation in barley by metabolic and proteomic reprogramming

Ghaffari, M. R., Mirzaei, M., Ghabooli, M., Khatabi, B., Wu, Y., Zabet-Moghaddam, M., Mohammadi-Nejad, G., Haynes, P. A., Hajirezaei, M. R., Sepehri, M. & Salekdeh, G. H., 1 Jan 2019, In : Environmental and Experimental Botany. 157, p. 197-210 14 p.

Research output: Contribution to journalArticleResearchpeer-review

proteomics
drought stress
barley
water stress
fungus

The quest for missing proteins in rice

Rahiminejad, M., Ledari, M. T., Mirzaei, M., Ghorbanzadeh, Z., Kavousi, K., Ghaffari, M. R., Haynes, P. A., Komatsu, S. & Salekdeh, G. H., 7 Jan 2019, In : Molecular Plant. 12, 1, p. 4-6 3 p.

Research output: Contribution to journalArticleResearchpeer-review

Protein Biosynthesis
Amyloid beta-Protein Precursor
Retina
Alzheimer Disease
Up-Regulation
2018

BDNF polymorphism: a review of its diagnostic and clinical relevance in neurodegenerative disorders

Shen, T., You, Y., Joseph, C., Mirzaei, M., Klistorner, A., Graham, S. L. & Gupta, V., 1 Jun 2018, In : Aging and Disease. 9, 3, p. 523-536 14 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Brain-Derived Neurotrophic Factor
Neurodegenerative Diseases
Valine
Methionine
Glaucoma

Bexarotene modulates Retinoid-X-receptor expression and is protective against neurotoxic endoplasmic reticulum stress response and apoptotic pathway activation

Dheer, Y., Chitranshi, N., Gupta, V., Abbasi, M., Mirzaei, M., You, Y., Chung, R., Graham, S. L. & Gupta, V., Dec 2018, In : Molecular Neurobiology. 55, 12, p. 9043-9056 14 p.

Research output: Contribution to journalArticleResearchpeer-review

Retinoid X Receptors
Endoplasmic Reticulum Stress
Retinoid X Receptor gamma
Retinoid X Receptor beta
Brain

Combining RNA-seq and proteomic profiling in cryopreserved human sperm exposed to sublethal stress: new biomarkers for stress-tolerance in sperm

Hezavehei, M., Shahverdi, A., Salekdeh, G. H., Mirzaei, M., Sharafi, M., Eftekhari-Yazdi, P., Nikmehr, B., Seifi, S. & Mirshahvaladi, S., Jul 2018, In : Human Reproduction. 33, Suppl. 1, p. 90-91 2 p., O-199.

Research output: Contribution to journalMeeting abstractResearch

Differential protein expression and post-translational modifications in metronidazole-resistant Giardia duodenalis

Emery, S. J., Baker, L., Ansell, B. R. E., Mirzaei, M., Haynes, P. A., McConville, M. J., Svärd, S. G. & Jex, A. R., 1 Apr 2018, In : GigaScience. 7, 4, p. 1-22 22 p., giy024.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File

Discovery of novel cell surface markers for purification of embryonic dopamine progenitors for transplantation in Parkinson's disease animal models

Fathi, A., Mirzaei, M., Dolatyar, B., Sharifitabar, M., Bayat, M., Shahbazi, E., Lee, J., Javan, M., Zhang, S-C., Gupta, V., Lee, B., Haynes, P. A., Baharvand, H. & Salekdeh, G. H., 1 Sep 2018, In : Molecular and Cellular Proteomics. 17, 9, p. 1670-1684 15 p.

Research output: Contribution to journalArticleResearchpeer-review

Pluripotent Stem Cells
Contactin 2
Stem cells
Purification
Parkinson Disease

Distinct changes in the proteome profile of endometrial tissues in polycystic ovary syndrome compared with healthy fertile women

Amjadi, F., Mehdizadeh, M., Ashrafi, M., Nasrabadi, D., Taleahmad, S., Mirzaei, M., Gupta, V., Salekdeh, G. H. & Aflatoonian, R., Aug 2018, In : Reproductive BioMedicine Online. 37, 2, p. 184-200 17 p.

Research output: Contribution to journalArticleResearchpeer-review

Polycystic Ovary Syndrome
Proteome
Proteins
14-3-3 Proteins
Luteal Phase

Distribution and development of molecularly distinct perineuronal nets in visual thalamus

Sabbagh, U., Monavarfeshani, A., Su, K., Zabet-Moghadam, M., Cole, J., Carnival, E., Su, J., Mirzaei, M., Gupta, V., Salekdeh, G. H. & Fox, M. A., Dec 2018, In : Journal of Neurochemistry. 147, 5, p. 626-646 21 p.

Research output: Contribution to journalArticleResearchpeer-review

Geniculate Bodies
Retinal Ganglion Cells
Thalamus
Retina
Rodentia

FTY720 promotes cellular pathways involved in myelination and anti-oxidant system in the brain cortex

Mirzaei, M., Gupta, V., Klistorner, A. & Graham, SL., 10 Apr 2018, In : Neurology. 90, 15 Supplement, P1.411.

Research output: Contribution to journalMeeting abstractResearch

Open Access
Oxidants
Brain
Proteins
Pharmaceutical Preparations
Multiple Sclerosis

Linking transcriptomics and proteomics in cryopreserved human sperm

Hezavehei, M., Mirzaei, M., Salekdeh, G. H., Shahverdi, A., Eftekhari-Yazdi, P. & Sharafi, M., Feb 2018, In : Cryobiology. 80, p. 175 1 p., S75.

Research output: Contribution to journalMeeting abstractResearch

transcriptomics
Proteomics
proteomics
Spermatozoa
spermatozoa

Molecular similarities and differences between human and rat retinas in glaucoma

Mirzaei, M., Gupta, V., Chitranshi, N., Wu, Y. & Graham, S. L., 2018, In : IOVS. 59, 9, p. 3531 1 p.

Research output: Contribution to journalMeeting abstractResearchpeer-review

Glaucoma
Retina
Up-Regulation
Down-Regulation
Retinal Ganglion Cells

Prospective isolation of ISL1+ cardiac progenitors from human ESCs for myocardial infarction therapy

Ghazizadeh, Z., Fattahi, F., Mirzaei, M., Bayersaikhan, D., Lee, J., Chae, S., Hwang, D., Byun, K., Tabar, M. S., Taleahmad, S., Mirshahvaladi, S., Shabani, P., Fonoudi, H., Haynes, P. A., Baharvand, H., Aghdami, N., Evans, T., Lee, B. & Salekdeh, G. H., 13 Mar 2018, In : Stem Cell Reports. 10, 3, p. 848-859 12 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Activated-Leukocyte Cell Adhesion Molecule
Muscle
Myocardial Infarction
Stem cells
Smooth Muscle Myocytes

Regulation of brain-derived neurotrophic factor and growth factor signaling pathways by tyrosine phosphatase Shp2 in the retina: a brief review

Abbasi, M., Gupta, V., Chitranshi, N., You, Y., Dheer, Y., Mirzaei, M. & Graham, S. L., 27 Mar 2018, In : Frontiers in Cellular Neuroscience. 12, p. 1-10 10 p., 85.

Research output: Contribution to journalShort surveyResearchpeer-review

Open Access
File
Brain-Derived Neurotrophic Factor
Phosphoric Monoester Hydrolases
Tyrosine
Retina
Intercellular Signaling Peptides and Proteins

Retinal changes in Alzheimer's disease: disease mechanisms to evaluation perspectives

Mirzaei, M., Gupta, V. B. & Gupta, V. K., 2018, In : Journal of Neurology & Neuromedicine. 3, 2, p. 11-13 3 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File

Stress preconditioning of sperm for cryopreservation: new approach based on proteomics characteristics

Hezavehei, M., Kouchesfahani, H. M., Salekdeh, G. H., Mirzaei, M., Sharafi, M., Eftekhari-Yazdi, P., Tobraggaleh, T. R. & Shahverdi, A., Feb 2018, In : Cryobiology. 80, p. 190 1 p., P42.

Research output: Contribution to journalMeeting abstractResearch

Cryopreservation
Proteomics
proteomics
cryopreservation
Spermatozoa

Surface markers of human embryonic stem cells: a meta analysis of membrane proteomics reports

Shekari, F., Han, C. L., Lee, J., Mirzaei, M., Gupta, V., Haynes, P. A., Lee, B., Baharvand, H., Chen, Y. J. & Hosseini Salekdeh, G., 2 Nov 2018, In : Expert Review of Proteomics. 15, 11, p. 911-922 12 p.

Research output: Contribution to journalReview articleResearchpeer-review

Stem cells
Proteomics
Meta-Analysis
Membrane Proteins
Membranes

The Art of validating quantitative proteomics data

Handler, D. C., Pascovici, D., Mirzaei, M., Gupta, V., Salekdeh, G. H. & Haynes, P. A., Dec 2018, In : Proteomics. 18, 23, p. 1-6 6 p., 1800222.

Research output: Contribution to journalArticleResearchpeer-review

Art
Proteomics
Western Blotting
Publications
Guidelines
2017

A comprehensive assessment of the biosynthetic pathways of ascorbate, alpha-tocopherol and free amino acids in Euglena gracilis var. saccharophila

Hasan, M. T., Sun, A., Mirzaei, M., Te'o, J., Hobba, G., Sunna, A. & Nevalainen, H., Nov 2017, In : Algal Research. 27, p. 140-151 12 p.

Research output: Contribution to journalArticleResearchpeer-review

Euglena gracilis
free amino acids
alpha-tocopherol
biochemical pathways
proteomics

Age-related neurodegenerative disease associated pathways identified in retinal and vitreous proteome from human glaucoma eyes

Mirzaei, M., Gupta, V. B., Chick, J. M., Greco, T. M., Wu, Y., Chitranshi, N., Wall, R. V., Hone, E., Deng, L., Dheer, Y., Abbasi, M., Rezaeian, M., Braidy, N., You, Y., Salekdeh, G. H., Haynes, P. A., Molloy, M. P., Martins, R., Cristea, I. M., Gygi, S. P. & 2 othersGraham, S. L. & Gupta, V. K., 4 Oct 2017, In : Scientific Reports. 7, 1, p. 1-16 16 p., 12685.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Proteome
Neurodegenerative Diseases
Glaucoma
Proteins
Vitreous Body

A proteomics approach to discover drought tolerance proteins in wheat pollen grain at meiosis stage

Fotovat, R., Alikhani, M., Valizadeh, M., Mirzaei, M. & Salekdeh, G. H., 2017, In : Protein and peptide letters. 24, 1, p. 26-36 11 p.

Research output: Contribution to journalArticleResearchpeer-review

Drought
Droughts
Meiosis
Pollen
Proteomics

Barley grain proteomics

Willows, R. D., Worden, P. & Mirzaei, M., 2017, Proteomics in food science: from farm to fork. Cosgrove, M. L. (ed.). London; San Diego; Cambridge; Oxford: Academic Press, p. 75-88 14 p.

Research output: Chapter in Book/Report/Conference proceedingChapterResearchpeer-review

Beer
Hordeum
Proteome
Proteomics
Beverages

Glaucoma is associated with plasmin proteolytic activation mediated through oxidative inactivation of neuroserpin

Gupta, V., Mirzaei, M., Gupta, V. B., Chitranshi, N., Dheer, Y., Vander Wall, R., Abbasi, M., You, Y., Chung, R. & Graham, S., 1 Dec 2017, In : Scientific Reports. 7, p. 1-18 18 p., 8412.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Fibrinolysin
Glaucoma
Retina
Methionine
Serpins

Low focal adhesion signaling promotes ground state pluripotency of mouse embryonic stem cells

Taleahmad, S., Mirzaei, M., Samadian, A., Hassani, S. N., Haynes, P. A., Salekdeh, G. H. & Baharvand, H., 2017, In : Journal of Proteome Research. 16, 10, p. 3585-3595 11 p.

Research output: Contribution to journalArticleResearchpeer-review

Focal Adhesions
Stem cells
Ground state
Adhesion
Serum

Mapping proteomics changes induced by fingolimod in different regions of the brain and retina

Gupta, V., Mirzaei, M., Klistorner, A. & Graham, SL., Oct 2017, In : Multiple Sclerosis Journal. 23, 3 suppl, p. 882-883 2 p., EP1679.

Research output: Contribution to journalMeeting abstractResearch

Proteomics
Retina
Brain
Frontal Lobe
Cerebellum

Proteomics of rice - our most valuable food crop

Wu, Y., Mirzaei, M. & Haynes, P. A., 5 Apr 2017, Proteomics in Food Science: from Farm to Fork. Colgrave, M. L. (ed.). London ; San Diego ; Cambridge ; Oxford: Elsevier, p. 17-33 17 p.

Research output: Chapter in Book/Report/Conference proceedingChapterResearchpeer-review

food crops
Climate change
Proteomics
proteomics
Crops

PTPN11 induces endoplasmic stress and apoptosis in SH-SY5Y cells

Chitranshi, N., Dheer, Y., Gupta, V., Abbasi, M., Mirzaei, M., You, Y., Chung, R., Graham, S. L. & Gupta, V., 19 Nov 2017, In : Neuroscience. 364, p. 175-189 15 p.

Research output: Contribution to journalArticleResearchpeer-review

Endoplasmic Reticulum Stress
Apoptosis
trkB Receptor
Up-Regulation
Dependovirus

Quantitative proteomic analysis of human testis reveals system-wide molecular and cellular pathways associated with non-obstructive azoospermia

Alikhani, M., Mirzaei, M., Sabbaghian, M., Parsamatin, P., Karamzadeh, R., Adib, S., Sodeifi, N., Gilani, M. A. S., Zabet-Moghaddam, M., Parker, L., Wu, Y., Gupta, V., Haynes, P. A., Gourabi, H., Baharvand, H. & Salekdeh, G. H., 6 Jun 2017, In : Journal of Proteomics. 162, p. 141-154 14 p.

Research output: Contribution to journalArticleResearchpeer-review

Azoospermia
Sertoli Cell-Only Syndrome
Proteomics
Testis
Male Infertility

The proteomic profile of rice mitosis under drought stress

Haynes, P. A., Wu, Y., Mirzaei, M., Pascovici, D. & Atwell, B. J., 2017.

Research output: Contribution to conferenceAbstractResearch

proteomics
mitosis
water stress
drought
rice

TMT one-stop shop: from reliable sample preparation to computational analysis platform

Mirzaei, M., Pascovici, D., Wu, J. X., Chick, J., Wu, Y., Cooke, B., Haynes, P. & Molloy, M. P., 2017, Proteome Bioinformatics: Methods in Molecular Biology. Keerthikumar, S. & Mathivanan, S. (eds.). New York: Humana Press Inc., Vol. 1549. p. 45-66 22 p. (Methods in Molecular Biology; vol. 1549).

Research output: Chapter in Book/Report/Conference proceedingChapterResearchpeer-review

Workflow
Proteome
Proteomics
Multivariate Analysis
2016

Applications of quantitative proteomics in plant research

Mirzaei, M., Wu, Y., Handler, D., Maher, T., Pascovici, D., Ravishankar, P., Moghaddam, M. Z., Haynes, P. A., Salekdeh, G. H., Chick, J. M. & Willows, R. D., 1 Jan 2016, Agricultural proteomics volume 1: Crops, horticulture, farm animals, food, insect and microorganisms. Salekdeh, G. H. (ed.). Switzerland: Springer, Springer Nature, Vol. 1. p. 1-29 29 p.

Research output: Chapter in Book/Report/Conference proceedingChapterResearchpeer-review

Proteomics
proteomics
Research
instrumentation
Bioinformatics

Extended exposure to sugar and/or caffeine produces distinct behavioral and neurochemical profiles in the orbitofrontal cortex of rats: Implications for neural function

Franklin, J. L., Mirzaei, M., Wearne, T. A., Homewood, J., Goodchild, A. K., Haynes, P. A. & Cornish, J. L., 1 Nov 2016, In : Proteomics. 16, 22, p. 2894-2910 17 p.

Research output: Contribution to journalArticleResearchpeer-review

Caffeine
Prefrontal Cortex
Sugars
Rats
Proteomics

How proteomics contributes to our understanding of drought tolerance

Mirzaei, M., Wu, Y., Worden, P., Jerkovic, A. & Atwell, B. J., 2016, Agricultural Proteomics Volume 2: Environmental Stresses. Salekdeh, G. H. (ed.). Cham: Springer, Springer Nature, p. 129-153 25 p.

Research output: Chapter in Book/Report/Conference proceedingChapterResearchpeer-review

Drought
Droughts
drought tolerance
Proteomics
proteomics
Inflammation
Biopsy
Immune Response
muscles
Acute

Induction of virulence factors in giardia duodenalis independent of host attachment

Emery, S. J., Mirzaei, M., Vuong, D., Pascovici, D., Chick, J. M., Lacey, E. & Haynes, P. A., 12 Feb 2016, In : Scientific Reports. 6, p. 1-16 16 p., 20765.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
Giardia lamblia
Trophozoites
Virulence Factors
Host-Parasite Interactions
Reactive Oxygen Species

PlantPReS: a database for plant proteome response to stress

Mousavi, S. A., Pouya, F. M., Ghaffari, M. R., Mirzaei, M., Ghaffari, A., Alikhani, M., Ghareyazie, M., Komatsu, S., Haynes, P. A. & Salekdeh, G. H., 30 Jun 2016, In : Journal of Proteomics. 143, p. 69-72 4 p.

Research output: Contribution to journalArticleResearchpeer-review

Proteome
Data Mining
Databases
Heat-Shock Proteins
Proteomics

Proteomic changes in the adrenal medulla following a single episode of glucoprivation: a time-course study

Goodchild, A., Bokiniec, P., Wall, R. V., Hassan, S., Parker, L., Moghaddam, M. Z. & Mirzaei, M., 2016, In : Journal of Neurochemistry. 134, S1, p. 232 1 p.

Research output: Contribution to journalMeeting abstractResearchpeer-review

Quantitative proteomic analysis of human testis reveals system-wide molecular pathways associated with non-obstructive Azoospermia: Poster presentation

Mirzaei, M., Alikhani, M., Sabbaghian, M., Gilani, M. A. S., Moghaddam, M. Z., Wu, Y., Haynes, P. A. & Salekdeh, H., 19 Jun 2016.

Research output: Contribution to conferencePosterResearchpeer-review

Posters
Azoospermia
Male Infertility
Proteomics
Testis