Paul A. Haynes, PhD - Publications

Affiliations: 
1994 Macquarie University, Macquarie Park, New South Wales, Australia 
 2000-2003 Torrey Mesa Research Institute 
 2003-2006 University of Arizona, Tucson, AZ 
 2006-2020 Molecular Sciences Macquarie University, Macquarie Park, New South Wales, Australia 
Area:
Proteomics, informatics
Website:
https://researchers.mq.edu.au/en/persons/paul-haynes

138 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Abyadeh M, Gupta V, Chitranshi N, Gupta V, Wu Y, Saks D, Wander Wall R, Fitzhenry MJ, Basavarajappa D, You Y, Salekdeh GH, Haynes PA, Graham SL, Mirzaei M. Mitochondrial Dysfunction in Alzheimer's Disease - a Proteomics Perspective. Expert Review of Proteomics. PMID 33874826 DOI: 10.1080/14789450.2021.1918550  0.96
2021 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, et al. Prospective Isolation of ISL1 Cardiac Progenitors from Human ESCs for Myocardial Infarction Therapy. Stem Cell Reports. 16: 666-668. PMID 33691147 DOI: 10.1016/j.stemcr.2021.01.012  0.96
2021 Deng L, Gupta VK, Wu Y, Pushpitha K, Chitranshi N, Gupta VB, Fitzhenry MJ, Moghaddam MZ, Karl T, Salekdeh GH, Graham SL, Haynes PA, Mirzaei M. Mouse model of Alzheimer's disease demonstrates differential effects of early disease pathology on various brain regions. Proteomics. e2000213. PMID 33559908 DOI: 10.1002/pmic.202000213  1
2020 Deng L, Handler DCL, Multari DH, Haynes PA. Comparison of protein and peptide fractionation approaches in protein identification and quantification from Saccharomyces cerevisiae. Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences. 1162: 122453. PMID 33279813 DOI: 10.1016/j.jchromb.2020.122453  1
2020 Masoomi-Aladizgeh F, Najeeb U, Hamzelou S, Pascovici D, Amirkhani A, Tan DKY, Mirzaei M, Haynes PA, Atwell BJ. Pollen development in cotton (Gossypium hirsutum) is highly sensitive to heat exposure during the tetrad stage. Plant, Cell & Environment. PMID 33047317 DOI: 10.1111/pce.13908  0.96
2020 Handler DCL, Cheng F, Shathili AM, Haynes PA. PeptideWitch-A Software Package to Produce High-Stringency Proteomics Data Visualizations from Label-Free Shotgun Proteomics Data. Proteomes. 8. PMID 32825686 DOI: 10.3390/Proteomes8030021  1
2020 Hamzelou S, Kamath KS, Masoomi-Aladizgeh F, Johnsen MM, Atwell BJ, Haynes PA. Wild and Cultivated Species of Rice Have Distinctive Proteomic Responses to Drought. International Journal of Molecular Sciences. 21. PMID 32825202 DOI: 10.3390/Ijms21175980  0.68
2020 Muralidharan S, Poon YY, Wright GC, Haynes PA, Lee NA. Quantitative proteomics analysis of high and low polyphenol expressing recombinant inbred lines (RILs) of peanut (Arachis hypogaea L.). Food Chemistry. 334: 127517. PMID 32711266 DOI: 10.1016/J.Foodchem.2020.127517  0.96
2020 Handler DCL, Haynes PA. Correction to "Statistics in Proteomics: A Meta-analysis of 100 Proteomics Papers Published in 2019". Journal of the American Society For Mass Spectrometry. PMID 32697095 DOI: 10.1021/Jasms.0C00253  1
2020 Mirzaei M, Gupta VK, Chitranshi N, Deng L, Pushpitha K, Abbasi M, Chick JM, Rajput R, Wu Y, McKay MJ, Salekdeh GH, Gupta VB, Haynes PA, Graham SL. Retinal proteomics of experimental glaucoma model reveal intraocular pressure-induced mediators of neurodegenerative changes. Journal of Cellular Biochemistry. PMID 32692886 DOI: 10.1002/Jcb.29822  1
2020 Deng L, Haynes PA, Wu Y, Amirkhani A, Kamath KS, Wu JX, Pushpitha K, Gupta V, Graham S, Gupta VK, Mirzaei M. Amyloid-beta peptide neurotoxicity in human neuronal cells is associated with modulation of insulin-like growth factor transport, lysosomal machinery and extracellular matrix receptor interactions. Neural Regeneration Research. 15: 2131-2142. PMID 32394972 DOI: 10.4103/1673-5374.282261  1
2020 Handler DCL, Haynes PA. Statistics in Proteomics: A Meta-analysis of 100 Proteomics Papers Published in 2019. Journal of the American Society For Mass Spectrometry. 31: 1337-1343. PMID 32324388 DOI: 10.1021/Jasms.9B00142  1
2020 Hamzelou S, Pascovici D, Kamath KS, Amirkhani A, McKay M, Mirzaei M, Atwell BJ, Haynes PA. Proteomic Responses to Drought Vary Widely Among Eight Diverse Genotypes of Rice (). International Journal of Molecular Sciences. 21. PMID 31935846 DOI: 10.3390/Ijms21010363  0.96
2019 Khatabi B, Gharechahi J, Ghaffari MR, Liu D, Haynes PA, McKay MJ, Mirzaei M, Salekdeh GH. Plant-microbe symbiosis: What has proteomics taught us? Proteomics. e1800105. PMID 31218790 DOI: 10.1002/Pmic.201800105  0.96
2019 Wu Y, Mirzaei M, Pascovici D, Haynes PA, Atwell BJ. Proteomes of leaf growing zones in rice genotypes with contrasting drought tolerance. Proteomics. e1800310. PMID 30891909 DOI: 10.1002/Pmic.201800310  0.96
2019 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, et al. Amyloid β Induces Early Changes in the Ribosomal Machinery, Cytoskeletal Organization and Oxidative Phosphorylation in Retinal Photoreceptor Cells. Frontiers in Molecular Neuroscience. 12: 24. PMID 30853886 DOI: 10.3389/Fnmol.2019.00024  1
2019 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, et al. Upregulation of Proteolytic Pathways and Altered Protein Biosynthesis Underlie Retinal Pathology in a Mouse Model of Alzheimer's Disease. Molecular Neurobiology. PMID 30707393 DOI: 10.1007/S12035-019-1479-4  1
2019 Wu Y, Mirzaei M, Atwell BJ, Haynes PA. Label-free and isobaric tandem mass tag (TMT) multiplexed quantitative proteomic data of two contrasting rice cultivars exposed to drought stress and recovery. Data in Brief. 22: 697-702. PMID 30656201 DOI: 10.1016/J.Dib.2018.12.041  0.96
2019 Rahiminejad M, Ledari MT, Mirzaei M, Ghorbanzadeh Z, Kavousi K, Ghaffari MR, Haynes PA, Komatsu S, Salekdeh GH. The Quest for Missing Proteins in Rice. Molecular Plant. 12: 4-6. PMID 30543994 DOI: 10.1016/J.Molp.2018.11.009  0.96
2019 Maher T, Mirzaei M, Pascovici D, Wright IJ, Haynes PA, Gallagher RV. Evidence from the proteome for local adaptation to extreme heat in a widespread tree species Functional Ecology. 33: 436-446. DOI: 10.1111/1365-2435.13260  0.96
2019 Ghaffari MR, Mirzaei M, Ghabooli M, Khatabi B, Wu Y, Zabet-Moghaddam M, Mohammadi-Nejad G, Haynes PA, Hajirezaei MR, Sepehri M, Salekdeh GH. Root endophytic fungus Piriformospora indica improves drought stress adaptation in barley by metabolic and proteomic reprogramming Environmental and Experimental Botany. 157: 197-210. DOI: 10.1016/J.Envexpbot.2018.10.002  0.96
2019 Khatabi B, Gharechahi J, Ghaffari MR, Liu D, Haynes PA, McKay MJ, Mirzaei M, Salekdeh GH. Front Cover: Plant–Microbe Symbiosis: What Has Proteomics Taught Us? Proteomics. 19: 1970141. DOI: 10.1002/Pmic.201970141  0.96
2019 Wu Y, Mirzaei M, Pascovici D, Haynes PA, Atwell BJ. Front Cover: Proteomes of Leaf‐Growing Zones in Rice Genotypes with Contrasting Drought Tolerance Proteomics. 19: 1970071. DOI: 10.1002/Pmic.201970071  0.96
2018 Shekari F, Han CL, Lee J, Mirzaei M, Gupta V, Haynes PA, Lee B, Baharvand H, Chen YJ, Hosseini Salekdeh G. Surface markers of human embryonic stem cells: a meta analysis of membrane proteomics reports. Expert Review of Proteomics. PMID 30358457 DOI: 10.1080/14789450.2018.1539669  0.96
2018 Handler D, Pascovici D, Mirzaei M, Gupta V, Salekdeh GH, Haynes PA. The Art of validating quantitative proteomics data. Proteomics. e1800222. PMID 30352137 DOI: 10.1002/Pmic.201800222  0.96
2018 George IS, Fennell AY, Haynes PA. Shotgun proteomic analysis of photoperiod regulated dormancy induction in grapevine. Journal of Proteomics. PMID 29857064 DOI: 10.1016/J.Jprot.2018.05.014  1
2018 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. Discovery of Novel Cell Surface Markers for Purification of Embryonic Dopamine progenitors for Transplantation in Parkinson's Disease Animal Models. Molecular & Cellular Proteomics : McP. PMID 29848781 DOI: 10.1074/Mcp.Ra118.000809  0.96
2018 Emery SJ, Baker L, Ansell BRE, Mirzaei M, Haynes PA, McConville MJ, Svärd SG, Jex AR. Differential protein expression and post-translational modifications in metronidazole-resistant Giardia duodenalis. Gigascience. 7. PMID 29688452 DOI: 10.1093/Gigascience/Giy024  0.96
2018 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, et al. Prospective Isolation of ISL1Cardiac Progenitors from Human ESCs for Myocardial Infarction Therapy. Stem Cell Reports. PMID 29503094 DOI: 10.1016/J.Stemcr.2018.01.037  0.96
2018 Vaibhav V, Thompson EL, Raftos DA, Haynes PA. Potential protein biomarkers of QX disease resistance in selectively bred Sydney Rock Oysters Aquaculture. 495: 144-152. DOI: 10.1016/J.Aquaculture.2018.05.035  0.44
2017 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, et al. Age-related neurodegenerative disease associated pathways identified in retinal and vitreous proteome from human glaucoma eyes. Scientific Reports. 7: 12685. PMID 28978942 DOI: 10.1038/S41598-017-12858-7  1
2017 Taleahmad S, Mirzaei M, Samadian A, Hassani SN, Haynes PA, Salekdeh GH, Baharvand H. Low Focal Adhesion Signaling Promotes Ground State Pluripotency of Mouse Embryonic Stem Cells. Journal of Proteome Research. 16: 3585-3595. PMID 28850235 DOI: 10.1021/Acs.Jproteome.7B00322  0.96
2017 Alikhani M, Mirzaei M, Sabbaghian M, Parsamatin P, Karamzadeh R, Adib S, Sodeifi N, Gilani MA, Zabet-Moghaddam M, Parker L, Wo Y, Gupta V, Haynes PA, Gourabi H, Baharvand H, et al. Quantitative proteomic analysis of human testis reveals system-wide molecular and cellular pathways associated with non-obstructive azoospermia. Journal of Proteomics. PMID 28213128 DOI: 10.1016/J.Jprot.2017.02.007  0.96
2017 Mirzaei M, Pascovici D, Wu JX, Chick J, Wu Y, Cooke B, Haynes P, Molloy MP. TMT One-Stop Shop: From Reliable Sample Preparation to Computational Analysis Platform. Methods in Molecular Biology (Clifton, N.J.). 1549: 45-66. PMID 27975283 DOI: 10.1007/978-1-4939-6740-7_5  0.96
2016 Raftos DA, Melwani AR, Haynes PA, Muralidharan S, Birch GF, Amaral V, Thompson EL, Taylor DA. Correction: The biology of environmental stress: molecular biomarkers in Sydney rock oysters (Saccostrea glomerata). Environmental Science. Processes & Impacts. PMID 27711878 DOI: 10.1039/c6em90036d  0.96
2016 Jones J, Mirzaei M, Ravishankar P, Xavier D, Lim DS, Shin DH, Bianucci R, Haynes PA. 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. Philosophical Transactions. Series a, Mathematical, Physical, and Engineering Sciences. 374. PMID 27644972 DOI: 10.1098/Rsta.2015.0373  1
2016 Franklin JL, Mirzaei M, Wearne TA, Homewood J, Goodchild AK, Haynes PA, Cornish JL. Extended exposure to sugar and/or caffeine produces distinct behavioral and neurochemical profiles in the orbitofrontal cortex of rats: Implications for neural function. Proteomics. PMID 27588558 DOI: 10.1002/Pmic.201600032  0.96
2016 Haynes PA, Stein SE, Washburn MP. Data quality issues in proteomics. Proteomics. PMID 27550836 DOI: 10.1002/Pmic.201600277  0.32
2016 Raftos DA, Melwani AR, Haynes PA, Muralidharan S, Birch GF, Amaral V, Thompson EL, Taylor DA. The biology of environmental stress: molecular biomarkers in Sydney rock oysters (Saccostrea glomerata). Environmental Science. Processes & Impacts. PMID 27548823 DOI: 10.1039/C6Em00322B  1
2016 Pascovici D, Handler D, Wu JX, Haynes PA. Multiple testing corrections in quantitative proteomics: A useful but blunt tool. Proteomics. PMID 27461997 DOI: 10.1002/Pmic.201600044  0.76
2016 Emery SJ, Lacey E, Haynes PA. Quantitative proteomics in Giardia duodenalis-Achievements and challenges. Molecular and Biochemical Parasitology. PMID 27449313 DOI: 10.1016/J.Molbiopara.2016.07.002  0.96
2016 Rattanakan S, George I, Haynes PA, Cramer GR. Relative quantification of phosphoproteomic changes in grapevine (Vitis vinifera L.) leaves in response to abscisic acid. Horticulture Research. 3: 16029. PMID 27366326 DOI: 10.1038/Hortres.2016.29  0.64
2016 Wu Y, Mirzaei M, Pascovici D, Chick JM, Atwell BJ, Haynes PA. 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. Journal of Proteomics. PMID 27195813 DOI: 10.1016/J.Jprot.2016.05.014  0.96
2016 Mousavi SA, Pouya FM, Ghaffari MR, Mirzaei M, Ghaffari A, Alikhani M, Ghareyazie M, Komatsu S, Haynes PA, Salekdeh GH. PlantPReS: A database for plant proteome response to stress. Journal of Proteomics. PMID 26947550 DOI: 10.1016/J.Jprot.2016.03.009  1
2016 Franklin JL, Mirzaei M, Wearne TA, Homewood J, Goodchild AK, Haynes PA, Cornish JL. 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. Journal of Proteome Research. PMID 26941107 DOI: 10.1021/Acs.Jproteome.5B01043  1
2016 Emery SJ, Mirzaei M, Vuong D, Pascovici D, Chick JM, Lacey E, Haynes PA. Induction of virulence factors in Giardia duodenalis independent of host attachment. Scientific Reports. 6: 20765. PMID 26867958 DOI: 10.1038/Srep20765  0.96
2016 Tacchi JL, Raymond BB, Haynes PA, Berry IJ, Widjaja M, Bogema DR, Woolley LK, Jenkins C, Minion FC, Padula MP, Djordjevic SP. Post-translational processing targets functionally diverse proteins in Mycoplasma hyopneumoniae. Open Biology. 6. PMID 26865024 DOI: 10.1098/Rsob.150210  1
2016 Emery SJ, Mirzaei M, Vuong D, Pascovici D, Chick JM, Lacey E, Haynes PA. Induction of virulence factors in giardia duodenalis independent of host attachment Scientific Reports. 6. DOI: 10.1038/srep20765  1
2016 Vaibhav V, Lepretre M, Thompson E, Raftos D, Haynes PA. Biomarkers of Winter Mortality resistance in selectively bred Sydney rock oysters (Saccostrea glomerata) Aquaculture. 465: 323-329. DOI: 10.1016/J.Aquaculture.2016.09.006  0.44
2015 Taleahmad S, Mirzaei M, Parker LM, Hassani SN, Mollamohammadi S, Sharifi-Zarchi A, Haynes PA, Baharvand H, Salekdeh GH. Proteome Analysis of Ground State Pluripotency. Scientific Reports. 5: 17985. PMID 26671762 DOI: 10.1038/Srep17985  1
2015 Franklin JL, Mirzaei M, Wearne TA, Sauer MK, Homewood J, Goodchild AK, Haynes PA, Cornish JL. 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. Proteomics. PMID 26621205 DOI: 10.1002/Pmic.201500126  1
2015 Ghan R, Van Sluyter SC, Hochberg U, Degu A, Hopper DW, Tillet RL, Schlauch KA, Haynes PA, Fait A, Cramer GR. Five omic technologies are concordant in differentiating the biochemical characteristics of the berries of five grapevine (Vitis vinifera L.) cultivars. Bmc Genomics. 16: 946. PMID 26573226 DOI: 10.1186/S12864-015-2115-Y  1
2015 Kaufman K, Jenkins Y, Alomari M, Mirzaei M, Best O, Pascovici D, Mactier S, Mulligan S, Haynes P, Christopherson RI. The Hsp90 inhibitor SNX-7081 is synergistic with fludarabine nucleoside via DNA damage and repair mechanisms in human, p53-negative chronic lymphocytic leukemia. Oncotarget. PMID 26556860 DOI: 10.18632/Oncotarget.5715  0.96
2015 Emery SJ, Lacey E, Haynes PA. Data from a proteomic baseline study of Assemblage A in Giardia duodenalis. Data in Brief. 5: 23-7. PMID 26380841 DOI: 10.1016/J.Dib.2015.08.003  1
2015 Jangravi Z, Tabar MS, Mirzaei M, Parsamatin P, Vakilian H, Alikhani M, Shabani M, Haynes PA, Goodchild AK, Gourabi H, Baharvand H, Salekdeh GH. Two Splice Variants of Y Chromosome-Located Lysine-Specific Demethylase 5D Have Distinct Function in Prostate Cancer Cell Line (DU-145). Journal of Proteome Research. 14: 3492-502. PMID 26215926 DOI: 10.1021/Acs.Jproteome.5B00333  1
2015 Vakilian H, Mirzaei M, Sharifi Tabar M, Pooyan P, Habibi Rezaee L, Parker L, Haynes PA, Gourabi H, Baharvand H, Salekdeh GH. DDX3Y, a Male-Specific Region of Y Chromosome Gene, May Modulate Neuronal Differentiation. Journal of Proteome Research. 14: 3474-83. PMID 26144214 DOI: 10.1021/Acs.Jproteome.5B00512  1
2015 Emery SJ, Pascovi D, Lacey E, Haynes PA. The generation gap: Proteome changes and strain variation during encystation in Giardia duodenalis. Molecular and Biochemical Parasitology. 201: 47-56. PMID 26045354 DOI: 10.1016/J.Molbiopara.2015.05.007  1
2015 Chakraborty S, Salekdeh GH, Yang P, Woo SH, Chin CF, Gehring C, Haynes PA, Mirzaei M, Komatsu S. Proteomics of Important Food Crops in the Asia Oceania Region: Current Status and Future Perspectives. Journal of Proteome Research. 14: 2723-44. PMID 26035454 DOI: 10.1021/Acs.Jproteome.5B00211  1
2015 George IS, Pascovici D, Mirzaei M, Haynes PA. Quantitative proteomic analysis of cabernet sauvignon grape cells exposed to thermal stresses reveals alterations in sugar and phenylpropanoid metabolism. Proteomics. 15: 3048-60. PMID 25959233 DOI: 10.1002/Pmic.201400541  1
2015 George IS, Fennell AY, Haynes PA. Protein identification and quantification from riverbank grape, Vitis riparia: Comparing SDS-PAGE and FASP-GPF techniques for shotgun proteomic analysis. Proteomics. 15: 3061-5. PMID 25929842 DOI: 10.1002/Pmic.201500085  1
2015 Halden RU, Hartmann EM, Denslow ND, Haynes PA, LaBaer J. Recent advances in proteomics applied to elucidate the role of environmental impacts on human health and organismal function. Journal of Proteome Research. 14: 1-4. PMID 25751307 DOI: 10.1021/Pr501224F  1
2015 Emery SJ, Lacey E, Haynes PA. Quantitative proteomic analysis of Giardia duodenalis assemblage A: A baseline for host, assemblage, and isolate variation. Proteomics. PMID 25728068 DOI: 10.1002/Pmic.201400434  1
2015 Wearne TA, Mirzaei M, Franklin JL, Goodchild AK, Haynes PA, Cornish JL. Methamphetamine-induced sensitization is associated with alterations to the proteome of the prefrontal cortex: implications for the maintenance of psychotic disorders. Journal of Proteome Research. 14: 397-410. PMID 25245100 DOI: 10.1021/Pr500719F  1
2015 Percy AJ, Tamura-Wells J, Albar JP, Aloria K, Amirkhani A, Araujo GDT, Arizmendi JM, Blanco FJ, Canals F, Cho JY, Colomé-Calls N, Corrales FJ, Domont G, Espadas G, Fernandez-Puente P, ... ... Haynes PA, et al. Inter-laboratory evaluation of instrument platforms and experimental workflows for quantitative accuracy and reproducibility assessment Eupa Open Proteomics. 8: 6-15. DOI: 10.1016/J.Euprot.2015.06.001  1
2015 Goodchild AK, Bokiniec P, Hassan SF, Haynes P, Parker LM, Wall RV, Moghaddam M, Mirzaei M. Molecular changes in the adrenal medulla and brain following glucoprivation Autonomic Neuroscience: Basic and Clinical. 192: 45-46. DOI: 10.1016/J.Autneu.2015.07.394  0.96
2014 George IS, Haynes PA. Current perspectives in proteomic analysis of abiotic stress in Grapevines. Frontiers in Plant Science. 5: 686. PMID 25538720 DOI: 10.3389/Fpls.2014.00686  1
2014 Emery SJ, van Sluyter S, Haynes PA. Proteomic analysis in Giardia duodenalis yields insights into strain virulence and antigenic variation. Proteomics. 14: 2523-34. PMID 25266764 DOI: 10.1002/Pmic.201400144  0.96
2014 Mirzaei M, Soltani N, Sarhadi E, George IS, Neilson KA, Pascovici D, Shahbazian S, Haynes PA, Atwell BJ, Salekdeh GH. Manipulating root water supply elicits major shifts in the shoot proteome. Journal of Proteome Research. 13: 517-26. PMID 24266738 DOI: 10.1021/Pr400696U  1
2014 Neilson KA, George IS, Emery SJ, Muralidharan S, Mirzaei M, Haynes PA. Analysis of rice proteins using SDS-PAGE shotgun proteomics. Methods in Molecular Biology (Clifton, N.J.). 1072: 289-302. PMID 24136530 DOI: 10.1007/978-1-62703-631-3_21  1
2013 Komatsu S, Haynes PA. Realizing the potential of agricultural and environmental proteomics. Journal of Proteome Research. 12: 4651. PMID 24175652 DOI: 10.1021/Pr4010426  0.4
2013 Kottapalli KR, Zabet-Moghaddam M, Rowland D, Faircloth W, Mirzaei M, Haynes PA, Payton P. Shotgun label-free quantitative proteomics of water-deficit-stressed midmature peanut (Arachis hypogaea L.) seed. Journal of Proteome Research. 12: 5048-57. PMID 24094305 DOI: 10.1021/Pr400936D  0.96
2013 Francis HM, Mirzaei M, Pardey MC, Haynes PA, Cornish JL. Proteomic analysis of the dorsal and ventral hippocampus of rats maintained on a high fat and refined sugar diet. Proteomics. 13: 3076-91. PMID 23963966 DOI: 10.1002/Pmic.201300124  1
2013 Chapman B, Castellana N, Apffel A, Ghan R, Cramer GR, Bellgard M, Haynes PA, Van Sluyter SC. Plant proteogenomics: from protein extraction to improved gene predictions. Methods in Molecular Biology (Clifton, N.J.). 1002: 267-94. PMID 23625410 DOI: 10.1007/978-1-62703-360-2_21  1
2013 Neilson KA, Keighley T, Pascovici D, Cooke B, Haynes PA. Label-free quantitative shotgun proteomics using normalized spectral abundance factors. Methods in Molecular Biology (Clifton, N.J.). 1002: 205-22. PMID 23625406 DOI: 10.1007/978-1-62703-360-2_17  0.96
2013 Neilson KA, Scafaro AP, Chick JM, George IS, Van Sluyter SC, Gygi SP, Atwell BJ, Haynes PA. The influence of signals from chilled roots on the proteome of shoot tissues in rice seedlings. Proteomics. 13: 1922-33. PMID 23580440 DOI: 10.1002/Pmic.201200475  1
2013 Cramer GR, Van Sluyter SC, Hopper DW, Pascovici D, Keighley T, Haynes PA. Proteomic analysis indicates massive changes in metabolism prior to the inhibition of growth and photosynthesis of grapevine (Vitis vinifera L.) in response to water deficit. Bmc Plant Biology. 13: 49. PMID 23514573 DOI: 10.1186/1471-2229-13-49  0.84
2013 Jangravi Z, Alikhani M, Arefnezhad B, Sharifi Tabar M, Taleahmad S, Karamzadeh R, Jadaliha M, Mousavi SA, Ahmadi Rastegar D, Parsamatin P, Vakilian H, Mirshahvaladi S, Sabbaghian M, Mohseni Meybodi A, Mirzaei M, ... ... Haynes PA, et al. A fresh look at the male-specific region of the human Y chromosome. Journal of Proteome Research. 12: 6-22. PMID 23253012 DOI: 10.1021/Pr300864K  1
2013 Monavarfeshani A, Mirzaei M, Sarhadi E, Amirkhani A, Khayam Nekouei M, Haynes PA, Mardi M, Salekdeh GH. Shotgun proteomic analysis of the Mexican lime tree infected with "CandidatusPhytoplasma aurantifolia". Journal of Proteome Research. 12: 785-95. PMID 23244174 DOI: 10.1021/Pr300865T  0.96
2013 Franklin JL, Mirzaei M, Sauer MK, Wearne TA, Goodchild AK, Haynes PA, Cornish JL. P.6.c.005 Exposure to caffeine and sucrose changes locomotor behaviour, neurobiology and response to acute methamphetamine challenge European Neuropsychopharmacology. 23. DOI: 10.1016/S0924-977X(13)70903-9  0.96
2012 Marangon M, Van Sluyter SC, Robinson EM, Muhlack RA, Holt HE, Haynes PA, Godden PW, Smith PA, Waters EJ. Degradation of white wine haze proteins by Aspergillopepsin I and II during juice flash pasteurization. Food Chemistry. 135: 1157-65. PMID 22953838 DOI: 10.1016/J.Foodchem.2012.05.042  0.84
2012 Muralidharan S, Thompson E, Raftos D, Birch G, Haynes PA. Quantitative proteomics of heavy metal stress responses in Sydney rock oysters Proteomics. 12: 906-921. PMID 22539440 DOI: 10.1002/Pmic.201100417  1
2012 Mirzaei M, Pascovici D, Atwell BJ, Haynes PA. Differential regulation of aquaporins, small GTPases and V-ATPases proteins in rice leaves subjected to drought stress and recovery. Proteomics. 12: 864-77. PMID 22539437 DOI: 10.1002/Pmic.201100389  0.96
2012 Dheilly NM, Haynes PA, Raftos DA, Nair SV. Time course proteomic profiling of cellular responses to immunological challenge in the sea urchin, Heliocidaris erythrogramma. Developmental and Comparative Immunology. 37: 243-56. PMID 22446733 DOI: 10.1016/J.Dci.2012.03.006  1
2012 Komatsu S, Haynes PA, Salekdeh GH. Promoting agriculture proteome research activities in the Asia and Oceania region. Journal of Proteome Research. 11: 1461. PMID 22324873 DOI: 10.1021/Pr300063Z  0.56
2012 Pascovici D, Keighley T, Mirzaei M, Haynes PA, Cooke B. PloGO: plotting gene ontology annotation and abundance in multi-condition proteomics experiments. Proteomics. 12: 406-10. PMID 22213732 DOI: 10.1002/Pmic.201100445  0.96
2012 Mirzaei M, Soltani N, Sarhadi E, Pascovici D, Keighley T, Salekdeh GH, Haynes PA, Atwell BJ. Shotgun proteomic analysis of long-distance drought signaling in rice roots. Journal of Proteome Research. 11: 348-58. PMID 22047206 DOI: 10.1021/Pr2008779  0.96
2012 Thompson EL, Taylor DA, Nair SV, Birch G, Haynes PA, Raftos DA. Proteomic discovery of biomarkers of metal contamination in Sydney Rock oysters (Saccostrea glomerata). Aquatic Toxicology (Amsterdam, Netherlands). 109: 202-12. PMID 22030410 DOI: 10.1016/J.Aquatox.2011.09.018  1
2012 Che Y, Mirzaei M, Best G, Zhong L, Raftery M, Mulligan SP, Haynes PA, Christopherson RI. Proteomic analysis of drug synergy between the Hsp90 inhibitor SNX7081 and fludarabine F1000research. 3. DOI: 10.7490/F1000Research.1089917.1  0.96
2011 Gammulla CG, Pascovici D, Atwell BJ, Haynes PA. Differential proteomic response of rice (Oryza sativa) leaves exposed to high- and low-temperature stress. Proteomics. 11: 2839-50. PMID 21695689 DOI: 10.1002/Pmic.201100068  0.76
2011 Thompson EL, Taylor DA, Nair SV, Birch G, Haynes PA, Raftos DA. A proteomic analysis of the effects of metal contamination on Sydney Rock Oyster (Saccostrea glomerata) haemolymph. Aquatic Toxicology (Amsterdam, Netherlands). 103: 241-9. PMID 21530475 DOI: 10.1016/J.Aquatox.2011.03.004  1
2011 Agrawal GK, Job D, Zivy M, Agrawal VP, Bradshaw RA, Dunn MJ, Haynes PA, van Wijk KJ, Kikuchi S, Renaut J, Weckwerth W, Rakwal R. Time to articulate a vision for the future of plant proteomics - A global perspective: An initiative for establishing the International Plant Proteomics Organization (INPPO). Proteomics. 11: 1559-68. PMID 21433283 DOI: 10.1002/Pmic.201000608  1
2011 Neilson KA, Mariani M, Haynes PA. Quantitative proteomic analysis of cold-responsive proteins in rice. Proteomics. 11: 1696-706. PMID 21433000 DOI: 10.1002/Pmic.201000727  0.96
2011 Neilson KA, Ali NA, Muralidharan S, Mirzaei M, Mariani M, Assadourian G, Lee A, Van Sluyter SC, Haynes PA. Less label, more free: Approaches in label-free quantitative mass spectrometry Proteomics. 11: 535-553. PMID 21243637 DOI: 10.1002/Pmic.201000553  1
2011 Marangon M, Van Sluyter SC, Neilson KA, Chan C, Haynes PA, Waters EJ, Falconer RJ. Roles of grape thaumatin-like protein and chitinase in white wine haze formation. Journal of Agricultural and Food Chemistry. 59: 733-40. PMID 21189017 DOI: 10.1021/Jf1038234  0.96
2011 Mirzaei M, Pascovici D, Keighley T, George I, Voelckel C, Heenan PB, Haynes PA. Shotgun proteomic profiling of five species of New Zealand Pachycladon. Proteomics. 11: 166-71. PMID 21182204 DOI: 10.1002/Pmic.200900816  0.96
2011 Lee A, Chick JM, Kolarich D, Haynes PA, Robertson GR, Tsoli M, Jankova L, Clarke SJ, Packer NH, Baker MS. Liver membrane proteome glycosylation changes in mice bearing an extra-hepatic tumor. Molecular & Cellular Proteomics : McP. 10: M900538MCP200. PMID 20167946 DOI: 10.1074/Mcp.M900538-Mcp200  1
2010 Gammulla CG, Pascovici D, Atwell BJ, Haynes PA. Differential metabolic response of cultured rice (Oryza sativa) cells exposed to high- and low-temperature stress. Proteomics. 10: 3001-19. PMID 20645384 DOI: 10.1002/Pmic.201000054  0.76
2010 Voelckel C, Mirzaei M, Reichelt M, Luo Z, Pascovici D, Heenan PB, Schmidt S, Janssen B, Haynes PA, Lockhart PJ. Transcript and protein profiling identify candidate gene sets of potential adaptive significance in New Zealand Pachycladon. Bmc Evolutionary Biology. 10: 151. PMID 20482888 DOI: 10.1186/1471-2148-10-151  0.96
2010 Kiesler P, Haynes PA, Shi L, Kao PN, Wysocki VH, Vercelli D. NF45 and NF90 regulate HS4-dependent interleukin-13 transcription in T cells. The Journal of Biological Chemistry. 285: 8256-67. PMID 20051514 DOI: 10.1074/Jbc.M109.041004  1
2010 Neilson KA, Gammulla CG, Mirzaei M, Imin N, Haynes PA. Proteomic analysis of temperature stress in plants. Proteomics. 10: 828-45. PMID 19953552 DOI: 10.1002/Pmic.200900538  0.96
2010 Scafaro AP, Haynes PA, Atwell BJ. Physiological and molecular changes in Oryza meridionalis Ng., a heat-tolerant species of wild rice. Journal of Experimental Botany. 61: 191-202. PMID 19819927 DOI: 10.1093/Jxb/Erp294  0.68
2009 Van Sluyter SC, Marangon M, Stranks SD, Neilson KA, Hayasaka Y, Haynes PA, Menz RI, Waters EJ. Two-step purification of pathogenesis-related proteins from grape juice and crystallization of thaumatin-like proteins. Journal of Agricultural and Food Chemistry. 57: 11376-82. PMID 19886666 DOI: 10.1021/Jf902365R  0.96
2009 Marangon M, Van Sluyter SC, Haynes PA, Waters EJ. Grape and wine proteins: their fractionation by hydrophobic interaction chromatography and identification by chromatographic and proteomic analysis. Journal of Agricultural and Food Chemistry. 57: 4415-25. PMID 19354294 DOI: 10.1021/Jf9000742  0.84
2009 Kelleher ES, Watts TD, LaFlamme BA, Haynes PA, Markow TA. Proteomic analysis of Drosophila mojavensis male accessory glands suggests novel classes of seminal fluid proteins. Insect Biochemistry and Molecular Biology. 39: 366-71. PMID 19328853 DOI: 10.1016/J.Ibmb.2009.03.003  1
2009 Lee A, Kolarich D, Haynes PA, Jensen PH, Baker MS, Packer NH. Rat liver membrane glycoproteome: Enrichment by phase partitioning and glycoprotein capture Journal of Proteome Research. 8: 770-781. PMID 19125615 DOI: 10.1021/Pr800910W  1
2008 Chick JM, Haynes PA, Bjellqvist B, Baker MS. A combination of immobilised pH gradienhts improves membrane proteomics Journal of Proteome Research. 7: 4974-4981. PMID 18837535 DOI: 10.1021/Pr800349F  1
2008 Naidoo N, Harrop SJ, Sobti M, Haynes PA, Szymczyna BR, Williamson JR, Curmi PM, Mabbutt BC. Crystal structure of Lsm3 octamer from Saccharomyces cerevisiae: implications for Lsm ring organisation and recruitment. Journal of Molecular Biology. 377: 1357-71. PMID 18329667 DOI: 10.1016/J.Jmb.2008.01.007  1
2008 Chick JM, Haynes PA, Molloy MP, Bjellqvist B, Baker MS, Len ACL. Characterization of the rat liver membrane proteome using peptide immobilized pH gradient isoelectric focusing Journal of Proteome Research. 7: 1036-1045. PMID 18211008 DOI: 10.1021/Pr700611W  1
2008 Baker MS, Haynes P, Len A, Molloy M, Lee A, Saldanha R, Chick J. Desperately Seeking Comprehensive Mammalian Membrane Proteomics Journal of Proteomics & Bioinformatics. 108-109. DOI: 10.4172/Jpb.S1000088  0.84
2007 Hattrup E, Neilson KA, Breci L, Haynes PA. Proteomic analysis of shade-avoidance response in tomato leaves Journal of Agricultural and Food Chemistry. 55: 8310-8318. PMID 17874839 DOI: 10.1021/Jf0713049  1
2007 Breci L, Haynes PA. Two-dimensional nanoflow liquid chromatography-tandem mass spectrometry of proteins extracted from rice leaves and roots Methods in Molecular Biology (Clifton, N.J.). 355: 249-266. PMID 17093316 DOI: 10.1385/1-59745-227-0:249  1
2007 Keeler M, Letarte J, Hattrup E, Hickman F, Haynes PA. Two-dimensional differential in-gel electrophoresis (DIGE) of leaf and roots of Lycopersicon esculentum. Methods in Molecular Biology (Clifton, N.J.). 355: 157-74. PMID 17093310 DOI: 10.1385/1-59745-227-0:157  0.6
2006 Rohrbough JG, Breci L, Merchant N, Miller S, Haynes PA. Verification of single-peptide protein identifications by the application of complementary database search algorithms. Journal of Biomolecular Techniques : Jbt. 17: 327-32. PMID 17122065  1
2006 Haynes PA, Miller S, Radabaugh T, Galligan M, Breci L, Rohrbough J, Hickman F, Merchant N. The wildcat toolbox: a set of perl script utilities for use in peptide mass spectral database searching and proteomics experiments. Journal of Biomolecular Techniques : Jbt. 17: 97-102. PMID 16741236  1
2006 Orsborn KI, Shubitz LF, Peng T, Kellner EM, Orbach MJ, Haynes PA, Galgiani JN. Protein expression profiling of Coccidioides posadasii by two-dimensional differential in-gel electrophoresis and evaluation of a newly recognized peroxisomal matrix protein as a recombinant vaccine candidate. Infection and Immunity. 74: 1865-72. PMID 16495561 DOI: 10.1128/Iai.74.3.1865-1872.2006  1
2005 Medina ML, Haynes PA, Breci L, Francisco WA. Analysis of secreted proteins from Aspergillus flavus. Proteomics. 5: 3153-61. PMID 16035112 DOI: 10.1002/Pmic.200401136  1
2005 Breci L, Hattrup E, Keeler M, Letarte J, Johnson R, Haynes PA. Comprehensive proteomics in yeast using chromatographic fractionation, gas phase fractionation, protein gel electrophoresis, and isoelectric focusing Proteomics. 5: 2018-2028. PMID 15852344 DOI: 10.1002/Pmic.200401103  1
2003 Panigrahi AK, Allen TE, Stuart K, Haynes PA, Gygi SP. Mass spectrometric analysis of the editosome and other multiprotein complexes in Trypanosoma brucei. Journal of the American Society For Mass Spectrometry. 14: 728-35. PMID 12837594 DOI: 10.1016/S1044-0305(03)00126-0  1
2002 Koller A, Washburn MP, Lange BM, Andon NL, Deciu C, Haynes PA, Hays L, Schieltz D, Ulaszek R, Wei J, Wolters D, Yates JR. Proteomic survey of metabolic pathways in rice Proceedings of the National Academy of Sciences of the United States of America. 99: 11969-11974. PMID 12163647 DOI: 10.1073/Pnas.172183199  1
2001 Steitz SA, Speer MY, Curinga G, Yang HY, Haynes P, Aebersold R, Schinke T, Karsenty G, Giachelli CM. Smooth muscle cell phenotypic transition associated with calcification: Upregulation of Cbfa1 and downregulation of smooth muscle lineage markers Circulation Research. 89: 1147-1154. PMID 11739279 DOI: 10.1161/Hh2401.101070  1
2000 Haynes PA, Aebersold R. Simultaneous detection and identification of O-GlcNAc-modified glycoproteins using liquid chromatography-tandem mass spectrometry. Analytical Chemistry. 72: 5402-10. PMID 11080893 DOI: 10.1021/Ac000512W  1
2000 Haynes PA, Goodlett DR, Gygi SP, Watts JD, Figeys D, Aebersold R. Towards an Integrated Analytical Technology for the Generation of Multidimensional Protein Expression Maps Journal of Protein Chemistry. 17: 143-162. DOI: 10.1007/978-1-59259-719-2_9  1
1999 Eberini I, Miller I, Gemeiner M, Haynes P, Aebersold R, Puglisi L, Sirtori CR, Gianazza E. A web site for the rat serum protein study group. Electrophoresis. 20: 3599-602. PMID 10612286 DOI: 10.1002/(Sici)1522-2683(19991201)20:18<3599::Aid-Elps3599>3.0.Co;2-K  1
1999 Miller I, Haynes P, Eberini I, Gemeiner M, Aebersold R, Gianazza E. Proteins of rat serum: III. Gender-related differences in protein concentration under baseline conditions and upon experimental inflammation as evaluated by two-dimensional electrophoresis. Electrophoresis. 20: 836-45. PMID 10344256 DOI: 10.1002/(Sici)1522-2683(19990101)20:4/5<836::Aid-Elps836>3.0.Co;2-6  1
1998 Ducret A, Bartone N, Haynes PA, Blanchard A, Aebersold R. A simplified gradient solvent delivery system for capillary liquid chromatography-electrospray ionization mass spectrometry. Analytical Biochemistry. 265: 129-38. PMID 9866717 DOI: 10.1006/Abio.1998.2873  1
1998 Haynes PA, Gygi SP, Figeys D, Aebersold R. Proteome analysis: biological assay or data archive? Electrophoresis. 19: 1862-71. PMID 9740046 DOI: 10.1002/Elps.1150191104  1
1998 Caler EV, Vaena de Avalos S, Haynes PA, Andrews NW, Burleigh BA. Oligopeptidase B-dependent signaling mediates host cell invasion by Trypanosoma cruzi. The Embo Journal. 17: 4975-86. PMID 9724634 DOI: 10.1093/Emboj/17.17.4975  1
1998 Miller I, Haynes P, Gemeiner M, Aebersold R, Manzoni C, Lovati MR, Vignati M, Eberini I, Gianazza E. Proteins of rat serum: II. Influence of some biological parameters of the two-dimensional electrophoresis pattern. Electrophoresis. 19: 1493-500. PMID 9694301 DOI: 10.1002/Elps.1150190846  1
1998 Haynes P, Miller I, Aebersold R, Gemeiner M, Eberini I, Lovati MR, Manzoni C, Vignati M, Gianazza E. Proteins of rat serum: I. Establishing a reference two-dimensional electrophoresis map by immunodetection and microbore high performance liquid chromatography-electrospray mass spectrometry. Electrophoresis. 19: 1484-92. PMID 9694300 DOI: 10.1002/Elps.1150190845  1
1998 Haynes PA, Fripp N, Aebersold R. Identification of gel-separated proteins by liquid chromatography-electrospray tandem mass spectrometry: comparison of methods and their limitations. Electrophoresis. 19: 939-45. PMID 9638940 DOI: 10.1002/Elps.1150190609  1
1996 Haynes PA, Cross GAM. Differential glycosylation of epitope-tagged glycoprotein Gp72 during the Trypanosoma cruzi life cycle Molecular and Biochemical Parasitology. 83: 253-256. PMID 9027759 DOI: 10.1016/S0166-6851(96)02764-8  1
1996 Haynes PA, Ferguson MAJ, Cross GAM. Structural characterization of novel oligosaccharides of cell-surface glycoproteins of Trypanosoma cruzi Glycobiology. 6: 869-878. PMID 9023550 DOI: 10.1093/Glycob/6.8.869  1
1996 Nozaki T, Haynes PA, Cross GAM. Characterization of the Trypanosoma brucei homologue of a Trypanosoma cruzi flagellum-adhesion glycoprotein Molecular and Biochemical Parasitology. 82: 245-255. PMID 8946390 DOI: 10.1016/0166-6851(96)02741-7  1
1996 Erwin AL, Haynes PA, Rice PA, Gotschlich EC. Conservation of the lipooligosaccharide synthesis locus lgt among strains of Neisseria gonorrhoeae: Requirement for lgtE in synthesis of the 2C7 epitope and of the β chain of strain 15253 Journal of Experimental Medicine. 184: 1233-1241. PMID 8879194 DOI: 10.1084/Jem.184.4.1233  1
1993 Haynes PA, Gooley AA, Ferguson MA, Redmond JW, Williams KL. Post-translational modifications of the Dictyostelium discoideum glycoprotein PsA. Glycosylphosphatidylinositol membrane anchor and composition of O-linked oligosaccharides. European Journal of Biochemistry. 216: 729-37. PMID 8404891 DOI: 10.1111/J.1432-1033.1993.Tb18192.X  0.92
1992 Haynes PA, Batley M, Peach RJ, Brennan SO, Redmond JW. Characterisation of oligosaccharides from a glycoprotein variant of human serum albumin (albumin Casebrook) using high-performance anion-exchange chromatography and nuclear magnetic resonance spectroscopy. Journal of Chromatography. 581: 187-93. PMID 1452609 DOI: 10.1016/0378-4347(92)80271-Q  0.92
1991 Haynes PA, Sheumack D, Kibby J, Redmond JW. Amino acid analysis using derivatisation with 9-fluorenylmethyl chloroformate and reversed-phase high-performance liquid chromatography. Journal of Chromatography. 540: 177-85. PMID 8786243 DOI: 10.1016/S0021-9673(01)88807-5  0.92
1991 Haynes PA, Sheumack D, Greig LG, Kibby J, Redmond JW. Applications of automated amino acid analysis using 9-fluorenylmethyl chloroformate. Journal of Chromatography. 588: 107-14. PMID 1687819 DOI: 10.1016/0021-9673(91)85012-5  0.92
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