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Items: 1 to 50 of 133

1.

Plant-Microbe Symbiosis: What Has Proteomics Taught Us?

Khatabi B, Gharechahi J, Ghaffari MR, Liu D, Haynes PA, McKay MJ, Mirzaei M, Salekdeh GH.

Proteomics. 2019 Aug;19(16):e1800105. doi: 10.1002/pmic.201800105. Review.

PMID:
31218790
2.

Proteomes of Leaf-Growing Zones in Rice Genotypes with Contrasting Drought Tolerance.

Wu Y, Mirzaei M, Pascovici D, Haynes PA, Atwell BJ.

Proteomics. 2019 May;19(9):e1800310. doi: 10.1002/pmic.201800310. Epub 2019 Apr 18.

PMID:
30891909
3.

Amyloid β Induces Early Changes in the Ribosomal Machinery, Cytoskeletal Organization and Oxidative Phosphorylation in Retinal Photoreceptor Cells.

Deng L, Pushpitha K, Joseph C, Gupta V, Rajput R, Chitranshi N, Dheer Y, Amirkhani A, Kamath K, Pascovici D, Wu JX, Salekdeh GH, Haynes PA, Graham SL, Gupta VK, Mirzaei M.

Front Mol Neurosci. 2019 Feb 22;12:24. doi: 10.3389/fnmol.2019.00024. eCollection 2019.

4.

Upregulation of Proteolytic Pathways and Altered Protein Biosynthesis Underlie Retinal Pathology in a Mouse Model of Alzheimer's Disease.

Mirzaei M, Pushpitha K, Deng L, Chitranshi N, Gupta V, Rajput R, Mangani AB, Dheer Y, Godinez A, McKay MJ, Kamath K, Pascovici D, Wu JX, Salekdeh GH, Karl T, Haynes PA, Graham SL, Gupta VK.

Mol Neurobiol. 2019 Sep;56(9):6017-6034. doi: 10.1007/s12035-019-1479-4. Epub 2019 Feb 1.

PMID:
30707393
5.

Label-free and isobaric tandem mass tag (TMT) multiplexed quantitative proteomic data of two contrasting rice cultivars exposed to drought stress and recovery.

Wu Y, Mirzaei M, Atwell BJ, Haynes PA.

Data Brief. 2018 Dec 15;22:697-702. doi: 10.1016/j.dib.2018.12.041. eCollection 2019 Feb.

6.

The Quest for Missing Proteins in Rice.

Rahiminejad M, Ledari MT, Mirzaei M, Ghorbanzadeh Z, Kavousi K, Ghaffari MR, Haynes PA, Komatsu S, Salekdeh GH.

Mol Plant. 2019 Jan 7;12(1):4-6. doi: 10.1016/j.molp.2018.11.009. Epub 2018 Dec 11. No abstract available.

PMID:
30543994
7.

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

Shekari F, Han CL, Lee J, Mirzaei M, Gupta V, Haynes PA, Lee B, Baharvand H, Chen YJ, Hosseini Salekdeh G.

Expert Rev Proteomics. 2018 Nov;15(11):911-922. doi: 10.1080/14789450.2018.1539669. Epub 2018 Oct 29. Review.

PMID:
30358457
8.

The Art of Validating Quantitative Proteomics Data.

Handler DC, Pascovici D, Mirzaei M, Gupta V, Salekdeh GH, Haynes PA.

Proteomics. 2018 Dec;18(23):e1800222. doi: 10.1002/pmic.201800222. Epub 2018 Nov 25.

PMID:
30352137
9.

Shotgun proteomic analysis of photoperiod regulated dormancy induction in grapevine.

George IS, Fennell AY, Haynes PA.

J Proteomics. 2018 Sep 15;187:13-24. doi: 10.1016/j.jprot.2018.05.014. Epub 2018 May 29.

PMID:
29857064
10.

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 SC, Gupta V, Lee B, Haynes PA, Baharvand H, Salekdeh GH.

Mol Cell Proteomics. 2018 Sep;17(9):1670-1684. doi: 10.1074/mcp.RA118.000809. Epub 2018 May 29.

11.

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

Emery SJ, Baker L, Ansell BRE, Mirzaei M, Haynes PA, McConville MJ, Svärd SG, Jex AR.

Gigascience. 2018 Apr 1;7(4). doi: 10.1093/gigascience/giy024.

12.

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 MS, Taleahmad S, Mirshahvaladi S, Shabani P, Fonoudi H, Haynes PA, Baharvand H, Aghdami N, Evans T, Lee B, Salekdeh GH.

Stem Cell Reports. 2018 Mar 13;10(3):848-859. doi: 10.1016/j.stemcr.2018.01.037. Epub 2018 Mar 1.

13.

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

Mirzaei M, Gupta VB, Chick JM, Greco TM, Wu Y, Chitranshi N, Wall RV, Hone E, Deng L, Dheer Y, Abbasi M, Rezaeian M, Braidy N, You Y, Salekdeh GH, Haynes PA, Molloy MP, Martins R, Cristea IM, Gygi SP, Graham SL, Gupta VK.

Sci Rep. 2017 Oct 4;7(1):12685. doi: 10.1038/s41598-017-12858-7.

14.

Low Focal Adhesion Signaling Promotes Ground State Pluripotency of Mouse Embryonic Stem Cells.

Taleahmad S, Mirzaei M, Samadian A, Hassani SN, Haynes PA, Salekdeh GH, Baharvand H.

J Proteome Res. 2017 Oct 6;16(10):3585-3595. doi: 10.1021/acs.jproteome.7b00322. Epub 2017 Sep 13.

PMID:
28850235
15.

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 MAS, Zabet-Moghaddam M, Parker L, Wu Y, Gupta V, Haynes PA, Gourabi H, Baharvand H, Salekdeh GH.

J Proteomics. 2017 Jun 6;162:141-154. doi: 10.1016/j.jprot.2017.02.007. Epub 2017 Feb 15.

PMID:
28213128
16.

Correction: The biology of environmental stress: molecular biomarkers in Sydney rock oysters (Saccostrea glomerata).

Raftos DA, Melwani AR, Haynes PA, Muralidharan S, Birch GF, Amaral V, Thompson EL, Taylor DA.

Environ Sci Process Impacts. 2016 Oct 12;18(10):1359.

PMID:
27711878
17.

Identification of proteins from 4200-year-old skin and muscle tissue biopsies from ancient Egyptian mummies of the first intermediate period shows evidence of acute inflammation and severe immune response.

Jones J, Mirzaei M, Ravishankar P, Xavier D, Lim do S, Shin DH, Bianucci R, Haynes PA.

Philos Trans A Math Phys Eng Sci. 2016 Oct 28;374(2079). pii: 20150373. doi: 10.1098/rsta.2015.0373.

18.

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

Franklin JL, Mirzaei M, Wearne TA, Homewood J, Goodchild AK, Haynes PA, Cornish JL.

Proteomics. 2016 Nov;16(22):2894-2910. doi: 10.1002/pmic.201600032. Epub 2016 Oct 14.

PMID:
27588558
19.

Data quality issues in proteomics - there are many paths to enlightenment.

Haynes PA, Stein SE, Washburn MP.

Proteomics. 2016 Sep;16(18):2433-4. doi: 10.1002/pmic.201600277. No abstract available.

PMID:
27550836
20.

The biology of environmental stress: molecular biomarkers in Sydney rock oysters (Saccostrea glomerata).

Raftos DA, Melwani AR, Haynes PA, Muralidharan S, Birch GF, Amaral V, Thompson EL, Taylor DA.

Environ Sci Process Impacts. 2016 Sep 14;18(9):1129-39. doi: 10.1039/c6em00322b. Epub 2016 Aug 22. Review. Erratum in: Environ Sci Process Impacts. 2016 Oct 12;18(10):1359.

PMID:
27548823
21.

Multiple testing corrections in quantitative proteomics: A useful but blunt tool.

Pascovici D, Handler DC, Wu JX, Haynes PA.

Proteomics. 2016 Sep;16(18):2448-53. doi: 10.1002/pmic.201600044.

PMID:
27461997
22.

Quantitative proteomics in Giardia duodenalis-Achievements and challenges.

Emery SJ, Lacey E, Haynes PA.

Mol Biochem Parasitol. 2016 Aug;208(2):96-112. doi: 10.1016/j.molbiopara.2016.07.002. Epub 2016 Jul 19.

PMID:
27449313
23.

Relative quantification of phosphoproteomic changes in grapevine (Vitis vinifera L.) leaves in response to abscisic acid.

Rattanakan S, George I, Haynes PA, Cramer GR.

Hortic Res. 2016 Jun 22;3:16029. doi: 10.1038/hortres.2016.29. eCollection 2016.

24.

Quantitative proteomic analysis of two different rice varieties reveals that drought tolerance is correlated with reduced abundance of photosynthetic machinery and increased abundance of ClpD1 protease.

Wu Y, Mirzaei M, Pascovici D, Chick JM, Atwell BJ, Haynes PA.

J Proteomics. 2016 Jun 30;143:73-82. doi: 10.1016/j.jprot.2016.05.014. Epub 2016 May 16.

PMID:
27195813
25.

PlantPReS: A database for plant proteome response to stress.

Mousavi SA, Pouya FM, Ghaffari MR, Mirzaei M, Ghaffari A, Alikhani M, Ghareyazie M, Komatsu S, Haynes PA, Salekdeh GH.

J Proteomics. 2016 Jun 30;143:69-72. doi: 10.1016/j.jprot.2016.03.009. Epub 2016 Mar 3.

PMID:
26947550
26.

Quantitative Proteomic Analysis of the Orbital Frontal Cortex in Rats Following Extended Exposure to Caffeine Reveals Extensive Changes to Protein Expression: Implications for Neurological Disease.

Franklin JL, Mirzaei M, Wearne TA, Homewood J, Goodchild AK, Haynes PA, Cornish JL.

J Proteome Res. 2016 May 6;15(5):1455-71. doi: 10.1021/acs.jproteome.5b01043. Epub 2016 Apr 11.

PMID:
26941107
27.

Induction of virulence factors in Giardia duodenalis independent of host attachment.

Emery SJ, Mirzaei M, Vuong D, Pascovici D, Chick JM, Lacey E, Haynes PA.

Sci Rep. 2016 Feb 12;6:20765. doi: 10.1038/srep20765.

28.

Post-translational processing targets functionally diverse proteins in Mycoplasma hyopneumoniae.

Tacchi JL, Raymond BB, Haynes PA, Berry IJ, Widjaja M, Bogema DR, Woolley LK, Jenkins C, Minion FC, Padula MP, Djordjevic SP.

Open Biol. 2016 Feb;6(2):150210. doi: 10.1098/rsob.150210.

29.

Proteome Analysis of Ground State Pluripotency.

Taleahmad S, Mirzaei M, Parker LM, Hassani SN, Mollamohammadi S, Sharifi-Zarchi A, Haynes PA, Baharvand H, Salekdeh GH.

Sci Rep. 2015 Dec 16;5:17985. doi: 10.1038/srep17985.

30.

Quantitative shotgun proteomics reveals extensive changes to the proteome of the orbitofrontal cortex in rats that are hyperactive following withdrawal from a high sugar diet.

Franklin JL, Mirzaei M, Wearne TA, Sauer MK, Homewood J, Goodchild AK, Haynes PA, Cornish JL.

Proteomics. 2016 Feb;16(4):657-73. doi: 10.1002/pmic.201500126. Epub 2016 Feb 2.

PMID:
26621205
31.

Five omic technologies are concordant in differentiating the biochemical characteristics of the berries of five grapevine (Vitis vinifera L.) cultivars.

Ghan R, Van Sluyter SC, Hochberg U, Degu A, Hopper DW, Tillet RL, Schlauch KA, Haynes PA, Fait A, Cramer GR.

BMC Genomics. 2015 Nov 16;16:946. doi: 10.1186/s12864-015-2115-y.

32.

The Hsp90 inhibitor SNX-7081 is synergistic with fludarabine nucleoside via DNA damage and repair mechanisms in human, p53-negative chronic lymphocytic leukemia.

Kaufman KL, Jenkins Y, Alomari M, Mirzaei M, Best OG, Pascovici D, Mactier S, Mulligan SP, Haynes PA, Christopherson RI.

Oncotarget. 2015 Dec 1;6(38):40981-97. doi: 10.18632/oncotarget.5715.

33.

Data from a proteomic baseline study of Assemblage A in Giardia duodenalis.

Emery SJ, Lacey E, Haynes PA.

Data Brief. 2015 Aug 19;5:23-7. doi: 10.1016/j.dib.2015.08.003. eCollection 2015 Dec.

34.

Two Splice Variants of Y Chromosome-Located Lysine-Specific Demethylase 5D Have Distinct Function in Prostate Cancer Cell Line (DU-145).

Jangravi Z, Tabar MS, Mirzaei M, Parsamatin P, Vakilian H, Alikhani M, Shabani M, Haynes PA, Goodchild AK, Gourabi H, Baharvand H, Salekdeh GH.

J Proteome Res. 2015 Sep 4;14(9):3492-502. doi: 10.1021/acs.jproteome.5b00333. Epub 2015 Aug 10.

PMID:
26215926
35.

DDX3Y, a Male-Specific Region of Y Chromosome Gene, May Modulate Neuronal Differentiation.

Vakilian H, Mirzaei M, Sharifi Tabar M, Pooyan P, Habibi Rezaee L, Parker L, Haynes PA, Gourabi H, Baharvand H, Salekdeh GH.

J Proteome Res. 2015 Sep 4;14(9):3474-83. doi: 10.1021/acs.jproteome.5b00512. Epub 2015 Jul 22.

PMID:
26144214
36.

The generation gap: Proteome changes and strain variation during encystation in Giardia duodenalis.

Emery SJ, Pascovi D, Lacey E, Haynes PA.

Mol Biochem Parasitol. 2015 May;201(1):47-56. doi: 10.1016/j.molbiopara.2015.05.007. Epub 2015 Jun 1.

PMID:
26045354
37.

Proteomics of Important Food Crops in the Asia Oceania Region: Current Status and Future Perspectives.

Chakraborty S, Salekdeh GH, Yang P, Woo SH, Chin CF, Gehring C, Haynes PA, Mirzaei M, Komatsu S.

J Proteome Res. 2015 Jul 2;14(7):2723-44. doi: 10.1021/acs.jproteome.5b00211. Epub 2015 Jun 11. Review.

PMID:
26035454
38.

Quantitative proteomic analysis of cabernet sauvignon grape cells exposed to thermal stresses reveals alterations in sugar and phenylpropanoid metabolism.

George IS, Pascovici D, Mirzaei M, Haynes PA.

Proteomics. 2015 Sep;15(17):3048-60. doi: 10.1002/pmic.201400541. Epub 2015 Jun 15.

PMID:
25959233
39.

Protein identification and quantification from riverbank grape, Vitis riparia: Comparing SDS-PAGE and FASP-GPF techniques for shotgun proteomic analysis.

George IS, Fennell AY, Haynes PA.

Proteomics. 2015 Sep;15(17):3061-5. doi: 10.1002/pmic.201500085. Epub 2015 Jun 22.

PMID:
25929842
40.

Recent advances in proteomics applied to elucidate the role of environmental impacts on human health and organismal function.

Halden RU, Hartmann EM, Denslow ND, Haynes PA, LaBaer J.

J Proteome Res. 2015 Jan 2;14(1):1-4. doi: 10.1021/pr501224f. No abstract available.

PMID:
25751307
41.

Quantitative proteomic analysis of Giardia duodenalis assemblage A: A baseline for host, assemblage, and isolate variation.

Emery SJ, Lacey E, Haynes PA.

Proteomics. 2015 Jul;15(13):2281-5. doi: 10.1002/pmic.201400434. Epub 2015 Mar 30.

PMID:
25728068
42.

Current perspectives in proteomic analysis of abiotic stress in Grapevines.

George IS, Haynes PA.

Front Plant Sci. 2014 Dec 8;5:686. doi: 10.3389/fpls.2014.00686. eCollection 2014.

43.

Proteomic analysis in Giardia duodenalis yields insights into strain virulence and antigenic variation.

Emery SJ, van Sluyter S, Haynes PA.

Proteomics. 2014 Nov;14(21-22):2523-34. doi: 10.1002/pmic.201400144.

PMID:
25266764
44.

Methamphetamine-induced sensitization is associated with alterations to the proteome of the prefrontal cortex: implications for the maintenance of psychotic disorders.

Wearne TA, Mirzaei M, Franklin JL, Goodchild AK, Haynes PA, Cornish JL.

J Proteome Res. 2015 Jan 2;14(1):397-410. doi: 10.1021/pr500719f. Epub 2014 Oct 17.

PMID:
25245100
45.

Manipulating root water supply elicits major shifts in the shoot proteome.

Mirzaei M, Soltani N, Sarhadi E, George IS, Neilson KA, Pascovici D, Shahbazian S, Haynes PA, Atwell BJ, Salekdeh GH.

J Proteome Res. 2014 Feb 7;13(2):517-26. doi: 10.1021/pr400696u. Epub 2013 Dec 3.

PMID:
24266738
46.

Realizing the potential of agricultural and environmental proteomics.

Komatsu S, Haynes PA.

J Proteome Res. 2013 Nov 1;12(11):4651. doi: 10.1021/pr4010426. No abstract available.

PMID:
24175652
47.

Analysis of rice proteins using SDS-PAGE shotgun proteomics.

Neilson KA, George IS, Emery SJ, Muralidharan S, Mirzaei M, Haynes PA.

Methods Mol Biol. 2014;1072:289-302. doi: 10.1007/978-1-62703-631-3_21.

PMID:
24136530
48.

Shotgun label-free quantitative proteomics of water-deficit-stressed midmature peanut (Arachis hypogaea L.) seed.

Kottapalli KR, Zabet-Moghaddam M, Rowland D, Faircloth W, Mirzaei M, Haynes PA, Payton P.

J Proteome Res. 2013 Nov 1;12(11):5048-57. doi: 10.1021/pr400936d. Epub 2013 Oct 14.

PMID:
24094305
49.

Proteomic analysis of the dorsal and ventral hippocampus of rats maintained on a high fat and refined sugar diet.

Francis HM, Mirzaei M, Pardey MC, Haynes PA, Cornish JL.

Proteomics. 2013 Oct;13(20):3076-91. doi: 10.1002/pmic.201300124. Epub 2013 Sep 18.

PMID:
23963966
50.

Plant proteogenomics: from protein extraction to improved gene predictions.

Chapman B, Castellana N, Apffel A, Ghan R, Cramer GR, Bellgard M, Haynes PA, Van Sluyter SC.

Methods Mol Biol. 2013;1002:267-94. doi: 10.1007/978-1-62703-360-2_21.

PMID:
23625410

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