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Abgrall, Rémi (2020). Letter from the Editor: About “A linear, second-order, energy stable, fully adaptive finite-element method for phase-field modelling of wetting phenomena” by B. Aymard, U. Vaes, M. Pradras and S. Kalliadasis [J. Comput. Phys. X 2 (2019) 100010]. Journal of Computational Physics, 410:109494.

Smakaj, Erand; Babrak, Lmar; Ohlin, Mats; Shugay, Mikhail; Briney, Bryan; Tosoni, Deniz; Galli, Christopher; Grobelsek, Vendi; D’Angelo, Igor; Olson, Branden; Reddy, Sai; Greiff, Victor; Trück, Johannes; Marquez, Susanna; Lees, William; Miho, Enkelejda (2020). Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences. Bioinformatics, 36(6):1731-1739.

Abgrall, Rémi; Lipnikov, Konstantin; Morgan, Nathaniel; Tokareva, Svetlana (2020). Multidimensional Staggered Grid Residual Distribution Scheme for Lagrangian Hydrodynamics. SIAM Journal on Scientific Computing, 42(1):A343-A370.


Casalicchio, Giuseppe; Bossek, Jakob; Lang, Michel; Kirchhoff, Dominik; Kerschke, Pascal; Hofner, Benjamin; Seibold, Heidi; Vanschoren, Joaquin; Bischl, Bernd (2019). OpenML: An R Package to Connect to the Networked Machine Learning Platform OpenML. Computational Statistics, 34(3):977-991.

Burovikhin, D; Sackmann, Benjamin; Schär, Merlin; Sim, J H; Eberhard, P; Lauxmann, M (2019). Investigation of Inhomogeneous Stiffness and Damping Characteristics of the Human Stapedial Annular Ligament. In: European Congress on Computational Methods in Applied Sciences and Engineering, Duisburg, 26 August 2019 - 26 August 2019, 18-25.

Sackmann, Benjamin; Warnholtz, Birthe; Sim, Jae Hoon; Burovikhin, Dmitrii; Dalhoff, Ernst; Eberhard, Peter; Lauxmann, Michael (2019). Investigation of Tympanic Membrane Influences on Middle-Ear Impedance Measurements and Simulations. In: European Congress on Computational Methods in Applied Sciences and Engineering, Duisburg, 26 August 2019 - 26 August 2019, 3-10.

Abgrall, Rémi (2019). Editorial. Journal of Computational Physics, 390:iii-iv.

Abgrall, Rémi; Bacigaluppi, Paola; Tokareva, Svetlana (2019). High-order residual distribution scheme for the time-dependent Euler equations of fluid dynamics. Computers & Mathematics with Applications, 78(2):274-297.

Lin, Jianfang; Abgrall, Rémi; Qiu, Jianxian (2019). High order residual distribution for steady state problems for hyperbolic conservation laws. Journal of Scientific Computing, 79(2):891-913.

Luber, Sandra (2019). Recent progress in computational exploration and design of functional materials. Computational Materials Science, 161:127-134.

Heyard, Rachel; Held, Leonhard (2019). The quantile probability model. Computational Statistics & Data Analysis, 132:84-99.

Crisovan, R; Torlo, D; Abgrall, Rémi; Tokareva, S (2019). Model order reduction for parametrized nonlinear hyperbolic problems as an application to uncertainty quantification. Journal of Computational and Applied Mathematics, 348:466-489.

Ohno, Koichi; Satoh, Hiroko; Iwamoto, Takeaki; Tokoyama, Hiroaki; Yamakado, Hideo (2019). Exploration of Carbon Allotropes with Four-membered Ring Structures on Quantum Chemical Potential Energy Surfaces. Journal of Computational Chemistry, 40(1):14-28.

Meier-Gibbons, Frances; Töteberg-Harms, Marc (2019). Aqueous Humor Dynamics and Its Influence on Glaucoma. In: Giodoboni, Giovanna; Harris, Alon Harris; Sacco, Riccardo. Ocular Fluid Dynamics: Anatomy, Physiology, Imaging Techniques, and Mathematical Modeling. Cham: Springer, 191-213.

Gasser, Rebekka; Gedicke, Joscha; Sauter, Stefan A (2019). Benchmark computation of eigenvalues with large defect for non-self-adjoint elliptic differential operators. SIAM Journal on Scientific Computing, 41(6):A3938-A3953.


Kedzierska, Katarzyna Z; Gerber, Livia; Cagnazzi, Daniele; Krützen, Michael; Ratan, Aakrosh; Kistler, Logan (2018). SONiCS: PCR stutter noise correction in genome-scale microsatellites. Bioinformatics, 34(23):4115-4117.

Perillo, Chiara; Battiston, Stefano (2018). A multiplex financial network approach to policy evaluation: the case of euro area Quantitative Easing. Applied Network Science, 3:49.

Abgrall, Rémi (2018). A general framework to construct schemes satisfying additional conservation relations. Application to entropy conservative and entropy dissipative schemes. Journal of Computational Physics, 372:640-666.

Vögeli, Urs; Nedaiasl, Khadijeh; Sauter, Stefan A (2018). A fully discrete Galerkin method for Abel-type integral equations. Advances in Computational Mathematics, 44(5):1601-1626.

Kresch, Andrew (2018). On the spaces generated by vectors with coordinates in incomplete residue systems. Research in the Mathematical Sciences, 5(3):36.

Grote, Marcus J; Mehlin, Michaela; Sauter, Stefan A (2018). Convergence analysis of energy conserving explicit local time-stepping methods for the wave equation. SIAM Journal on Numerical Analysis, 56(2):994-1021.

James, A Pappachen; Salama, K Nabil; Li, H; Biolek, D; Indiveri, G; Chua, L O (2018). Guest Editorial: Special Issue on Large-Scale Memristive Systems and Neurochips for Computational Intelligence. IEEE Transactions on Emerging Topics in Computational Intelligence, 2(5):320-323.

Singer, Jochen; Ruscheweyh, Hans-Joachim; Hofmann, Ariane L; Thurnherr, Thomas; Singer, Franziska; Toussaint, Nora C; Ng, Charlotte K Y; Piscuoglio, Salvatore; Beisel, Christian; Christofori, Gerhard; Dummer, Reinhard; Hall, Michael N; Krek, Wilhelm; Levesque, Mitchell P; Manz, Markus G; Moch, Holger; Papassotiropoulos, Andreas; Stekhoven, Daniel J; Wild, Peter; Wüst, Thomas; Rinn, Bernd; Beerenwinkel, Niko (2018). NGS-pipe: a flexible, easily extendable, and highly configurable framework for NGS analysis. Bioinformatics, 34(1):107-108.

Seibold, Heidi; Bernau, Christoph; Boulesteix, Anne-Laure; De Bin, Riccardo (2018). On the choice and influence of the number of boosting steps for high-dimensional linear Cox-models. Computational Statistics, 33(3):1195-1215.

Abgrall, Rémi (2018). Some remarks about conservation for residual distribution schemes. Computational Methods in Applied Mathematics, 18(3):327-351.

Soneson, Charlotte; Robinson, Mark D (2018). Towards unified quality verification of synthetic count data with countsimQC. Bioinformatics, 34(4):691-692.

Scherrer, Luca; Tomko, Martin; Ranacher, Peter; Weibel, Robert (2018). Travelers or locals? Identifying meaningful sub-populations from human movement data in the absence of ground truth. EPJ Data Science:7:19.


Ledoit, Olivier; Wolf, Michael (2017). Numerical implementation of the QuEST function. Computational Statistics & Data Analysis, 115:199-223.

Deng, Jun; Xu, Xinzhou; Zhang, Zixing; Frühholz, Sascha; Schuller, Bjorn (2017). Semi-supervised autoencoders for speech emotion recognition. IEEE/ACM Transactions on Audio, Speech, and Language Processing, (99):1.

Abgrall, Rémi; Mishra, S (2017). Uncertainty quantification for hyperbolic systems of conservation laws. Handbook of Numerical Analysis, 18:507-544.

Abgrall, Rémi; Koren, Barry (2017). Computational science for energy research. Journal of Computational Physics, 345:A1.

Abgrall, Rémi; Viville, Q; Beaugendre, H; Dobrzynski, C (2017). Construction of a p-adaptive continuous residual distribution scheme. Journal of Scientific Computing, 72(3):1232-1268.

Muff, Stefanie; Ott, Manuela; Braun, Julia; Held, Leonhard (2017). Bayesian two-component measurement error modelling for survival analysis using INLA—A case study on cardiovascular disease mortality in Switzerland. Computational Statistics & Data Analysis, 113:177-193.

Rodrigues, João F Matias; Schmidt, Thomas Sebastian Benedikt; Tackmann, Janko; von Mering, Christian (2017). MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis. Bioinformatics, 33(23):3808-3810.

Abgrall, Rémi (2017). High order schemes for hyperbolic problems using globally continuous approximation and avoiding mass matrices. Journal of Scientific Computing, 73(2-3):461-494.

Weymuth, Monika; Sauter, Stefan; Repin, Sergey (2017). A posteriori modelling-discretization error estimate for elliptic problems with L ∞-Coefficients. Computational Methods in Applied Mathematics, 17(3):515-531.

Kappeler, Thomas; Molnar, Jan-Cornelius (2017). On the Well-posedness of the defocusing mKdV equation below $L^{2}$. SIAM Journal on Mathematical Analysis, 49(3):2191-2219.

Abgrall, Rémi (2017). Some Failures of Riemann Solvers. In: Abgrall, Rémi; Shu, Chi-Wang. Handbook of Numerical Methods for Hyperbolic Problems - Applied and Modern Issues. North Holland: Elsevier, 351-360.

Sauter, Stefan A; Schanz, Martin (2017). Convolution quadrature for the wave equation with impedance boundary conditions. Journal of Computational Physics, 334:442-459.

Grimm, Alexander; Tessone, Claudio J (2017). Analysing the sensitivity of nestedness detection methods. Applied Network Science:2:37.

Ohno, Koichi; Kishimoto, Naoki; Iwamoto, Takeaki; Satoh, Hiroko (2017). Global exploration of isomers and isomerization channels on the quantum chemical potential energy surface of H3 CNO3. Journal of Computational Chemistry, 38(10):669-687.


Montazeri, Hesam; Kuipers, Jack; Kouyos, Roger; Böni, Jürg; Yerly, Sabine; Klimkait, Thomas; Aubert, Vincent; Günthard, Huldrych F; Beerenwinkel, Niko (2016). Large-scale inference of conjunctive Bayesian networks. Bioinformatics, 32(17):i727-i735.

Mennle, Timo; Seuken, Sven (2016). The Pareto frontier for random mechanisms. In: The 2016 ACM Conference on Economics and Computation, Maastricht, The Netherlands, 24 August 2016 - 28 August 2016, 769.

Lopez-Fernandez, Maria; Sauter, Stefan A (2016). Generalized convolution quadrature based on Runge-Kutta methods. Numerische Mathematik, 133(4):743-779.

Tang, Kunkun; Congedo, Pietro M; Abgrall, Rémi (2016). Adaptive surrogate modeling by ANOVA and sparse polynomial dimensional decomposition for global sensitivity analysis in fluid simulation. Journal of Computational Physics, 314:557-589.

Repin, Sergey; Samrowski, Tatiana; Sauter, Stefan (2016). Estimates of the modeling error generated by homogenization of an elliptic boundary value problem. Journal of Numerical Mathematics, 24(1):1-15.

Geraci, Gianluca; Congedo, Pietro Marco; Abgrall, Rémi; Iaccarino, Gianluca (2016). A novel weakly-intrusive non-linear multiresolution framework for uncertainty quantification in hyperbolic partial differential equations. Journal of Scientific Computing, 66(1):358-405.

Falletta, Silvia; Sauter, Stefan A (2016). The panel-clustering method for the wave equation in two spatial dimensions. Journal of Computational Physics, 305:217-243.

Buzdugan, Laura; Kalisch, Markus; Navarro, Arcadi; Schunk, Daniel; Fehr, Ernst; Bühlmann, Peter (2016). Assessing statistical significance in multivariable genome wide association analysis. Bioinformatics, 32(13):1990-2000.

Abgrall, Rémi; Bacigaluppi, Paola; Tokareva, Svetlana (2016). How to avoid mass matrix for linear hyperbolic problems. In: Karasözen, B; Manguoglu, M; Tezer-Sezgin, M; Göktepe, S; Ugur, Ö. Numerical Mathematics and Advanced Applications ENUMATH 2015. Cham: Springer, 75-86.

Ciarlet, Phillip G; Ciarlet, Patrick; Sauter, Stefan A; Simian, C (2016). Intrinsic finite element methods for the computation of fluxes for Poisson’s equation. Numerische Mathematik, 132(3):433-462.

Franceschini, Andrea; Lin, Jianyi; von Mering, Christian; Jensen, Lars Juhl (2016). SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles. Bioinformatics, 32(7):1085-1087.


Bertram, Nora (2015). Tagungsbericht. In: „Computing all their cost and trouble“. Finanzmärkte, Spekulationen und Regulierung in der Frühen Neuzeit und in der Moderne. Diskurse, Narrative, Strategien, Zürich, 8 October 2015 - 9 October 2015.

Abgrall, Rémi; Congedo, Pietro Marco; Geraci, Gianluca; Rodio, Maria Giovanna (2015). Stochastic discrete equation method (sDEM) for two-phase flows. Journal of Computational Physics, 299:281-306.

Schaper, Elke; Korsunsky, Alexander; Pečerska, Jūlija; Messina, Antonio; Murri, Riccardo; Stockinger, Heinz; Zoller, Stefan; Xenarios, Ioannis; Anisimova, Maria (2015). TRAL: tandem repeat annotation library. Bioinformatics, 31(18):3051-3053.

Lopez-Fernandez, Maria; Sauter, Stefan (2015). Generalized convolution quadrature with variable time stepping. Part II: Algorithm and numerical results. Applied Numerical Mathematics, 94:88-105.

Röst, Hannes L; Rosenberger, George; Aebersold, Ruedi; Malmström, Lars (2015). Efficient visualization of high-throughput targeted proteomics experiments: TAPIR. Bioinformatics, 31(14):2415-2417.

Koornwinder, Tom H; Sauter, Stefan A (2015). The intersection of bivariate orthogonal polynomials on triangle patches. Mathematics of Computation, 84(294):1795-1812.

Arpaia, Luca; Ricchiuto, Mario; Abgrall, Rémi (2015). An ALE formulation for explicit Runge–Kutta residual distribution. Journal of Scientific Computing, 63(2):502-547.

Panse, Christian; Trachsel, Christian; Grossmann, Jonas; Schlapbach, Ralph (2015). specL - An R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics. Bioinformatics, 31(13):2228-2231.

Teleman, Johan; Röst, Hannes L; Rosenberger, George; Schmitt, Uwe; Malmström, Lars; Malmström, Johan; Levander, Fredrik (2015). DIANA - algorithmic improvements for analysis of data-independent acquisition MS data. Bioinformatics, 31(4):555-562.

Abgrall, Rémi; de Santis, Dante (2015). Linear and non-linear high order accurate residual distribution schemes for the discretization of the steady compressible Navier–Stokes equations. Journal of Computational Physics, 283:329-359.

Metz, Andreas; Wolf, Martin; Achermann, Peter; Scholkmann, Felix (2015). A new approach for automatic removal of movement artifacts in near-infrared spectroscopy time series by means of acceleration data. Algorithms, 8(4):1052-1075.

Sauter, Stefan A; Zech, J (2015). A posteriori error estimation of $\mathit{hp}$-dG finite element methods for highly indefinite Helmholtz problems. SIAM Journal on Numerical Analysis, 53(5):2414-2440.

Sala, Oliver; Lüthi, Hans Peter; Togni, Antonio; Iannuzzi, Marcella; Hutter, Jürg (2015). Dividing a complex reaction involving a hypervalent iodine reagent into three limiting mechanisms byab initiomolecular dynamics. Journal of Computational Chemistry, 36(11):785-794.

Munglani, Gautam; Vetter, Roman; Wittel, Falk K; Herrmann, Hans J (2015). Orthotropic rotation-free thin shell elements. Computational Mechanics, 56(5):785-793.

Schmid, Marc W; Grossniklaus, Ueli (2015). Rcount: simple and flexible RNA-Seq read counting. Bioinformatics, 31(3):436-437.


Henshaw, Jonathan M; Jennions, Michael D; Kokko, Hanna (2014). The Economics of Egg Trading: Mating Rate, Sperm Competition and Positive Frequency-Dependence. Dynamic Games and Applications, 4(4):379-390.

Vilar, François; Maire, Pierre-Henri; Abgrall, Rémi (2014). A discontinuous Galerkin discretization for solving the two-dimensional gas dynamics equations written under total Lagrangian formulation on general unstructured grids. Journal of Computational Physics, 276:188-234.

Dall'Olio, Giovanni M; Vahdati, Ali R; Bertranpetit, Jaume; Wagner, Andreas; Laayouni, Hafid (2014). VCF2Networks: applying genotype networks to single-nucleotide variants data. Bioinformatics, 31(3):438-439.

Jennings, G I; Prigge, D; Carney, S; Karni, S; Rauch, J B; Abgrall, Rémi (2014). Water wave propagation in unbounded domains. Part II: Numerical methods for fractional PDEs. Journal of Computational Physics, 275:443-458.

Wiewiórka, Marek S; Messina, Antonio; Pacholewska, Alicja; Maffioletti, Sergio; Gawrysiak, Piotr; Okoniewski, Michał J (2014). SparkSeq: fast, scalable and cloud-ready tool for the interactive genomic data analysis with nucleotide precision. Bioinformatics, 30(18):2652-2653.

Rosenberger, George; Ludwig, Christina; Röst, Hannes L; Aebersold, Ruedi; Malmström, Lars (2014). aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data. Bioinformatics, 30(17):2511-2513.

Abgrall, Rémi; Kumar, Harish (2014). Robust finite volume schemes for two-fluid plasma equations. Journal of Scientific Computing, 60(3):584-611.

Abgrall, Rémi; Smolarkiewicz, Piotr; Xiao, Feng; Zaleski, Stéphane (2014). Frontiers in computational physics: modeling the earth system. Journal of Computational Physics, 271:1.

Marz, Manja; Beerenwinkel, Niko; Drosten, Christian; Fricke, Markus; Frishman, Dmitrij; Hofacker, Ivo L; Hoffmann, Dieter; Middendorf, Martin; Rattei, Thomas; Stadler, Peter F; Töpfer, Armin (2014). Challenges in RNA virus bioinformatics. Bioinformatics, 30(13):1793-1799.

Sauter, S; Veit, A (2014). Retarded boundary integral equations on the sphere: exact and numerical solution. IMA Journal of Numerical Analysis, 34(2):675-699.

Zhou, Yu; Ma, Xiaoxing; Gall, Harald (2014). A middleware platform for the dynamic evolution of distributed component-based systems. Computing, 96(8):725-747.

Balsara, Dinshaw S; Dumbser, Michael; Abgrall, Rémi (2014). Multidimensional HLLC Riemann solver for unstructured meshes – with application to Euler and MHD flows. Journal of Computational Physics, 261:172-208.

Omasits, Ulrich; Ahrens, Christian H; Müller, Sebastian; Wollscheid, Bernd (2014). Protter: interactive protein feature visualization and integration with experimental proteomic data. Bioinformatics, 30(6):884-886.

Abgrall, Rémi; Congedo, P M; Geraci, G (2014). A one-time truncate and encode multiresolution stochastic framework. Journal of Computational Physics, 257(Part A):19-56.

Abgrall, Rémi; Beaugendre, H; Dobrzynski, C (2014). An immersed boundary method using unstructured anisotropic mesh adaptation combined with level-sets and penalization techniques. Journal of Computational Physics, 257(Part A):83-101.

Samrowski, Tatiana (2014). Combined error estimates in the case of dimension reduction. Computational Methods in Applied Mathematics, 14(1):113-134.

Eigel, Martin; Samrowski, Tatiana (2014). Functional A posteriori error estimation for stationary reaction-convection-diffusion problems. Computational Methods in Applied Mathematics, 14(2):135-150.

Eugster, Manuel J A; Leisch, Friedrich; Strobl, Carolin (2014). (Psycho-)analysis of benchmark experiments : a formal framework for investigating the relationship between data sets and learning algorithms. Computational Statistics & Data Analysis, 71:986-1000.

Fu, Biao; Sahakyan, Aleksandr B; Camilloni, Carlo; Tartaglia, Gian Gaetano; Paci, Emanuele; Caflisch, Amedeo; Vendruscolo, Michele; Cavalli, Andrea (2014). ALMOST: an all atom molecular simulation toolkit for protein structure determination. Journal of Computational Chemistry, 35(14):1101-1105.

Hutter, Juerg; Iannuzzi, Marcella; Schiffmann, Florian; VandeVondele, Joost (2014). CP2K: Atomistic simulations of condensed matter systems. Wiley Interdisciplinary Reviews. Computational Molecular Science, 4(1):15-25.

Braun, Julia; Held, Leonhard; Sabanés Bové, Daniel (2014). Choice of generalized linear mixed models using predictive crossvalidation. Computational Statistics & Data Analysis, 75:190-202.

Matias Rodrigues, João F; von Mering, Christian (2014). HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences. Bioinformatics, 30(2):287-288.

Abgrall, Rémi; de Santis, Dante; Ricchiuto, M (2014). High-order preserving residual distribution schemes for advection-diffusion scalar problems on arbitrary grids. SIAM Journal on Scientific Computing, 36(3):A955-A983.

Sunnaker, M; Zamora-Sillero, E; Lopez Garcia de Lomana, A; Rudroff, F; Sauer, U; Stelling, J; Wagner, A (2014). Topological augmentation to infer hidden processes in biological systems. Bioinformatics, 30(2):221-227.

Gomez, F; Stoop, R-L; Stoop, R (2014). Universal dynamical properties preclude standard clustering in a large class of biochemical data. Open Bioinformatics Journal, 30(17):2486-2493.


Melenk, Jens Markus; Parsani, Asieh; Sauter, Stefan A (2013). General DG-methods for highly indefinite Helmholtz problems. Journal of Scientific Computing, 57(3):536-581.

López-Fernándes, María; Sauter, Stefan A (2013). Generalized convolution quadrature with variable time stepping. IMA Journal of Numerical Analysis, 33(4):1156-1175.

Dörfler, Willy; Sauter, Stefan A (2013). A posteriori error estimation for highly indefinite Helmholtz problems. Computational Methods in Applied Mathematics, 13(3):333-347.

Croset, Samuel; Overington, John P; Rebholz-Schuhmann, Dietrich (2013). Brain: biomedical knowledge manipulation. Open Bioinformatics Journal, 29(9):1238-1239.

Ballani, Jonas; Banjai, Lehel; Sauter, Stefan A; Veit, Alexander (2013). Numerical solution of exterior Maxwell problems by Galerkin BEM and Runge–Kutta convolution quadrature. Numerische Mathematik, 123(4):643-670.

Maire, Pierre-Henri; Abgrall, Rémi; Breil, Jérôme; Loubière, Raphaël; Rebourset, Bernard (2013). A nominally second-order cell-centered Lagrangian scheme for simulating elastic–plastic flows on two-dimensional unstructured grids. Journal of Computational Physics, 235(15):626-665.

Abfrall, Rémi; Congedo, Pietro Marco (2013). A semi-intrusive deterministic approach to uncertainty quantification in non-linear fluid flow problems. Journal of Computational Physics, 235:828-845.

Sauter, Stefan A; Veit, Alexander (2013). A Galerkin method for retarded boundary integral equations with smooth and compactly supported temporal basis functions. Numerische Mathematik, 123(1):145-176.

Loewe, Kristian; Grueschow, Marcus; Borgelt, Christian (2013). Mining local connectivity patterns in fMRI data. In: Christian, Borgelt; María Ángeles, Gil; João M C, Sousa; Michel, Verleysen. Towards Advanced Data Analysis by Combining Soft Computing and Statistics. Berlin: Springer (Bücher), 305-317.

Busetto, Alberto Giovanni; Hauser, Alain; Krummenacher, Gabriel; Sunnåker, Mikael; Dimopoulos, Sotiris; Ong, Cheng Soon; Stelling, Jörg; Buhmann, Joachim M (2013). Near-optimal experimental design for model selection in systems biology. Bioinformatics:online.

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


Repin, S I; Samrowski, T S; Sauter, S A (2012). Combined a posteriori modelling-discretization error estimate for elliptic problems with variable coefficients. Mathematical Modelling and Numerical Analysis, 46(6):1389-1405.

Sakoparnig, T; Beerenwinkel, N (2012). Efficient sampling for Bayesian inference of conjunctive Bayesian networks. Bioinformatics, 28(18):2318-2324.

Zoppi, Laura; Siegel, Jay S; Baldridge, Kim K (2012). Electron transport and optical properties of curved aromatics. Wiley Interdisciplinary Reviews: Computational Molecular Science, 3(1):1-12.

Hutter, Juerg (2012). Car-Parrinello molecular dynamics. Wiley Interdisciplinary Reviews: Computational Molecular Science, 2(4):604-612.

Dessimoz, C; Gabaldon, T; Roos, D S; Sonnhammer, E L L; Herrero, J; Altenhoff, A; Apweiler, R; Ashburner, M; Blake, J; Boeckmann, B; Bridge, A; Bruford, E; Cherry, M; Conte, M; Dannie, D; Datta, R; Dessimoz, C; Domelevo Entfellner, J-B; Ebersberger, I; Gabaldon, T; Galperin, M; Herrero, J; Joseph, J; Koestler, T; Kriventseva, E; Lecompte, O; Leunissen, J; Lewis, S; Linard, B; Livstone, M S; et al (2012). Toward community standards in the quest for orthologs. Bioinformatics, 28(6):900-904.

Hess, Franziska; Farkas, Attila; Seitsonen, Ari P; Over, Herbert (2012). “First-Principles” kinetic monte carlo simulations revisited: CO oxidation over RuO2(110). Journal of Computational Chemistry, 33(7):757-766.

Dickhaus, Thorsten; Straßburger, Klaus; Schunk, Daniel; Morcillo-Suarez, Carlos; Illig, Thomas; Navarro, Arcadi (2012). How to analyze many contingency tables simultaneously in genetic association studies. Statistical Applications in Genetics and Molecular Biology, 11(4):Article 12.

Maze, Gérard (2012). Analysis of a key distribution scheme in secure multicasting. Journal of mathematical cryptology, 6(1):69-80.

Reboux, Sylvain; Schrader, Birte; Sbalzarini, Ivo F (2012). A self-organizing Lagrangian particle method for adaptive-resolution advection–diffusion simulations. Journal of Computational Physics, 231(9):3623-3646.

Scholkmann, F; Boss, J; Wolf, M (2012). An efficient algorithm for automatic peak detection in noisy periodic and quasi-periodic signals. Algorithms, 5(4):588-603.

Würsch, Michael; Ghezzi, Giacomo; Hert, Matthias; Reif, Gerald; Gall, Harald C (2012). SEON: A pyramid of ontologies for software evolution and its applications. Computing, 94(11):857-885.

Siebourg, Juliane; Merdes, Gunter; Misselwitz, Benjamin; Hardt, Wolf-Dietrich; Beerenwinkel, Niko (2012). Stability of gene rankings from RNAi screens. Bioinformatics, 28(12):1612-1618.


Holmström, L; Pasanen, L; Furrer, R; Sain, S R (2011). Scale space multiresolution analysis of random signals. Computational Statistics and Data Analysis, 55(10):2840-2855.

Longair, M H; Baker, D A; Armstrong, J D (2011). Simple neurite tracer. Bioinformatics, 27(17):2453-2454.

Eastman, J M; Paine, C E T; Hardy, O J (2011). spacodiR: structuring of phylogenetic diversity in ecological communities. Bioinformatics, 27(17):2437-2438.

Guillet, T; Teyssier, R (2011). A simple multigrid scheme for solving the Poisson equation with arbitrary domain boundaries. Journal of Computational Physics, 230(12):4756-4771.

Kascha, Christian; Trenkler, Carsten (2011). Bootstrapping the likelihood ratio cointegration test in error correction models with unknown lag order. Computational Statistics and Data Analysis, 55(2):1008-1017.

Preusser, T; Rumpf, M; Sauter, S; Schwen, L O (2011). 3D composite finite elements for elliptic boundary value problems with discontinuous coefficients. SIAM Journal on Scientific Computing (SISC), 33(5):2115-2143.

Schrödle, B; Held, L (2011). A primer on disease mapping and ecological regression using INLA. Computational Statistics, 26(2):241-258.

Khoromskij, B; Sauter, S; Veit, A (2011). Fast quadrature techniques for retarded potentials based on TT/QTT tensor approximation. Computational Methods in Applied Mathematics, 11(3):342-362.

Schaffter, Thomas; Marbach, Daniel; Floreano, Dario (2011). GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods. Bioinformatics, 27(16):2263-2270.

Melenk, J M; Sauter, S (2011). Wave-number explicit convergence analysis for Galerkin discretizations of the Helmholtz equation (extended version). SIAM Journal on Numerical Analysis, 49(3):1210-1243.

Melenk, J M; Sauter, S (2011). Wavenumber explicit convergence analysis for Galerkin discretizations of the Helmholtz equation. SIAM Journal on Numerical Analysis, 49(3):1210-1243.

Seeber, M; Felline, A; Raimondi, F; Muff, S; Friedman, R; Rao, F; Caflisch, A; Fanelli, F (2011). Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. Journal of Computational Chemistry, 32(6):1183-1194.


Saalfeld, S; Cardona, A; Hartenstein, V; Tomancak, P (2010). As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets. Bioinformatics, 26(12):i57-i63.

Rufibach, K (2010). An active set algorithm to estimate parameters in generalized linear models with ordered predictors. Computational Statistics and Data Analysis, 54(6):1442-1456.

Melenk, J M; Sauter, S (2010). Convergence analysis for finite element discretizations of the Helmholtz equation with Dirichlet-to-Neumann boundary conditions. Mathematics of Computation, 79(272):1871-1914.

Sauter, S (2010). hp-Finite Elements for Elliptic Eigenvalue Problems: Error estimates which are explicit with respect to λ, h, and p. SIAM Journal on Numerical Analysis, 48(1):95-108.

Cerdonio, M; de Marchi, F; de Pietri, R; Jetzer, P; Marzari, F; Mazzolo, G; Ortolan, A; Sereno, M (2010). Effects of interplanetary dust on the LISA drag-free constellation. Celestial Mechanics and Dynamical Astronomy, 107(1-2):255-264.

Schrader, Birte; Reboux, Sylvain; Sbalzarini, Ivo F (2010). Discretization correction of general integral PSE Operators for particle methods. Journal of Computational Physics, 229(11):4159-4182.

Groeber, Patrick; Rauhut, Heiko (2010). Does ignorance promote norm compliance? Computational & Mathematical Organization Theory, 16(1):1-28.

Huang, D; Zhou, T; Lafleur, K; Nevado, C; Caflisch, A (2010). Kinase selectivity potential for inhibitors targeting the ATP binding site: A network analysis. Bioinformatics, 26(2):198-204.

Sannomiya, T; Hafner, C (2010). Multiple multipole program modelling for nano plasmonic sensors. Journal of Computational and Theoretical Nanoscience, 7(8):1587-1595.

Ostafe, A; Shparlinski, I (2010). On the degree growth in some polynomial dynamical systems and nonlinear pseudorandom number generators. Mathematics of Computation, 79(269):501-511.


Liu, J; Bandyopadhyay, N; Ranka, S; Baudis, Michael; Kahveci, T (2009). Inferring progression models for CGH data. Bioinformatics, 25(17):2208-2215.

Bayati, B; Chatelain, P; Koumoutsakos, P (2009). D-leaping: Accelerating stochastic simulation algorithms for reactions with delays. Journal of Computational Physics, 228(16):5908-5916.

Saalfeld, S; Cardona, A; Hartenstein, V; Tomancak, P (2009). CATMAID: collaborative annotation toolkit for massive amounts of image data. Bioinformatics, 25(15):1984-1986.

Claassen, M; Aebersold, R; Buhmann, J M (2009). Proteome coverage prediction with infinite Markov models. Bioinformatics, 25(12):i154-i160.

Gehlenborg, N; Yan, W; Lee, I Y; Yoo, H; Nieselt, K; Hwang, D; Aebersold, R; Hood, L (2009). Prequips--an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data. Bioinformatics, 25(5):682-683.

Broda, Simon; Paolella, Marc S (2009). Evaluating the density of ratios of noncentral quadratic forms in normal variables. Computational Statistics and Data Analysis, 53(4):1264-1270.

Haas, Markus; Mittnik, Stefan; Paolella, Marc S (2009). Asymmetric multivariate normal mixture GARCH. Computational Statistics and Data Analysis, 53(6):2129-2154.

Kotte, Oliver; Heinemann, Matthias (2009). A divide-and-conquer approach to analyze underdetermined biochemical models. Bioinformatics, 25(4):519-525.

Brooks, B R; Brooks, C L; Mackerell, A D; Nilsson, L; Petrella, R J; Roux, B; Won, Y; Archontis, G; Bartels, C; Boresch, S; Caflisch, A; Caves, L; Cui, Q; Dinner, A R; Feig, M; Fischer, S; Gao, J; Hodoscek, M; Im, W; Kuczera, K; Lazaridis, T; Ma, J; Ovchinnikov, V; Paci, E; Pastor, R W; Post, C B; Pu, J Z; Schaefer, M; Tidor, B; Venable, R M; Woodcock, H L; Wu, X; Yang, W; York, D M; Karplus, M (2009). CHARMM: the biomolecular simulation program. Journal of Computational Chemistry, 30(10):1545-1614.

Marbach, Daniel; Schaffter, Thomas; Mattiussi, Claudio; Floreano, Dario (2009). Generating realistic in silico gene networks for performance assessment of reverse engineering methods. Journal of Computational Biology, 16(2):229-39.

Gerstung, M; Baudis, Michael; Moch, H; Beerenwinkel, N (2009). Quantifying cancer progression with conjunctive Bayesian networks. Bioinformatics, 25(21):2809-2815.

Hackbusch, W; Kress, W; Sauter, S (2009). Sparse convolution quadrature for time domain boundary integral formulations of the wave equation. IMA Journal of Numerical Analysis, 29(1):158-179.

Corvellec, Jean-Noël; Motreanu, Viorica (2009). Stability of global minimum points of lower semicontinuous functions. Pac. J. Optim., 5(1):75-86.

Park, J; Gasser, T; Rousson, V (2009). Structural components in functional data. Computational Statistics and Data Analysis, 53(9):3452-3465.

Sannomiya, T; Vörös, J; Hafner, C (2009). Symmetry decomposed multiple multipole program calculation of plasmonic particles on substrate for biosensing applications. Journal of Computational and Theoretical Nanoscience, 6(3):749-756.


Hwang, D; Zhang, N; Lee, H; Yi, E; Zhang, H; Lee, I Y; Hood, L; Aebersold, R (2008). MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis. Bioinformatics, 24(22):2641-2642.

Heitmann, K; Lukić, Z; Fasel, P; Habib, S; Warren, M S; White, M; Ahrens, J; Ankeny, L; Armstrong, R; O'Shea, B; Ricker, P M; Springel, V; Stadel, J; Trac, H (2008). The cosmic code comparison project. Computational Science & Discovery, 1(1):015003.

Ramos, H; Shannon, P; Aebersold, R (2008). The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data. Bioinformatics, 24(18):2110-2111.

Rehrauer, H; Schönmann, S; Eberl, L; Schlapbach, R (2008). PhyloDetect: a likelihood-based strategy for detecting microorganisms with diagnostic microarrays. Bioinformatics, 24(16):i83-i89.

Babuska, I; Sauter, S (2008). Efficient solution of anisotropic lattice equations by the recovery method. SIAM Journal on Scientific Computing (SISC), 30(5):2386-2404.

Höhle, M; Paul, M (2008). Count data regression charts for the monitoring of surveillance time series. Computational Statistics and Data Analysis, 52(9):4357-4368.

Oudet, Édouard; Rieger, Marc Oliver (2008). Local minimizers of functionals with multiple volume constraints. ESAIM: Control, Optimisation and Calculus of Variations, 14(4):780-794.

Kress, W; Sauter, S (2008). Numerical treatment of retarded boundary integral equations by sparse panel clustering. IMA Journal of Numerical Analysis, 28(1):162-185.

Heinzmann, D (2008). A filtered polynomial approach to density estimation. Computational Statistics, 23(3):343-360.

Haberthür, U; Caflisch, A (2008). FACTS: Fast analytical continuum treatment of solvation. Journal of Computational Chemistry, 29(5):701-715.

Banjai, L; Hackbusch, W (2008). Hierarchical matrix techniques for low- and high-frequency Helmholtz problems. IMA Journal of Numerical Analysis, 28(1):46-79.

Graham, I G; Grasedyck, L; Hackbusch, W; Sauter, S (2008). Optimal panel-clustering in the presence of anisotropic mesh refinement. SIAM Journal on Numerical Analysis, 46(1):517-543.

Banjai, L; Sauter, S (2008). Rapid solution of the wave equation in unbounded domains. SIAM Journal on Numerical Analysis, 47(1):227-249.

Banjai, L (2008). Revisiting the crowding phenomenon in Schwarz-Christoffel mapping. SIAM Journal on Scientific Computing (SISC), 30(2):618-636.

Cinquemani, Eugenio; Milias-Argeitis, Andreas; Summers, Sean; Lygeros, John (2008). Stochastic dynamics of genetic networks: modelling and parameter identification. Bioinformatics, 24(23):2748-2754.

Petersheim, D; Sauter, S (2008). The composite mini element-coarse mesh computation of Stokes flows on complicated domains. SIAM Journal on Numerical Analysis, 46(6):3181-3206.


Seeber, M; Cecchini, M; Rao, F; Settanni, G; Caflisch, A (2007). Wordom: a program for efficient analysis of molecular dynamics simulations. Bioinformatics, 23(19):2625-2627.

Broda, Simon; Paolella, Marc S; Carstensen, Kai (2007). Bias-adjusted estimation in the ARX(1) model. Computational Statistics and Data Analysis, 51(7):3355-3367.

Broda, Simon; Paolella, Marc S (2007). Saddlepoint approximations for the doubly noncentral t distribution. Computational Statistics and Data Analysis, 51(6):2907-2918.

Banjai, L; Sauter, S (2007). A refined Galerkin error and stability analysis for highly indefinite variational problems. SIAM Journal on Numerical Analysis, 45(1):37-53.

Hackbusch, W; Khoromskij, B; Sauter, S (2007). Adaptive Galerkin boundary element methods with panel clustering. Numerische Mathematik, 105(4):603-631.

Roos, F F; Jacob, R; Grossmann, J; Fischer, B; Buhmann, J M; Gruissem, W; Baginsky, S; Widmayer, P (2007). PepSplice: cache-efficient search algorithms for comprehensive identification of tandem mass spectra. Bioinformatics, 23(22):3016-3023.

Repin, S; Sauter, S; Smolianski, A (2007). Two-sided a posteriori error estimates for mixed formulations of elliptic problems. SIAM Journal on Numerical Analysis, 45(3):928-945.


Steiger, Olivier (2006). Navier–Stokes equations with first order boundary conditions. Journal of mathematical fluid mechanics, 8(4):456-481.

Fischer, B; Grossmann, J; Roth, V; Gruissem, W; Baginsky, S; Buhmann, J M (2006). Semi-supervised LC/MS alignment for differential proteomics. Bioinformatics, 22(14):e132-40.

Sauter, S (2006). A refined finite element convergence theory for highly indefinite Helmholtz problems. Computing, 78(2):101-115.

Paolella, Marc; Hartz, Christoph; Mittnik, Stefan (2006). Accurate value-at-risk forecasting based on the Normal-GARCH model. Computational Statistics & Data Analysis, 51(4):2295-2312.

Hackbusch, W; Löhndorf, M; Sauter, S (2006). Coarsening of boundary-element spaces. Computing, 77(3):253-273.

Sauter, S; Warnke, R (2006). Composite finite elements for elliptic boundary value problems with discontinuous coefficients. Computing, 77(1):29-55.

Liu, J; Mohammed, J; Carter, J; Ranka, S; Kahveci, T; Baudis, Michael (2006). Distance-based clustering of CGH data. Bioinformatics, 22(16):1971-1978.

Nicaise, S; Sauter, S A (2006). Efficient numerical solution of Neumann problems on complicated domains. Calcolo, 43(2):95-120.

Noetzli, J; Huggel, C; Hoelzle, M; Haeberli, W (2006). GIS-based modelling of rock-ice avalanches from Alpine permafrost areas. Computational Geosciences, 10(2):161-178.

Anza Hafsa, O; Mandallena, J-P; Michaille, G (2006). Homogenization of periodic nonconvex integral functionals in terms of Young measures. ESAIM: Control, Optimisation and Calculus of Variations, 12(1):35-51 (electronic).

Buffa, A; Sauter, S (2006). On the acoustic single layer potential: stabilization and Fourier analysis. SIAM Journal on Scientific Computing (SISC), 28(5):1974-1999.

Rech, M; Sauter, S; Smolianski, A (2006). Two-scale composite finite element method for Dirichlet problems on complicated domains. Numerische Mathematik, 102(4):681-708.


Börm, S; Sauter, S (2005). BEM with linear complexity for the classical boundary integral operators. Mathematics of Computation, 74(251):1139-1177 (electronic).

Elliptic and parabolic problems. Edited by: Bandle, C; Berestycki, H; Brighi, B; Brillard, A; Chipot, M; Coron, J-M; Sbordone, C; Shafrir, I; Valente, V (2005). Basel: Birkhäuser Verlag.

Graham, I; Hackbusch, W; Sauter, S (2005). Finite elements on degenerate meshes: inverse-type inequalities and applications. IMA Journal of Numerical Analysis, 25(2):379-407.


Repin, S; Sauter, S; Smolianski, A (2004). A posteriori error estimation for the Poisson equation with mixed Dirichlet/Neumann boundary conditions. Journal of Computational and Applied Mathematics, 164/16:601-612.

Carstensen, C; Sauter, S (2004). A posteriori error analysis for elliptic PDEs on domains with complicated structures. Numerische Mathematik, 96(4):691-721.

Repin, S; Sauter, S; Smolianski, A (2004). A posteriori estimation of dimension reduction errors. In: Feistauer, M. Numerical mathematics and advanced applications. Berlin: Springer, 716-725.

Repin, S; Sauter, S; Smolianski, A (2004). A posteriori estimation of dimension reduction errors for elliptic problems on thin domains. SIAM Journal on Numerical Analysis, 42(4):1435-1451.

Babuska, I; Sauter, S (2004). Algebraic algorithms for the analysis of mechanical trusses. Mathematics of Computation, 73(248):1601-1622 (electronic).

Dahmen, W; Faermann, B; Graham, I; Hackbusch, W; Sauter, S (2004). Inverse inequalities on non-quasi-uniform meshes and application to the mortar element method. Mathematics of Computation, 73(247):1107-1138 (electronic).

Chipot, M; Hastings, S; Kinderlehrer, D (2004). Transport in a molecular motor system. M2AN. Mathematical Modelling and Numerical Analysis, 38(6):1011-1034.


Repin, S; Sauter, S; Smolianski, A (2003). A posteriori error estimation for the Dirichlet problem with account of the error in the approximation of boundary conditions. Computing, 70(3):205-233.

Paolella, Marc (2003). Computing moments of ratios of quadratic forms in normal variables. Computational Statistics & Data Analysis, 42(3):313-331.

Krzebek, N; Sauter, S (2003). Fast cluster techniques for BEM. Engineering Analysis with Boundary Elements, 27(5):455-467.


De Lellis, C (2002). An example in the gradient theory of phase transitions. ESAIM: Control, Optimisation and Calculus of Variations, 7:285-289 (electronic).


Kappeler, T; Mityagin, B (2001). Estimates for periodic and Dirichlet eigenvalues of the Schrödinger operator. SIAM Journal on Mathematical Analysis, 33(1):113-152.

Chipot, M; March, R; Vitulano, D (2001). Numerical analysis of oscillations in a nonconvex problem related to image selective smoothing. Journal of Computational and Applied Mathematics, 136(1-2):123-133.

Sauter, S; Lage, C (2001). Transformation of hypersingular integrals and black-box cubature. Mathematics of Computation, 70(233):223-250 (electronic).


Graham, I; Hackbusch, W; Sauter, S (2000). Discrete boundary element methods on general meshes in 3D. Numerische Mathematik, 86(1):103-137.

Graham, I; Hackbusch, W; Sauter, S (2000). Hybrid Galerkin boundary elements: theory and implementation. Numerische Mathematik, 86(1):139-172.

Sauter, S (2000). Variable order panel clustering. Computing, 64(3):223-261.


Sauter, S; Warnke, R (1999). Extension operators and approximation on domains containing small geometric details. East-West Journal of Numerical Mathematics, 7(1):61-77.

Chipot, M (1999). The appearance of microstructures in problems with incompatible wells and their numerical approach. Numerische Mathematik, 83(3):325-352.


Brighi, B; Chipot, M (1998). Approximation of infima in the calculus of variations. Journal of Computational and Applied Mathematics, 98(2):273-287.

Brighi, B; Chipot, M; Gut, E (1998). Finite differences on triangular grids. Numerical Methods for Partial Differential Equations, 14(5):567-579.


Hackbusch, W; Sauter, S (1997). Composite finite elements for the approximation of PDEs on domains with complicated micro-structures. Numerische Mathematik, 75(4):447-472.

Babuska, I; Sauter, S (1997). Is the pollution effect of the FEM avoidable for the Helmholtz equation considering high wave numbers? SIAM Journal on Numerical Analysis, 34(6):2392-2423.

Sauter, S; Schwab, C (1997). Quadrature for hp-Galerkin BEM in lR3. Numerische Mathematik, 78(2):211-258.


Sauter, S; Krapp, A (1996). On the effect of numerical integration in the Galerkin boundary element method. Numerische Mathematik, 74(3):337-359.

André, N; Chipot, M (1996). Uniqueness and nonuniqueness for the approximation of quasilinear elliptic equations. SIAM Journal on Numerical Analysis, 33(5):1981-1994.


Chipot, M; Collins, C; Kinderlehrer, D (1995). Numerical analysis of oscillations in multiple well problems. Numerische Mathematik, 70(3):259-282.


Weber, H (1994). A multigrid method for a Petrov-Galerkin discretization of the Stokes equations. Numerische Mathematik, 66(4):525-541.

Brighi, B; Chipot, M (1994). Approximated convex envelope of a function. SIAM Journal on Numerical Analysis, 31(1):128-148.

Hackbusch, W; Sauter, S (1994). On numerical cubatures of nearly singular surface integrals arising in BEM collocation. Computing, 52(2):139-159.


Yang, H (1993). Conjugate gradient methods for the Rayleigh quotient minimization of generalized eigenvalue problems. Computing, 51(1):79-94.


Heusser, C (1992). Conjugate gradient-type algorithms for a finite-element discretization of the Stokes equations. Journal of Computational and Applied Mathematics, 39(1):23-37.

Chipot, M; Collins, C (1992). Numerical approximations in variational problems with potential wells. SIAM Journal on Numerical Analysis, 29(4):1002-1019.


Verfürth, R (1991). A posteriori error estimators for the Stokes equations II non-conforming discretizations. Numerische Mathematik, 60(2):235-249.

Verfürth, R (1991). Finite element approximation of incompressible Navier-Stokes equations with slip boundary condition II. Numerische Mathematik, 59(6):615-636.

Chipot, M (1991). Numerical analysis of oscillations in nonconvex problems. Numerische Mathematik, 59(8):747-767.

Sauter, S (1991). The ILU method for finite-element discretizations. Journal of Computational and Applied Mathematics, 36(1):91-106.


Braess, D; Verfürth, R (1990). Multigrid methods for nonconforming finite element methods. SIAM Journal on Numerical Analysis, 27(4):979-986.


Verfürth, R (1989). A posteriori error estimators for the Stokes equations. Numerische Mathematik, 55(3):309-325.

This list was generated on Fri Jul 10 01:27:56 2020 CEST.