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A Mutation in Hnrnph1 That Decreases Methamphetamine-Induced Reinforcement, Reward, and Dopamine Release and Increases Synaptosomal hnRNP H and Mitochondrial Proteins.

Ruan QT, Yazdani N, Blum BC, Beierle JA, Lin W, Coelho MA, Fultz EK, Healy AF, Shahin JR, Kandola AK, Luttik KP, Zheng K, Smith NJ, Cheung J, Mortazavi F, Apicco DJ, Ragu Varman D, Ramamoorthy S, Ash PEA, Rosene DL, Emili A, Wolozin B, Szumlinski KK, Bryant CD.

J Neurosci. 2020 Jan 2;40(1):107-130. doi: 10.1523/JNEUROSCI.1808-19.2019. Epub 2019 Nov 8.


Protein-Protein Interaction Profiling in Candida albicans Revealed by Biochemical Purification-Mass Spectrometry (BP/MS).

Pourhaghighi R, O'Meara TR, Cowen LE, Emili A.

Methods Mol Biol. 2019;2049:203-211. doi: 10.1007/978-1-4939-9736-7_12.


EPIC: software toolkit for elution profile-based inference of protein complexes.

Hu LZ, Goebels F, Tan JH, Wolf E, Kuzmanov U, Wan C, Phanse S, Xu C, Schertzberg M, Fraser AG, Bader GD, Emili A.

Nat Methods. 2019 Aug;16(8):737-742. doi: 10.1038/s41592-019-0461-4. Epub 2019 Jul 15.


Mapping global protein contacts.

Vajda S, Emili A.

Science. 2019 Jul 12;365(6449):120-121. doi: 10.1126/science.aay1440. No abstract available.


Global proteomic analyses define an environmentally contingent Hsp90 interactome and reveal chaperone-dependent regulation of stress granule proteins and the R2TP complex in a fungal pathogen.

O'Meara TR, O'Meara MJ, Polvi EJ, Pourhaghighi MR, Liston SD, Lin ZY, Veri AO, Emili A, Gingras AC, Cowen LE.

PLoS Biol. 2019 Jul 8;17(7):e3000358. doi: 10.1371/journal.pbio.3000358. eCollection 2019 Jul.


Egr1 mediates the effect of insulin on leptin transcription in adipocytes.

Mohtar O, Ozdemir C, Roy D, Shantaram D, Emili A, Kandror KV.

J Biol Chem. 2019 Apr 12;294(15):5784-5789. doi: 10.1074/jbc.AC119.007855. Epub 2019 Mar 7.


Two-Dimensional Biochemical Purification for Global Proteomic Analysis of Macromolecular Protein Complexes.

Pourhaghighi R, Emili A.

Methods Mol Biol. 2019;1871:445-454. doi: 10.1007/978-1-4939-8814-3_26.


Single-platform 'multi-omic' profiling: unified mass spectrometry and computational workflows for integrative proteomics-metabolomics analysis.

Blum BC, Mousavi F, Emili A.

Mol Omics. 2018 Oct 8;14(5):307-319. doi: 10.1039/c8mo00136g. Review.


Automated Computational Inference of Multi-protein Assemblies from Biochemical Co-purification Data.

Goebels F, Hu L, Bader G, Emili A.

Methods Mol Biol. 2018;1764:391-399. doi: 10.1007/978-1-4939-7759-8_25.


Global Characterization of Protein Complexes by Biochemical Purification-Mass Spectrometry (BP/MS).

Pourhaghighi R, Emili A.

Methods Mol Biol. 2018;1764:185-191. doi: 10.1007/978-1-4939-7759-8_12.


FZD4 Marks Lateral Plate Mesoderm and Signals with NORRIN to Increase Cardiomyocyte Induction from Pluripotent Stem Cell-Derived Cardiac Progenitors.

Yoon C, Song H, Yin T, Bausch-Fluck D, Frei AP, Kattman S, Dubois N, Witty AD, Hewel JA, Guo H, Emili A, Wollscheid B, Keller G, Zandstra PW.

Stem Cell Reports. 2018 Jan 9;10(1):87-100. doi: 10.1016/j.stemcr.2017.11.008. Epub 2017 Dec 14.


The Nitrogen Regulatory PII Protein (GlnB) and N-Acetylglucosamine 6-Phosphate Epimerase (NanE) Allosterically Activate Glucosamine 6-Phosphate Deaminase (NagB) in Escherichia coli.

Rodionova IA, Goodacre N, Babu M, Emili A, Uetz P, Saier MH Jr.

J Bacteriol. 2018 Feb 7;200(5). pii: e00691-17. doi: 10.1128/JB.00691-17. Print 2018 Mar 1.


Panomics for Precision Medicine.

Sandhu C, Qureshi A, Emili A.

Trends Mol Med. 2018 Jan;24(1):85-101. doi: 10.1016/j.molmed.2017.11.001. Epub 2017 Dec 5. Review.


Global landscape of cell envelope protein complexes in Escherichia coli.

Babu M, Bundalovic-Torma C, Calmettes C, Phanse S, Zhang Q, Jiang Y, Minic Z, Kim S, Mehla J, Gagarinova A, Rodionova I, Kumar A, Guo H, Kagan O, Pogoutse O, Aoki H, Deineko V, Caufield JH, Holtzapple E, Zhang Z, Vastermark A, Pandya Y, Lai CC, El Bakkouri M, Hooda Y, Shah M, Burnside D, Hooshyar M, Vlasblom J, Rajagopala SV, Golshani A, Wuchty S, F Greenblatt J, Saier M, Uetz P, F Moraes T, Parkinson J, Emili A.

Nat Biotechnol. 2018 Jan;36(1):103-112. doi: 10.1038/nbt.4024. Epub 2017 Nov 27.


Native KCC2 interactome reveals PACSIN1 as a critical regulator of synaptic inhibition.

Mahadevan V, Khademullah CS, Dargaei Z, Chevrier J, Uvarov P, Kwan J, Bagshaw RD, Pawson T, Emili A, De Koninck Y, Anggono V, Airaksinen M, Woodin MA.

Elife. 2017 Oct 13;6. pii: e28270. doi: 10.7554/eLife.28270.


Mass spectrometry methods to study protein-metabolite interactions.

Guo H, Peng H, Emili A.

Expert Opin Drug Discov. 2017 Dec;12(12):1271-1280. doi: 10.1080/17460441.2017.1378178. Epub 2017 Sep 21. Review.


Protein complexes, big data, machine learning and integrative proteomics: lessons learned over a decade of systematic analysis of protein interaction networks.

Havugimana PC, Hu P, Emili A.

Expert Rev Proteomics. 2017 Oct;14(10):845-855. doi: 10.1080/14789450.2017.1374179. Epub 2017 Sep 18. Review.


Exercise-responsive phosphoproteins in the heart.

Guo H, Isserlin R, Emili A, Burniston JG.

J Mol Cell Cardiol. 2017 Oct;111:61-68. doi: 10.1016/j.yjmcc.2017.08.001. Epub 2017 Aug 4.


Hypoxia-Induced Changes in the Fibroblast Secretome, Exosome, and Whole-Cell Proteome Using Cultured, Cardiac-Derived Cells Isolated from Neonatal Mice.

Cosme J, Guo H, Hadipour-Lakmehsari S, Emili A, Gramolini AO.

J Proteome Res. 2017 Aug 4;16(8):2836-2847. doi: 10.1021/acs.jproteome.7b00144. Epub 2017 Jul 6.


The phosphocarrier protein HPr of the bacterial phosphotransferase system globally regulates energy metabolism by directly interacting with multiple enzymes in Escherichia coli.

Rodionova IA, Zhang Z, Mehla J, Goodacre N, Babu M, Emili A, Uetz P, Saier MH Jr.

J Biol Chem. 2017 Aug 25;292(34):14250-14257. doi: 10.1074/jbc.M117.795294. Epub 2017 Jun 20.


Mercury uptake by halophytes in response to a long-term contamination in coastal wetland salt marshes (northern Adriatic Sea).

Pellegrini E, Petranich E, Acquavita A, Canário J, Emili A, Covelli S.

Environ Geochem Health. 2017 Dec;39(6):1273-1289. doi: 10.1007/s10653-017-9981-y. Epub 2017 May 29.


Managing multiple chronic conditions in the community: a Canadian qualitative study of the experiences of older adults, family caregivers and healthcare providers.

Ploeg J, Matthew-Maich N, Fraser K, Dufour S, McAiney C, Kaasalainen S, Markle-Reid M, Upshur R, Cleghorn L, Emili A.

BMC Geriatr. 2017 Jan 31;17(1):40. doi: 10.1186/s12877-017-0431-6.


DLG5 connects cell polarity and Hippo signaling protein networks by linking PAR-1 with MST1/2.

Kwan J, Sczaniecka A, Heidary Arash E, Nguyen L, Chen CC, Ratkovic S, Klezovitch O, Attisano L, McNeill H, Emili A, Vasioukhin V.

Genes Dev. 2016 Dec 15;30(24):2696-2709. doi: 10.1101/gad.284539.116.


A Global Analysis of the Receptor Tyrosine Kinase-Protein Phosphatase Interactome.

Yao Z, Darowski K, St-Denis N, Wong V, Offensperger F, Villedieu A, Amin S, Malty R, Aoki H, Guo H, Xu Y, Iorio C, Kotlyar M, Emili A, Jurisica I, Neel BG, Babu M, Gingras AC, Stagljar I.

Mol Cell. 2017 Jan 19;65(2):347-360. doi: 10.1016/j.molcel.2016.12.004. Epub 2017 Jan 5.


The profile of adsorbed plasma and serum proteins on methacrylic acid copolymer beads: Effect on complement activation.

Wells LA, Guo H, Emili A, Sefton MV.

Biomaterials. 2017 Feb;118:74-83. doi: 10.1016/j.biomaterials.2016.11.036. Epub 2016 Nov 25.


Multiparameter functional diversity of human C2H2 zinc finger proteins.

Schmitges FW, Radovani E, Najafabadi HS, Barazandeh M, Campitelli LF, Yin Y, Jolma A, Zhong G, Guo H, Kanagalingam T, Dai WF, Taipale J, Emili A, Greenblatt JF, Hughes TR.

Genome Res. 2016 Dec;26(12):1742-1752. Epub 2016 Nov 16.


Global phosphoproteomic profiling reveals perturbed signaling in a mouse model of dilated cardiomyopathy.

Kuzmanov U, Guo H, Buchsbaum D, Cosme J, Abbasi C, Isserlin R, Sharma P, Gramolini AO, Emili A.

Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):12592-12597. Epub 2016 Oct 14.


Systematic Genetic Screens Reveal the Dynamic Global Functional Organization of the Bacterial Translation Machinery.

Gagarinova A, Stewart G, Samanfar B, Phanse S, White CA, Aoki H, Deineko V, Beloglazova N, Yakunin AF, Golshani A, Brown ED, Babu M, Emili A.

Cell Rep. 2016 Oct 11;17(3):904-916. doi: 10.1016/j.celrep.2016.09.040.


An Unbiased Chemical Proteomics Method Identifies FabI as the Primary Target of 6-OH-BDE-47.

Peng H, Guo H, Pogoutse O, Wan C, Hu LZ, Ni Z, Emili A.

Environ Sci Technol. 2016 Oct 18;50(20):11329-11336. doi: 10.1021/acs.est.6b03541. Epub 2016 Oct 7.


G9a and ZNF644 Physically Associate to Suppress Progenitor Gene Expression during Neurogenesis.

Olsen JB, Wong L, Deimling S, Miles A, Guo H, Li Y, Zhang Z, Greenblatt JF, Emili A, Tropepe V.

Stem Cell Reports. 2016 Sep 13;7(3):454-470. doi: 10.1016/j.stemcr.2016.06.012. Epub 2016 Aug 18.


Bioaccumulation of thallium and other trace metals in Biscutella laevigata nearby a decommissioned zinc-lead mine (Northeastern Italian Alps).

Pavoni E, Petranich E, Adami G, Baracchini E, Crosera M, Emili A, Lenaz D, Higueras P, Covelli S.

J Environ Manage. 2017 Jan 15;186(Pt 2):214-224. doi: 10.1016/j.jenvman.2016.07.022. Epub 2016 Jul 30.


Extracellular histones identified in crocodile blood inhibit in-vitro HIV-1 infection.

Kozlowski HN, Lai ET, Havugimana PC, White C, Emili A, Sakac D, Binnington B, Neschadim A, McCarthy SD, Branch DR.

AIDS. 2016 Aug 24;30(13):2043-52. doi: 10.1097/QAD.0000000000001159.


DoE optimization of a mercury isotope ratio determination method for environmental studies.

Berni A, Baschieri C, Covelli S, Emili A, Marchetti A, Manzini D, Berto D, Rampazzo F.

Talanta. 2016 May 15;152:179-87. doi: 10.1016/j.talanta.2016.02.012. Epub 2016 Feb 3.


Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes.

Phanse S, Wan C, Borgeson B, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, Tillier ER, Wallingford JB, Parkinson J, Marcotte EM, Emili A.

Data Brief. 2015 Dec 12;6:715-21. doi: 10.1016/j.dib.2015.11.062. eCollection 2016 Mar.


Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli.

Kumar A, Beloglazova N, Bundalovic-Torma C, Phanse S, Deineko V, Gagarinova A, Musso G, Vlasblom J, Lemak S, Hooshyar M, Minic Z, Wagih O, Mosca R, Aloy P, Golshani A, Parkinson J, Emili A, Yakunin AF, Babu M.

Cell Rep. 2016 Jan 26;14(3):648-661. doi: 10.1016/j.celrep.2015.12.060. Epub 2016 Jan 8.


Investigating Bacterial Protein Synthesis Using Systems Biology Approaches.

Gagarinova A, Emili A.

Adv Exp Med Biol. 2015;883:21-40. doi: 10.1007/978-3-319-23603-2_2. Review.


Determining composition of micron-scale protein deposits in neurodegenerative disease by spatially targeted optical microproteomics.

Hadley KC, Rakhit R, Guo H, Sun Y, Jonkman JE, McLaurin J, Hazrati LN, Emili A, Chakrabartty A.

Elife. 2015 Sep 29;4. pii: e09579. doi: 10.7554/eLife.09579.


Panorama of ancient metazoan macromolecular complexes.

Wan C, Borgeson B, Phanse S, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, Tillier ER, Wallingford JB, Parkinson J, Marcotte EM, Emili A.

Nature. 2015 Sep 17;525(7569):339-44. doi: 10.1038/nature14877. Epub 2015 Sep 7.


Mobility of heavy metals from polluted sediments of a semi-enclosed basin: in situ benthic chamber experiments in Taranto's Mar Piccolo (Ionian Sea, Southern Italy).

Emili A, Acquavita A, Covelli S, Spada L, Di Leo A, Giandomenico S, Cardellicchio N.

Environ Sci Pollut Res Int. 2016 Jul;23(13):12582-95. doi: 10.1007/s11356-015-5281-1. Epub 2015 Sep 4.


Integrative genomics positions MKRN1 as a novel ribonucleoprotein within the embryonic stem cell gene regulatory network.

Cassar PA, Carpenedo RL, Samavarchi-Tehrani P, Olsen JB, Park CJ, Chang WY, Chen Z, Choey C, Delaney S, Guo H, Guo H, Tanner RM, Perkins TJ, Tenenbaum SA, Emili A, Wrana JL, Gibbings D, Stanford WL.

EMBO Rep. 2015 Oct;16(10):1334-57. doi: 10.15252/embr.201540974. Epub 2015 Aug 11.


Unbiased phosphoproteomic method identifies the initial effects of a methacrylic acid copolymer on macrophages.

Chamberlain MD, Wells LA, Lisovsky A, Guo H, Isserlin R, Talior-Volodarsky I, Mahou R, Emili A, Sefton MV.

Proc Natl Acad Sci U S A. 2015 Aug 25;112(34):10673-8. doi: 10.1073/pnas.1508826112. Epub 2015 Aug 10.


Phosphoproteomic network analysis in the sea urchin Strongylocentrotus purpuratus reveals new candidates in egg activation.

Guo H, Garcia-Vedrenne AE, Isserlin R, Lugowski A, Morada A, Sun A, Miao Y, Kuzmanov U, Wan C, Ma H, Foltz K, Emili A.

Proteomics. 2015 Dec;15(23-24):4080-95. doi: 10.1002/pmic.201500159. Epub 2015 Sep 7.


Oxygen, carbon, and nutrient exchanges at the sediment-water interface in the Mar Piccolo of Taranto (Ionian Sea, southern Italy).

De Vittor C, Relitti F, Kralj M, Covelli S, Emili A.

Environ Sci Pollut Res Int. 2016 Jul;23(13):12566-81. doi: 10.1007/s11356-015-4999-0. Epub 2015 Jul 9.


Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation.

Marcon E, Jain H, Bhattacharya A, Guo H, Phanse S, Pu S, Byram G, Collins BC, Dowdell E, Fenner M, Guo X, Hutchinson A, Kennedy JJ, Krastins B, Larsen B, Lin ZY, Lopez MF, Loppnau P, Miersch S, Nguyen T, Olsen JB, Paduch M, Ravichandran M, Seitova A, Vadali G, Vogelsang MS, Whiteaker JR, Zhong G, Zhong N, Zhao L, Aebersold R, Arrowsmith CH, Emili A, Frappier L, Gingras AC, Gstaiger M, Paulovich AG, Koide S, Kossiakoff AA, Sidhu SS, Wodak SJ, Gräslund S, Greenblatt JF, Edwards AM.

Nat Methods. 2015 Aug;12(8):725-31. doi: 10.1038/nmeth.3472. Epub 2015 Jun 29.


Extracting high confidence protein interactions from affinity purification data: at the crossroads.

Pu S, Vlasblom J, Turinsky A, Marcon E, Phanse S, Trimble SS, Olsen J, Greenblatt J, Emili A, Wodak SJ.

J Proteomics. 2015 Apr 6;118:63-80. doi: 10.1016/j.jprot.2015.03.009. Epub 2015 Mar 14.


Large-scale label-free phosphoproteomics: from technology to data interpretation.

Guo H, Isserlin R, Lugowski A, Kuzmanov U, Emili A.

Bioanalysis. 2014 Sep;6(18):2403-20. doi: 10.4155/bio.14.188. Review.


Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy.

Isserlin R, Merico D, Wang D, Vuckovic D, Bousette N, Gramolini AO, Bader GD, Emili A.

Mol Biosyst. 2015 Jan;11(1):239-51. doi: 10.1039/c4mb00265b. Epub 2014 Oct 31.


Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli.

Vlasblom J, Zuberi K, Rodriguez H, Arnold R, Gagarinova A, Deineko V, Kumar A, Leung E, Rizzolo K, Samanfar B, Chang L, Phanse S, Golshani A, Greenblatt JF, Houry WA, Emili A, Morris Q, Bader G, Babu M.

Bioinformatics. 2015 Feb 1;31(3):306-10. doi: 10.1093/bioinformatics/btu671. Epub 2014 Oct 13.


Roles for Pbp1 and caloric restriction in genome and lifespan maintenance via suppression of RNA-DNA hybrids.

Salvi JS, Chan JN, Szafranski K, Liu TT, Wu JD, Olsen JB, Khanam N, Poon BP, Emili A, Mekhail K.

Dev Cell. 2014 Jul 28;30(2):177-91. doi: 10.1016/j.devcel.2014.05.013.

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