Below you find a list of publications related to our work. Former and current members of SIS are highlighted.

Publications in Scientific Journals in 2016

Katherine Wolstencroft; Olga Krebs; Jacky L. Snoep; Natalie J. Stanford; Finn Bacall; Martin Golebiewski; Rostyk Kuzyakiv; Quyen Nguyen; Stuart Owen; Stian Soiland-Reyes; Jakub Straszewski; David D. van Niekerk; Alan R. Williams; Lars Malmström; Bernd Rinn; Wolfgang Müller; Carole Goble
FAIRDOMHub: a repository and collaboration environment for sharing systems biology research
Nucleic Acids Research 2016
DOI: 10.1093/nar/gkw1032

Hannes L Röst, Timo Sachsenberg, Stephan Aiche, Chris Bielow, Hendrik Weisser, Fabian Aicheler, Sandro Andreotti, Hans-Christian Ehrlich, Petra Gutenbrunner, Erhan Kenar, Xiao Liang, Sven Nahnsen, Lars Nilse, Julianus Pfeuffer, George Rosenberger, Marc Rurik, Uwe Schmitt, Johannes Veit, Mathias Walzer, David Wojnar, Witold E Wolski, Oliver Schilling, Jyoti S Chou dhary, Lars Malmström, Ruedi Aebersold, Knut Reinert and Oliver Kohlbacher
OpenMS: a flexible open-source software platform for mass spectrometry data analysis
Nature Methods, 30 Aug 2016 (online), Vol. 13, pp 741-748
DOI:10.1038/nmeth.3959

Tarik A. Khan, Simon Friedensohn, Arthur R. Gorter de Vries, Jakub Straszewski, Hans-Joachim Ruscheweyh and Sai T. Reddy
Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting
Science Advances, 11 Mar 2016, Vol. 2, no. 3
DOI:10.1126/sciadv.1501371

Szczerba M, Wiewiórka MS, Okoniewski MJ, Rybiński H
Scalable Cloud-Based Data Analysis Software Systems for Big Data from Next Generation Sequencing
chapter in: Big Data Analysis: New Algorithms for a New Society, Studies in Big Data, Springer, 2016, pp. 263-283
DOI:10.1007/978-3-319-26989-4

Ludovico Fusco, Riwal Lefort, Kevin Smith, Fethallah Benmansour, German Gonzalez, Caterina Barillari, Bernd Rinn, Francois Fleuret, Pascal Fua and Olivier Pertz
Computer vision profiling of neurite outgrowth dynamics reveals spatiotemporal modularity of Rho GTPase signaling
J Cell Biol 2016 212:91-111
DOI:10.1083/jcb.201506018

Publications in Scientific Journals in 2015

SIB Swiss Institute of Bioinformatics Members (including Schmid E, Okoniewski MJ, Straszewski J, Blum L, Kohler M, Kupczyk P, Luomi A, Elmer FJ, Barillari C, Fuentes J)
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases
Nucleic Acids Research, Volume 44, Issue D1.
DOI:10.1093/nar/gkv1310

Urosevic-Maiwald M, Barysch MJ, Cheng PF, Karpova MB, Steinert H, Okoniewski MJ, Dummer R.
In vivo profiling reveals immunomodulatory effects of sorafenib and dacarbazine on melanoma
Oncoimmunology, 4(2), 2015
DOI:10.4161/2162402X.2014.988458

Cheryl de Vallière, Solange Vidal, Ieuan Clay, Giorgia Jurisic, Irina Tcymbarevich, Silvia Lang, Marie-Gabrielle Ludwig, Michal Okoniewski, Jyrki J. Eloranta, Gerd A. Kullak-Ublick, Carsten A. Wagner, Gerhard Rogler, Klaus Seuwen
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases
American Journal of Physiology - Gastrointestinal and Liver Physiology
September 2015 Vol. 309 no. 6
DOI:10.1152/ajpgi.00408.2014

Okoniewski M, Płoski R, Wiewiórka MS, Demków U
Future Directions
chapter in: Clinical Applications for Next-Generation Sequencing, Elsevier, 2015, pp.281-294
DOI:10.1016/B978-0-12-801739-5.00015-5

Jörg Wicker, Tim Lorsbach, Martin Gütlein, Emanuel Schmid, Diogo Latino, Stefan Kramer and Kathrin Fenner
enviPath – The environmental contaminant biotransformation pathway resource
Nucl. Acids Res.
DOI:10.1093/nar/gkv1229

Barillari C, Ottoz D, Fuentes-Serna JM, Ramakrishnan C, Rinn B, Rudoelf F
openBIS ELN-LIMS: an open-source database for academic laboratories
Bioinformatics
DOI:10.1093/bioinformatics/btv606

Shi G, Wüst T, Li YW and Landau DP
Protein folding of the HOP model: A parallel Wang—Landau study
J. Phys.: Conf. Ser. 640, 012017 (2015)
DOI:10.1088/1742-6596/640/1/012017

Kiefer P, Schmitt U, Müller J, Hartl J, Meyer F, Ryffel F, Vorholt J
DynaMet: A Fully Automated Pipeline for Dynamic LC-MS Data
Analytical Chemistry (2015) 87 (19), pp 9679-9686.
DOI:10.1021/acs.analchem.5b01660

Guo T, Kouvonen p, Koh CC, Gillet L, Wolski W, Röst H, Rosenberger G, Collins B, Blum L, Gillessen S, Joerger M, Jouchum W, Aebersold R
Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps
Nature Medicine 21, 407–413
DOI:10.1038/nm.3807

Bitton DA, Schubert F, Dey S, Okoniewski M, Smith GC, Khadayate S, Pancaldi V, Wood V, Bähler J
AnGeLi: a tool for the analysis of gene lists from fission yeast
Frontiers in Genetics
DOI:10.3389/fgene.2015.00330

Wiewiorka MS, Szabelska A, Okoniewski M
Analysis of AmpliSeq RNA-Sequencing Enrichment Panels
Pattern Recognition and Machine Intelligence, Springer
DOI:10.1007/978-3-319-19941-2 47

Surace L, Lysenko V, Fontana A, Cecconi V, Janssen H, Bicvic A, Okoniewski M, Pruschy M, Dummer R, Neefjes J, Knuth A, Gupta A, van den Broek M
Complement is a central mediator of radiotherapy-induced tumor-specific immunity and clinical response
Immunity. Apr 21;42(4):767-77
DOI:10.1016/j.immuni.2015.03.009.

Meienberg J, Zerjavic K, Keller I, Okoniewski M et al
New insights into the performance of human whole-exome capture platforms
Nucleic Acids Research 43 (11): e76
DOI:10.1093/nar/gkv216

Röst H, Schmitt U, Aebersold R, Malmström L
Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry.
PLoS ONE 10(4):e0125108.
DOI:10.1371/journal.pone.0125108

Wüst T, Reith D and Virnau P
Sequence Determines Degree of Knottedness in a Coarse-Grained Protein Model
Phys. Rev. Lett. 114, 028102
DOI:10.1103/PhysRevLett.114.028102

Herpich J, Stinson GS, Dutton AA, Rix HW, Martig M, Roškar R, Macciò AV, Quinn TR, Wadsley J
How to bend galaxy disc profiles: the role of halo spin
Monthly Notices of the Royal Astronomical Society, 448 L99, March 2015
DOI:10.1093/mnrasl/slv006

Roškar R, Fiacconi D, Mayer L, Kazantzidis S, Quinn TR, Wadsley J
Orbital decay of supermassive black hole binaries in clumpy multiphase merger remnants
Monthly Notices of the Royal Astronomical Society, 449, 494, May 2015
DOI:10.1093/mnras/stv312

Marasco A, Debattista VP, Fraternali F, van der Hulst T, Wadsley J, Quinn T, Roškar R
The effect of stellar feedback on a Milky Way-like galaxy and its gaseous halo
Monthly Notices of the Royal Astronomical Society, 451, 4223, August 2015
DOI:10.1093/mnras/stv1240

Mayer L, Fiacconi D, Bonoli S, Quinn T, Roškar R, Shen S, Wadsley J
Direct Formation of Supermassive Black Holes in Metal-enriched Gas at the Heart of High-redshift Galaxy Mergers
The Astrophysical Journal, 810, 51, September 2015
DOI:10.1088/0004-637X/810/1/51

Debattista VP, van den Bosch FC, Roškar R, Quinn T, Moore B, Cole DR
Internal alignments of red versus blue discs in dark matter haloes
Monthly Notices of the Royal Astronomical Society, 452, 4094, October 2015
DOI:10.1093/mnras/stv1563

Chen IW, Helmchen F, Lütcke H
Specific Early and Late Oddball-Evoked Responses in Excitatory and Inhibitory Neurons of Mouse Auditory Cortex.
Journal of Neuroscience
DOI:10.1523/JNEUROSCI.2240-15.2015

Publications in Scientific Journals in 2014

Kunszt P, Blum L, Hullár B, Schmid E, Srebniak A, Wolski W, Rinn B, Elmer FJ, Ramakrishnan C, Quandt A, Malmström L
iPortal: the swiss grid proteomics portal: Requirements and new features based on experience and usability considerations
Concurrency Computat.: Pract. Exper.
DOI:10.1002/cpe.3294

Osterwalder M, Speziale D, Shoukry M, Mohan R, Ivanek R, Kohler M, Beisel C, Wen X, Scales SJ, Christoffels VM, Visel A, Lopez-Rios J, Zeller R.
HAND2 targets define a network of transcriptional regulators that compartmentalize the early limb bud mesenchyme.
Dev Cell. 31(3):345-57
DOI: 10.1016/j.devcel.2014.09.018.

Shi G, Vogel T, and Wüst T, Li YW and Landau DP
Effect of single-site mutations on hydrophobic-polar lattice proteins
Phys. Rev. E 90, 033307
DOI:10.1103/PhysRevE.90.033307

Vogel T, Li YW, Wüst T and Landau DP
Scalable replica-exchange framework for Wang-Landau sampling
Phys. Rev. E 90, 023302
DOI:10.1103/PhysRevE.90.023302

Gevensleben H, Albrecht B, Lütcke H, Auer T, Dewiputri WI, Schweizer R, Moll G, Heinrich H, Rothenberger A
Neurofeedback of slow cortical potentials: neural mechanisms and feasibility of a placebo-controlled design in healthy adults
Frontiers in Human Neuroscience
DOI:10.3389/fnhum.2014.00990

Teleman J, Röst H, Rosenberger G, Schmitt U, Malmström L, Malmström J, Levandar F
DIANA – algorithmic improvements for analysis of data-independent acquisition MS data
Bioinformatics, 31(4), pp 555-562
DOI:10.1093/bioinformatics/btu686

Schmitt U, Röst H, Aebersold R, Malmström L
pyOpenMS: A Python-based interface to the OpenMS mass-spectroscopy algorithm library
Proteomics 14(1).
DOI:10.1002/pmic.201300246

Ramakrishnan C, Bieri A, Sauter N, Roizard S, Ringer P, Müller S, Goldie K, Enimanev K, Stahlberg H, Rinn B, Braun T
openBEB: open biological experiment browser for correlative measurements
BMC Bioinformatics 15(1):84.
DOI:10.1186/1471-2105-15-84

Rämö P, Drewek A, Arrieumerlou C, Beerenwinkel N, Ben-Tekaya H, Cardel B, Casanova A, Conde-Alvarez R, Cossart P, Csúcs G, Eicher S, Emmenlauer M, Greber U, Hardt WD, Helenius A, Kasper C, Kaufmann A, Kreibich S, Kühbacher A, Kunszt P, Low SH, Mercer J, Mudrak D, Muntwiler S, Pelkmans L, Pizarro-Cerdá J, Podvinec M, Pujadas E, Rinn B, Rouilly V, Schmich F, Siebourg-Polster J, Snijder B, Stebler M, Studer G, Szczurek E, Truttmann M, von Mering C, Vonderheit A, Yakimovich A, Bühlmann P, Dehio C
Simultaneous analysis of large-scale RNAi screens for pathogen entry
BMC genomics 15(1):1162
DOI:10.1186/1471-2164-15-1162

Selected Publications in Scientific Journals before 2014

Schmitt U, Kiefer P, Vorholt J
eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows
Bioinformatics (2013) 29(7), pp 963-964
DOI:10.1093/bioinformatics/btt080

Peter Kunszt, Lorenz Blum, Bela Hullar, Emanuel Schmid, Adam Srebniak, Witold Wolski, Bernd Rinn, Franz-Josef Elmer, Chandrasekhar Ramakrishnan, Andreas Quandt, Lars Malmström
Improving the Swiss Grid Proteomics Portal: Requirements and new Features based on Experience and Usability Considerations
Proceedings of the 5th International Workshop on Science Gateways Zurich
http://ceur-ws.org/Vol-993/paper18.pdf

Bauch A, Adamczyk I, Buczek P, Elmer FJ, Enimanev K, Glyzewski P, Kohler M, Pylak T, Quandt A, Ramakrishnan C, Beisel C, Malmström L, Aebersold R, Rinn B
openBIS: a flexible framework for managing and analyzing complex data in biology research
BMC Bioinformatics 2011, 12:468
DOI:1471-2105-12-468

Buller F, Steiner M, Scheuermann J, Mannocci L, Nissen I, Kohler M, Beisel C, Neri D.
High-throughput sequencing for the identification of binding molecules from DNA-encoded chemical libraries.
Bioorg Med Chem Lett. 2010 Jul 15;20(14):4188-92.
DOI:10.1016/j.bmcl.2010.05.053

Other Types of Publications

Rinn B
Data Management in Large Collaborative Biology Research Projects
it – Information Technology 53 (2011) 5
DOI:10.1524/itit.2011.0647

Kozak K, Bauch A, Csucs G, Pylak T and Rinn B
Towards a comprehensive open source platform for management and analysis of High Content Screening data
European Pharmaceutical Review (2010) August 19, 4:34-39
www.europeanpharmaceuticalreview.com

Schmitt U
Herr der Kerne – Rechnen auf Graphikkarten mit CUDA
iX 4/2009, heise Zeitschriften Verlag, pp 149-151.
(Article in German computer magazine about GPU computing)

Kirsch R, Schmitt U
Programmieren in C – eine mathematikorientierte Einführung
Springer Lehrbuch, Springer Verlag, 2007.
DOI:10.1007/978-3-540-45384-0
(Book in German language teaching C as first programming language additionally introducing basic concepts of numerical programming)