Below you find a list of publications related to our work. Former and current members of SIS are highlighted.
Scientific and other Publications
2022
Tanzila Mukhtar,
Jeremie Breda,
Manal A Adam,
Marcelo Boareto,
Pascal Grobecker,
Zahra Karimaddini,
Alice Grison,
Katja Eschbach,
Ramakrishnan Chandrasekhar,
Swen Vermeul,
Michal Okoniewski,
Mikhail Pachkov,
Corey C Harwell,
Suzana Atanasoski,
Christian Beisel,
Dagmar Iber,
Erik van Nimwegen,
Verdon Taylor
Temporal and sequential transcriptional dynamics define lineage shifts in corticogenesis
The EMBO Journal
https://doi.org/10.15252/embj.2022111132
Melanie Generali, Debora Kehl, Debora Wanner, Michal J Okoniewski, Simon P
Hoerstrup, Paolo Cinelli
Heterogeneous expression of ACE2 and TMPRRS2 in mesenchymal stromal cells
Journal of cellular and molecular medicine, 2022,
https://doi.org/10.1111/jcmm.17048
Juan Carlos Juárez-Cruz, Michal Okoniewski, Mónica Ramírez, Carlos
Ortuño-Pineda, Napoleón Navarro-Tito, Eduardo Castañeda-Saucedo
Chronic Leptin Treatment Induces Epithelial-Mesenchymal Transition in MCF10A Mammary Epithelial Cells
Journal of Mammary Gland Biology and Neoplasia, 2022,
https://doi.org/10.1007/s10911-022-09515-9
Uwe Schmitt, Beatrice Moser, Christiane S. Lorenz, Alexandre Refregier
sympy2c: From symbolic expressions to fast C/C++ functions and ODE solvers in Python
Astronomy and Computing
https://doi.org/10.1016/j.ascom.2022.100666
Beatrice Moser, Christiane S. Lorenz, Uwe Schmitt, Alexandre Refregier, Janis Fluri, Raphael Sgier, Federica Tarsitano, Lavinia Heisenberg
Symbolic Implementation of Extensions of the PyCosmo Boltzmann Solver
Astronomy and Computing
https://doi.org/10.1016/j.ascom.2022.100603
2021
publications mentioning our HPC cluster
Davide Vanzo , Samuel Peter, Lukas Vonwiller, Matthias Bürgler, Manuel Weberndorfer, Annunziato Siviglia, Daniel Conde, David F.Vetsch
Basement v3: a modular freeware for river process modelling over multiple computational backends
Environmental Modelling & Software (105102)
https://doi.org/10.1016/j.envsoft.2021.105102
Tiannan Guo, .., Uwe Schmitt et al
Rapid proteotyping reveals cancer biology and drug response determinants in the NCI-60 cells
www.biorxiv.org,
DOI:10.1101/268953
Roland Goers, Diana Coman Schmid, Vera F. Jäggi, Paolo Paioni, Michal J.
Okoniewski, Althea Parker, Beat Bangerter, Sofia Georgakopoulou, Thierry
Sengstag, Julia Bielicki, Romy Tilen, Swen Vermeul, Stefanie D. Krämer,
Christoph Berger, Bernd Rinn, Henriette E. Meyer zu Schwabedissen
SwissPKcdw – A clinical data warehouse for the optimization of pediatric dosing regimens
CPT: Pharmacometrics & Systems Pharmacology, https://doi.org/10.1002/psp4.12723
Paolo Paioni, Vera F. Jäggi, Romy Tilen, Michelle Seiler,Philipp Baumann,
Dominic S. Bräm, Carole Jetzer, Robin T. U. Haid, Aljoscha N. Goetschi, Roland
Goers, Daniel Müller, Diana Coman Schmid, Henriette E. Meyer zu
Schwabedissen, Bernd Rinn, Christoph Berger, and Stefanie D. Krämer5
Gentamicin Population Pharmacokinetics in Pediatric Patients - A Prospective Study with Data Analysis Using the saemix Package in R
Pharmaceutics. 2021 Oct; 13(10): 1596. https://doi.org/10.3390%2Fpharmaceutics13101596
Kurmann, Lisa, Michal Okoniewski, and Raghvendra K. Dubey
Estradiol Inhibits Human Brain Vascular Pericyte Migration Activity: A Functional and Transcriptomic Analysis
Cells. 2021; 10(9):2314. https://doi.org/10.3390/cells10092314
Kurmann, Lisa, Michal Okoniewski, and Raghvendra K. Dubey
Transcryptomic Analysis of Human Brain -Microvascular Endothelial Cell Driven Changes in -Vascular Pericytes
Cells. 2021; 10(7):1784.
https://doi.org/10.3390/cells10071784
Kurmann L, Okoniewski M, Ogunshola OO, Leeners B, Imthurn B, Dubey RK
Transcryptomic Analysis of Human Brain-Microvascular Endothelial Response to
-Pericytes: Cell Orientation Defines Barrier Function.
Cells. 2021; 10(4):963.
https://doi.org/10.3390/cells10040963
Cléry, A., Krepl, M., Nguyen, C.K.X. Okoniewski, M et al.
Structure of SRSF1 RRM1 bound to
RNA reveals an unexpected bimodal mode of interaction and explains its
involvement in SMN1 exon7 splicing.
Nat Commun 12, 428 (2021).
https://doi.org/10.1038/s41467-020-20481-w
2020
Töwe, Barillari
Who Does What? – Research Data Management at ETH Zurich
Data Science Journal,
DOI:10.5334/dsj-2020-036
Kühne, Iannuzzi, Del Ben, Rybkin, Seewald, Stein, Laino, Khaliullin, Schütt, Schiffmann, Golze, Wilhelm, Chulkov, Bani-Hashemian, Weber, Borštnik, et al.
CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations
J. Chem. Phys. 152, 194103 (2020) DOI:10.1063/5.0007045
SPHN – The BioMedIT Network: A Secure IT Platform for Research with Sensitive Human Data
Studies in Health Technology and Informatics,
Volume 270: Digital Personalized Health and Medicine, p 1170ff,
DOI:10.3233/SHTI200348
Pierre Millard, Uwe Schmitt, Patrick Kiefer, Julia A. Vorholt, Stéphanie Heux, Jean-Charles Portais
ScalaFlux: A scalable approach to quantify fluxes in metabolic subnetworks
PLOS Computational Biology
DOI:10.1371/journal.pcbi.1007799
Mikołaj Rybiński, Simon Möller, Mikael Sunnåker, Claude Lormeau, Jörg Stelling
TopoFilter: a MATLAB package for mechanistic model identification in systems biology
BMC Bioinformatics
DOI:10.1186/s12859-020-3343-y
Egli A, Koch D, Danuser J, Hendriksen R, Driesen S, Schmid DC, Neher R, Mäusezahl M, Seth-Smith HMB, Bloemberg G, Tschudin-Sutter S, Endimiani A, Perreten V, Greub G, Schrenzel J, Stephan R.
Symposium report: One Health meets sequencing
Microbes and Infection
DOI:10.1016/j.micinf.2019.07.004
Tanmay Tanna, Florian Schmid, Mariia Y. Cherepkova, Michal Okoniewski and Randall J. Platt
Recording transcriptional histories using Record-seq
Nature Protocals
DOI:10.1038/s41596-019-0253-4
2019
Grzegorz Dudziuk, Weronika Wronowska, Anna Gambin, Zuzanna Szymańska, Mikołaj Rybińsk
Biologically sound formal model of Hsp70 heat induction
Journal of Theoretical Biology
DOI:10.1016/j.jtbi.2019.05.022
Fischer M, Belanger SE, Berckmans P, Bernhard MJ, Bláha L4, Coman Schmid DE, Dyer SD, Haupt T, Hermens JLM, Hultman MT, Laue H, Lillicrap A, Mlnaříková M, Natsch A, Novák J, Sinnige TL, Tollefsen KE, von Niederhäusern V, Witters H, Županič A, Schirmer K
Repeatability and Reproducibility of the RTgill-W1 Cell Line Assay for Predicting Fish Acute Toxicity
Toxicological Sciences
DOI:10.1093/toxsci/kfz057
Wolfgang Omlor, Anna-Sophia Wahl, Pia Sipilä1, Henry Lütcke, Balazs Laurenczy, I-Wen Chen, Lazar T. Sumanovski, Marcel van’t Hoff, Philipp Bethge, Fabian F. Voigt,Martin E. Schwab& Fritjof Helmchen
Context-dependent limb movement encoding in neuronal populations of motor cortex
Nature Communications
DOI:10.1038/s41467-019-12670-z
Thomas L. Russell, Jichang Zhang, Michal Okoniewski, Felix Franke, Sandrine Bichet and Andreas Hierlemann
Medullary Respiratory Circuit Is Reorganized by a Seasonally-Induced Program in Preparation for Hibernation
Frontiers in Neuroscience
DOI:10.3389/fnins.2019.00376
2018
Marc W. Schmid, Christian Heichinger, Diana Coman Schmid et al.
Contribution of epigenetic variation to adaptation in Arabidopsis
Nature Communications 2018
DOI:10.1038/s41467-018-06932-5
Christoph Lippuner, Chandra Ramakrishnana, Walter U.Bassoa, Marc W.Schmid, Michal Okoniewski et al.
RNA-Seq analysis during the life cycle of Cryptosporidium parvum reveals significant differential gene expression between proliferating stages in the intestine and infectious sporozoites
International Journal for Parasitology 2018
DOI:10.1016/j.ijpara.2017.10.007
Josias B. Frazão, Martino Colombo, Cedric Simillion, Adem Bilican, Irene Keller, Daniel Wüthrich, Zhiqing Zhu, Michal J. Okoniewski et al.
Gene expression in chronic granulomatous disease and interferon‐γ receptor‐deficient cells treated in vitro with interferon‐γ
Journal of Cellular Biochemistry
DOI:10.1002/jcb.27718
Guangjie Shi, Thomas Wüst and David P. Landau
Elucidating thermal behavior, native contacts, and folding funnels of simple lattice proteins using replica exchange Wang-Landau sampling
Journal of Chemical Physics
DOI:10.1063/1.5026256
Anna Leśniewska, Joanna Zyprych-Walczak, Alicja Szabelska-Beręsewicz and Michal J. Okoniewski
Genes sharing the protein family domain decrease the performance of classification with RNA-seq genomic signatures
Biology Direct 2018
DOI:10.1186/s13062-018-0205-x
Alfred C.K. Farris, Guangjie Shi, Thomas Wüst and David P. Landau
The role of chain-stiffness in lattice protein models: A replica-exchange Wang-Landau study
Journal of Chemical Physics
DOI:10.1063/1.5045482
J. Panyasantisuk, E. Dall'Ara, M. Pretterklieber, D.H. Pahr and P.K. Zysset
Mapping anisotropy improves QCT-based finite element estimation of hip strength in pooled stance and side-fall load configurations
Medical Engineering & Physics 2018
DOI:10.1016/j.medengphy.2018.06.004
Marek Wiewiórka, Anna Leśniewska, Agnieszka Szmurło, Kacper Stępień, Mateusz Borowiak, Michal Okoniewski and Tomasz Gambin
SeQuiLa: An elastic, fast and scalable SQL-oriented solution for processing and querying genomic intervals
Bioinformatics 2018
DOI:10.1093/bioinformatics/bty940
Matthew S. Wilson, Guangjie Shi, Thomas Wüst, Ying Wai Li and David P. Landau
Influence of substrate pattern on the adsorption of HP lattice proteins
Journal of Molecular Simulation 2018
DOI:10.1080/08927022.2018.1471691
2017
Claude Lormeau, Mikołaj Rybiński, Jörg Stelling
Multi-objective design of synthetic biological circuits
IFAC-PapersOnLine
DOI:10.1016/j.ifacol.2017.08.1601
Alex Upton, Miguel Blanca, Jose Antonio Cornejo-García and James Richard Perkins
Weighted Epistatic Analysis of NSAIDs Hypersensitivity Data
Engineering Applications of Artificial Intelligence, June 2017, Volume 62
DOI: 10.1016/j.engappai.2016.09.007
Marek D Wiewiórka, Dawid P Wysakowicz, Michal J Okoniewski and Tomasz Gambin
Benchmarking distributed data warehouse solutions for storing genomic variant information
Database - The Journal of Biological Databases and Curation, Vol 2017
DOI: 10.1093/database/bax049
George Rosenberger, Isabell Bludau, Uwe Schmitt, Moritz Heusel, Christie L Hunter, Yansheng Liu, Michael J MacCoss, Brendan X MacLean, Alexey I Nesvizhskii, Patrick G A Pedrioli, Lukas Reiter, Hannes L Röst, Stephen Tate, Ying S Ting, Ben C Collins and Ruedi Aebersold
Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses
Nature Methods 2017
DOI: 10.1038/nmeth.4398
Ravi B Anjanappa, Devang Mehta, Michal J Okoniewski, Alicja Szabelska, Wilhelm Gruissem and Hervé Vanderschuren
Molecular insights into cassava brown streak virus susceptibility and resistance by profiling of the early host response
Molecular Plant Pathology
DOI: 10.1111/mpp.12565
J. Singer, H-J. Ruscheweyh, A. L. Hofmann, T. Thurnherr, F. Singer, N. C. Toussaint, C. K.Y. Ng, S. Piscuoglio, C. Beisel, G. Christofori, R. Dummer, M. N. Hall, W. Krek, M. Levesque, M. G. Manz, H. Moch, A.Papassotiropoulos, D. J. Stekhoven, P.Wild, T. Wüst, B. Rinn and N.Beerenwinkel
NGS-pipe: a flexible, easily extendable, and highly configurable framework for NGS analysis
Bioinformatics 2017
DOI: 10.1093/bioinformatics/btx540
Urs Graf, Elisa A Casanova, Sarah Wyck, Damian Dalcher, Marco Gatti, Eva Vollenweider, Michal J Okoniewski, Fabienne A Weber, Sameera S Patel, Marc W Schmid, Jiwen Li, Jafar Sharif, Guido A Wanner, Haruhiko Koseki, Jiemin Wong, Pawel Pelczar, Lorenza Penengo, Raffaella Santoro and Paolo Cinelli
Pramel7 mediates ground-state pluripotency through proteasomal-epigenetic combined pathways
Nature Cell Biology 19, 763–773
DOI: 10.1038/ncb3554
Oliver Fuhrer, Tarun Chadha, Torsten Hoefler, Grzegorz Kwasniewski, Xavier Lapillonne, David Leutwyler, Daniel Lüthi, Carlos Osuna, Christoph Schär, Thomas C. Schulthess, and Hannes Vogts
Near-global climate simulation at 1 km resolution: establishing a performance baseline on 4888 GPUs with COSMO 5.0
Geoscientific Model Development 2017
DOI: 10.5194/gmd-2017-230
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
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
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
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
Barillari, Lütcke, Petrus, Töwe, Thomas Wüst, Bernd Rinn
Supporting Scientists with FAIR Research Data Management – Initiatives at ETH Zurich and beyond
Bulletin der Vereinigung der Schweizerischen Hochschuldozierenden, August 2020
https://sis.id.ethz.ch/documents/VSH_Bulletin_August_2020_WEB.pdf
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)