Selected Publications


Refereed Journal Articles

M. Bollhöfer, O. Schenk, F. Verbosio
High Performance Block Incomplete LU Factorization
Applied Numerical Mathematics, Volume 162, April 2021, Pages 265-2021,
A. Eftekhari, D. Pasadakis, S. Scheidegger, M. Bollhöfer, O. Schenk
Block-Enhanced Precision Matrix Estimation for Large-Scale Datasets
Journal of Computational Science, Volume 53, July 2021, Pages 1-39,


Refereed Journal Articles

A. Buetti-Dinh, M. Herold, S. Christel, M.E. Hajjami, S. Bellenberg, O. Ilie, P. Wilmes, A. Poetsch, W. Sand, M. Vera, I.V. Pivkin, M. Dopson
Systems biology of acidophile biofilms for efficient metal extraction
Scientific Data, 2020
S. Bellenberg , A. Buetti-Dinh, V. Galli, O. Ilie, M. Herold, S. Christel, M. Boretska, I.V. Pivkin, P. Wilmes, W. Sand, M. Vera, M. Dopson
Automated microscopic analysis of metal sulfide colonization by acidophilic microorganisms
Applied and Environmental Microbiology, 6-86, 2020
A. Buetti-Dinh, M. Herold, S. Christel , M.E.Hajjami, F. Delogu, O. Ilie, S. Bellenberg, P. Wilmes, A. Poetsch, W. Sand, M. Vera, I.V. Pivkin, R. Friedman, M. Dopson
Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations
BMC Bioinformatics, 1-21, 2020
I. Horenko, G. Marchenko, P. Gagliardini
On a computationally-scalable sparse formulation of the multidimensional and non-stationary maximum entropy principle
Communications in Applied Mathematics and Computational Science, Volume 15, Number 2, Pages 1-38, 2020
I. Horenko, D. Rodrigues, T. O'Kane, K. Everschor-Sitte
Physically-inspired computational tools for sharp detection of material inhomogeneities in magnetic imaging
I. Horenko
On a scalable entropic breaching of the overfitting barrier in machine learning
Neural Computation, Volume 32, Number 8, pages 1563-1579, 2020
S. Gerber, L. Pospisil, M. Navandar, I. Horenko
Low-cost scalable discretization, prediction and feature selection for complex systems.
Science Advances, Volume 6, Number 5, eaaw0961, 2020 DOI: 10.1126/sciadv.aaw0961
R. Užupytė, E. C. Wit
Test for triadic closure and triadic protection in temporal relational event data
Social Network Analysis and Mining, 1-21(10), 2020
V. Vinciotti, E. C. Wit
Statistica Neerlandica special issue on Statistical Network Science
Statistica Neerlandica, 74(3), 220-221, 2020.
F. Richter, B. Haegeman, R. S. Etienne, E. C. Wit
Introducing a general class of species diversification models for phylogenetic trees
Statistica Neerlandica, 74(3), 261-274, 2020
S. Ranciati., E.C. Wit, C. Viroli
Bayesian smooth-and-match inference for ordinary differential equations models linear in the parameters
Statistica Neerlandica, 74(3), 125-144, 2020
E. C. Wit, L. Augugliaro, H. Pazira, J. González, F. Abegaz
Sparse relative risk regression models
Biostatistics, 21(2), e131–e147, 2020
W. Kruijer, P. Behrouzi, D. Bustos-Korts, M. X. Rodríguez-Álvarez, S. M. Mahmoudi, B. Yandell, E. C. Wit, F. A. van Eeuwijk
Reconstruction of Networks with Direct and Indirect Genetic Effects
Genetics, 214(4), 781-807, 2020
M. Signorelli, E. C. Wit
Model-based clustering for populations of networks
Statistical Modelling, 20(1), 9-29, 2020
S. de Vos, S. Patten, E. C. Wit, E. H. Bos, K. J. Wardenaar, P. de Jonge
Subtyping psychological distress in the population: A semi-parametric network approach
Epidemiology and psychiatric sciences, 29, 1-8, 2020
S. N. Wood, E. C. Wit, M.Fasiolo, P. J. Green
COVID-19 and the difficulty of inferring epidemiological parameters from clinical data
Lancet Infectious Diseases, 2020
I. Artico, I. Smolyarenko, V. Vinciotti, E. C. Wit
How rare are power-law networks really?
Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 476(2241), 2020
P. Arbenz, L. Giraud, O. Schenk.W. Vanroose
Guest editorial: Special Issue on Parallel Matrix Algorithms and Applications (PMAA’18)
Parallel Computing, Volume 84, December 2020, Pages 1-2
P. Sanan. D. May, B. Bollhöfer, O. Schenk
Pragmatic Solvers for 3D Stokes and Elasticity Problems with Heterogeneous Coefficients: Evaluating Modern Incomplete LDLT Preconditioners
Solid Earth Discussions, 1-23, 2020,
A. Klawonn, M. Lanser, M. Uran, O. Rheinbach, S. Köhler, J. Schröder, L. Scheunemann, D. Brands, D. Balzani, A. Gandhi, G. Wellein, M. Wittmann, O. Schenk, R. Janalík
Towards A Virtual Laboratory - Computation of Forming Limit Curves
In: Bungartz HJ., Reiz S., Uekermann B., Neumann P., Nagel W. (eds) Software for Exascale Computing - SPPEXA 2016-2019. Lecture Notes in Computational Science and Engineering, vol 136. Springer, Cham,
J. van Niekerk, H. Bakka, H. Rue, and O. Schenk
New frontiers in Bayesian modeling using the INLA package in R
Journal of Statistical Software, accepted, in press.
J. Kardos, D. Kourounis, and O. Schenk
Two-Level Parallel Augmented Schur Complement Interior-Point Algorithms for the Solution of Security Constrained Optimal Power Flow Problems
IEEE Transactions on Power Systems, 1340 - 1350, Volume: 35 , Issue: 2 , March 2020,
C. Alappat, G. Hager, O. Schenk, J. Thies, A. Basermann, A. Bischop, H. Fehske, G. Wellein
A Recursive Algebraic Coloring Technique for Hardware-Efficient Symmetric Sparse Matrix-Vector Multiplication
ACM Transactions on Parallel Computing, Vol. 7, No. 3, Article 19, June 2020


Book Contributions

M. Bollhöfer, O. Schenk , R. Janalik, S. Hamm, and K. Gullapalli
State-of-The-Art Sparse Direct Solvers
In: Grama A., Sameh A. (eds) Parallel Algorithms in Computational Science and Engineering. Modeling and Simulation in Science, Engineering and Technology. pp 1-32, Birkhäuser, Cham.
J. Kardos, D. Kourounis, and O. Schenk
Parallel Structure Exploiting Interior Point Methods
In: Grama A., Sameh A. (eds) Parallel Algorithms in Computational Science and Engineering. Modeling and Simulation in Science, Engineering and Technology. pp 63-93, Birkhäuser, Cham.

Refereed Journal Articles

A. Buetti-Dinh, V. Galli, S. Bellenberg, O. Ilie, M. Herold, S. Christel, M. Boretska, I.V. Pivkin, P. Wilmes, W. Sand, M. Vera, M. Dopson
Deep neural networks outperform human expert's capacity in characterizing bioleaching bacterial biofilm composition
Biotechnology Reports, 2019
D. Pellin, L. Biasco, A. Aiuti, M.C. Di Serio, E.C. Wit
Penalized inference of the hematopoietic cell differentiation network via high-dimensional clonal tracking
Applied Network Science, 1-115, 2019
K. Kamphorst, B.C. Oosterloo, A.M. Vlieger, N.B. Rutten, C.M. Bunkers, E.C. Wit, R.M Van Elburg
Antibiotic Treatment in the First Week of Life Impacts the Growth Trajectory in the First Year of Life in Term Infants
Journal of Pediatric Gastroenterology and Nutrition, 131-136, 2019
A. Abbruzzo , I. Vujačić, A.M. Mineo, E.C. Wit
Selecting the tuning parameter in penalized Gaussian graphical models
Statistics and Computing, 559-569, 2019
P. Behrouzi, E.C. Wit
De novo construction of polyploid linkage maps using discrete graphical models
Bioinformatics, 1-3, 2019
N. Demetrashvili, N. Smidt, H. Snieder, E.R. Van Den Heuvel, E.C. Wit
Variance components models for analysis of big family data of health outcomes in the lifelines cohort study
Twin Research and Human Genetics, 1083-1093, 2019
E.C. Wit
Introduction to network inference in genomics
Network Science: An Aerial View, 99-119, 2019
R. Mohammadi, E.C. Wit
BDgraph: An R package for Bayesian structure learning in graphical models
Journal of Statistical Software, 1-2, 2019
S. E. Balafas, W. P. Krijnen, W. J. Post, E. C. Wit
An R Package for Nonparametric IRT Modelling of Unfolding Processes
The R Journal,
N. P. Gill, L. D’Arrigo, E. C Wit
Comparison of Postoperative Fever and Effectiveness of Percutaneous Nephrolithotomy (PCNL) Versus Retrograde Intrarenal Surgery (RIRS) for the Treatment of Renal Stones
SN Comprehensive Clinical Medicine, 1(3), 154-159.019, 2019
P. Behrouzi, E. C. Wit
Detecting epistatic selection with partially observed genotype data by using copula graphical models
Journal of the Royal Statistical Society. Series C: Applied Statistics, 68(1), 141-160, 2019
M. Rosenau, I. Horenko, F. Corbi, M. Rudolf, R. Kornhuber and O. Oncken
Synchronization of great subduction megathrust earthquakes: Insights from scale model analysis.
Journal of Geophysical Research: Solid Earth, 124(4):3646-3661, 2019
M. Bollhoefer, A. Eftekhari, S. Scheidegger, and O. Schenk
Large-Scale Sparse Inverse Covariance Matrix Estimation
SIAM J. Sci. Comput., 41(1), A380–A401, January 2019, DOI: