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

Scientific and other Publications

2024

Silvan Fischbacher, Beatrice Moser, Tomasz Kacprzak, Joerg Herbel, Luca Tortorelli, Uwe Schmitt, Alexandre Refregier, Adam Amara
𝚐𝚊𝚕𝚜𝚋𝚒: A Python package for the GalSBI galaxy population model
https://arxiv.org/abs/2412.08722v1

Silvan Fischbacher, Beatrice Moser, Tomasz Kacprzak, Luca Tortorelli, Joerg Herbel, Claudio Bruderer, Uwe Schmitt, Alexandre Refregier, Joel Berge, Lukas Gamper, Adam Amara
𝚄𝙵𝚒𝚐 𝚟𝟷: The ultra-fast image generator
https://arxiv.org/abs/2412.08716

Franziska Menti, José A. Caballero, Mark C. Wyatt, Antonio García Muñoz, Keivan G. Stassun, Eleonora Alei, Markus Demleitner, Grant Kennedy, Tim Lichtenberg, Uwe Schmitt, Jessica S. Schonhut-Stasik, Haiyang S. Wang, Sascha P. Quanz, the LIFE Collaboration
Database of Candidate Targets for the LIFE Mission
Research Notes of the AAS
https://doi.org/10.3847/2515-5172/ad887e

Lara Fuhrmann, Kim Philipp Jablonski, Ivan Topolsky, Aashil A Batavia, Nico Borgsmüller, Pelin Icer Baykal, Matteo Carrara, Chaoran Chen, Arthur Dondi, Monica Dragan, David Dreifuss, Anika John, Benjamin Langer, Michal Okoniewski, Louis du Plessis, Uwe Schmitt, Franziska Singer, Tanja Stadler, Niko Beerenwinkel
V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation
GigaScience
https://doi.org/10.1093/gigascience/giae065

Gerhard Bräunlich, Shashank Saxena, Manuel Weberndorfer, Miguel Spinola, Prateek Gupta, Dennis M. Kochmann
AQCNES: A Quasi-Continuum Non-Equilibrium Solver
Journal of Open Source Software
https://doi.org/10.21105/joss.07068

Michal J. Okoniewski, Anna Wiegand, Diana Coman Schmid, Christian Bolliger, Cristian Bovino, Mattia Belluco, Thomas Wüst, Olivier Byrde, Sergio Maffioletti, Bernd Rinn
Leonhard Med, a trusted research environment for processing sensitive research data
Journal of Integrative Bioinformatics
https://www.degruyter.com/document/doi/10.1515/jib-2024-0021

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

Chahan M. Kropf, Alessio Ciullo, Laura Otth, Simona Meiler, Arun Rana, Emanuel Schmid, Jamie W. McCaughey, David N. Bresch
Uncertainty and sensitivity analysis for probabilistic weather and climate-risk modelling: an implementation in CLIMADA v.3.1.0
Geoscientific Model Development
https://doi.org/10.5194/gmd-15-7177-2022

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

Minju Lee, Lorenz C. Blum, Emanuel Schmid, Kathrin Fenner, Urs von Gunten
A computer-based prediction platform for the reaction of ozone with organic compounds in aqueous solution: kinetics and mechanisms
Environmental Science: Processes & Impacts
DOI: 10.1039/c6em00584e

Diogo A. R. S. Latino, Jörg Wicker, Martin Gütlein, Emanuel Schmid, Stefan Kramer, Kathrin Fenner
Eawag-Soil in enviPath: a new resource for exploring regulatory pesticide soil biodegradation pathways and half-life data
Environmental Science: Processes & Impacts
DOI: 10.1039/c6em00697c

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 A. R. S. 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)