Publications

• Bettinger JQ, Welle KA, Hryhorenko JR, Ghaemmaghami S. Quantitative analysis of in vivo methionine oxidation of the human proteome. Journal of Proteome Research. 2019 Feb.
• Yang S, Li H, Bhatti S, Zhou S, Yang Y, Fish T, Thannhauser TW. The Al-induced proteomes of epidermal and outer cortical cells in root apex of cherry tomato ‘LA 2710’. Journal of proteomics. 2020 Jan 16;211:103560.
• Sheller-Miller S, Radnaa E, Arita Y, Getahun D, Jones RJ, Peltier MR, Menon R. Environmental pollutant induced cellular injury is reflected in exosomes from placental explants. Placenta. 2020 Jan 1;89:42-9.
• Nkamba I, Mulet C, Dubey GP, Gorgette O, Couesnon A, Salles A, Moya-Nilges M, Jung V, Gaboriau-Routhiau V, Guerrera IC, Shima T. Intracellular offspring released from SFB filaments are flagellated. Nature Microbiology. 2020 Jan;5(1):34-9.
• Bhagwat AR, Le Sage V, Nturibi E, Kulej K, Jones J, Guo M, Kim ET, Garcia BA, Weitzman MD, Shroff H, Lakdawala SS. Quantitative live cell imaging reveals influenza virus manipulation of Rab11A transport through reduced dynein association. Nature Communications. 2020 Jan 7;11(1):1-4.
• Gibbs KD, Washington EJ, Jaslow SL, Bourgeois JS, Foster MW, Guo R, Brennan RG, Ko DC. The Salmonella Secreted Effector SarA/SteE Mimics Cytokine Receptor Signaling to Activate STAT3. Cell Host & Microbe. 2020 Jan 8;27(1):129-39.
• Carabetta VJ, Greco TM, Cristea IM, Dubnau D. YfmK is an Nε-lysine acetyltransferase that directly acetylates the histone-like protein HBsu in Bacillus subtilis. Proceedings of the National Academy of Sciences. 2019 Feb 26;116(9):3752-7.
• Christakopoulos C, Cehofski LJ, Christensen SR, Vorum H, Honoré B. Proteomics reveals a set of highly enriched proteins in epiretinal membrane compared with inner limiting membrane. Experimental eye research. 2019 Sep 1;186:107722.
• Cremer SE, Catalfamo JL, Goggs R, Seemann SE, Kristensen AT, Brooks MB. Proteomic profiling of the thrombin-activated canine platelet secretome (CAPS). PloS one. 2019;14(11).
• Dehghan E, Goodarzi M, Saremi B, Lin R, Mirzaei H. Hydralazine targets cAMP-dependent protein kinase leading to sirtuin1/5 activation and lifespan extension in C. elegans. Nature communications. 2019 Oct 28;10(1):1-6.
• Eliash N, Thangarajan S, Goldenberg I, Sela N, Kupervaser M, Barlev J, Altman Y, Knyazer A, Kamer Y, Zaidman I, Rafaeli A. Varroa chemosensory proteins: some are conserved across Arthropoda but others are arachnid specific. Insect molecular biology. 2019 Jun;28(3):321-41.
• Even A, Morelli G, Broix L, Scaramuzzino C, Turchetto S, Gladwyn-Ng I, Le Bail R, Shilian M, Freeman S, Magiera MM, Jijumon AS. ATAT1-enriched vesicles promote microtubule acetylation via axonal transport. Science Advances. 2019 Dec 1;5(12):eaax2705.
• Bosserman RE, Nicholson KR, Champion MM, Champion PA. A new ESX-1 substrate in Mycobacterium marinum that is required for hemolysis but not host cell lysis. Journal of bacteriology. 2019 Jul 15;201(14):e00760-18.
• Guergues J, Zhang P, Liu B, Stevens Jr SM. Improved Methodology for Sensitive and Rapid Quantitative Proteomic Analysis of Adult‐Derived Mouse Microglia: Application to a Novel In Vitro Mouse Microglial Cell Model. Proteomics. 2019 Jun;19(11):1800469.
• Javitt A, Barnea E, Kramer M, Wolf-Levy H, Levin Y, Admon A, Merbl Y. Pro-inflammatory cytokines alter the immunopeptidome landscape by modulation of HLA-B expression. Frontiers in immunology. 2019;10:141.
• Johnson T, Payne S, Grove R, McCarthy S, Oeltjen E, Mach C, Adamec J, Wilson MA, Van Cott K, Blum P. Methylation deficiency of chromatin proteins is a non-mutational and epigenetic-like trait in evolved lines of the archaeon Sulfolobus solfataricus. Journal of Biological Chemistry. 2019 May 10;294(19):7821-32.
• Lopez CA, Beavers WN, Weiss A, Knippel RJ, Zackular JP, Chazin W, Skaar EP. The Immune Protein Calprotectin Impacts Clostridioides difficile Metabolism through Zinc Limitation. mBio. 2019 Dec 17;10(6).
• Agosto LM, Gazzara MR, Radens CM, Sidoli S, Baeza J, Garcia BA, Lynch KW. Deep profiling and custom databases improve detection of proteoforms generated by alternative splicing. Genome research. 2019 Dec 1;29(12):2046-55.
• Ma L, Herren AW, Espinal G, Randol J, McLaughlin B, Martinez-Cerdeño V, Pessah IN, Hagerman RJ, Hagerman PJ. Composition of the Intranuclear Inclusions of Fragile X-associated Tremor/Ataxia Syndrome. Acta neuropathologica communications. 2019 Dec 1;7(1):143.
• Michailowsky V, Li H, Mittra B, Iyer SR, Mazála DA, Corrotte M, Wang Y, Chin ER, Lovering RM, Andrews NW. Defects in sarcolemma repair and skeletal muscle function after injury in a mouse model of Niemann-Pick type A/B disease. Skeletal muscle. 2019 Dec;9(1):1-5.
• Miyazaki Y, Murayama K, Fathi I, Imura T, Yamagata Y, Watanabe K, Maeda H, Inagaki A, Igarashi Y, Miyagi S, Shima H. Strategy towards tailored donor tissue-specific pancreatic islet isolation. PloS one. 2019;14(5).
• Naamati A, Williamson JC, Greenwood EJ, Marelli S, Lehner PJ, Matheson NJ. Functional proteomic atlas of HIV infection in primary human CD4+ T cells. Elife. 2019 Mar 12;8:e41431.
• Lum KK, Howard TR, Pan C, Cristea IM. Charge-Mediated Pyrin Oligomerization Nucleates Antiviral IFI16 Sensing of Herpesvirus DNA. mBio. 2019 Aug 27;10(4):e01428-19.
• Anderson AP, Luo X, Russell W, Yin YW. Oxidative damage diminishes mitochondrial DNA polymerase replication fidelity. Nucleic Acids Research. 2020 Jan 24;48(2):817-29.
• Peng C, Andersen B, Arshid S, Larsen MR, Albergaria H, Lametsch R, Arneborg N. Proteomics insights into the responses of Saccharomyces cerevisiae during mixed-culture alcoholic fermentation with Lachancea thermotolerans. FEMS microbiology ecology. 2019 Sep;95(9):fiz126.
• Rezazadeh S, Yang D, Tombline G, Simon M, Regan SP, Seluanov A, Gorbunova V. SIRT6 promotes transcription of a subset of NRF2 targets by mono-ADP-ribosylating BAF170. Nucleic acids research. 2019 Sep 5;47(15):7914-28.
• Rojas A, Baneth G. Secretome of the carcinogenic helminth Spirocerca lupi reveals specific parasite proteins associated with its different life stages. Veterinary parasitology. 2019 Nov 1;275:108935.
• van Oostrum M, Müller M, Klein F, Bruderer R, Zhang H, Pedrioli PG, Reiter L, Tsapogas P, Rolink A, Wollscheid B. Classification of mouse B cell types using surfaceome proteotype maps. Nature Communications. 2019 Dec 16;10(1):1-9.
• Antelo-Varela M, Bartel J, Quesada-Ganuza A, Appel K, Bernal-Cabas M, Sura T, Otto A, Rasmussen M, van Dijl JM, Nielsen A, Maaß S. Ariadne’s Thread in the Analytical Labyrinth of Membrane Proteins: Integration of Targeted and Shotgun Proteomics for Global Absolute Quantification of Membrane Proteins. Analytical chemistry. 2019 Aug 19;91(18):11972-80.
• Sheller-Miller S, Trivedi J, Yellon SM, Menon R. Exosomes cause preterm birth in mice: Evidence for paracrine signaling in pregnancy. Scientific reports. 2019 Jan 24;9(1):1-8.
• Swearingen KE, Eng JK, Shteynberg D, Vigdorovich V, Springer TA, Mendoza L, Sather DN, Deutsch EW, Kappe SH, Moritz RL. A tandem mass spectrometry sequence database search method for identification of O-fucosylated proteins by mass spectrometry. Journal of proteome research. 2018 Dec 7;18(2):652-63.
• Serebryany E, Yu S, Trauger SA, Budnik B, Shakhnovich EI. Dynamic disulfide exchange in a crystallin protein in the human eye lens promotes cataract-associated aggregation. Journal of Biological Chemistry. 2018 Nov 16;293(46):17997-8009.
• Li H, Zhu Y, Rangu M, Wu X, Bhatti S, Zhou S, Yang Y, Fish T, Thannhauser TW. Identification of Heat-Induced Proteomes in Tomato Microspores Using LCM-Proteomics Analysis. Single Cell Biol. 2018;7(173):2.
• Parrine D, Wu BS, Muhammad B, Rivera K, Pappin D, Zhao X, Lefsrud M. Proteome modifications on tomato under extreme high light induced-stress. Proteome science. 2018 Dec 1;16(1):20.
• Arredondo SA, Swearingen KE, Martinson T, Steel R, Dankwa DA, Harupa A, Camargo N, Betz W, Vigdorovich V, Oliver BG, Kangwanrangsan N. The micronemal plasmodium proteins P36 and P52 act in concert to establish the replication-permissive compartment within infected hepatocytes. Frontiers in cellular and infection microbiology. 2018 Nov 27;8:413.

bioRxiv Publications

• Pinals RL, Yang D, Rosenberg DJ, Chaudhary T, Crothers AR, Iavarone AT, Hammel M, Landry MP. Protein Corona Composition and Dynamics on Carbon Nanotubes in Blood Plasma and Cerebrospinal Fluid. bioRxiv. 2020 Jan 1.
• Sanders B, D'Andrea D, Collins MO, Rees EE, Steward TG, Zhu Y, Chapman G, Legge SE, Pardiñas AF, Harwood AJ, Gray WP. Synaptic protein DLG2 controls neurogenic transcriptional programs disrupted in schizophrenia and related disorders. bioRxiv. 2020 Jan 1.
• Canestrari JG, Lasek-Nesselquist E, Upadhyay A, Rofaeil M, Champion MM, Wade JT, Derbyshire KM, Gray TA. Leaderless short ORFs in mycobacteria comprise a translational regulon. bioRxiv. 2019 Jan 1:834739.
• Herrera JA, Mallikarjun V, Rosini S, Montero MA, Warwood S, O'Caulian R, Knight D, Schwartz MA, Swift J. Laser capture microdissection coupled mass spectrometry (LCM-MS) for spatially resolved analysis of formalin-fixed and stained human lung tissues. bioRxiv. 2019 Jan 1:721373.
• Hilchey SP, Palshikar MG, Emo JA, Li D, Garigen J, Wang J, Mendelson ES, Cipolla V, Thakar J, Zand MS. Cyclosporine a directly affects human and mouse b cell migration in vitro by disrupting a hIF-1 α dependent, o 2 sensing, molecular switch. BMC immunology. 2020 Dec;21(1):1-8.
• Hutti CR, Welle KA, Hryhorenko JR, Ghaemmaghami S. Global analysis of protein degradation in prion infected cells. bioRxiv. 2019 Jan 1:712927.
• Johnson AG, Flynn RA, Lapointe CP, Ooi YS, Zhao ML, Yamada SB, Couthouis J, Gitler AD, Carette JE, Puglisi JD. A memory of RPS25 loss drives resistance phenotypes. bioRxiv. 2019 Jan 1:805663.
• La Cono V, Messina E, Rohde M, Arcadi E, Ciordia S, Crisafi F, Denaro R, Ferrer M, Giuliano L, Golyshin PN, Golyshina OV. Differential polysaccharide utilization is the basis for a nanohaloarchaeon: haloarchaeon symbiosis. bioRxiv. 2019 Jan 1:794461.
• Lasch P, Schneider A, Blumenscheit C, Doellinger J. Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS1) and in silico Peptide Mass Data. bioRxiv. 2019 Jan 1:870089.
• Lin Y, Zhou X, Kato M, Liu D, Ghaemmaghami S, Tu BP, McKnight SL. Redox-mediated regulation of a labile, evolutionarily conserved cross-β structure formed by the TDP43 low complexity domain. bioRxiv. 2019 Jan 1.
• Marelli S, Williamson JC, Protasio AV, Naamati A, Greenwood EJ, Deane JE, Lehner PJ, Matheson NJ. Antagonism of PP2A is an independent and conserved function of HIV-1 Vif and causes cell cycle arrest. BioRxiv. 2019 Jan 1:825752.
• Marinić M, Lynch VJ. Derivation of endometrial gland organoids from term post-partum placenta. bioRxiv. 2019 Jan 1:753780.
• Su Z, Chang Q, Drelich A, Shelite T, Judy B, Liu Y, Xiao J, Zhou C, He X, Saito T, Tang S. Annexin A2 depletion exacerbates the intracerebral microhemorrhage induced by acute rickettsia and Ebola virus infections. bioRxiv. 2019 Jan 1:862037.
• Vari B, Bloechl C, Raninger AM, Poupardin R, Beez CM, Hoog A, Brachtl G, Eminger E, Binder HM, Oeller M, Spittler A. Extracellular vesicles from therapeutic grade allogeneic human placental stromal cells induce angiogenesis and modulate immunity. bioRxiv. 2019 Jan 1:808808.
• Serebryany E, Yu S, Trauger SA, Budnik B, Shakhnovich EI. Catalysis of cataract-associated human γD crystallin aggregation via dynamic disulfide exchange. bioRxiv. 2018 Jan 1:300608.