Publications

Please note that Prof. Macek's publications prior to 2010 are not included.

For a selection of our publications, please check our Research page. 

263. Mattern S, Hollfoth V, Riemenschneider P, Dickemann A, Sulyok M, Jarboui MA, Boldt K, Luibrand J, Fusco S, Franz-Wachtel M, Singer K, Goeppert B, Ueffing M, Schilling O, Malek N, Macek B, Fend F, Singer S. 2024. A mass spectrometry-based morphomolecular approach identifies distinct proteomic signatures of frequent esophagitis types and is a powerful tool in precision medicine. EMBO Mol Med, accepted

262. Buchert R, Burkhalter MD, ..., Velic A, ..., Rieß O, Weber JJ, Philipp M, Haack TB. 2024. Bi-allelic KICS2 mutations impair KICSTOR complex-mediated mTORC1 regulation causing intellectual disability and epilepsy. Am J Hum Genetics, accepted

261. Hundsdorfer L, Muenkel M, Aparicio-Yuste R, Sánchez-Rendón JC, Gómez-Benito MJ, Balmes A, Schäffer TE, Velic A, Yeh T, Constantinou I, WrightK, Güler GÖ, Brokatzky D, Maček B, Mostowy S, Bastounis EE. 2024. ERK activation waves coordinate mechanical cell competition leading to collective elimination via extrusion of bacterially-infected cells. Cell Rep, accepted

260. Nashier P, Samp I, Adler M, Ebner F, Thai Lê L, Göppel M, Jers C, Mijakovic I, Schwarz S, Macek B. 2024. Deep phosphoproteomics of Klebsiella pneumoniae reveals HipA-mediated tolerance to ciprofloxacin. PLOS Pathogens, accepted

259. Malmsheimer S, Grin I, Bohn E, Franz-Wachtel M, Macek B, Sahr T, Smollich F, Chetrit D, Meir A, Roy C, Buchrieser C, Wagner S. 2024. The T4bSS of Legionella features a two-step secretion pathway with an inner membrane intermediate for secretion of transmembrane effectors. PLOS Pathogens, accepted

258. Cavarischia-Rega C, Sharma K, Fitzgerald JC, Macek B. 2024. Proteome dynamics in iPSC-derived human dopaminergic neurons. Mol Cell Proteomics 23(10):100838. doi: 10.1016/j.mcpro.2024.100838.

257. Broeckaert N, Longin H, Hendrix H, De Smet J, Franz-Wachtel M, Maček B, van Noort V, Lavigne R. 2024. Acetylomics reveals an extensive acetylation diversity within Pseudomonas aeruginosa. microLife, accepted

256. Mangilet AF, Weber J, Schüler S, Adler M, Mjema EY, Heilmann P, Herold A, Renneberg M, Nagel L, Droste-Borel I, Streicher S, Schmutzer T, Rot G, Macek B, Schmidtke C, Laubinger S. 2024. The Arabidopsis U1 snRNP regulates mRNA 3’-end processing. Nat Plants, accepted

255. Köbler C, Schmelling NM, Wiegard A, Pawlowski A, Pattanayak GK, Spät P, Scheurer NM, Sebastian KN, Stirba FP, Berwanger LC, Kolkhof P, Maček B, Rust MJ, Axmann IM, Wilde A. 2024. Two KaiABC systems control circadian oscillations in one cyanobacterium. Nat Communications, accepted

254. Ammanath AV, Matsuo M, Wang H, Kraus F, Bleisch A, Peslalz P, Mohammad M, Deshmukh M, Grießhammer A, Purkayastha M, Vorbach A, Macek B, Brötz-Oesterhelt H, Maier L, Kretschmer D, Peschel A, Jin T, Plietker B, Götz F. 2024. Antimicrobial evaluation of two Polycyclic Polyprenylated Acylphloroglucinol compounds: PPAP23 and PPAP53. Int J Mol Sci, in press

253. Frey Y, Lungu C, Meyer F, Hauth F, Hahn D, Kersten C, Heller V, Franz-Wachtel M, Macek B, Barsukov I, Olayioye MA. 2024. Regulation of the DLC3 tumor suppressor by a novel phosphoswitch. iScience 27(7):110203. doi: 10.1016/j.isci.2024.110203

252. Froehlich T, Jenner A, Cavarischia-Rega C, Fagbadebo F, Lurz Y, Frecot D, Kaiser P, Nueske S, Scholz A, Schäffer E, Garcia-Saez A, Macek B, Rothbauer U. 2024. Nanobodies as novel tools to monitor the mitochondrial fission factor Drp1. Life Science Alliance 7(8):e202402608. doi: 10.26508/lsa.202402608

251. Wyss N, ..., Macek B, ..., Walz J, Rammensee HG,...Flatz L. 2024. Autoimmunity Against Surfactant Protein B Is Associated with Pneumonitis During Checkpoint Blockade. Am J Respir Crit Care Med., in press

250. Hoffmann A, Steffens U, Macek B, Franz-Wachtel M, Nieselt K, Harbig T, Scherlach K, Hertweck C, Sahl HG, Bierbaum G. 2024. The unusual mode of action of the polyketide glycoside antibiotic cervimycin C. mSphere 9(5):e0076423. doi: 10.1128/msphere.00764-23

249. Brown A, Meiborg A, Franz-Wachtel M, Macek B, Gordon S, Rog O, Weadick C, Werner M. 2024. Characterization of the Pristionchus pacificus "epigenetic toolkit" reveals the evolutionary loss of the histone methyltransferase complex PRC2. Genetics 227(1):iyae041. doi: 10.1093/genetics/iyae041

248. Kraus A, Spät P, Timm S, Wilson A, Schumann R, Hagemann M, Macek B, Hess WR. 2024. Protein NirP1 regulates nitrite reductase and nitrite excretion in cyanobacteria. Nat Communications 15(1):1911. doi: 10.1038/s41467-024-46253-4

247. Pranjic M, Spät P, Semanjski Curkovic M, Macek B, Gruic-Sovulj I, Mocibob M. 2024. Resilience and Proteome Response of Escherichia coli to High Levels of Isoleucine Mistranslation. Biol Macromol, Volume 262/1 doi: 10.1016/j.ijbiomac.2024.130068.

246. Hanswillemenke A, Hofacker DT, Sorgenfrei M, Fruhner C, Franz-Wachtel M, Schwarzer D, Macek B, Stafforst T. 2024. Profiling the Interactome of Oligonucleotide Drugs by Proximity Biotinylation. Nat Chem Biol 20(5):555-565. doi: 10.1038/s41589-023-01530-z

245. Meraz-Torres F, Niessner H, Plöger S, Riel S, Schörg B, Casadei N, Kneilling M, Macek B, Eigentler T, Rieß O, Garbe C, Amaral T, Sinnberg T. 2024. Augmenting MEK inhibitor efficacy in BRAF wild-type melanoma: synergistic effects of disulfiram combination therapy. J Exp Clin Canc Res 43(1):30. doi: 10.1186/s13046-023-02941-5.

244. Zittlau K, Nashier P, Cavarischia-Rega C, Macek B, Spät P*, Nalpas N*. 2023. Recent progress in quantitative phosphoproteomics. Exp Rev Proteomics 20(12):469-482.

243. Barske T*, Spät P*, Schubert H, Walke P, Maček B, Hagemann M. 2023. The role of serine/threonine-specific protein kinases in cyanobacteria - SpkB is involved in acclimation to fluctuating conditions in Synechocystis sp. PCC 6803. Mol Cell Proteomics, 20(11):100656. doi: 10.1016/j.mcpro.2023.100656

242. Einig E, Jin C, Andrioletti V, Macek B, Popov N. 2023. RNAPII-dependent ATM signaling at collisions with replication forks. Nat Commun. 14(1):5147. doi: 10.1038/s41467-023-40924-4.

241. Park J, Tucci A, Cipriani V, Demidov G, Rocca C, Senderek J, Butryn M, Velic A, ..., Maček B, Synofzik M, Ossowski S, Timmann D, Wolf ME, Smedley D, Riess O, Schöls L, Houlden H, Haack TB, Hengel H. 2023. Heterozygous UCHL1 loss-of-function variants cause a neurodegenerative disorder with spasticity, ataxia, neuropathy, and optic atrophy. Genet Med. 24(10):2079-2090. doi: 10.1016/j.gim.2023.100961.

240. Sporbeck K, Haas ML, Pastor-Maldonado CJ, Schüssele DS, Hunter C, Takacs Z, Diogo de Oliveira AL, Franz-Wachtel M, Charsou C, Pfisterer SG, Gubas A, Haller PK, Knorr RL, Kaulich M, Macek B, Eskelinen EL, Simonsen A, Proikas-Cezanne T. 2023. The ABL-MYC axis controls WIPI1-enhanced autophagy in lifespan extension. Commun Biol. 6(1):872. doi: 10.1038/s42003-023-05236-9.

239. Gómez-Pérez D, Schmid M, Chaudhry V, Hu Y, Velic A, Maček B, Ruhe J, Kemen A, Kemen E. 2023. Proteins released into the plant apoplast by the obligate parasitic protist Albugo selectively repress phyllosphere-associated bacteria. New Phytol, 239(6):2320-2334.

238. Aly A, Laszlo ZI, Rajkumar S, Demir T, Hindley N, Lamont DJ, Lehmann J, Seidel M, Sommer D, Franz-Wachtel M, Barletta F, Heumos S, Czemmel S, Kabashi E, Ludolph A, Boeckers TM, Henstridge CM, Catanese A. 2023. Integrative proteomics highlight presynaptic alterations and c-Jun misactivation as convergent pathomechanisms in ALS. Acta Neuropathol. 146(3):451-475. doi: 10.1007/s00401-023-02611-y

237. Pereira Sena P, Weber JJ, Bayezit S, Saup R, Eltemur RDI, Li X, Velic A, Jung J, Macek B, Nguyen HP, Riess O, Schmidt T. 2023. Implications of specific lysine
residues within ataxin-3 for the molecular pathogenesis of Machado-Joseph disease. Front Mol Neurosci, 16:1133271

236. Spät P, Krauspe V, Hess WR, Macek B*, Nalpas N*. 2023. Deep proteogenomics of a photosynthetic cyanobacterium. J Prot Res, 22(6):1969-1983

235. Werner MS, Loschko T, King T, Reich S, Theska T, Franz-Wachtel M, Macek B, Sommer RJ. 2023. Histone 4 lysine 5/12 acetylation enables developmental plasticity of Pristionchus mouth form. Nat Commun. 14(1):2095.

234. Glumac M, Polovic M, Batel A, Gelemanovic A, Macek B, Velic A, Marinovic-Terzic I. 2023. SPRTN-dependent DPC degradation precedes repair of damaged DNA: A proof of concept revealed by the STAR assay. Nucleic Acid Res, 51(6):e35

233. Gratani FL, Englert T, Nashier P, Sass P, Mann P, Czech L, Neumann N, Doello S, Blobelt R, Alberti S, Forchhammer K, Bange G, Höfer K, Macek B. 2023. E. coli toxin YjjJ (HipH) is a Ser/Thr protein kinase that impacts cell division, carbon metabolism and ribosome assembly. mSystems, 8(1):e0104322

232. Krauss S, Harbig TA, Rapp J, Schaefle T, Franz-Wachtel M, Reetz L, Elsherbini AMA, Macek B, Grond S, Link H, Nieselt K, Krismer B, Peschel A, Heilbronner S. 2022. Horizontal Transfer of Bacteriocin Biosynthesis Genes Requires Metabolic Adaptation To Improve Compound Production and Cellular Fitness. Microbiol Spectr. 6:e0317622.

231. Schulze S, Yu L, Hua C, Zhang L, Kolb D, Weber H, Ehinger A, Saile SC, Stahl M, Franz-Wachtel M, Li L, El Kasmi F, Nürnberger T, Cevik V, Kemmerling B. 2022. The Arabidopsis TIR-NBS-LRR protein CSA1 guards BAK1-BIR3 homeostasis and mediates convergence of pattern- and effector-induced immune responses. Cell Host & Microbe, 30(12):1717-1731

230. Ammanath AV, Jarneborn A, Nguyen M, Wessling L, Tribelli P, Nega M,  Beck C, Luqman A, Selim K, Kalbacher H, Macek B, Beer Hammer S, Jin T, Götz F. 2022. From a Hsp90 - binding protein to a peptide drug. microLife, 4, 1–12

229. Lechado-Terradas A, Schepers S, Zittlau KI, Sharma K, Ok O, Fitzgerald JC, Geimer S, Westermann B, Macek B*, Kahle PJ*. 2022. Parkin-dependent mitophagy occurs via proteasome-dependent steps sequentially targeting separate mitochondrial sub-compartments for autophagy. Autophagy Rep, 1(1), 576–602

228. Dietrich A, Steffens U, Gajdiss M, Boschert AL, Dröge JK, Szekat C, Sass P, Malik IT, Bornikoel J, Reinke L, Maček B, Franz-Wachtel M, Nieselt K, Harbig T, Scherlach K, Brötz-Oesterhelt H, Hertweck C, Sahl HG, Bierbaum G. 2022. Cervimycin-Resistant Staphylococcus aureus Strains Display Vancomycin-Intermediate Resistant Phenotypes. Microbiol Spectr. 29:e0256722.

227. Birkle K, Renschler F, Angelov A, Wilharm G, Franz-Wachtel M, Maček B, Bohn E, Weber E, Müller J, Friedrich L, Schütz M. 2022. An Unprecedented Tolerance to Deletion of the Periplasmic Chaperones SurA, Skp, and DegP in the Nosocomial Pathogen Acinetobacter baumannii. J Bacteriol 15:e0005422.

226. Sinnberg T, Lichtensteiger C, Hasan Ali O, ..., Velic A, ..., Röcken M, ..., Macek B, Twerenbold R, Penninger JM, Matter MS, Flatz L. 2022. Pulmonary Surfactant Proteins are Inhibited by IgA Autoantibodies in Severe COVID-19. Am J Respir Crit Care Med, 207(1):38-49.

225. Khozooei S, Lettau K, Barletta F, Jost T, Rebholz S, Veerappan S, Franz-Wachtel M, Macek B, Iliakis G, Distel LV, Zips D, Toulany M. 2022. Fisetin induces DNA double-strand break and interferes with the repair of radiation-induced damage to radiosensitize triple negative breast cancer cells. J Exp Clin Cancer Res 22;41(1):256

224. Drwesh L, Heim B, Graf M, Kehr L, Hansen-Palmus L, Franz-Wachtel M, Macek B, Kalbacher H, Buchner J, Rapaport D. 2022. A network of cytosolic (co)chaperones promotes the biogenesis of mitochondrial signal-anchored outer membrane proteins. eLife, 11:e77706

223. Park J, Tucci A, Cipriani V,..., Velic A,..., Macek B,..., Riess O, Schöls L, Houlden H, Haack TB, Hengel H. 2022. Heterozygous UCHL1 loss-of-function variants cause a neurodegenerative disorder with spasticity, ataxia, neuropathy, and optic atrophy. Genetics in Medicine, (10):2079-2090

222. Saric E, Quinn G, Nalpas N, Paradzik T, Kazazic S, Filic Z, Semanjski M, Herron P, Hunter I, Macek B*, Vujaklija D*. 2022. Phosphoproteome dynamics of Streptomyces rimosus during submerged growth and antibiotic production. mSystems, 7(5):e0019922

221. Lebecq A, Doumane M, Fangain A, Bayle V, Leong JX, Rozier F, Marques-Bueno MD, Armengot L, Boisseau R, Simon ML, Franz-Wachtel M, Macek B, Üstün S, Jaillais Y, Caillaud MC. 2022. The Arabidopsis SAC9 enzyme is enriched in a cortical population of early endosomes and restricts PI(4,5)P2 at the plasma membrane. Elife 11:e73837

220. Große-Berkenbusch K, Avci-Adali M, Arnold M, Cahalan L, Cahalan P, Velic A, Macek B, Schlensak C, Wendel HP, Stoppelkamp S. 2022. Profiling of time-dependent human plasma protein adsorption on non-coated and heparin-coated oxygenator membranes. Biomaterials Adv. 139, 213014.

219. Abeditashi M, Weber JJ, Pereira Sena P, Velic A, Kalimeri M, Incebacak Eltemur RD, Schmidt J, Hübener-Schmid J, Hauser S, Macek B, Riess O, Schmidt T. 2022. KPNB1 modulates the Machado-Joseph disease protein ataxin-3 through activation of the mitochondrial protease CLPP. Cell Mol Life Sci. 79(8):401.

218. Leong JX, Raffeiner M, Spinti D, Langin G, Franz-Wachtel M, Guzman AR, Kim JG, Pandey P, Minina AE, Macek B, Hafrén A, Bozkurt TO, Mudgett MB, Börnke F, Hofius D, Üstün S. 2022. A bacterial effector counteracts host autophagy by promoting degradation of an autophagy component. EMBO J. 27:e110352.

217. Frey Y, Franz-Wachtel M, Macek B, Olayioye MA. 2022. Proteasomal turnover of the RhoGAP tumor suppressor DLC1 is regulated by HECTD1 and USP7. Sci Rep, 12(1):5036

216. Fagbadebo FO, Kaiser PD, Zittlau K, Bartlick N, Wagner TR, Froehlich T, Jarjour G, Nueske S, Scholz A, Traenkle B, Macek B, Rothbauer U. 2022. A nanobody-based toolset to monitor and modify the mitochondrial GTPase Miro1. Front Mol Biosci, 9: 835302

215. Zittlau KI, Terradas AL, Nalpas N, Geisler S, Kahle PJ, Macek B. 2022. Temporal Analysis of Protein Ubiquitylation and Phosphorylation During Parkin-dependent Mitophagy. Mol Cell Proteomics, 21(2):100191

214. Reuter L, Schmidt T, Manishankar P, Throm C, Keicher J, Bock A, Droste-Borel I, Oecking C. 2022. Light-triggered and phosphorylation-dependent 14-3-3 association with NON-PHOTOTROPIC HYPOCOTYL 3 is required for hypocotyl phototropism. Nat Communications, 12, 6128

213. Jenner A, Peña-Blanco A, Salvador-Gallego R, Ugarte-Uribe B, Zollo C, Ganief T, Bierlmeier J, Mund M, Lee J, Ries J, Schwarzer D, Macek B, Garcia-Saez A. 2022. Direct interaction with DRP1 activates BAX and induces apoptosis. EMBO J. 13:e108587

212. Schmitt M, Sinnberg T, Niessner H, Forschner A, Garbe C, Macek B*, Nalpas NC*. 2021. Individualized proteogenomics reveals mutational landscape of melanoma patients in response to immunotherapy. Cancers 13(21), 5411

211. Terradas AL, Zittlau K, Macek B, Fraiberg M, Elazar Z, Kahle PJ. 2021. Regulation of mitochondrial cargo-selective autophagy by post-translational modifications. J. Biol Chem 297(5):101339

210. Singh N, Kronenberger T, Eipper A, Weichel F, Franz M, Macek B, Wagner S. 2021. Conserved salt bridges facilitate assembly of the helical core export apparatus of a Salmonella enterica type III secretion system. J Mol Bio. 433(19):167175.

209. Hengel H, Hannan SB, Dyack S, MacKay SB, Schatz U, Fleger M, Kurringer A, Balousha G, Ghanim Z, Alkuraya FS, Alzaidan H, Alsaif HS, Mitani T, Bozdogan S, Pehlivan D, Lupski JR, Gleeson JJ, Dehghani M, Mehrjardi MYV, Sherr EH, Parks KC, Argilli E, Begtrup A, Galehdari H, Balousha O, Shariati G, Mazaheri N, Malamiri RA, Pagnamenta AT, Kingston H, Banka S, Jackson A, Osmond M; Care4Rare Canada Consortium; Genomics England Research Consortium, Rieß A, Haack TB, Nägele T, Schuster S, Hauser S, Admard J, Casadei N, Velic A, Macek B, Ossowski S, Houlden H, Maroofian R, Schöls L. 2021. Bi-allelic loss-of-function variants in BCAS3 cause a syndromic neurodevelopmental disorder. Am J Hum Genet. 108(6):1069-1082.

208. Spät P, Barske T, Macek B, Hagemann M. 2021. Alterations in the CO₂ availability induce alterations in the phospho-proteome of the cyanobacterium Synechocystis sp. PCC 6803. New Phytologist 231(3):1123-1137

207. Sultan A, Jers C, Ganief TA, Shi L, Senissar M, Køhler JB, Macek B, Mijakovic I. 2021. Phosphoproteome Study of Escherichia coli Devoid of Ser/Thr Kinase YeaG During the Metabolic Shift From Glucose to Malate. Front Microbiol 12:657562

206. Halova L, Cobley D, Franz-Wachtel M, Wang T, Morrison KR, Krug K, Nalpas N, Maček B, Hagan IM, Humphrey SJ, Petersen J. 2021. A TOR (target of rapamycin) and nutritional phosphoproteome of fission yeast reveals novel targets in networks conserved in humans. Open Biol. 11(4):200405.

205. Schmitt M, Sinnberg T, Bratl K, Zittlau K,Garbe C, Macek B*, Nalpas NC*. 2021. Proteogenomics reveals perturbed signalling networks in Malignant Melanoma Cells Resistant to BRAF inhibition. Mol Cell Proteomics 20:100163

204. Nalpas N, Hoyles L, Anselm V, Ganief T, Martinez-Gili L, Grau C, Droste-Borel I, Davidovic L, Altafaj X, Dumas M, Macek B. 2021. An Integrated Workflow for Enhanced Taxonomic and Functional Coverage of the Mouse Faecal Metaproteome. Gut Microbes 13:1, 199483

203. Semanjski M, Gratani FL, Englert T, Nashier P, Beke V, Nalpas N, Germain E, George S, Wolz C, Gerdes K, Macek B. 2021. Proteome Dynamics during Antibiotic Persistence and Resuscitation. mSystems 6(4):e0054921

202. Ferrari E, Barbero F, Busquets-Fité M, Franz-Wachtel M, Köhler HR, Puntes V, Kemmerling B. 2021. Growth-Promoting Gold Nanoparticles Decrease Stress Responses in Arabidopsis Seedlings. Nanomaterials (Basel). 11(12):3161

201. Thiel D, Yañez-Guerra LA, Franz-Wachtel M, Hejnol A, Jékely G. Nemertean, Brachiopod, and Phoronid Neuropeptidomics Reveals Ancestral Spiralian Signaling Systems. 2021. Mol Biol Evol. 38(11):4847-4866

200. Krauspe V, Fahrner M, Spät P, Steglich C, Frankenberg-Dinkel N, Macek B, Schilling O, Hess WR. 2021. Discovery of a novel small protein factor involved in the coordinated degradation of phycobilisomes in cyanobacteria. Proc Natl Acad Sci USA 118 (5) e2012277118

199. Orthwein T, Scholl J, Spät P, Lucius S, Koch M, Macek B, Hagemann M, Forchhammer K. 2021. The Novel PII-Interactor PirC Identifies Phosphoglycerate Mutase as Key Control Point of Carbon Storage Metabolism in Cyanobacteria. Proc Natl Acad Sci USA 118 (6) e2019988118

198. Riediger M, Spät P, Bilgera R, Voigt K, Macek B, Hess WR. 2020. Analysis of a Photosynthetic Cyanobacterium Rich in Internal Membrane Systems via Gradient Profiling by Sequencing (Gradseq). Plant Cell 33(2):248-269

197. Hegenauer V, Slaby P, Körner M, Bruckmüller JA, Burggraf R, Albert I, Kaiser B, Löffelhardt B, Droste-Borel I, Sklenar J, Menke FLH, Maček B, Ranjan A, Sinha N, Nürnberger T, Felix G, Krause K, Stahl M, Albert M. 2020. The tomato receptor CuRe1 senses a cell wall protein to identify Cuscuta as a pathogen. Nat Commun. 11(1):5299.

196. Hauser S, Schuster S, Heuten E, Höflinger P, Admard J, Schelling Y, Velic A, Macek B, Ossowski S, Schoels L. 2020. Comparative transcriptional profiling of motor neuron disorder-associated genes in various human cell culture models. Front Cell Dev Biol 8: 544043

195. Slane D, Lee CH, Kolb M, Dent C, Miao Y, Franz-Wachtel M, Lau S, Macek B, Balasubramanian S, Bayer M, Jürgens G. 2020. The integral spliceosomal component CWC15 is required for development in Arabidopsis. Sci Rep. 2020 10(1):13336.

194. Bansal P, Madlung J, Schaaf K, Macek B, Bono F. 2020. An interaction network of RNA-binding proteins involved in Drosophila oogenesis. Mol Cell Proteomics 19(9):1485-1502

193. Schlöffel M, Salzer A, Wan WL, van Wijk R, Del Corvo R, Semanjski M, Symeonidi E, Slaby P, Kilian J, Macek B, Munnik T, Gust AA. 2020. The BIR2/BIR3-associated Phospholipase D gamma 1 negatively regulates plant immunity. Plant Physiol. pii: pp.01292.2019.

192. Meinohl C, Barnard SJ, Fritz-Wolf K, Unger M, Porr A, Heipel M, Wirth S, Madlung J, Nordheim A, Menke A, Becker K, Giehl K. 2020. Galectin-8 binds to the Farnesylated C-terminus of K-Ras4B and Modifies Ras/ERK Signaling and Migration in Pancreatic and Lung Carcinoma Cells. Cancers 12, 30; doi:10.3390/cancers12010030

191. Mukherjee J, Franz-Wachtel M, Maček B, Jansen RP. RNA Interactome Identification via RNA-BioID in Mouse Embryonic Fibroblasts. Bio Protoc. 2020 Jan 5;10(1):e3476. doi: 10.21769/BioProtoc.3476. PMID: 33654709; PMCID: PMC7842539.

190. Kraemer BF, Geimer M, Franz-Wachtel M, Lamkemeyer T, Mannell H, Lindemann S. Extracellular Matrix-Specific Platelet Activation Leads to a Differential Translational Response and Protein De Novo Synthesis in Human Platelets. Int J Mol Sci. 2020 Oct 31;21(21):8155. doi: 10.3390/ijms21218155. PMID: 33142786; PMCID: PMC7672557.

189. Pelletier A, Freton C, Gallay C, Trouve J, Cluzel C, Franz-Wachtel M, Macek B, Jault JM, Grangeasse C, Guiral S. 2019. The Tyrosine-Autokinase UbK Is Required for Proper Cell Growth and Cell Morphology of Streptococcus pneumoniae. Front Microbiol 10:1942

188. Macek B, Forchhammer K, Hardouin J, Weber-Ban E, Grangeasse C, Mijakovic I. 2019. Protein post-translational modifications in bacteria. Nat Rev Microbiol 17(11):651-664

187. Tribelli PM, Luqman A, Nguyen MT, Madlung J, Fan SH, Macek B, Sass P, Bitschar K, Sauer B, Kretschmer D, Götz F. 2019. Staphylococcus aureus Lpl protein triggers human host cell invasion via activation of Hsp90 receptor. Cellular Microbiology, 22(1):e13111

186. El Maadidi S, Weber AN, Motshwene P, Schüssler JM, Backes D, Dickhöfer S, Wang H, Liu X, Garcia MD, Taumer C, Soufi B, Wolz O, Klimosch S, Franz-Wachtel M, Macek B, Gay NJ. 2019. Putative link between Polo-like kinases (PLKs) and Toll-like receptor (TLR) signaling in transformed and primary human immune cells. Sci Reports, 9(1):13168

185. Singer-Krüger B, Fröhlich T, Franz-Wachtel M, Nalpas N, Macek B, Jansen RP. 2019. APEX2-mediated proximity labeling resolves protein networks in Saccharomyces cerevisiae cells. FEBS J, 287(2):325-344

184. Watzer B, Spät P, Neumann N, Koch M, Sobotka R, Macek B, Hennrich O, Forchhammer K. 2019. The Signal Transduction Protein PII Controls Ammonium, Nitrate and Urea Uptake in Cyanobacteria. Front Microbiol 10:1428.

183. Mukherjee, J., Hermesh, O., Eliscovich, C., Nalpas, N., Franz-Wachtel, M., Macek, B., Jansen, R. 2019. β-actin mRNA interactome mapping by proximity biotinylation. Proc Natl Acad Sci USA 116(26):12863-12872

182. Nielsen, S., Turnbull, K., Roghanian, M., Bærentsen, R., Semanjski, M., Brodersen, D., Macek, B., Gerdes, K. 2019. Serine-Threonine Kinases Encoded by Split hipA Homologs Inhibit Tryptophanyl-tRNA Synthetase. mBio 10(3). pii: e01138-19

181. Zhou, B., Semanjski, M., Orlovetskie, N., Bhattacharya, S., Alon, S., Jarrous, N., Zhang, Y., Macek, B., Sinai, L., Ben-Yehuda, S. 2019. Arginine dephosphorylation propels spore germination in bacteria. Proc Natl Acad Sci USA 116(28):14228-14237

180. Michel T, Golombek S, Steinle H, Hann L, Velic A, Macek B, Krajewski S, Schlensak C, Wendel HP, Avci-Adali M. 2019. Efficient reduction of synthetic mRNA induced immune activation by simultaneous delivery of B18R encoding mRNA. J Biol Eng 13:40.

179. Löffler MW, Mohr C, Bichmann L, Freudenmann LK, Walzer M, Schroeder CM, Trautwein N, Hilke FJ, Zinser RS, Mühlenbruch L, Kowalewski DJ, Schuster H, Sturm M, Matthes J, Riess O, Czemmel S, Nahnsen S, Königsrainer I, Thiel K, Nadalin S, Beckert S, Bösmüller H, Fend F, Velic A, Maček B, Haen SP, Buonaguro L, Kohlbacher O, Stevanović S, Königsrainer A; HEPAVAC Consortium, Rammensee HG. 2019. Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma. Genome Med. 11(1):28.

178. Schmitt M, Sinnberg T, Nalpas NC, Maass A, Schittek B, Macek B. 2019. Quantitative proteomics links the intermediate filament nestin to resistance to targeted BRAF inhibition in melanoma cells. Mol Cell Proteomics 18(6):1096-1109

177. Forte GM, Davie E, Lie S, Franz-Wachtel M, Ovens AJ, Wang T, Oakhill JS, Macek B, Hagan IM, Petersen J. 2019. Import of extracellular ATP in yeast and man modulates AMPK and TORC1 signalling. J Cell Sci. 132(7). pii: jcs223925

176. Bilus, M., Semanjski, M., Mocibob, M., Zivkovic, I., Cvetesic, N., Tawfik, D.S., Toth-Petroczy, A., Macek, B., Gruic-Sovulj, I. 2019. On the mechanism and origin of isoleucyl-tRNA synthetase editing against norvaline. J Mol Biol 431(6):1284-1297

175. Klein, K., Sonnabend, M.S., Frank, L., Leibiger, K., Franz-Wachtel, M., Macek, B., Trunk, T., Leo, J.C., Autenrieth, I.B., Schütz M., Bohn, E. 2019. Deprivation of the Periplasmic Chaperone SurA Reduces Virulence and Restores Antibiotic Susceptibility of Multidrug-Resistant Pseudomonas aeruginosa. Front Microbiol 10:100

174. Leboucher, A., Pisani,D.F., Martinez-Gili, L., Chilloux, J., Bermudez-Martin, P., Van Dijck, A., Ganief, T., Macek, B., Becker, J.A.J., Le Merrer, J., Kooy, R.F., Amri, E., Khandjian,E.W., Dumas, M., Davidovic, L. 2019. The translational regulator FMRP controls lipid and glucose metabolism in mice and humans. Mol Metab 21:22-35

173. Kraemer BF, Lamkemeyer T, Franz-Wachtel M, Lindemann S. The Integrin Activating Protein Kindlin-3 Is Cleaved in Human Platelets during ST-Elevation Myocardial Infarction. Int J Mol Sci. 2019 Dec 6;20(24):6154. doi: 10.3390/ijms20246154. PMID: 31817594; PMCID: PMC6941114.

172. Kraemer BF, Mannell H, Lamkemeyer T, Franz-Wachtel M, Lindemann S. Heat-Shock Protein 27 (HSPB1) Is Upregulated and Phosphorylated in Human Platelets during ST-Elevation Myocardial Infarction. Int J Mol Sci. 2019 Nov 27;20(23):5968. doi: 10.3390/ijms20235968. PMID: 31783528; PMCID: PMC6928972.

171. Ravikumar V, Nalpas NC, Anselm V, Krug K, Lenuzzi M, Šestak MS, Domazet-Lošo T, Mijakovic I, Macek B. 2018. In-depth analysis of Bacillus subtilis proteome identifies new ORFs and traces the evolutionary history of modified proteins. Sci Reports 8(1):17246.

170. Singh MK, Richter S, Beckmann H, Kientz M, Stierhof YD, Anders N, Fäßler F, Nielsen M, Knöll C, Thomann A, Franz-Wachtel M, Macek B, Skriver K, Pimpl P, Jürgens G. 2018. A single class of ARF GTPase activated by several pathway-specific ARF-GEFs regulates essential membrane traffic in Arabidopsis. PLOS Genetics 14(11):e1007795.

169. Thiel D, Franz-Wachtel M, Hejnol FAA. 2018. Xenacoelomorph Neuropeptidomes Reveal a Major Expansion of Neuropeptide Systems during Early Bilaterian Evolution. Mol Biol Evol 35(10):2528–2543

168. Fuchs, K., Cardona Gloria, Y., Wolz, O., Herster, F., Sharma, L., Dillen, C.A, Täumer, C., Dickhöfer, S., Bittner, Z., Dang, T., Singh, A., Haischer, D., Schlöffel, M.A., Koymans, K.J., Sanmuganantham, T., Krach, M., Roger, T., Le Roy, D., Schilling, N.A., Frauhammer, F., Miller, L.S., Nürnberger, T., LeibundGut-Landmann, S., Gust, A.A., Macek, B., Frank, M., Gouttefangeas, C., Dela Cruz, C.S., Hartl, D., Weber, A.N.R. 2018. The fungal ligand chitin directly binds TLR and triggers inflammation dependent on oligomer size. EMBO Reports 19(12). pii: e46065.

167. de Francisco Amorim M, Willing EM, Szabo EX, Francisco-Mangilet AG, Droste-Borel I, Macek B, Schneeberger K, Laubinger S. 2018. The U1 snRNP subunit LUC7 modulates plant development and stress responses via regulation of alternative splicing. Plant Cell 30(11):2838-2854.

166. Stoll H, Ost M, Singh A, Mehling R, Neri D, Schäfer I, Velic A, Macek B, Kretschmer D, Weidenmaier C, Hector A, Handgretinger R, Götz F, Peschel A, Hartl D, Rieber N. 2018. Staphylococcal Enterotoxins Dose-Dependently Modulate the Generation of Myeloid-Derived Suppressor Cells. Front Cell Infect Microbiol 8:321.

165. Semanjski, M., Germain, E., Bratl, K., Kiessling, A., Gerdes K., Macek, B. 2018. The kinases HipA and HipA7 phosphorylate different substrate pools in Escherichia coli to promote multidrug tolerance. Science Signaling 11, eaat5750

164. Speth C, Szabo EX, Martinho C, Collani S, Zur Oven-Krockhaus S, Richter S, Droste-Borel I, Macek B, Stierhof YD, Schmid M, Liu C, Laubinger S. 2018. Arabidopsis RNA processing factor SERRATE regulates the transcription of intronless genes. Elife 7. pii: e37078.

163. Terfrüchte M, Wewetzer S, Sarkari P, Stollewerk D, Franz-Wachtel M, Macek B, Schlepütz T, Feldbrügge M, Büchs J, Schipper K. 2018. Tackling destructive proteolysis of unconventionally secreted heterologous proteins in Ustilago maydis. J Biotechnol 284:37-51

162. Soufi, B., Täumer, C., Semanjski, M., Macek, B. 2018. Phosphopeptide Enrichment from Bacterial Samples Utilizing Titanium Oxide Affinity Chromatography. Meth Mol Biol 1841:231-247

161. Gratani FL, Horvatek P, Geiger T, Borisova M, Mayer C, Grin I, Wagner S, Steinchen W, Bange G, Velic A, Macek B, Wolz C. 2018. Regulation of the opposing (p)ppGpp synthetase and hydrolase activities in a bifunctional RelA/SpoT homologue from Staphylococcus aureus. PLoS Genet 14(7):e1007514.

160. Cheng MHK, Hoffmann PC, Franz-Wachtel M, Sparn C, Seng C, Macek B, Jansen RP. 2018. The RNA-Binding Protein Scp160p Facilitates Aggregation of Many Endogenous Q/N-Rich Proteins. Cell Rep 24(1):20-26

159. Kuhlen L, Abrusci P, Johnson S, Gault J, Deme J, Caesar J, Dietsche T, Mebrhatu MT, Ganief T, Macek B, Wagner S, Robinson CV, Lea SM. 2018. Structure of the core of the type III secretion system export apparatus. Nat Struct Mol Biol 25(7):583-590.

158. Jores, T., Lawatscheck, J., Beke, V., Franz-Wachtel, M., Yunoki, K., Fitzgerald, J., Macek, B., Endo, T., Kalbacher, H., Buchner, J., Rapaport, D. 2018. Cytosolic Hsp70 and Hsp40 chaperones enable the biogenesis of mitochondrial β-barrel proteins. J Cell Biol 217(9):3091-3108.

157. Bryce C, Franz-Wachtel M, Nalpas N, Miot J, Benzerara K, Byrne JM, Kleindienst S, Macek B, Kappler A. 2018. Proteome response of a metabolically flexible anoxygenic phototroph to Fe(II) oxidation. Appl Environ Microbiol 84(16). pii: e01166-18.

156. Spät P, Klotz A, Rexroth S, Macek B, Forchhammer K. 2018. Chlorosis as a developmental program in cyanobacteria: the proteomic fundament for survival and awakening. Mol Cell Proteomics 17(9):1650-1669.

155. Sauter RJ, Sauter M, Reis ES, Emschermann FN, Nording H, Ebenhöch S, Kraft P, Münzer P, Mauler M, Rheinlaender J, Madlung J, Edlich F, Schäffer TE, Meuth SG, Düerschmied D, Geisler T, Borst O, Gawaz M, Kleinschnitz C, Lambris JD, Langer HF. 2018. A Functional Relevance of the Anaphylatoxin Receptor C3aR for Platelet Function and Arterial Thrombus Formation Marks an Intersection Point Between Innate Immunity and Thrombosis. Circulation 138(16):1720-1735.

154. Taumer, C., Griesbaum, L., Kovacevic, A., Soufi, B., Nalpas, N.C., Macek, B. 2018. Parallel Reaction Monitoring on a Q Exactive Mass Spectrometer Increases Reproducibility of Phosphopeptide Detection in Bacterial Phosphoproteomics Measurements. J Proteomics 189:60-66.

153. Bornikoel J, Staiger J, Madlung J, Forchhammer K, Maldener I. 2018. LytM factor Alr3353 affects filament morphology and cell-cell communication in the multicellular cyanobacterium Anabaena sp. PCC 7120. Mol Microbiol. 108(2):187-203.

152. van de Poel S, Dreer M, Velic A, Macek B, Baskaran P, Iftner T, Stubenrauch F. 2018. Identification and functional characterization of phosphorylation sites of the HPV31 E8^E2 protein. J Virol 92(4). pii: e01743-17.

151. Korkmaz AG, Popov T, Peisl L, Codrea MC, Nahnsen S, Steimle A, Velic A, Macek B, von Bergen M, Bernhardt J, Frick JS. 2018. Proteome and phosphoproteome analysis of commensally induced dendritic cell maturation states. J Proteomics 180:11-24.

150. Fitzgerald JC, Zimprich, A, Carvajal Berrio DA, Schindler KM, Maurer B, Schulte C, Bus C, Hauser AK, Kübler M, Reddy Bobbili RL, Schwarz LM, Vartholomaiou E, Brockmann K, Wüst R, Madlung J, Nordheim A, Riess O, Martins LM, Glaab E, May P, Schenke-Layland K, Picard D, Sharma M, Gasser T, Krüger R. 2017. Metformin reverses TRAP1 mutation-associated alterations in mitochondrial function in Parkinson’s disease. Brain 140(9):2444–2459

149. Laboucarié, T., Detilleux, D., Rodriguez, R., Romeo, Y., Franz-Wachtel, M., Krug, K., Maček, B., Petersen, J., Villén J., Helmlinger, D. 2017. The TORC1 and TORC2 signaling pathways converge to regulate the SAGA transcriptional co-activator in response to nutrient availability. EMBO Reports 18(12):2197-2218.

148. Fabiani, F., Renault, T.T., Peters, B., Dietsche, T., Galvez, E., Guse, A., Freier, K., Charpentier, E., Strowig, T., Franz-Wachtel, M., Macek, B., Wagner, S., Hensel, M., Erhardt, M. 2017. A flagellum-specific chaperone facilitates assembly of the core type III export apparatus of the bacterial flagellum. PLOS Biology 15(8):e2002267

147. Murali, A., Shin, J., Yurugi, H., Krishnan, A., Akutsu, M., Carpy, A., Macek, B., Rajalingam K. 2017 Ubiquitin dependent regulation of Cdc42 by XIAP. Cell Death & Disease 8(6):e2900

146. Bakula, D., Müller, A.J., Takacs, Z., Franz-Wachtel, M., Thost, A., Zuleger, T., Brigger, D., Tschan, M.P., Frickey, T., Robenek, H., Macek, B., Proikas-Cezanne, T. 2017. WIPI3 and WIPI4 β-propellers act as scaffolds for LKB1-AMPK and TSC1-TSC2 in the control of autophagy. Nat Communications 8:15637

145. Kliza, K., Taumer, C., Pinzuti, I., Franz-Wachtel, M., Kunzelmann, S., Stieglitz, B., Macek, B., Husnjak, K. 2017. Internally tagged ubiquitin: a tool to identify linear polyubiquitin-modified proteins by mass spectrometry. Nat Methods 14(5):504-512

144. Cobley, D., Halova, L., Schauries, M, Franz-Wachtel, M., Du, W., Krug, K., Macek, B., Petersen, J. 2017. Ste12/Fab1 phosphatidylinositol-3-phosphate 5-kinase is required for nitrogen-regulated mitotic commitment and cell size control. PLOS One 12 (3), e0172740

143. Liu, X., Pichulik, T., Wolz, O.-O., Dang, T.-M., Stutz, A, Page, C., Garcia, M.D., Kraus, H., Dickhöfer, S., Daiber, E., Münzenmayer, L., Wahl, S., Rieber, N., Kümmerle-Deschner, J., Yazdi, A., Franz-Wachtel, M., Macek, B., Radsak, M., Vogel, S., Schulte, B., Stickel, J.S., Hartl, D., Latz, E., Slgenbauer, S., Grimbacher, B., Miller, L., Brunner, C., Wolz, C., Weber, A.N. 2017. Human NLRP3 inflammasome activity is regulated by and potentially targetable via BTK. Journal of Allergy and Clinical Immunology 6749(17)30232-4

142. Weirich, J., Bräutigam, C., Mühlenkamp, M., Franz-Wachtel, M., Macek, B., Meuskens, I., Bohn, E., Autenrieth, I., Schütz, M. 2017. Components of the OMP biogenesis machinery required for virulence – an approach to identify new targets for antivirulence therapy. Virulence 24:1-20

141. Derouiche, A., Petranovic, D., Macek, B., Mijakovic, I. 2017. Bacillus subtilis single-stranded DNA-binding protein SsbA is phosphorylated at threonine 38 by the serine/threonine kinase YabT. Period Biol 118 (4), 399-404

140. Dietsche, T., Mebrhatu, M.T., Brunner, M.J., Abrusci, P., Yan, J., Franz-Wachtel, M., Schärfe, C., Zilkenat, S., Grin, I., Galán, J.E., Kohlbacher, O., Lea, S., Macek, B., Marlovits, T.C., Robinson, C., Wagner, S. 2016. Structural and functional characterization of the bacterial type III secretion export apparatus. PLOS Pathogens 12(12):e100607

139. Hendrick, J., Franz-Wachtel, M., Moeller, Y., Schmid, S., Macek, B, Olayioye, M. 2016. The polarity protein Scribble positions DLC3 at adherens junctions to regulate Rho signaling. J Cell Biol 129(19):3583-3596.

138. Amin, R., Franz-Wachtel, M., Tiffert, Y., Heberer, M., Meky, M., Ahmed, Y., Matthews, A., Krysenko, S., Jakobi, M., Hinder, M., Moore, J., Okoniewski, N., Macek, B., Wohlleben, W., Bera, A. 2016. Post-translational serine/threonine phosphorylation and lysine acetylation: a novel regulatory aspect of the global nitrogen response regulator GlnR in S. coelicolor M145. Frontiers in Molecular Biosciences 3:38.

137. Hoseini, H., Pandey, S., Jores, T., Schmitt, A., Franz-Wachtel, M., Macek, B., Buchner, J., Dimmer, K., Rapaport, D. 2016. The cytosolic co-chaperone Sti1 is involved in mitochondrial biogenesis. FEBS J 283(18):3338-52.

136. Hanzelmann, D., Joo, H., Franz-Wachtel, M., Hertlein, T., Stevanovic, S., Macek, B., Wolz, C., Götz, F., Otto, M., Kretschmer, D., Peschel, A. 2016. Toll-like receptor 2 activation depends on lipopeptide shedding by bacterial surfactants. Nat Communications 7:12304.

135. Cvetesic, N., Semanjski, M., Soufi, B., Krug, K., Gruic-Sovulj, I., Macek, B. 2016. Proteome-wide measurement of non-canonical bacterial mistranslation by quantitative mass spectrometry of protein modifications. Sci Reports 6:28631.

134. Marei, H., Carpy, A., Macek, B., Malliri, A. 2016. Proteomic Analysis of Rac1 Signalling Regulation by Guanine Nucleotide Exchange Factors. Cell Cycle 15(15):1961-74.

133. Baker, K., Kirkham, S., Halova, L., Atkin, J., Franz-Wachtel, M., Cobley, D., Krug, K., Macek, B., Mulvihill, D., Petersen, J. 2016. TOR Complex 2 localises to the Cytokinetic Actomyosin ring and controls the fidelity of cytokinesis. J Cell Sci 129(13):2613-24.

132. Sinnberg, T., Makino, E, Krueger, M.A., Velic, A., Macek, B., Rothbauer, U., Groll, N., Pötz, O., Czemmel, S., Niessner, H., Meier, F., Schittek, B. 2016. A novel nexus consisting of beta-catenin and Stat3 attenuates BRAF inhibitor efficacy and mediates secondary resistance to vemurafenib. EBioMedicine 8:132-49.

131. Shi, L., Ravikumar, V., Derouiche, A., Kalantari, A., Macek, B., Mijakovic, I. 2016. Tyrosine 601 of Bacillus subtilis DnaK Undergoes Phosphorylation and Is Crucial for Chaperone Activity and Heat Shock Survival. Frontiers in Microbiology 7:533.

130. Dreer, M., Fertey, J., van de Poel, S., Straub, E., Madlung, J., Macek, B., Iftner, T., Stubenrauch, F. 2016. Interaction of NCOR/SMRT repressor complexes with papillomavirus E8^E2C proteins 1 inhibits viral replication. PLOS Pathogens 12(4):e1005556.

129. Zilkenat, S., Franz-Wachtel, M., Stierhof, Y., Galán, J.E., Macek, B., Wagner, S. 2016. Determination of the stoichiometry of the complete bacterial type III secretion needle complex using a combined quantitative proteomic approach. Mol Cell Proteomics 15(5):1598-609.

128. Marei, H., Carpy, A., Woroniuk, A., Vennin, C., White, G., Timpson, P., Macek, B., Malliri A. 2016. Differential Rac1 signalling by guanine nucleotide exchange factors implicates FLII in regulating Rac1-driven cell migration. Nat Communications 7:10664.

127. Bekiesch, P., Franz-Wachtel, M., Forchhammer, K., Kulik, A., Brocker, M., Gust, B., Apel A.K. 2016. DNA affinity capturing identifies new regulators of the heterologously expressed novobiocin gene cluster in Streptomyces coelicolor M512. Appl Microbiol Biotechnol 100(10):4495-509.

126. Semanjski, M., Macek, B. 2016. Shotgun proteomics of bacterial pathogens: Advances, challenges and clinical implications. Exp Rev Proteomics 13(2):139-56.

125. Meyer zu Reckendorf, C., Anastasiadou, S., Bachhuber, F., Franz-Wachtel, M., Macek, B., Knöll, B. 2016. Proteomic analysis of SRF associated transcription complexes identified TFII-I as modulator of SRF function in neurons. Eur J Cell Biol 95(1):42-56.

124. Ravikumar, V.,Macek, B., Mijakovic, I. 2016. Resources for assignment of phosphorylation sites on peptides and proteins. Meth Mol Biol, 1355:293-306.

123. Carpy, A., Koch, A., Bicho, C.C., Borek, W.E., Hauf, S., Sawin, K.E., Macek, B. 2016. Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC)-Based Quantitative Proteomics and Phosphoproteomics in Fission Yeast. Cold Spring Harbor Protocols, doi:10.1101/pdb.prot091686

122. Macek, B., Carpy, A., Koch, A., Bicho, C.C, Borek, W.E, Hauf, S., Sawin, K.E.2016. Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) Technology in Fission Yeast. Cold Spring Harbor Protocols, doi:10.1101/pdb.top079814

121. Koch, A., Bicho, C.C., Borek, W.E., Carpy, A., Macek, B., Hauf, S., Sawin. K.E. 2016. Construction, Growth, and Harvesting of Fission Yeast SILAC Strains. Cold Spring Harbor Protocols, doi:10.1101/pdb.prot091678

120. Rosenberg, A., Soufi, B., Ravikumar, V., Soares, N.C., Krug, K., Smith, Y, Macek, B., Ben-Yehuda, S. 2015. Phosphoproteome Dynamics Mediate Revival of Bacterial Spores. BMC Biology 13:76.

119. Cavignac Y, Lieber D, Laib Sampaio K, Madlung J, Lamkemeyer T, Jahn G, Nordheim A, Sinzger C. 2015. The Cellular Proteins Grb2 and DDX3 Are Increased upon Human Cytomegalovirus Infection and Act in a Proviral Fashion. PLoS One, 10(6):e0131614.

118. Derouiche A, Shi L, Bidnenko V, Ventroux M, Pigonneau N, Franz-Wachtel M, Kalantari A, Nessler S, Noirot-Gros MF, Mijakovic I. 2015. Bacillus subtilis SalA is a phosphorylation-dependent transcription regulator which represses scoC and activates the production of the exoprotease AprE. Mol Microbiol, 97(6):1195-208.

117. Walker B, Schmid E, Russo A, Schmidt EM, Burk O, Münzer P, Velic A, Macek B, Schaller M, Schwab M, Seabra MC, Gawaz M, Lang F, Borst O. 2015. Impact of the Serum- & Glucocorticoid-inducible Kinase 1 (SGK1) on platelet dense granule biogenesis and secretion. J Thromb Haemost, 13(7):1325-34.

116. Ladwig, N., Franz-Wachtel, M., Hezel, F., Soufi, B., Macek, B., Wohlleben, W., Muth, G. 2015. The serine/threonine protein kinase PkaI (SCO4778) phosphorylates MreC and PBP2 during morphological differentiation of Streptomyces coelicolor A3(2). PLOS One 10(4):e0125425.

115. Spät, P., Macek, B., Forchhammer, K. 2015. Phosphoproteome of the cyanobacterium Synechocystis sp. PCC 6803 and its dynamics during nitrogen starvation. Frontiers in Microbiology 6:248.

114. Soufi, B., Krug, K., Harst, A.,Macek, B. 2015. Characterization of the E.coli proteome and its modifications during growth and ethanol stress. Frontiers in Microbiology 6:103.

113. Burian, M., Velic, A., Matic, K., Günther, S., Kraft, B., Gonser, L., Forchhammer, S., Tiffert, Y., Naumer, C., Krohn, M., Berneburg, M., Yazdi, A.S., Macek, B., Schittek, B. 2015. Quantitative Proteomics of the Human Skin Secretome reveals a Reduction of Immune Defense Mediators in Ectodermal Dysplasia Patients. J Invest Dermatol 135(3):759-67.

112. Umbach, A.T., Zhang, B., Daniel, C., Fajol, A., Velic, A., Hosseinzadeh, Z., Bhavsar, S.K., Bock, C.T., Kandolf, R., Pichler, B.J., Amann, K.U., Föller, M., Lang, F. 2015. Janus kinase 3 regulates renal 25-hydroxyvitamin D 1α-hydroxylase expression, calcitriol formation, and phosphate metabolism. Kidney Int 87(4):728-37.

111. Soufi, B., Macek, B. 2015. Global analysis of bacterial membrane proteins and their modifications. Int J Med Microbiol 305(2):203-8.

110. McEwan, D.G., Richter, B., Claudi, B., Wigge, C., Wild, P., Farhan, H., McGourty, K., Coxon, F.P., Franz-Wachtel, M., Perdu, B., Akutsu, M., Habermann, A., Kirchof, A., Helfrich, M.H., Odgren, P.R., Van Hul, W., Frangakis, A.S., Rajalingam, K., Macek, B., Holden, D.W., Bumann, D., Dikic, I. 2015. PLEKHM1 Regulates Salmonella-Containing Vacuole Biogenesis and Infection. Cell Host Microbe 17(1):58-71.

109. Carpy, A., Patel, A., Krug, K., Hagan, I., Macek, B. 2015. Nic1 Inactivation Enables Stable Isotope Labeling with ¹³C₆¹⁵N₄-Arginine in Schizosaccharomyces pombe. Mol Cell Proteomics 14(1):243-50.

108. Magalska A, Schellhaus AK, Moreno-Andres D, Zanini F, Schooley A, Sachdev R, Schwarz H, Madlung J, Antonin W. 2014. RuvB-like ATPases Function in Chromatin Decondensation at the End of Mitosis. Dev Cell. 31(3):305-318

107. Fleurie, A., Lesterlin, C., Manuse, S., Zhao, C., Cluzel, C., Lavergne, J-P., Franz-Wachtel, M., Macek, B., Combet, C., Kuru, E., VanNieuwenhze, M.S., Brun, Y.V., Sherratt, D., Grangeasse, C. 2014. MapZ marks the division sites and positions FtsZ rings in Streptococcus pneumaniae. Nature 516(7530):259-62.

106. Krug, K., Popic, S., Carpy, A., Täumer, C.,Macek, B. 2014. Construction and assessment of individualized proteogenomic databases for large-scale analysis of non-synonymous single nucleotide variants. Proteomics 14(23-24):2699-708

105. Shi, L., Pigonneau, N., Ravikumar, V., Dobrinic, P., Macek, B., Franjevic, D., Noirot-Gros, M., Mijakovic, I. 2014.Cross-phosphorylation of bacterial serine/threonine and tyrosine protein kinases on key regulatory residues. Frontiers in Microbiology17;5:495.

104. Matic, K., Eninger, T., Bardoni, B., Davidovic, L., Macek, B. 2014. Quantitative Phosphoproteomics of Murine Fmr1-KO Cell Lines Provides New Insights into FMRP-Dependent Signal Transduction Mechanisms. J Prot Res 13(10):4388-97.

103. Liu X, Grabherr HM, Willmann R, Kolb D, Brunner F, Bertsche U, Kühner D, Franz-Wachtel M, Amin B, Felix G, Ongena M, Nürnberger T, Gust AA. 2014. Host-induced bacterial cell wall decomposition mediates pattern-triggered immunity in Arabidopsis. Elife 3. doi: 10.7554/eLife.01990.

102. Takeda, A., Oberoi-Khanuja, T.K., Glatz, G., Peter-Scholz, R., Carpy, A., Macek, B., Remenyi, A., Rajalingam, K. 2014. Ubiquitin dependent regulation of MEKK2/3-MEK5-ERK5 signaling module by IAPs. EMBO J33(16):1784-801.

101. Carpy, A., Krug, K., Graf, S., Koch, A., Popic, S., Hauf, S., Macek,B. 2014. Absolute proteome and phosphoproteome dynamics during the cell cycle of fission yeast. Mol Cell Proteomics13(8):1925-36.

100. Utrobicic, I., Novak, I., Marinovic-Terzic, I., Matic, K., Salamunic, I.,Saraga Babic, M., Kunac, N., Kostic Mesin, A., Macek, B., Terzic, J. 2014. Idiopathic carpal tunnel syndrome associated with elevated plasma fibrinogen and fibrinogen deposits at the transverse carpal ligament. Neurosurgery 75(3):276-85.

99. Blaum, B.S., Mazzotta, S., Nöldeke, E.R., Halter, T., Madlung, J., Kemmerling, B., Stehle, T. 2014. Structure of the pseudokinase domain of BIR2, a regulator of BAK1-mediated immune signaling in Arabidopsis. J Struct Biol 186(1):112-21.

98. Fleurie, A., Manuse, S., Zhao, C., Campo, N., Cluzel, C., Lavergne, J.-P., Freton, C., Combet, C., Guiral, S., Soufi, B., Macek, B., Di Guilmi, A., Claverys, J.-P., Galinier, A., Grangeasse, C. 2014. Interplay of the serine/threonine-kinase StkP and the paralogs DivIVA and GpsB in pneumococcal cell elongation and division. PLOS Genetics 10(4):e1004275.

97. Ravikumar, V., Shi, L., Krug, K., Derouiche, A., Jers, C., Cousin, C., Kobir, A., Mijakovic, I., Macek, B. 2014. Quantitative phosphoproteome analysis of Bacillus subtilis reveals novel substrates of the kinase PrkC and phosphatase PrpC. Mol Cell Proteomics 13(8):1965-78.

96. Braune, E., Schuster-Gossler, K., Lyszkiewicz, M., Serth, K., Preuße, K., Madlung, J.,Macek, B., Krueger, A., Gossler, A. 2014. S/T phosphorylation of DLL1 is required for full ligand activity in vitro but dispensable for DLL1 function in vivo during embryonic patterning and marginal zone B cell development. Mol Cell Biol 34(7):1221-33.

95. Grin, I., Hartmann, M.D., Sauer, G.,Hernandez Alvarez, B., Schütz, M., Madlung, J., Macek, B., Felipe-Lopez, A., Hensel, M., Lupas, A., Linke, D. 2014. A trimeric lipoprotein assists in trimeric autotransporter biogenesis in Enterobacteria. J Biol Chem 289(11):7388-98.

94. Soufi, B.,Macek, B. 2014. Stable Isotope Labeling by Amino Acids (SILAC) applied to Bacterial Cell Culture. Meth Mol Biol 1188:9-22.

93. Conzelmann M, Williams EA, Krug K, Franz-Wachtel M, Macek B, Jékely G. 2013. The neuropeptide complement of the marine annelid Platynereis dumerilii. BMC Genomics 14(1):906.

92. Bäsell, K., Otto, A., Zühlke, D., Rappen, G., Schmidt, S., Hentschker, C., Macek, B., Ohlsen, K., Hecker, M., Becher, D. 2013. The phosphoproteome and its physiological dynamics in Staphylococcus aureus. Int J Med Microbiol 304(2):121-32.

91. Derouiche A, Bidnenko V, Grenha R, Pigonneau N, Ventroux M, Franz-Wachtel M, Nessler S, Noirot-Gros MF, Mijakovic I. 2013. Interaction of bacterial fatty-acid-displaced regulators with DNA is interrupted by tyrosine phosphorylation in the helix-turn-helix domain. Nucleic Acids Res 41(20):9371-81.

90. Krug, K., Carpy, A., Behrends, G., Matic, K., Soares, N. C., and Macek, B. 2013. Deep coverage of the Escherichia coli proteome enables the assessment of false discovery rates in simple proteogenomic experiments. Mol Cell Proteomics 12(11):3420-30.

89. Gauthier NP, Soufi B, Walkowicz WE, Pedicord VA, Mavrakis KJ, Macek B, Gin DY, Sander C and Miller ML. 2013. Cell-selective labeling using amino acid precursors for proteomic studies of multicellular environments. Nature Methods 10(8):768-73.

88. Scharf M, Neef S, Freund R, Geers-Knörr C, Franz-Wachtel M, Brandis A, Krone D, Schneider H, Groos S, Menon MB, Chang KC, Kraft T, Meissner JD, Boheler KR, Maier LS, Gaestel M, Scheibe RJ. 2013. Mitogen-Activated Protein Kinase-Activated Protein Kinases 2 and 3 Regulate SERCA2a Expression and Fiber Type Composition To Modulate Skeletal Muscle and Cardiomyocyte Function. Mol Cell Biol 33(13):2586-602.

87.Soares, N.C., Spät, P., Krug, K.,Macek, B.2013.Global dynamics of the Escherichia coli proteome and phosphoproteome during growth in minimal medium. J Prot Res 12(6):2611-21.

86. Hausmann, N., Fengler, S., Hennig, A., Franz-Wachtel, M., Hampp, R., Neef, M. 2013. Cytosolic Calcium, hydrogen peroxide, and related gene expression and protein modulation in Arabidopsis thaliana cell cultures respond immediately to altered gravitation: Parabolic flight data. Plant Biology, in press

85. Geiger, T., Velic, A., Macek, B., Lundberg, E., Kampf, C., Nagaraj, N., Uhlen, M., Cox, J., Mann, M. 2013. Initial quantitative proteomic map of twenty-eight mouse tissues using the SILAC mouse. Mol Cell Proteomics12(6):1709-22.

84. Sturm, T., Leinders-Zufall, T., Macek, B., Jung, S., Pömmerl, B., Stevanović, S., Zufall, F., Rammensee, H.G., Overath, P. 2013. MHC-binding peptides occurring in mouse urine stimulate vomeronasal neurons. Nature Communications 4:1616

83. Manavella, P.A., Hagmann, J., Ott, F., Laubinger, S., Franz-Wachtel, M., Macek, B., Weigel, D. 2012.Fast-forward genetics identifies plant CPL phosphatases as regulators of miRNA-processing. Cell 151(4):859-70.

82. Forouzan D, Ammelburg M, Hobel CF, Ströh LJ, Sessler N, Martin J, Lupas AN. 2012. The archaeal proteasome is regulated by a network of AAA ATPases. J Biol Chem 287(46):39254-62.

81. Vujaklija, D., Macek, B. 2012. Detecting posttranslational modifications on bacterial SSB proteins. Methods Mol Biol 922: 205-18.

80. Vollmer, B., Sachdev, R., Eisenhardt, N., Schneider, A.M., Sieverding, C., Madlung, J., Gerken, U., Macek, B., Antonin, W. 2012. Nuclear pore complex assembly depends on a direct interaction of Nup53 with nuclear membranes. EMBO J 31(20):4072-84.

79. Borchert, N., Krug, K., Gand, F., Sinha, A., Sommer, R., Macek, B. 2012. Phosphoproteome of Pristionchus pacificus provides insights into architecture of signaling networks in nematode models. Mol Cell Proteomics 11(12):1631-9.

78. Huck, B., Kemkemer, R., Franz-Wachtel, M., Macek, B., Hausser, A., Olayioye, M.A. 2012. GIT1 phosphorylation on serine 46 by PKD3 regulates paxillin trafficking and cellular protrusive activity. J Biol Chem 287(41):34604-13.

77. Soufi, B., Soares, N.C., Ravikumar, V., Macek, B. 2012. Proteomics reveals evidence of cross-talk between protein modifications in bacteria: Focus on protein acetylation and phosphorylation. Curr Opin Microbiol 15(3):357-63.

76. Franz-Wachtel, M., Eisler, S., Krug, K., Wahl, S., Carpy, A., Nordheim, A., Pfizenmaier, K., Hausser, A., Macek, B. 2012. Global detection of Protein Kinase D-dependent phosphorylation events in nocodazole-treated human cells. Mol Cell Proteomics11(5):160-70.

75. Zelenak, C., Eberhard, M., Jilani, K., Qadri, S.M., Macek, B., Lang, F. 2012. Protein Kinase CK1α Regulates Erythrocyte Survival. Cell Physiol Biochem. 29(1-2):171-80.

74. Doppler K, Lindner A, Schütz W, Schütz M, Bornemann A.2012. Gain and loss of extracellular molecules in sporadic inclusion body myositis and polymyositis--a proteomics-based study. Brain Pathol. 22(1):32-40.
73. Sharma, K., Vabulas, M., Macek, B., Pinkert, S., Cox, J., Mann, M., Hartl, U. 2012. Quantitative proteomics reveals that Hsp90 inhibition preferentially targets kinases and the DNA damage response. Mol Cell Proteomics. 11.3:M111.014654
72. Sessler, N., Krug, K., Nordheim, A., Mordmüller, B., Macek, B. 2012. Analysis of the P. falciparum proteasome using Blue Native PAGE and label-free quantitative mass spectrometry. Amino Acids 43(3):1119-29.

71. Mijakovic, I., Macek, B. 2012. Impact of phosphoproteomics on studies of bacterial physiology. FEMS Microbiology Reviews 36(4):877-92.

70. Oberoi, T.K., Dogan, T., Hocking, J.C., Scholz, R.P., Mooz, J., Anderson, C.L., Karreman, C., Meyer zu Heringdorf, D., Schmidt, G., Ruonala, M., Namikawa, K., Harms, G.S., Carpy, A., Macek, B., Köster, R.W., Rajalingam, K. 2011. IAPs regulate the plasticity of cell migration by directly targeting Rac1 for degradation. EMBO J. 31(1):14-28

69. Djamei, A., Schipper, K., Rabe, F., Vincon, V., Kahnt, J., Osorio, S., Fernie, A.R., Johannsen, M., Maier, U., Mörschel, E., Feussner, I., Feussner, K., Meinicke, P., Stierhoff, Y., Schwarz, H., Macek, B., Mann, M., Kahmann, R. 2011. Metabolomic priming by a secreted fungal effector. Nature 478:395-400

68. Koch, A., Krug, K., Pengelley, S.,Macek, B^#., Hauf, S^#. 2011. Mitotic substrates of the kinase Aurora with roles in chromatin regulation identified through quantitative phosphoproteomics of fission yeast. Science Signaling. 4 (179): rs6.

67. Macek, B. 2011. LC-MS for the identification of posttranslational modifications on proteins. (A book chapter in “Protein and Peptide Analysis by LC-MS”, Royal Society of Chemistry, ISBN-10: 1849731829)

66. Schütz, W., Hausmann, N., Krug, K., Hampp, R., Macek, B. 2011. Extending SILAC to proteomics of plant cell lines. Plant Cell. 23(5):1701-5.

65. Ikeda F, Deribe YL, Skånland SS, Stieglitz B, Grabbe C, Franz-Wachtel M, van Wijk SJ, Goswami P, Nagy V, Terzic J, Tokunaga F, Androulidaki A, Nakagawa T, Pasparakis M, Iwai K, Sundberg JP, Schaefer L, Rittinger K, Macek B, Dikic I. SHARPIN forms a linear ubiquitin ligase complex regulating NF-kappaB activity and apoptosis. Nature. 2011 Mar 31;471(7340):637-41.

64. Grgurevic L, Macek B, Mercep M, Jelic M, Smoljanovic T, Erjavec I, Dumic-Cule I, Prgomet S, Durdevic D, Vnuk D, Lipar M, Stejskal M, Kufner V, Brkljacic J, Maticic D, Vukicevic S. Bone morphogenetic protein (BMP)1-3 enhances bone repair. Biochem Biophys Res Commun. 408(1):25-31.
63. Hausser, A., Barisic, S., Nagel, A., Franz-Wachtel, M., Macek, B., Preiss, A., Maier, D. and Link, G. Phosphorylation of serine 402 impedes slingshot 1 (SSH1) phosphatase activity. 2011 EMBO Reports. 12(6):527-33.
62. Löffler, A.S., Alers, S., Dieterle, A.M., Keppeler, H., Franz-Wachtel, M., Kundu, M., Campbell, D.G., Wesselborg, S., Alessi, D.R., Stork, B. Ulk1-mediated phosphorylation of AMPK constitutes a negative regulatory feedback loop. 2011 Autophagy. 7(7):696-706.

61. Nestler J, Schütz W, Hochholdinger F. Conserved and unique features of the maize (Zea mays L.) root hair proteome. J Proteome Res. 10(5):2525-37.

60. Macek B, Mijakovic I. Site-specific analysis of bacterial phosphoproteomes. 2011. Proteomics. 11(15):3002-11.

59. Grgurevic L, Macek B, Healy DR, Brault AL, Erjavec I, Cipcic A, Grgurevic I, Rogic D, Galesic K, Brkljacic J, Stern-Padovan R, Paralkar VM, Vukicevic S. Circulating bone morphogenetic protein 1-3 isoform increases renal fibrosis. J Am Soc Nephrol. 2011 Apr;22(4):681-92.

58. Zelenak C, Föller M, Velic A, Krug K, Qadri SM, Viollet B, Lang F, Macek B. Proteome Analysis of Erythrocytes Lacking AMP-Activated Protein Kinase Reveals a Role of PAK2 Kinase in Eryptosis. J Proteome Res. 2011 Apr 1;10(4):1690-1697.

57. Tiffert Y, Franz-Wachtel M, Fladerer C, Nordheim A, Reuther J, Wohlleben W, Mast Y. Proteomic analysis of the GlnR-mediated response to nitrogen limitation in Streptomyces coelicolor M145.Appl Microbiol Biotechnol. 2011 Feb;89(4):1149-59.

56. Krug, K., Nahnsen, S., Macek, B. 2011. Mass spectrometry at the interface of genomics and proteomics. Mol Biosystems 7(2):284-91.

55. Tschan S, Kreidenweiss A, Stierhof YD, Sessler N, Fendel R, Mordmüller B. Mitochondrial localization of the threonine peptidase PfHslV, a ClpQ ortholog in Plasmodium falciparum. Int J Parasitol. 2010 Nov;40(13):1517-23.

54. Menon MB, Schwermann J, Singh AK, Franz-Wachtel M, Pabst O, Seidler U, Omary MB, Kotlyarov A, Gaestel M. p38 MAP kinase and MAPKAP kinases MK2/3 cooperatively phosphorylate epithelial keratins. J Biol Chem. 2010 Oct 22;285(43):33242-51.

53. Pasztor L, Ziebandt AK, Nega M, Schlag M, Haase S, Franz-Wachtel M, Madlung J, Nordheim A, Heinrichs DE, Götz F. Staphylococcal major autolysin (Atl) is involved in excretion of cytoplasmic proteins. J Biol Chem. 2010 Nov 19;285(47):36794-803. Epub 2010 Sep 16.

52. Burbulla LF, Schelling C, Kato H, Rapaport D, Woitalla D, Schiesling C, Schulte C, Sharma M, Illig T, Bauer P, Jung S, Nordheim A, Schöls L, Riess O, Krüger R. Dissecting the role of the mitochondrial chaperone mortalin in Parkinson's disease: functional impact of disease-related variants on mitochondrial homeostasis.Hum Mol Genet. 2010 Nov 15;19(22):4437-52. Epub 2010 Sep 2.

51. Velic, A., Macek, B., Wagner, C. 2010. Towards quantitative proteomics of organ substructures: implications for renal physiology. Seminars in Nephrology 30(5):487-499

50. Marcon, C., Schützenmeister, A., Schütz, W., Madlung, J., Piepho, H.P., Hochholdinger, F. 2010. Nonadditive protein accumulation patterns in maize (Zea mays L.) hybrids during embryo development. J Prot Res 2010 Dec 3;9(12):6511-6522.

49. Schütz, W., Franz-Wachtel, M., Macek, B. 2010. SILAC in Mikroorganismen. (in German) Biospektrum 5: 552-554

48. Soufi, B., Kumar, C., Gnad, F., Mann, M., Mijakovic, I., Macek, B. Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) applied to quantitative proteomics of Bacillus subtilis. 2010 J Prot Res 9(7):3638-3646, Epub 2010 May 28

47. Jers C, Pedersen MM, Paspaliari DK, Schütz W, Johnsson C, Soufi B, Macek B, Jensen PR, Mijakovic I. Bacillus subtilis BY-kinase PtkA controls enzyme activity and localisation of its protein substrates. Mol Microbiol. 2010 Jul;77(2):287-299. Epub 2010 May 24.

46. Jung S, Fladerer C, Braendle F, Madlung J, Spring O, Nordheim A. Identification of a novel Plasmopara halstedii elicitor protein combining de novo peptide sequencing algorithms and RACE-PCR. 2010 Proteome Sci. 8(1):24.

45. Bertsch A, Jung S, Zerck A, Pfeifer N, Nahnsen S, Henneges C, Nordheim A, Kohlbacher O. Optimal de novo design of MRM experiments for rapid assay development in targeted proteomics. J Proteome Res. 2010 May 7;9(5):2696-704.

44. Ma W, Muthreich N, Liao C, Franz-Wachtel M, Schütz W, Zhang F, Hochholdinger F, Li C. The mucilage proteome of maize (Zea mays L.) primary roots. J Proteome Res. 2010 Jun 4;9(6):2968-2976. Epub 2010 Apr 21

43. Alsheimer M, Baier A, Schramm S, Schütz W, Benavente R. Synaptonemal Complex Protein SYCP3 exists in two isoforms showing different Conservation in Mammalian Evolution. Cytogenet. Genome Res. 2010;128(1-3):162-168. Epub 2010 Mar 25.

42. Borchert N, Dieterich C, Krug K, Schütz W, Jung S, Nordheim A, Sommer RJ, Macek B. Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models. Genome Res. 2010 Jun;20(6):837-846. Epub 2010 Mar 17.

41. Saleem M, Lamkemeyer T, Schützenmeister A, Madlung J, Sakai H, Piepho HP, Nordheim A, Hochholdinger F. Specification of cortical parenchyma and stele of maize primary roots by asymmetric levels of auxin, cytokinin, and cytokinin-regulated proteins. Plant Physiol. 2010;152(1):4-18.

40. Muthreich N., Schützenmeister A., Schütz W., Madlung J., Krug K., Nordheim A., Piepho H.-P., Hochholdinger F. (2009): Regulation of the maize (Zea mays L.) embryo proteome by RTCS which controls seminal root initiation. Eur. J. Cell Biol. 2010 Feb-Mar;89(2-3):242-249. Epub 2009 Dec 3.

39. Liu Y., von BehrensI., Muthreich N., Schütz W., Nordheim A., Hochholdinger F. (2009): Regulation of the pericycle proteome in maize (Zea mays L.) primary roots by RUM1 which is required for lateral root initiation. Eur. J. Cell Biol. 2010 Feb-Mar;89(2-3):236-241. Epub 2009 Dec 4.

38. Henneges C, Hinselmann G, Jung S, Madlung J, Schütz W, Nordheim A, Zell A. Ranking Methods for the Prediction of Frequent Top Scoring Peptides from Proteomics Data. J Proteomics Bioinformatics. 2009; 2: 226-235

37. Gröbner S, Linke D, Schütz W, Fladerer C, Madlung J, Autenrieth IB, Witte W, Pfeifer Y. Emergence of carbapenem-non-susceptible extended-spectrum beta-lactamase-producing Klebsiella pneumoniae isolates at the university hospital of Tübingen, Germany. J Med Microbiol. 2009;58(Pt 7):912-22.

36. Biswas L, Biswas R, Nerz C, Ohlsen K, Schlag M, Schäfer T, Lamkemeyer T, Ziebandt AK, Hantke K, Rosenstein R, Götz F. Role of the twin-arginine translocation pathway in Staphylococcus. J Bacteriol. 2009;191(19):5921-9.

35. Saleem M, Lamkemeyer T, Schützenmeister A, Fladerer C, Piepho HP, Nordheim A, Hochholdinger F. Tissue specific control of the maize (Zea mays L.) embryo, cortical parenchyma, and stele proteomes by RUM1 which regulates seminal and lateral root initiation. J Proteome Res. 2009 May;8(5):2285-97.

34. Sprossmann F, Pankert P, Sausbier U, Wirth A, Zhou XB, Madlung J,Zhao H, Bucurenciu I, Jakob A, Lamkemeyer T, Neuhuber W, Offermanns S, Shipston MJ, Korth M, Nordheim A, Ruth P, Sausbier M. Inducible knockout mutagenesis reveals compensatory mechanisms elicited by constitutive BK channel deficiency in overactive murine bladder. FEBS J. 2009;276(6):1680-97

33. Pirow R, Buchen I, Richter M, Allmer C, Nunes F, Günsel A, Heikens W, Lamkemeyer T, von Reumont BM, Hetz SK. Cationic composition and acid-base state of the extracellular fluid, and specific buffer value of hemoglobin from the branchiopod crustacean Triops cancriformis. J Comp Physiol B. 2009 Apr;179(3):369-81.

32. Zhang F, Skoda MWA, Jacobs RMJ, Dressen DG, Martin RA, Martin CM, Clark GF, Lamkemeyer T, Schreiber F. Gold Nanoparticles Decorated with Oligo(ethylene glycol) Thiols: Enhanced Hofmeister Effects in Colloid-Protein Mixtures. J Phys. Chem. C 2009; 113(12):4839-4847

31. Barjaktorovic Z, Babbick M, Nordheim A, Lamkemeyer T, Magel E, Hampp R. Alterations in Protein Expression of Arabidopsis thaliana Cell Cultures During Hyper- and Simulated Micro-Gravity. Microgravity Science and Technology. 2009; 21(1-2): 191-196

30. Eisenbeis S, Lohmiller S, Valdebenito M, Leicht S and Braun V (2008) NagA-dependent uptake of N-Acetyl-gGlucosamine and N-Acetyl-Chitin Oligosaccharides across the Outer Membrane of Caulobacter crescentus. Journal of Bacteriology, 190 (15): 5230-5238.

29. Meyer VS, Kastenmuller W, Gasteiger G, Franz-Wachtel M, Lamkemeyer T, Rammensee HG, Stevanovic S, Sigurdardottir D and Drexle I (2008) Long-term immunity against actual poxviral HLA ligands as identified by differential stable isotope labeling. J Immunol, 181 (9): 6371-83

28. Hala M, Cole R, Synek L, Drdova E, Pecenkova T, Nordheim A, Lamkemeyer T, Madlung J, Hochholdinger F, Fowler J and Zarsky V (2008) An exocyst complex functions in plant cell growth. Plant Cell, 20(5): 1330-45

27. Siemoneit U, Hofmann B, Kather N, Lamkemeyer T, Madlung J, Franke L, Schneider G, Jauch J, Poeckel D and Werz O (2008) Identification and functional analysis of cyclooxygenase-1 as a molecular target of boswellic acids. Biochem Pharmacol, 75 (2): 503-513.

26. Duechting A, Tschöpe C, Kaiser H, Lamkemeyer T, Tanaka N Aberle S, Lang F, Torresi J, Kandolf R and Bock CT (2008) Human parvovirus B19-NS1 protein modulates inflammatory signaling by activation of STAT3/PIAS3 in human endothelial cells J Virol, 82(16): 7942-52

25. Hoecker N, Lamkemeyer T, Keller B, Fladerer C, Madlung J, Piepho HP, Nordheim A and Hochholdinger F (2008) Analysis of non-additive protein accumulation in young primary roots of a maize (Zea mays L.) F1-hybrid compared to its parental inbred lines. Proteomics, 8(16): 3882-94.

24. Barjaktarović Z, Nordheim A, Lamkemeyer T, Fladerer C, Madlung J and Hampp R (2007) Time-course of changes in amounts of specific proteins upon exposure to hyper-g, 2-D clinorotation, and 3-D random positioning of Arabidopsis cell cultures. Journal of Experimental Botany, 58 (15/16): 4357-63.

23. Dembinsky D, Woll K, Saleem M, Liu Y, Fu Y, Borsuk LA, Lamkemeyer T, Fladerer C, Madlung J, Barbazuk B, Nordheim A, Nettleton D, Schnable PS, Hochholdinger F (2007) Transcriptomic and proteomic analyses of pericycle cells of the maize (Zea mays L.) primary root. Plant Physiol, 145: 575-588.

22. del Val C, Ernst P, Falkenhahn M, Fladerer C, Glatting KH, Suhai S (2007) ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ. Nucleic Acids Res, 35: W444-W450.

21. Weinzierl AO, Lemmel C, Schoor O, Müller M, Krüger T, Wernet D, Hennenlotter J, Stenzl A, Klingel K, Rammensee HG and Stevanović S (2007) Distorted relation between mRNA copy number and corresponding major histocompatibility complex ligand density on the cell surface. Mol Cell Proteomics, 6: 102-13.

20. Dengjel J, Nastke MD, Gouttefangeas C, Gitsioudis G, Schoor O, Altenberend F, Müller M, Krämer B, Missiou A, Sauter M, Hennenlotter J, Wernet D, Stenzl A, Rammensee HG, Klingel K and Stevanović S (2006) Unexpected Abundance of HLA Class II Presented Peptides in Primary Renal Cell Carcinomas. Clin Cancer Res, 12: 4163-4170.

19. Proikas-Cezanne T, Gaugel A, Frickey T and Nordheim A (2006) Rab14 is part of the early endosomal clathrin-coated TGN microdomain. FEBS Lett., 580: 5241-5246.

18. Rönnefarth VM, Erbacher AIM, Lamkemeyer T, Madlung J, Nordheim A, Rammensee HG and Decker P (2006) TLR2/TLR4-independent neutrophil activation and recruitment upon endocytosis of nucleosomes reveals a new pathway of innate immunity in systemic lupus erythematosus. J Immunol, 177: 7740-7749.

17. Crisóstomo MI, Vollmer W, Kharat A, Inhülsen S, Gehre F, Buckenmaier S and Tomasz A (2006) Attenuation of penicillin resistance in a peptidoglycan O-acetyl transferase mutant of Streptococcus pneumoniae. Mol Microbiol, published online.

16. Berg CP, Stein GM, Klein R, Pascu M, Berg T, Kammer W, Priemer M, Nordheim A, Gregor M, Berg PA and Wesselborg S (2006) Demonstration of PDC-E1 subunits as major antigens in the complement fixing fraction M4 and re-evaluation of PDC-E1-specific antibodies in PBC patients. Liver Int, 26: 846-855.

15. Sauer M, Jakob A, Nordheim A and Hochholdinger F (2006) Proteomic analysis of shoot-borne root initiation in maize (Zea mays L.). Proteomics, 6: 2530-2541.

14. Rousselot M, Jaenicke E, Lamkemeyer T, Harris RJ, and Pirow R (2006) Native and subunit molecular mass and quarternary structure of the haemoglobin from the primitive branchiopod crustacean Triops cancriformis. FEBS J, 273: 4055-4071.

13. Liu Y, Lamkemeyer T, Jakob A, Mi G, Zhang F, Nordheim A, and Hochholdinger F (2006) Comparative proteome analyses of maize (Zea mays L.) primary roots prior to lateral root initiation reveal differential protein expression in the lateral root initiation mutant rum1. Proteomics, 6: 4300-4308.

12. Lamkemeyer T, Zeis B, Decker H, Jaenicke E, Waschbüsch D, Gebauer W, Markl J, Meissner U, Rousselot M, Zal F and Paul RJ (2006) Molecular mass of macromolecules and subunits and quaternary structure of hemoglobin from the microcrustacean Daphnia magna. FEBS J, 273: 3393-3410.

11. Mordmüller B, Fendel R, Kreidenweiss A, Gille C, Hurwitz R, Metzger WG, Kun JFJ, Lamkemeyer T, Nordheim A, and Kremsner PG (2006) Plasmodia express two threonine-peptidase complexes during asexual development. Mol Biochem Parasitol, 148: 79-85.

10. Neubauer H, Clare SE, Kurek R, Fehm T, Wallwiener D, Sotlar K, Nordheim A, Wozny W, Schwall GP, Poznanović S, Sastri C, Hunzinger C, Stegmann W, Schrattenholz A and Cahill MA (2006) Breast cancer proteomics by laser capture microdissection, sample pooling, 54-cm IPG IEF, and differential iodine radioisotope detection. Electrophoresis, 27: 1840-1852.

9. Zimmermann U, Junker H, Krämer F, Balabanov S, Kleist B, Kammer W, Nordheim A and Walther R (2006) Comparative proteomic analysis of neoplastic and non-neoplastic germ cell tissue. Biol Chem, 387: 437-440.

8. Resch A, Leicht S, Saric M, Pasztor L, Jakob A, Götz F, and Nordheim A (2006) Comparative proteome analysis of Staphylococcus aureus biofilm and planktonic cells and correlation with transcriptome profiling. Proteomics, 6: 1867-1877.

7. Tolson JP, Flad T, Gnau V, Dihazi H, Hennenlotter J, Beck A, Mueller GA, Kuczyk M, and Mueller CA. (2006). Differential detection of S100A8 in transitional cell carcinoma of the bladder by pair wise tissue proteomic and immunohistochemical analysis. Proteomics, 6: 697-708.

6. Lamkemeyer T, Paul RJ, Stöcker W, Yiallouros I and Zeis B (2005) Macromolecular isoforms of Daphnia magna haemoglobin. Biol Chem, 386: 1087-1096.

5. Neugebauer H, Herrmann C, Kammer W, Schwarz G, Nordheim A, and Braun V (2005) ExbBD-dependent transport of maltodextrins through the novel MalA protein across the outer membrane of Caulobacter crescentus. J Bacteriol, 187: 8300-11.

4. Hennersdorf F, Florian S, Jakob A, Baumgartner K, Sonneck K, Nordheim A, Biedermann T, Valent P, and Bühring HJ. (2005) Identification of CD13, CD107a, and CD164 as novel basophil-activation markers and dissection of two response patterns in time kinetics of IgE-dependent upregulation, Cell Res, 15: 325 - 335.

3. Hoschle B, Gnau V, and Jendrossek D. (2005). Methylcrotonyl-CoA and geranyl-CoA carboxylases are involved in leucine/isovalerate utilization (Liu) and acyclic terpene utilization (Atu), and are encoded by liuB/liuD and atuC/atuF, in Pseudomonas aeruginosa. Microbiology, 151: 3649-56.

2. Bera A, Herbert S, Jakob A, Vollmer W and Götz F (2005). Why are pathogenic staphylococci so lysozyme resistant? The peptidoglycan O-acetyltransferase OatA is the major determinant for lysozyme resistance of Staphylococcus aureus. Mol Microbiol, 55: 778-787.

1. Proikas-Cezanne T, Waddell S, Gaugel A, Frickey T, Lupas A, and Nordheim A (2004). WIPI-1alpha (WIPI49), a member of the novel 7-bladed WIPI protein family, is aberrantly expressed in human cancer and is linked to starvation-induced autophagy. Oncogene, 23: 9314-9325.