Core Facility Proteomics & Mass Spectrometry

Publications

  1. Ajiboye J, Uldry AC, Heller M, Fan E,  VanVoorhis WC, Hemphill A, Müller J. (2024) Molecular targets of the 5-amido-carboxamidebased bumped kinase inhibitor BKI-1748 in Cryptosporidium parvum and HCT-8 host cells. Int. J. Mol. Sci. . 25,2707. https://doi.org/10.3390/ijms25052707.
  2. Akshay A, Gheinani AH, Besic M, Braga S, Uldry AC, Heller M, Rehrauer H, Fournier CA, Burkhard FC, Monastyrskaya K. (2024) De-obstruction of bladder outlet in humans reverses organ remodelling by normalizing the expression of key transcription factors. BMC Urology, 24:33. https://doi.org/10.1186/s12894-024-01417-8.
  3. Gurzeler LA, Link M, Ibig Y, Schmidt I, Galuba O, Schoenbett J, Gasser-Didierlaurant C, Parker CN, Mao X, Bitsch F, Schirle M, Couttet P, Sigoillot F, Ziegelmüller J, Uldry AC, Teodorowicz W, Schmiedeberg N, Mühlemann O, Reinhardt J. (2023) Drug-induced eRF1 degradation promotes readthrough and reveals a new branch of ribosome quality control. Cell Rep. 42:113056. doi: 10.1016/j.celrep.2023.113056. Epub 2023 Aug 30. Erratum in: Cell Rep. 2023 Sep 26;42(9):113159. PMID: 37651229.
  4. Nasif S, Colombo M, Uldry AC, Schröder MS, de Brot S, Mühlemann O. Inhibition of nonsense-mediated mRNA decay reduces the tumorigenicity of human fibrosarcoma cells. NAR Cancer. 2023 Sep 6;5(3):zcad048. doi: 10.1093/narcan/zcad048. PMID: 37681034
  5. Bartos K, Ramakrishnan SK, Braga-Lagache S, Hänzi B, Durussel F, Prakash Sridharan A, Zhu Y, Sheehan D, Hynes NE, Bonny O, Moor MB. (2023) Renal FGF23 signaling depends on redox protein Memo1 and promotes orthovanadate-sensitive protein phosphotyrosyl phosphatase activity. J Cell Commun Signal. 17:705-722. doi: 10.1007/s12079-022-00710-1. PMID: 36434320
  6. Hänggeli KPA, Hemphill A, Müller N, Heller M, Uldry AC, Braga-Lagache S, Müller J, Boubaker G. (2023) Comparative Proteomic Analysis of Toxoplasma gondii RH Wild-Type and Four SRS29B (SAG1) Knock-Out Clones Reveals Significant Differences between Individual Strains. Int. J. Mol. Sci. 2023, 24, 10454. https://doi.org/10.3390/ijms241310454. PMID: 37445632
  7. Pilotto F, Douthwaite C, Diab R, Ye XQ, Al Qassab Z, Tietje C, Mounassir M, Odriozola A, Thapa A, Buijsen RAM, Lagache S, Uldry AC, Heller M, Müller S, van Roon-Mom WMC, Zuber B, Liebscher S, Saxena S. (2023) Early molecular layer interneuron hyperactivity triggers Purkinje neuron degeneration in SCA1. Neuron 111:1–21. https://doi.org/10.1016/j.neuron.2023.05.016. PMID: 37321222
  8. Müller J, Preza M, Kaethner M, Rufener R, Braga S, Uldry AC, Heller M, Lundström-Stadelmann B. (2023) Targeted and non-targeted proteomics to characterize the parasite proteins of Echinococcus multilocularis metacestodes. Front Cell Infect Microbiol. 13:1170763. doi: 10.3389/fcimb.2023.1170763. PMID: 37325510
  9. Memedovski R, Preza M, Müller J, Kämpfer T, Rufener R, de Souza MVN, da Silva ET, de Andrade GF, Braga S, Uldry AC, Buchs N, Heller M, Lundström-Stadelmann B. (2023) Investigation of the mechanism of action of mefloquine and derivatives against the parasite Echinococcus multilocularis. Int J Parasitol: Drugs Drug Resist. 21: 114-124. doi: 10.1016/j.ijpddr.2023.03.002. PMID: 36921443
  10. Timpanaro A, Piccand C, Uldry AC, Bode PK, Dzhumashev D, Sala R, Heller M, Rössler J, Bernasconi M. (2023) Surfaceome Profiling of Cell Lines and Patient-Derived Xenografts Confirm FGFR4, NCAM1, CD276, and Highlight AGRL2, JAM3, and L1CAM as Surface Targets for Rhabdomyosarcoma. Int. J. Mol. Sci. 24, 2601. https://doi.org/10.3390/ijms24032601. PMID: 36768928
  11. Lux J, Holivololona L, San Millan Gutierrez R, Hilty M, Ramette A, Heller M, Hathaway LJ. (2022), AmiA and AliA peptide ligands are secreted by Klebsiella pneumoniae and inhibit growth of Streptococcus pneumoniae. Sci Rep. 12(1):22268. doi: 10.1038/s41598-022-26838-z. PMID: 36564446.
  12. Müller J, Schlange C, Heller M, Uldry A-C, Braga-Lagache S, Haynes RK, Hemphill A. (2022) Proteomic characterization of Toxoplasma gondii ME49 derived strains resistant to the artemisinin derivatives artemiside and artemisone reveals potential mode of action independent of ROS formation. Int J Parasitol: Drugs Drug Resist., 21:1-12. doi: 10.1016/j.ijpddr.2022.11.005.
  13. Müller J, Boubaker G, Imhof D, Hänggeli K, Haudenschild N, Brage-Lagache S, Uldry A-C, Heller M, Ortega-Mora LM, Hemphill A (2022) Differential affinity chromatography coupled to mass spectrometry: a suitable tool to identify common binding proteins of a broad-range antimicrobial peptide derived from leucinostatin. Biomedicines, 10, 2675. doi: 10.3390/biomedicines10112675.
  14. Domanski M, Dedic E, Pérez ME, Clery A, Campagne S, Uldry AC, Braga S, Heller M, Rabl J, Afanasyev P, Boehringer D, Novacek J, Allain FT, Mühlemann, O. (2022) 40S hnRNP particles are a novel class of nuclear biomolecular condensates, Nucleic Acids Res., 50(11):6300-6312. doi: 10.1093/nar/gkac457.
  15. Uldry A-C, Maciel-Dominguez A, Jornod M, Buchs N, Braga-Lagache S, Brodard J, Jankovic J, Bonadies N, Heller M. (2022) Effect of Sample Transportation on the Proteome of Human Circulating Blood Extracellular Vesicles. Int. J. Mol. Sci. 23, 4515. https://doi.org/10.3390/ijms23094515.
  16. Müller J, Nicoleta A, Imhof D, Hänggeli K, Uldry AC, Lagache S, Heller M, Ojo KK, Ortega Mora LM, Van Voorhis WC, Hemphill A (2022) Common molecular targets of a quinolone based bumped kinase inhibitor in Neospora caninum and Danio rerio. Int. J. Mol. Sci., 23(4), 2381; doi: 10.3390/ijms23042381.
  17. Colomé N, Abian J, Aloria K, Arizmendi JM, Barceló-Batllori S, Braga-Lagache S, … Heller M, … Corrales FJ (2022) ProteoRed-ISCIII; EuPA. Multi-laboratory experiment PME11 for the standardization of phosphoproteome analysis. J Proteomics. 251:104409. doi: 10.1016/j.jprot.2021.104409. PMID: 34758407.
  18. Hill V, Akarsu H, Sánchez Barbarroja R, Cippà VL, Kuhnert P, Heller M, Falquet L, Heller M, Stoffel MH, Labroussaa F, Jores J (2021) Minimalistic mycoplasmas harbor different functional toxin-antitoxin systems. PLoS Genet. 17(10):e1009365. doi: 10.1371/journal.pgen.1009365. PMID: 34673769.
  19. Anghel N, Müller J, Serricchio M, Jelk J, Bütikofer P, Boubaker G, Imhof D, Ramseier J, Desiatkina O, Păunescu E, Braga-Lagache S, Heller M, Furrer J, Hemphill A (2021) Cellular and Molecular Targets of Nucleotide-Tagged Trithiolato-Bridged Arene Ruthenium Complexes in the Protozoan Parasites Toxoplasma gondii and Trypanosoma brucei. Int J Mol Sci. 22: 10787. doi: 0.3390/ijms221910787.
  20. Schniering J, Maciukiewicz M, Gabrys HS, Brunner M, Blüthgen C, Meier C, Braga-Lagache S, Uldry A-C, Heller M, Guckenberger M, Fretheim H, Nakas CT, Hoffmann-Vold A-M, Distler O, Frauenfelder T, Tanadini-Lang S, Maurer B (2021) Radiomic fingerprinting decodes phenotypes of systemic sclerosis-associated interstitial lung disease. Eur Respir J. 14:2004503. doi: 10.1183/13993003.04503-2020. PMID: 34649979.
  21. Zysset-Burri DC, Schlegel I, Lincke JB, Jaggi D, Keller I, Heller M, Braga-Lagache, Wolf S, Zinkernagel MS. (2021) Understanding the interactions between the ocular surface microbiome and the tear proteome. Invest Ophthalmol Vis Sci. 62(10):8. doi: 10.1167/iovs.62.10.8.
  22. Hallal M, Braga-Lagache S, Jankovic J, Simillion C, Bruggmann R, Uldry AC, Allam R, Heller M, Bonadies N. (2021) Inference of Kinase-Signaling Networks in Human Myeloid Cell Line Models by Phosphoproteomics using Kinase Activity Enrichment Analysis (KAEA). BMC Cancer. 21:789. doi.org/10.1186/s12885-021-08479-z.
  23. Contu L, Balistreri G, Domanski M, Uldry AC, Mühlemann O. (2021) Characterisation of the Semliki Forest Virus-host cell interactome reveals the viral capsid protein as an inhibitor of nonsense-mediated mRNA decay. PLoS Pathog. 17(5):e1009603. doi: 10.1371/journal.ppat.1009603. PMID: 34019569.
  24. Müller J, Heller M, Uldry A.C., Braga S, Mueller N. (2021) Nitroreductase activites in Giardia lamblia: ORF 17150 encodes a quinone reductase with nitroreductase activity. Pathogens.10, 129. doi.org/10.3390/pathogens10020129
  25. Bevkal S, Naguleswaran A, Rehmann R, Kaiser M, Heller M, Roditi I. (2021) An Alba-domain protein required for proteome remodeling during differentiation of Trypanosoma brucei. PLoSPathog 17(1): e1009239. doi: 10.1371/journal.ppat.1009239.
  26. Tamò L, Fytianos K, Caldana F, Simillion C, Feki A, Nita I, Heller M, Geiser T, Gazdhar A (2021) Interactome analysis of iPSC secretome and its effect on macrophages in vitro. Int J Mol Sci. 22: 958. doi: 10.3390/ijms22020958.
  27. Heller M, Braga S, Mueller N, Müller J. (2020) Transfection with plasmid causing stable expression of a foreign gene affects general proteome pattern in Giardia lamblia trophozoites. Frontiers: Cellular and Infection Microbiology, published:18.Dec.2020. doi: 10.3389/fcimb.2020.602756
  28. Cyrta J, Augspach A, de Filippo MR, Prandi D, Thienger P, Benelli M, Cooley V, Bareja R, Wilkes D, Chae S-S, Cavaliere P, Dephoure N, Uldry A-C, Lagache SB, Roma L, Cohen S, Jaquet M, Brandt LP, Alshalalfa M, Sboner A, Feng F, Wang S, Beltran H, Lotan T, Spahn M, Kruithof-de Julio M, Chen Y, Ballman KV, Demichelis F, Piscuoglio S, Rubin MA. (2020) Role of Specialized Composition of SWI/SNF Complexes in Prostate Cancer Lineage Plasticity. Nat Commun. 11: 5549 doi.org/10.1038/s41467-020-19328-1.
  29. Duman M, Vaquié A, Nocera G, Heller M, Stumpe M, Sankar DS, Dengjel J, Meijer D, Yamaguchi T, Matthias P, Zeis T, Schaeren-Wiemers N, Hayoz A, Ruff S, Jacob C. (2020) EEF1A1 Deacetylation Enables Transcriptional Activation of Remyelination. Nat. Commun. 11:3420 doi.org/10.1038/s41467-020-17243-z.
  30. Winzer P, Müller J, Imhof D, Ritler D, Uldry A-C, Braga-Lagache S, Heller M, Ojo KK, Van Voorhis WC, Ortega L, Hemphill A. (2020) Neospora caninum: Differential proteome of multinucleated complexes induced by the bumped kinase inhibitor BKI-1294. Microorganism, 8, 801; doi:10.3390/microorganisms8060801.
  31. Müller J, Braga S, Uldry AC, Heller M, Müller N. (2020) Comparative proteomics of three Giardia lamblia strains: Investigation of antigenic variation in the post-genomic era. Parasitology. 147: 1008-1018. doi:10.1017/S0031182020000657
  32. Briand ML, Gebleux R, Richina F, Correro MR, Grether Y, Dudal Y, Braga-Lagache S, Heller M, Beerli RR, Grawunder U, Corvini PF, Shahgaldian P. (2020) Partially shielded enzymes capable of processing large protein substrates. Chem. Commun. 56: 5170-5173. doi: 10.1039/d0cc01150a.
  33. Cosgrove J, Novkovic M, Albrecht S, Pikor N, Zhou Z, Onder L, Mörbe U, Cupovic J, Miller H, Alden K, Thuery A, O'Toole P, Pinter R, Jarrett S, Taylor E, Venetz D, Heller M, Uguccioni M, Legler D, Lacey C, Coatesworth A, Polak W, Cupedo T, Manoury B, Thelen M, Stein J, Wolf M, Leake M, Timmis J, Ludewig B, Coles M. (2020) B-cell Zone Reticular Cell Microenvironments Shape CXCL13 Gradient Formation. Nat. Commun. 11: 3677. doi.org/10.1038/s41467-020-17135
  34. Nasher FNA, Kwun MJ, Croucher NJ, Heller M, Hathaway LJ. (2019) Peptide occurring in Enterobacteriaceae triggers Streptococcus pneumoniae cell death. Frontiers in Cell & Infection Microbiol. 9:320. doi: 10.3389/fcimb.2019.00320.
  35. Müller J, Braga S, Heller M, Müller N. (2019) Resistance formation to nitro drugs in Giardia lamblia: No common markers identified by comparative proteomics. Int J Parasitol-Drug., 9: 112-119. doi: 10.1016/j.ijpddr.2019.03.002.
  36. Kuhn-Nentwig L, Langenegger N, Heller M, Koua D, Nentwig W. (2019) The dual prey-inactivation strategy of spiders - In-depth venomic analysis of Cupiennius salei. Toxins, 11:167, doi:10.3390/toxins11030167.
  37. Kehl D, Mallone A, Generali M, Heller M, Uldry AC, Cheng P, Gantenbein B, Hoerstrup SP, Weber B. (2019) Proteomic analysis of human mesenchymal stromal cell secretomes: a systematic comparison of the angiogenic potential. NPJ Regen Med. 4:8. doi: 10.1038/s41536-019-0070-y.
  38. Zahnd S, Braga-Lagache S, Buchs N, Lugli A, Dawson H, Heller M, Zlobec I. (2019) A Digital Pathology based Shotgun-Proteomics Approach to Biomarker Discovery in Colorectal Cancer. J Pathol Inform. 10:40. doi: 10.4103/jpi.jpi_65_18.
  39. Nicholson P, Furrer J, Hässig M, Strauss C, Heller M, Braga-Lagache S, Frey J. (2019) Production of neutralizing antibodies against the secreted Clostridium chauvoei toxin A (CctA) upon blackleg vaccination. Anaerobe. 56: 78-87. doi: 10.1016/j.anaerobe.2019.02.011.
  40. Brunner MAT, Rüfenacht S, Bauer A, Erpel S, Buchs N, Braga-Lagache S, Heller M, Leeb T, Jagannathan V, Wiener DJ, Welle MM. (2019) Bald Thigh Syndrome in sighthounds – revisiting the cause of a well-known disease. Plos one, 14: e0212645. DOI: 10.1371/journal.pone.0212645.
  41. Jack T, Leuenberger M, Ruepp MD, Vernekar SKV, Thompson AJ, Braga-Lagache S, Heller M, Lochner M. (2019) Mapping the Orthosteric Binding Site of the Human 5-HT(3) Receptor Using Photo-crosslinking Antagonists. ACS Chem Neurosci. 10:438-450. doi: 10.1021/acschemneuro.8b00327.
  42. V’kovski P, Gerber M, Kelly J, Pfaender S, Ebert N, Braga Lagache S, Simillion C, Portmann J, Stalder H, Gaschen V, Bruggmann R, Stoffel M, Heller M, Dijkman R, Thiel V. (2019) Determination of host cell proteins constituting the molecular microenvironment of coronavirus replicase complexes by proximity-labeling. eLife, 8:e42037 doi: 10.7554/eLife.42037.002.
  43. Basaco T, Pektor S, Bermudez JM, Meneses N, Heller M, Galván JA, Boligán KF, Schürch S, von Gunten S, Türler A, Miederer M. (2018) Evaluation of radiolabeled Girentuximab in vitro and in vivo. Pharmaceuticals. 132; doi:10.3390/ph11040132.
  44. Nasher F, Aguilar F, Aebi S, Hermans P, Heller M, Hathaway LJ. (2018) Peptide ligands of AmiA, AliA and AliB proteins determine pneumococcal phenotype. Frontiers in Microbiol. 9:3013.
  45. Buchs N, Braga-Lagache S, Uldry A-C, Brodard J, Debonneville C, Reynard J-S, Heller M. (2018) Absolute Quantification of Grapevine Red Blotch Virus in Grapevine Leaf and Petiole Tissues by Proteomics. Frontiers in Plant Science. 9:1735. 10.3389/fpls.2018.01735.
  46. Pieróg J, Fytianos K, Tamò L, Simillion C, Taddeo A, Kocher G, Gugger M, Grodzki T, Heller M, Geiser T, Blank F, Gazdhar A, Schmid RA. (2018) Stem cell secretome attenuate acute rejection in rat lung allotransplantation. Interactive CardioVascular and Thoracic Surgery. 1-7, doi:10.1093/icvts/ivy306.
  47. Taboada H, Meneses N, Dunn MF, Vargas-Lagunas C, Buchs N, Castro-Mondragon JA, Heller M, Encarnación S. (2018) Proteins in the periplasmic space and outer membrane vesicles of Rhizobium etli CE3 grown in minimal medium are largely distinct and change with growth phase. Microbiology. doi: 10.1099/mic.0.000720.
  48. Nasher F, Förster S, Yildirim EC, Grandgirard D, Leib SL, Heller M, Hathaway LJ. (2018) Foreign peptide triggers boost in pneumococcal metabolism and growth. BMC Microbiol. 18:23.
  49. Nasher F, Heller M, Hathaway LJ. (2018) Streptococcus pneumoniae Proteins AmiA, AliA, and AliB Bind Peptides Found in Ribosomal Proteins of Other Bacterial Species. Frontiers in Microbiol. 8:2688. doi: 10.3389/fmicb.2017.02688.
  50. Gazdhar A, Ravikumar P, Pastor J, Heller M, Ye J, Zhang J, Moe OW, Geiser T, Hsia CCW. (2018) Alpha-Klotho Enrichment in Induced Pluripotent Stem Cell Secretome Contributes to Antioxidative Protection in Acute Lung Injury. Stem Cells. 36: 616-625. doi: 10.1002/stem.2752. PubMed PMID: 29226550.
  51. Langenegger N, Koua D, Schürch S, Heller M, Nentwig W, Kuhn-Nentwig L. (2017) Identification of a precursor processing protease from the spider Cupiennius salei essential for venom neurotoxin maturation. J Biol Chem. pii: jbc.M117.810911. doi: 10.1074/jbc.M117.810911. [Epub ahead of print] PubMed PMID: 29269415.
  52. Meneses N, Taboada H, Dunn MF, Vargas MD, Buchs N, Heller M, Encarnación S. (2017) The naringenin-induced exoproteome of Rhizobium etli CE3. Arch Microbiol. 199(5):737-755. doi: 10.1007/s00203-017-1351-8. PMID: 28255691.
  53. Brügger V, Duman M, Bochud M, Münger E, Heller M, Ruff S, Jacob C. (2017) Delaying Histone Deacetylase Response to Injury Accelerates Conversion into Repair Schwann Cells and Nerve Regeneration. Nature Commun. 8:14272. doi: 10.1038/ncomms14272. PMID: 28139683
  54. Braga-Lagache S, Buchs N, Iacovache M-I, Zuber B, Jackson CB, Heller M. (2016) Robust Label-Free, Quantitative Profiling of Circulating Plasma Microparticle Associated Proteins. Mol Cell Proteomics. 15: 3640-3652. (doi: 10.1074/mcp.M116.060491).
  55. Ruegsegger C, Maharjan N, Goswami A, de L'Etang AF, Weis J, Troost D, Heller M, Gut H, Saxena S. (2016) Aberrant association of misfolded SOD1 with Na(+)/K(+)ATPase-α3 impairs its activity and contributes to motor neuron vulnerability in ALS. Acta Neuropathol. 131:427-451.
  56. Naguleswaran A, Gunasekera K, Schimanski B, Heller M, Hemphill A, Ochsenreiter T, Roditi I. (2015) Trypanosoma brucei RRM1 is a nuclear RNA-binding protein and modulator of chromatin structure. MBio. 6(2):e00114.
  57. Petrovic M, Simillion C, Kruzliak P, Sabo J, Heller M. (2015) Doxorubicin Affects Expression of Proteins of Neuronal Pathways in MCF-7 Breast Cancer Cells. Cancer Genomics Proteomics. 12:347-358.
  58. Raczynska KD, Ruepp MD, Brzek A, Reber S, Romeo V, Rindlisbacher B, Heller M, Szweykowska-Kulinska Z, Jarmolowski A, Schümperli D. (2015) FUS/TLS contributes to replication-dependent histone gene expression by interaction with U7 snRNPs and histone-specific transcription factors. Nucleic Acids Res. pii: gkv794.
  59. Karin Stettler, Xiaoming Li, Björn Sandrock, Sophie Lagache Braga, Manfred Heller, Lutz Dümbgen, and Beat Suter. (2014) A Drosophila XPD model links cell cycle coordination with neuro-development and suggests links to cancer. Dis Models Mech. dmm.016907.
  60. Cristodero M, Schimanski B, Heller M, Roditi I. (2014) Functional characterization of the trypanosome translational repressor SCD6. Biochem J. 457(1):57-67. doi: 10.1042/BJ20130747. PubMed PMID: 24087925.
  61. Denise C Zysset-Burri, Norbert Müller, Christian Beuret, Manfred Heller, Nadia Schürch, Bruno Gottstein and Matthias Wittwer (2014) Genome-wide identification of pathogenicity factors of the free-living amoeba Naegleria fowleri. BMC Genomics. 15: 496.
  62. Hansjürg Engel, Moana Mika, Dalia Denapaite, Regine Hakenbeck, Kathrin Mühlemann, Manfred Heller, Lucy Hathaway, and Markus Hilty (2014) A low affinity penicillin-binding protein 2x is required for heteroresistance in Streptococcus pneumonia. Antimicrob Agents Chemother. 58(7):3934-41.
  63. Lucy J. Hathaway, Patrick Bättig, Sandra Reber, Jeannine U. Rotzetter, Suzanne Aebi, Christoph Hauser, Manfred Heller, Aras Kadioglu, and Kathrin Mühlemann (2014) Streptococcus pneumoniae detects and responds to foreign bacterial peptide fragments in its environment. Open Biology, 4, 130224.
  64. Philippe Vanden Bergh, Manfred Heller, Sophie Braga-Lagache and Joachim Frey (2013) The Aeromonas salmonicida subsp. salmonicida exoproteome: global analysis, moonlighting proteins and putative antigens for vaccination against furunculosis. Proteome Sci., 11(1): 44.
  65. Philippe Vanden Bergh, Manfred Heller, Sophie Braga-Lagache and Joachim Frey (2013) The Aeromonas salmonicida subsp. salmonicida exoproteome. Determination of the complete repertoire of Type-Three Secretion System effectors and identification of other virulence factors. Proteome Sci., 11(1): 42.
  66. Gabriela Schumann Burkard, Sandro Käser, Patricia de Araujo, Bernd Schimanski, Arunasalam Naguleswaran, Sebastian Knüsel, Manfred Heller, Isabel Roditi (2013) Nucleolar proteins regulate stage-specific gene expression and ribosomal RNA maturation in Trypanosoma brucei. Mol. Microbiol., 88(4):827-40. doi: 10.1111/mmi.12227.
  67. Kapila Gunasekera, Daniel Wuethrich, Sophie Braga-Lagache, Manfred Heller and Torsten Ochsenreiter (2012) Proteome remodeling during development from blood to insect form Trypanosoma brucei parasites quantified by SILAC and mass spectrometry. BMC Genomics, 13:556 doi:10.1186/1471-2164-13-556.
  68. Ali Al Kaabi, Tobias Traupe, Monika Stutz, Natasha Buchs, Manfred Heller (2012) Cause or Effect of Arteriogenesis: Compositional Alterations of Microparticles from CAD Patients Undergoing External Counterpulsation Therapy. PLoS ONE 7(10): e46822. doi:10.1371/journal.pone.0046822
  69. Sandra Eltschinger, Eva Greganova, Manfred Heller, Peter Buetikofer, Michael Altmann (2012) Eukaryotic translation elongation factor 1A (eEF1A) domain I from S. cerevisiae is required but not sufficient for inter-species complementation. PloS ONE, 7(7): e42338. doi:10.1371/journal.pone.0042338
  70. Jan Mani, Andreas Güttinger, Bernd Schimanski, Manfred Heller, Alvaro Acosta-Serrano, Pascale Pescher, Gerald Späth and Isabel Roditi (2011) Alba-domain proteins of Trypanosoma brucei are cytoplasmic RNA-binding proteins that interact with the translation machinery. Plos ONE, 6(7): e22463.
  71. Bruno Vincent, Martha Kaeslin, Thomas Roth, Manfred Heller, Julie Poulain, François Cousserans, Johann Schaller, Marylène Poirié, Beatrice Lanzrein, Jean-Michel Drezen, Sébastien JM Moreau (2010) The venom composition of the parasitic wasp Chelonus inanitus resolved by combined transcriptome analysis and proteomic approach. BMC Genomics, 11, 693.
  72. Christoph Wetterwald, Thomas Roth, Martha Kaeslin, Marc Annaheim, Gabriela Wespi, Manfred Heller, Pascal Mäser, Isabel Roditi, Rita Pfister-Wilhelm, Annie Bézier, Gabor Gyapay, Jean-Michel Drezen, Beatrice Lanzrein (2010) Identification of bracovirus particle proteins and analysis of their transcript levels at the stage of virion formation. J. Gen. Virol., 91, 2610-2619.
  73. Eva Greganova, Manfred Heller, Peter Bütikofer (2010) A structural domain mediates attachment of ethanolamine phosphoglycerol to eukaryotic elongation factor 1A in Trypanosoma brucei. PloS ONE, 5, e9486.
  74. Serricchio M, Heller M, Bütikofer P. (2010) An unconventional biosynthetic route for cardiolipin in Trypanosoma brucei. CHEM PHYS LIPIDS 08/2010:163.
  75. Rafael Koch, Romana Ledermann, Olivier Urwyler, Manfred Heller, Beat Suter (2009) Systematic Functional Analysis of BicD Serine Phosphorylation and Intragenic Suppression of a Female Sterile Allele of BicD. PloS ONE, 4(2), e4552.
  76. Bézier, A., Annaheim, M., Herbinière, J., Wetterwald, C., Gyapay, G., Bernard-Samain, S., Wincker, P., Roditi, I., Heller, M., Belghazi, M., Pfister-Wilhem, R., Periquet, G., Dupuy, C., Huguet, E., Volkoff, A.N., Lanzrein, B., Drezen, J.M. (2009) Polydnaviruses of braconid wasps derive from an ancestral nudivirus. Science, 323(5916), 926-930.
  77. Luis Da Silva-Azevedo, Sebastian Jähne, Christian Hoffmann, Daniel Stalder, Manfred Heller, Axel R Pries, Andreas Zakrzewicz, Oliver Baum (2009) Up-regulation of the peroxiredoxin-6 related metabolism of reactive oxygen species in skeletal muscle of mice lacking neuronal nitric oxide synthase. J. Physiol., 587, 655-668.
  78. Daniel Stalder, Trinh Cung, Steffen Gloekler, Pascal Meier, Evelyn Schlappritzi; André Haeberli, Santica Marcovina, Christian Seiler, Manfred Heller (2008) Apolipoprotein(a) Size and Lipoprotein(a) Concentrations in Patients with Good and Poor Coronary Collateral Flow - an Interrelation Discovered by Proteomic Screening of Pooled Plasma Samples. J. Prot. Bioinfo., 1, 389-400.
  79. Ambort, D., Stalder, D., Lottaz, D., Huguenin, M., Oneda, B., Heller, M., Sterchi, E.E. (2008) The metalloendopeptidase meprin - a novel 2D-based approach to the discovery of candidate substrates. FEBS J., 275, 4490-4509.
  80. Stalder, D., Haeberli, A., Heller, M. (2008) Evaluation of Reproducibility of Protein Identification Results after Multidimensional Human Serum Protein Separation. Proteomics, 8, 414-424.
  81. SCHAUB, A., WYMANN, S., HELLER, M., GHIELMETTI, M., BELEZNAY, Z., STADLER, B.M., BOLLI, R., MIESCHER, S. (2007) Self-Reactivity in the Dimeric Intravenous Immunoglobulin Fraction. Ann. N.Y. Acad. Sci., 1110, 681-693.
  82. Heller, M., Schlappritzi, E., Stalder, D., Nuoffer, J.M., Haeberli, A. (2007) Compositional Protein Analysis of High Density Lipoproteins in Hypercholesterolemia by Shotgun LC-MS/MS and Probabilistic Peptide Scoring. Mol. Cell. Proteomics, 6, 1059-1072.
  83. Michel, P.E., Crettaz, D., Morier, P., Heller, M., Gallot, D., Tissot, J.D., Reymond, F., Rossier, J.S. (2006) Proteome analysis of human plasma and amniotic fluid by Off-Gel isoelectric focusing followed by nano-LC-MS/MS. Electrophoresis, 27, 1169-1181.
  84. Rentsch, C.A., Cecchini, M.G., Schwaninger, R., Germann, M., Markwalder, R., Heller, M., Van der Pluijm, G., Thalmann, G.N., Wetterwald, A. (2006) Differential expression of TGFbeta-stimulated clone 22 in normal prostate and prostate cancer. Int. J. Cancer, 118, 899-906.
  85. Heller, M., Ye, M., Michel, P.E., Morier, P., Stalder, D., Jünger, M.A., Aebersold, R., Reymond, F., Rossier, J.S. (2005) Added Value for Tandem Mass Spectrometry Shotgun Proteomics Data Validation through Isoelectric Focusing of Peptides. J. Proteome Res. 4(6), 2273-2282.
  86. Heller, M., Stalder, D., Schlappritzi, E., Hayn, G., Matter, U., Haeberli, A. (2005) Mass Spectrometry based Analytical Tools for the Molecular Protein Characterization of Human Plasma Lipoproteins. Proteomics 5, 2619-2630.
  87. Heller,, M., Michel, P.E., Morier, P., Crettaz, D., Wenz, C., Tissot, J.D., Reymond, F., Rossier, J.S. (2005) Two Stage Off-Gel Isoelectric Focusing: Protein Followed by Peptide Fractionation and Application to Proteome Analysis of Human Plasma. Electrophoresis 26, 1174-1188.
  88. Rose, K., Bougueleret, L, Baussant, T., Böhm, G., Botti, P., Colinge, J., Cusin, I., Gaertner, H., Gleizes, A., Heller, M., et al. (2004) Industrial-scale proteomics: From litres of plasma to chemically synthesized proteins. Proteomics 4, 2125-2150.
  89. Sanchez, JC; Converset, V; Nolan, A; Schmid, G; Wang, S; Heller, M; Sennitt, MV; Hochstrasser, DF; Cawthorne, MA (2003) Effect of rosiglitazone on the differential expression of obesity and insulin resistance associated proteins in lep/lep mice. Proteomics 3 (8): 1500-1520.
  90. Haendeler J, Yin G, Hojo Y, Saito Y, Melaragno M, Yan C, Sharma VK, Heller M, Aebersold R, Berk BC. (2003) GIT1 mediates Src-dependent activation of phospholipase Cgamma by angiotensin II and epidermal growth factor. J Biol Chem. 278: 49936-49944.
  91. Heller M., Mattou H., Menzel C., Yao X. (2003) Trypsin Catalyzed 16O-to-18O Exchange for Comparative Proteomics: Tandem Mass Spectrometry Comparison using MALDI-TOF, ESI-QTOF and ESI-Ion Trap Mass Spectrometers. J. Am. Soc. Mass Spectrom. 14 (7): 704-718.
  92. Sanchez, J.-C., Converset, V., Nolan, A., Schmid, G., Wang, S., Heller, M., Sennitt, M.V., Hochstrasser, D.F., Cawthorne, M.A. (2002) Effect of rosiglitazone on the differential expression of diabetes associated proteins in pancreatic islets of C57B1/6 lep/lep mice. Mol. & Cell. Proteomics 1 (7): 509-516.
  93. Rabilloud, T., Heller, M., Gasnier, F., Luche, S., Rey, C., Aebersold, R., Benahmed, M., Louisot, P., Lunardi, J. (2002) Proteomics analysis of cellular response to oxidative stress: Evidence for in vivo over-oxidation of peroxiredoxins at their active site. J. Biol. Chem. 277: 19396-19401.
  94. Bienvenut, W.V., Hoogland, C., Greco, A., Heller, M., Gasteiger, E., Appel, R.D., Diaz, J.-J., Sanchez, J.-C., and Hochstrasser, D.F. (2002) Hydrogen/Deuterium Exchange for Higher Specificity of Protein Identification by Peptide Mass Fingerprinting. J. Rapid Com. Mass Spectrom. 16(6):616-626.
  95. W.V. Bienvenut, M. Müller, P.M. Palagi, E. Gasteiger, M. Heller, E. Jung, M. Giron, R. Gras, S. Gay, P.-A. Binz, G. J. Hughes, J.-C. Sanchez, R.D. Appel, D.F. Hochstrasser; Mass spectrometry and genomic analysis; Proteomics and mass spectrometry: Some aspects and recent developments. J.N. Houby Ed.; Kluwer Academic Publishers, 2001, pp93-145.
  96. Rabilloud, T., Heller, M., Rigobello, M.P., Bindoli, A., Aebersold R., and Lunardi, J. (2001) The mitochondrial antioxidant defence system and its response to oxidative stress. Proteomics 1:1105-1110.
  97. Heller, M., Watts, J.D., and Aebersold, R. (2001) CD28 stimulation regulates its association with N-ethylmaleimide-sensitive fusion protein and other proteins involved in vesicle sorting. Proteomics 1:70-78.
  98. Heller, M., Loomes, K. M., and Cooper, G. J. S. (2000) Synthesis of biologically active tritiated amylin and salmon calcitonin analogues. Analytical Biochemistry 285:100-104.
  99. Jung, E., Heller, M., Sanchez, J.-C., and Hochstrasser, D. F. (2000) Proteomics meets cell biology: The establishment of subcellular proteomes [Review]. Electrophoresis 21: 3369-3377.
  100. Heller, M., Goodlett, D. R., Watts, J.D., and Aebersold, R. (2000) A Comprehensive Characterization of the T Cell Antigen Receptor Complex Composition by Micro-Capillary Liquid Chromatography Tandem Mass Spectrometry. Electrophoresis 21: 2180-2195.
  101. Rabilloud, T., Blisnick, T., Heller, M., Luche, S., Aebersold, R., Lunardi, J., and Braun-Breton, C. (1999) Analysis of membrane proteins by two-dimensional electrophoresis: Comparison of the proteins extracted from normal or Plasmodium falciparum-infected erythrocyte ghosts. Electrophoresis 20: 3603-3610.
  102. M. Hettiarachchi, S. Chalkley, S.M. Furler, Y-S. Choong, M. Heller, G.J.S. Cooper and E.W. Kraegen (1997) Rat amylin8-37 enhances insulin action and alters lipid metabolism in normal and insulin-resistant rats. American Journal of Physiology 273 (Endocrinol. Metab. 36): E859-E867.
  103. Heller, M., Buetikofer, P., and Brodbeck, U. (1994) Generation by limited proteolysis of a catalytically active 39-kDa protein from the 115-kDa form of phosphatidylinositol-glycan-specific phospholipase D from bovine serum. European Journal of Biochemistry 224: 823-833.
  104. Heller, M., Bieri, S., and Brodbeck, U. (1992) A novel form of glycosylphosphatidyl-inositol-anchor converting activity with a specificity of a phospholipase D in mammalian liver membranes. Biochimica et Biophysica Acta 1109: 109-116.
  105. Sänger, M., Borle, F., Heller, M., and Sigrist, H. (1992) Light-induced Coupling of Aqueous-Soluble Proteins to Liposomes formed from Carbene-Generating Phospholipids. Bioconjugate Chemistry 3: 308-314.