Publications

List of publications produced by members of S3IT.

2016

  • Schneider, Aurel; Teyssier, Romain; Potter, Doug; Stadel, Joachim; Onions, Julian; Reed, Darren S; Smith, Robert E; Springel, Volker; Pearce, Frazer R; Scoccimarro, Roman; Matter power spectrum and the challenge of percent accuracy. JCAP (2016) 04-047 arXiv
  • Fiacconi, Davide; Madau, Piero; Potter, Doug; Stadel, Joachim; Cold Dark Matter Substructures in Early-Type Galaxy Halos. ApJ arXiv
  • Malmstrom, Erik; Kilsgard, Ola; Hauri, Simon; Smeds, Emanuel; Herwald, Heiko; Malmstrom, Lars; Malmstrom, Johan; Large-scale inference of protein tissue origin in gram-positive sepsis plasma using quantitative targeted proteomics. Nat Commun (2016), 7: 10261.
  • Tykesson, Emil; Mao, Yang; Maccarana, Marco; Pu, Yi; Gao, Jinshan; Lin, Cheng; Zaia, Joseph; Westergren-Thorsson, Gunilla; Ellervik, Ulf; - Malmstrom, Lars; Malmstrom, Anders; Deciphering the mode of action of the processive polysaccharide modifying enzyme dermatan sulfate epimerase 1 by hydrogen-deuterium exchange mass spectrometry. Chem. Sci (2016), 7: 1447-1456.
  • Gossmann, T.I., Saleh, D., Schmid, M.W., Spence, M.A., Schmid, K.J. (2016): Plant reproductive development is characterised by a transcriptomic evolutionary bulge. Molecular Biology and Evolution, advanced access

2015

  • Malmstrom, Lars; Bakochi, Anahita; Svensson, Gabriel; Kilsgard, Ola; Lantz, Henrik; Petersson, Ann; Hauri, Simon; Karlsson, Christofer; Malmstrom, Johan; Quantitative proteogenomics of human pathogens using DIA-MS. J Proteomics (2015), 0: Epub ahead of print.
  • Walzthoeni, Thomas; Joachimiak, Lukasz; Rosenberger, George; Rost, Hannes; Malmstrom, Lars; Leitner, Alexander; Frydman, Judith; Aebersold, Ruedi; xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry. Nat Methods (2015), 0: Epub ahead of print.
  • Rost, Hannes; Malmstrom, Lars; Aebersold, Ruedi; Reproducible quantitative proteotype data matrices for systems biology. Mol Biol Cell (2015), 26: 3926-31.
  • E. Schaper, A. Korsunsky, A. Messina, R. Murri, J. Pecerska, H. Stockinger, S. Zoller, I. Xenarios, M. Anisimova: TRAL: Tandem repeat annotation library, Bioinformatics (2015), http://dx.doi.org/10.1093/bioinformatics/btv306
  • R. Kümmerli, L. A. Santorelli, E. T. Granato, Z. Dumas, A. Dobay, A. S. Griffin and S. A. West (2015): Co-evolutionary dynamics between public good producers and cheats in the bacterium Pseudomonas aeruginosa. J Evol Biol. 28: 2264–2274.
  • Parker, Sarah; Roest, Hannes; Rosenberger, George; Collins, Ben; Malmstrom, Lars; Amodei, Dario; Venkatraman, Vidya; Raedschelders, Koen; Van Eyk, Jennifer; Aebersold, Ruedi; Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-Independent Acquisition Mass Spectrometry. Mol Cell Proteomics (2015), -1: Epub ahead of print.
    pubmed | journal
  • Sjostrom, Martin; Ossola, Reto; Breslin, Thomas; Rinner, Oliver; Malmstrom, Lars; Schmidt, Alexander; Aebersold, Ruedi; Malmstrom, Johan; Nimaus, Emma; A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery. J Proteome Res (2015), : Epub ahead of print.
  • Rost, Hannes; Schmitt, Uwe; Aebersold, Ruedi; Malmstrom, Lars; Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry. PLoS One (2015), 10(4): e0125108.
  • Rost, Hannes; Rosenberger, George; Aebersold, Ruedi; Malmstrom, Lars; Efficient visualization of high-throughput targeted proteomics experiments: TAPIR. Bioinformatics (2015), 0: -.
  • Schmid, M.W., Schmidt, A., Grossniklaus, U. (2015): The female gametophyte: An emerging model for cell type-specific systems biology in plant development. Frontiers in Plant Science, 6: 907.
  • Schmid, M.W., Grob, S., Grossniklaus, U. (2015): HiCdat: a fast and easy-to-use Hi-C data analysis tool. BMC Bioinformatics, 16: 277.
  • Schmid, M.W., Grossniklaus, U. (2015): Rcount: simple and flexible RNA-Seq read counting. Bioinformatics, 31(3): 436-437.
  • Schmidt, A., Schmid, M.W., Grossniklaus, U. (2015): Plant germline formation: molecular insights define common concepts and illustrate developmental flexibility in apomictic and sexual reproduction. Development, 142: 229-241.

2014

  • Quandt, Andreas; Espona Pernas, Lucia; Balasko, Akos; Weisser, Hendrik; Brusniak, Mi-Youn; Kunszt, Peter; Aebersold, Ruedi; Malmstrom, Lars; Using synthetic peptides to benchmark peptide identification software and search parameters for MS/MS data analysis. EuPA Open Proteomics (2014), 5: 21-31.
  • Teleman, Johan; Rost, Hannes; Rosenberger, George; Schmitt, Uwe; Malmstrom, Lars; Malmstrom, Johan; Levander, Fredrik; DIANA - algorithmic improvements for analysis of data-independent acquisition MS data. Bioinformatics (2014), : .
  • Wisniewska, Magdalena; Happonen, Lotta; Kahn, Fredrik; Varjosalo, Markku; Malmstrom, Lars; Rosenberger, George; Karlsson, Christofer; Cazzamali, Giuseppe; Pozdnyakova, Irina; Frick, Inga-Maria; Bjorck, Lars; Streicher, Werner; Malmstrom, Johan; Wikstrom, Mats; Functional and Structural Properties of a Novel Protein and Virulence Factor (sHIP) in Streptococcus pyogenes. J Biol Chem (2014), 289(26): 18175-88.
  • Kunszt, Peter; Blum, Lorenz; Hullar, Bela; Schmid, Emanuel; Srebniak, Adam; Wolski, Witold; Rinn, Bernd; Elmer, Franz-Josef; Ramakrishnan, Chandrasekhar; Quandt, Andreas; Malmstrom, Lars; iPortal: the swiss grid proteomics portal: Requirements and new features based on experience and usability considerations. Concurrency and Computation: Practice and Experience (2014), 0: -.
  • Rosenberger, George; Ludwig, Christina; Rost, Hannes; Aebersold, Ruedi; Malmstrom, Lars; aLFQ: An R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data. Bioinformatics (2014), Epub ahead of print: .
  • Rost, Hannes; Rosenberger, George; Navarro, Pedro; Gillet, Ludovic; Miladinovia, Saja; Schubert, Olga; Wolski, Witold; Collins, Ben; Malmstrom, Johan; Malmstrom, Lars; Aebersold, Ruedi; OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nat Biotechnol (2014), 32: 219-23.
  • Teleman, Johan; Dowsey, Andrew; Gonzalez-Galarza, Faviel; Perkins, Simon; Pratt, Brian; Rost, Hannes; Malmstrom, Lars; Malmstrom, Johan; Jones, Andrew; Deutsch, Eric; Levander, Fredrik; Numerical compression schemes for proteomics mass spectrometry data. Mol Cell Proteomics (2014), -: .
  • Rost, Hannes; Schmitt, Uwe; Aebersold, Ruedi; Malmstrom, Lars; pyOpenMS: A Python-based interface to the OpenMS mass-spectrometry algorithm library. Proteomics (2014), 14: 74-7.
  • Grob, S., Schmid, M.W., Grossniklaus, U. (2014): HiC Analysis in Arabidopsis Identifies the KNOT, a Structure with Similarities to the flamenco Locus of Drosophila. Molecular Cell, 55(5): 678-693.
  • Schmidt, A., Schmid, M.W., Klostermeier, U.C., Qi, W., Guthörl, D., Sailer, C., Waller, M., Rosenstiel, P., and Grossniklaus, U. (2014): Apomictic and sexual germline development differ with respect to cell cycle, transcriptional, hormonal and epigenetic regulation. PLOS Genetics, 10(7): e1004476.
  • Gossmann, T.I., Schmid, M.W., Grossniklaus, U., and Schmid, K.J. (2014): Selection-driven evolution of sex-biased genes is consistent with sexual selection in Arabidopsis thaliana. Molecular Biology and Evolution, 31(3): 574-583.

2013

  • P. Kunszt, S. Maffioletti, R. Murri, V. Tschopp: GridCertLib: A Single Sign-on Solution for Grid Web Applications and Portals, Journal of Grid Computing vol.~9 no.~4 (2013), pp.~441--453. Pre-print available at: http://arxiv.org/abs/1101.4116.
  • R. Murri: Performance of Python runtimes on a non-numeric scientific code, in: Proceedings of the EuroSciPy2013 Conference, 2013
  • D. Menghini, M. Di Paola, R. Murri, F. Costanzo, C. Caltagirone, S. Vicari, L. Petrosini Cerebellar vermis abnormalities and cognitive functions in individuals with Williams syndrome. Research in developmental disabilities, 04/2013; 34(7):2118-2126.
  • T. Aleksiev, S. Barkow-Oesterreicher, P. Kunszt, S. Maffioletti, R. Murri, C. Panse, VM-MAD: A Cloud/Cluster Software for Service-Oriented Academic Environments, In: International Supercomputing Conference 2013, Lecture Notes in Computer Science 7905, pp. 447--461. Pre-print available at: http://arxiv.org/abs/1302.2529.
  • Kahraman, Abdullah; Herzog, Franz; Leitner, Alexander; Rosenberger, George; Aebersold, Ruedi; Malmstrom, Lars; Cross-Link Guided Molecular Modeling with ROSETTA. PLoS One (2013), 8: e73411.
  • Kunszt, Peter; Blum, Lorenz; Hullar, Bela; Schmid, Emanuel; Srebniak, Adam; Wolski, Witold; Rinn, Bernd; Elmer, Franz-Josef; Ramakrishnan, Chandrasekhar; Quandt, Andreas; Malmstrom, Lars; Improving the Swiss Grid Proteomics Portal: Requirements and new Features based on Experience and Usability Considerations. conf proc. of the 5th International Workshop on Science Gateways (IWSG 2013), Zurich, 3-5 June 2013, in CEUR Workshop Proceedings Vol 993 (2013), 993: -.
  • Weisser, Hendrik; Nahnsen, Sven; Grossmann, Jonas; Nilse, Lars; Quandt, Andreas; Brauer, Hendrik; Sturm, Marc; Kenar, Erhan; Kohlbacher, Oliver; Aebersold, Ruedi; Malmstrom, Lars; An automated pipeline for high-throughput label-free quantitative proteomics. J Proteome Res (2013), -: Epub ahead of print.
  • Grob, S., Schmid, M.W., Luedtke, N.W., Wicker, T., and Grossniklaus, U. (2013): Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture. Genome Biology, 14:R129.
  • Wuest, S.E., Schmid, M.W., and Grossniklaus, U. (2013): Cell-specific expression profiling of rare cell types as exemplified by its impact on our understanding of female gametophyte development. Current Opinion in Plant Biology, 16: 1-9.

2012

  • S. Moretti, R. Murri, S. Maffioletti, A. Kuzniar, B. Castella, N. Salamin, M. Robinson-Rechavi, H. Stockinger: gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution In: HealthGrid Applications and Technologies Meet Science Gateways for Life Sciences, March 2012. Pre-print available at: http://arxiv.org/abs/1203.3092
  • S. Maffioletti, R. Murri: GC3Pie: A Python framework for high-throughput computing, In: Proceedings of the EGI Community Forum 2012 / EMI Second Technical Conference (EGICF12-EMITC2), 2012. Published online at http://pos.sissa.it/cgi-bin/reader/conf.cgi?confid=162.
  • R. Murri, S. Maffioletti: AppPot: bridging the Grid and Cloud worlds. In: Proceedings of the EGI Community Forum 2012 / EMI Second Technical Conference (EGICF12-EMITC2), 2012. Published online at http://pos.sissa.it/cgi-bin/reader/conf.cgi?confid=162.
  • Malmstrom, Lars; Nordenfelt, Pontus; Malmstrom, Johan; Business intelligence strategies enables rapid analysis of quantitative proteomics data. Journal of Proteome Science and Computational Biology (2012), 1 (1): -.
  • Karlsson, Christofer; Malmstrom, Lars; Aebersold, Ruedi; Malmstrom, Johan; Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes. Nat Commun (2012), 3: 1301.
  • Herzog, Franz; Kahraman, Abdullah; Boehringer, Daniel; Mak, Raymond; Bracher, Andreas; Walzthoeni, Thomas; Leitner, Alexander; Beck, Martin; Hartl, Franz-Ulrich; Ban, Nenad; Malmstrom, Lars; Aebersold, Ruedi; Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometry. Science (2012), 337: 1348-52.
  • Reker, Daniel; Malmstrom, Lars; Bioinformatic challenges in targeted proteomics. J Proteome Res (2012), 11: 4393-402.
  • Rost, Hannes; Malmstrom, Lars; Aebersold, Ruedi; A computational tool to detect and avoid redundancy in selected reaction monitoring. Mol Cell Proteomics (2012), 11: 540-9.
  • Malmstrom, Lars; Malmstrom, Johan; Selevsek, Nathalie; Rosenberger, George; Aebersold, Ruedi; Automated workflow for large-scale Selected Reaction Monitoring experiments. J Proteome Res (2012), 11: 1644-53.
  • You, W., Tyczewska, A., Spencer, M., Daxinger, L., Schmid, M.W., Grossniklaus, U., Simon, S., Meyers, B.C., Matzke, A.J.M., and Matzke, M. (2012): Atypical DNA methylation of genes encoding cysteine-rich peptides in Arabidopsis thaliana. BMC Plant Biology, 12: 51.
  • Schmidt, A., Schmid, M.W., and Grossniklaus, U. (2012): Analysis of plant germline development by high-throughput RNA profiling: technical advances and new insights. The Plant Journal, 70(1): 18-29.
  • Schmid, M.W., Schmidt, A., Klostermeier, U.C., Barann, M., Rosenstiel, P., and Grossniklaus, U. (2012): A powerful method for transcriptional profiling of specific cell types in eukaryotes: laser-assisted microdissection and RNA sequencing. PLOS ONE, 7(1): e29685.

2011

  • R. Murri: A novel parallel algorithm for Gaussian Elimination of sparse unsymmetric matrices. In: Roman Wyrzykowski, editor, Proceedings of the PPAM2011 Conference, volume 7203/7204 of Lecture Notes in Computer Science. Springer-Verlag, 2012. Pre-print available at: http://arxiv.org/abs/1105.4136.
  • Bauch, Angela; Adamczyk, Izabela; Buczek, Piotr; Elmer, Franz-Josef; Enimanev, Kaloyan; Glyzewski, Pawel; Kohler, Manuel; Pylak, Tomasz; Quandt, Andreas; Ramakrishnan, Chandrasekhar; Beisel, Christian; Malmstrom, Lars; Aebersold, Ruedi; Rinn, Bernd; openBIS: a flexible framework for managing and analyzing complex data in biology research. BMC Bioinformatics (2011), 12: 468.
  • Malmstrom, Johan; Karlsson, Christofer; Nordenfelt, Pontus; Ossola, Reto; Weisser, Hendrik; Quandt, Andreas; Hansson, Karin; Aebersold, Ruedi; Malmstrom, Lars; Bjorck, Lars; Streptococcus pyogenes in human plasma: adaptive mechanisms analyzed by mass spectrometry based proteomics. J Biol Chem (2011), 287: 1415-25.
  • Kunszt, Peter; Malmstrom, Lars; Fantini, Nicola; Subholt, Wibke; Lautenschlager, Marcel; Reifler, Roland; Ruckstuhl, Stefan; Accelerating 3D Protein Modeling Using Cloud Computing. Seventh IEEE International Conference on e-Science Workshops (2011), --: 166-169.
  • Drew, Kevin; Winters, Patrick; Butterfoss, Glenn; Berstis, Viktors; Uplinger, Keith; Armstrong, Jonathan; Riffle, Michael; Schweighofer, Erik; Bovermann, Bill; Goodlett, David; Davis, Trisha; Shasha, Dennis; Malmstrom, Lars; Bonneau, Richard; The proteome folding project: Proteome-scale prediction of structure and function. Genome Res (2011), 21: 1981-94.
  • Malmstrom, Lars; Malmstrom, Johan; Aebersold, Ruedi; Quantitative proteomics of microbes: Principles and applications to virulence. Proteomics (2011), 11: 2947-56.
  • Kahraman, Abdullah; Malmstrom, Lars; Aebersold, Ruedi; Xwalk: Computing and Visualizing Distances in Cross-linking Experiments. Bioinformatics (2011), 27: 2163-4.
  • Kunszt, Peter; Espona Pernas, Lucia; Quandt, Andreas; Schmid, Emanuel; Hunt, Ela; Malmstrom, Lars; The Swiss Grid Proteomics Portal. Proceedings of the Second International Conference on Parallel, Distributed, Grid and Cloud Computing for Engineering (2011), -: 81.
  • McKeown, P.C., Laouielle-Duprat, S., Prins, P., Wolff, P., Schmid, M.W., Donoghue, M.T.A., Fort, A., Duszynska, D., Comte, A., Lao, N.T., Wennblom, T.J., Smant, G., Köhler, C., Grossniklaus, U., and Spillane, C. (2011): Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thaliana seeds. BMC Plant Biology, 11: 113.