Publications from 2022

WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads In Proceedings

M.D. Patterson (Murray), T. Marschall (Tobias), N. Pisanti (Nadia), L.J.J. van Iersel (Leo), L. Stougie (Leen), G.W. Klau (Gunnar) and A. Schönhuth (Alexander)

Exact protein structure classification using the maximum contact map overlap metric In Proceedings

I. Wohlers (Inken), M. Le Boudic-Jamin (Mathilde), H. Djidjev (Hristo), G.W. Klau (Gunnar) and R. Andonov (Rumen)

NatalieQ: a web server for protein-protein interaction network querying Article

M. El-Kebir (Mohammed), B.W. Brandt (Bernd), J. Heringa (Jaap) and G.W. Klau (Gunnar)

eXamine: Exploring annotated modules in networks In Proceedings

K. Dinkla, M. El-Kebir (Mohammed), C.I. Bucur (Cristina-Iulia), M. Siderius, M.J. Smit, M.A. Westenberg and G.W. Klau (Gunnar)

Synergy of vacuolation and cell-cell repulsion in lumen formation Presentation

S.E.M. Boas (Sonja) and R.M.H. Merks (Roeland)

Tip cell overtaking arises spontaneously in computational models of angiogenic sprouting Presentation

S.E.M. Boas (Sonja) and R.M.H. Merks (Roeland)

Mechanical cell-ECM interactions amplifies response to substrate stretch and induces cell alignment Presentation

E.G. Rens (Lisanne) and R.M.H. Merks (Roeland)

Semidefinite Optimization Lecture

E. de Klerk (Etienne) and M. Laurent (Monique)

Functional module search in protein networks based on semantic similarity improves the analysis of proteomics data Article

D. Boyanova, S. Nilla, G.W. Klau (Gunnar), T. Dandekar, T. Müller (Tobias) and M. Dittrich (Marcus)

Kugelblitz in freier Wildbahn Article

U. Ebert (Ute)

Advanced 3-D Reconstruction Algorithms for Electron Tomography In Proceedings

T. Sanders, J.D. Roehling, K.J. Batenburg (Joost), B.C. Gates, A. Katz, P. Binev and I. Arslan

Discrete representation of local orientation in grains using diffraction contrast tomography In Proceedings

N.R. Viganò (Nicola), W. Ludwig (Wolfgang) and K.J. Batenburg (Joost)

Adaptive Grid Refinement for Discrete Tomography In Proceedings

T. van Leeuwen (Tristan) and K.J. Batenburg (Joost)

A compositional model to reason about end-to-end QoS in Stochastic Reo Connectors Article

Y.-J. Moon (Young-Joo), A.M. Silva (Alexandra), C. Krause (born Köhler) (Christian) and F. Arbab (Farhad)

Mechanisms for Hiring a Matroid Base Without Money In Proceedings

E. Pountourakis and G. Schäfer (Guido)

Orchestrating web services using Reo: from circuits and behaviors to automatically generated code Article

S.-S.T.Q. Jongmans (Sung), F. Santini (Francesco), M Sargolzaei, F. Arbab (Farhad) and H. Afsarmanesh

Partially-distributed coordination with Reo In Proceedings

S.-S.T.Q. Jongmans (Sung), F. Santini (Francesco) and F. Arbab (Farhad)

The Strong Price of Anarchy of Linear Bottleneck Congestion Games Article

B. de Keijzer (Bart), G. Schäfer (Guido) and O. Telelis (Orestis)

Automata-based optimization of interaction protocols for scalable multicore platforms In Proceedings

S.-S.T.Q. Jongmans (Sung), S. Halle and F. Arbab (Farhad)

3D imaging of semiconductor components by discrete laminography In Proceedings

K.J. Batenburg (Joost), W.J. Palenstijn (Willem Jan) and J. Sijbers (Jan)

Supervisory controller synthesis for safe software adaptation In Proceedings

N. Khakpour (Narges), F. Arbab (Farhad) and É. Rutten (Éric)

Toward sequentializing overparallelized protocol code In Proceedings

S.-S.T.Q. Jongmans (Sung) and F. Arbab (Farhad)

Efficient Cost-Sharing Mechanisms for Price-Collecting Problems Article

A. Gupta (Anupam), J. Könemann (Jochen), S. Leonardi (Stefano), R. Ravi and G. Schäfer (Guido)

High-level protocol engineering without performance penalty for multi-core Article

F. Arbab (Farhad), S.-S.T.Q. Jongmans (Sung) and F.S. de Boer (Frank)

Altruism and its impact on the price of anarchy Article

P. Chen (Po-An), B. de Keijzer (Bart), D. Kempe and G. Schäfer (Guido)

Adaptive zooming in X-ray computed tomography Article

A. Dabravolski (Andrei), K.J. Batenburg (Joost) and J. Sijbers (Jan)

Aligning Projection Images from Binary Volumes Article

F. Bleichrodt (Folkert), J. De Beenhouwer (Jan), J. Sijbers (Jan) and K.J. Batenburg (Joost)

Quality bounds for binary tomography with arbitrary projection matrices Article

W.R. Fortes (Wagner) and K.J. Batenburg (Joost)

Super-Resolution for Computed Tomography Based on Discrete Tomography Article

W. van Aarle (Wim), K.J. Batenburg (Joost), G. van Gompel (Gert), E. van de Casteele and J. Sijbers (Jan)

Dynamic angle selection in X-ray computed tomography Article

A. Dabravolski (Andrei), K.J. Batenburg (Joost) and J. Sijbers (Jan)

Scheduling over Scenarios on Two Machines Tech Report

E. Feuerstein, A. Marchetti Spaccamela (Alberto), F. Schalekamp (Frans), R.A. Sitters (René), S.L. van der Ster (Suzanne), L. Stougie (Leen) and A. van Zuylen (Anke)

A Multiresolution Approach to Discrete Tomography Using DART Article

A. Dabravolski (Andrei), K.J. Batenburg (Joost) and J. Sijbers (Jan)

Polynomial time approximation schemes for the traveling repairman and other minimum latency problems In Proceedings

R.A. Sitters (René)

The traveling salesman problem on cubic and subcubic graphs Article

S. Boyd, R.A. Sitters (René), S.L. van der Ster (Suzanne) and L. Stougie (Leen)

Material Profile Influences in Bulk-Heterojunctions Article

J.D. Roehling, C.W. Rochester, H.W. Ro, P. Wang (Pengfei), J. Majewski, K.J. Batenburg (Joost), I. Arslan, D.M. Delongchamp and A.J. Moulé

The Generalized Work Function Algorithm Is Competitive for the Generalized 2-Server Problem Article

R.A. Sitters (René)

Designing engines for data analysis Inaugural Lecture

P.A. Boncz (Peter)

The properties of SIRT, TVM, and DART for 3D imaging of tubular domains in nanocomposite thin-films and sections Article

D. Chen, B. Goris (Bart), F. Bleichrodt (Folkert), H.H. Mezerji, S. Bals (Sara), K.J. Batenburg (Joost), G. de With and H. Friedrich

Turing in Quantumland Book Chapter

H.M. Buhrman (Harry)

Improving Filtered Backprojection Reconstruction by Data-Dependent Filtering Article

D.M. Pelt (Daniël) and K.J. Batenburg (Joost)

The reconstructed residual error: a novel segmentation evaluation measure for reconstructed images in tomography Article

T. Roelandts (Tom), K.J. Batenburg (Joost), A.J. den Dekker and J. Sijbers (Jan)

Reductions to the set of random strings: The resource-bounded case Article

E. Allender, H.M. Buhrman (Harry), L. Friedman and B. S. Loff Barreto (Bruno Serra)

Region-Based Iterative Reconstruction of Structurally Changing Objects in CT Article

G. Van Eyndhoven (Geert), K.J. Batenburg (Joost) and J. Sijbers (Jan)

Position-Based Quantum Cryptography: Impossibility and Constructions Article

H.M. Buhrman (Harry), S. Chandran, S. Fehr (Serge), R. Gelles, V. Goyal, R. Ostrovsky and C. Schaffner (Christian)

Approximating algebraic tomography methods by filtered backprojection: a local filter approach Article

L. Plantagie (Linda) and K.J. Batenburg (Joost)

Object Redundancy Profiling in Java Presentation

M.J. Steindorfer (Michael)

Proceedings of the 4th Workshop on Linked Science 2014 - Making Sense Out of Data Proceedings

INVENiT: Exploring Cultural Heritage Collections While Adding Annotations In Proceedings

C. Dijkshoorn (Chris), J.R. van Ossenbruggen (Jacco), L. Aroyo (Lora) and T. Schreiber

Understanding fish behavior during typhoon events in real-life underwater environments Article

C. Spampinato (Concetto), S. Palazzo, B.J. Boom (Bas), J.R. van Ossenbruggen (Jacco), I. Kavasidis, R. Di Salvo, F.-P. Lin (Fang-Pang), D. Giordano (Daniela), L. Hardman (Lynda) and R.B. Fisher (Robert)

Editorial — Special issue on multimedia in ecology Article

C. Spampinato (Concetto), V Mezaris, B. Huet and J.R. van Ossenbruggen (Jacco)

Propagation of negative planar streamer fronts in noble gases In Proceedings

S. Dujko (Sasa), A. Markosyan (Aram) and U. Ebert (Ute)

PumpKin: A tool to find principal pathways in plasma chemical models Article

A. Markosyan (Aram), A. Luque (Alejandro), F.J. Gordillo-Vazquez (Francisco) and U. Ebert (Ute)

A time scale for electrical screening in pulsed gas discharges Article

H.J. Teunissen (Jannis), A.B. Sun (Anbang) and U. Ebert (Ute)

Impact of lightning on the lower ionosphere of Saturn and possible generation of halos and sprites Article

D. Dubrovin, A. Luque (Alejandro), F.J. Gordillo-Vazquez (Francisco), Y. Yair, F.C. Parra-Rojas, U. Ebert (Ute) and C. Price

The inception of pulsed discharges in air: simulations in background fields above and below breakdown Article

A.B. Sun (Anbang), H.J. Teunissen (Jannis) and U. Ebert (Ute)

3D particle simulation of positive streamer inception from a needle electrode in supercritical nitrogen Article

A.B. Sun (Anbang), H.J. Teunissen (Jannis) and U. Ebert (Ute)

Stroboscopic images of streamers through air and over dielectric surfaces Article

D.J.M. Trienekens (Dirk), S. Nijdam (Sander) and U. Ebert (Ute)

Propagation of a positive streamer towards a dielectric tip in pure nitrogen and in air Article

A. A. Dubinova (Anna), H.J. Teunissen (Jannis) and U. Ebert (Ute)

Streamer discharges can move perpendicularly to the electric field Article

S. Nijdam (Sander), E. Takahashi, H.J. Teunissen (Jannis) and U. Ebert (Ute)

Coupling between atmospheric layers in gaseous giant planets due to lightning-generated electromagnetic pulses Article

A. Luque (Alejandro), D. Dubrovin, F.J. Gordillo-Vazquez (Francisco), U. Ebert (Ute), F.C. Parra-Rojas, Y. Yair and C. Price

Driedimensionale visualisatie van atomen met discrete tomografie - 10 jaar NWD Magazine Article

K.J. Batenburg (Joost)

RealKrimp - Finding Hyperintervals that Compress with MDL for Real-Valued Data In Proceedings

J.E. Witteveen, W. Duijvestein, A.J. Knobbe (Arno) and P.D. Grünwald (Peter)

Neutral Vlasov kinetic theory of magnetized plasmas Tech Report

C. Tronci and E. Camporeale (Enrico)

Wave-particle interactions with parallel whistler waves: nonlinear and time-dependent effects revealed by Particle-in-Cell simulations Tech Report

E. Camporeale (Enrico) and G. Zimbardo

Resonant and non-resonant whistlers-particle interaction in the radiation belts Tech Report

E. Camporeale (Enrico)

Tracing the molecular basis of transcriptional dynamics in noisy data by using an experiment-based mathematical model Article

K.N. Rybakova, A. Tomaszewska, S. van Mourik (Simon), J.G. Blom (Joke), H.V. Westerhoff (Hans), C. Carlberg and F.J. Bruggeman (Frank)

'Geld is een bijverschijnsel' - Leeuwarder Courant Magazine Article

P. Beertema (Piet) and CWI CWI

A practical approximation algorithm for solving massive instances of hybridization number for binary and nonbinary trees Article

L.J.J. van Iersel (Leo), S.M. Kelk (Steven), N. Lekic (Nela) and C. Scornavacca

Approximation algorithms for nonbinary agreement forests Article

L.J.J. van Iersel (Leo), S.M. Kelk (Steven), N. Lekic (Nela) and L. Stougie (Leen)

Sterrenkundigen genomineerd voor Gordon Bell-prijs voor snelste computerberekeningen - Astroblogs Magazine Article

J. Bédorf (Jeroen)

Database Innovator Peter Boncz to Present on Expanded Actian Analytics Platform SQL-in-Hadoop Capabilities at Hadoop - Fort Mill Times Summit Magazine Article

P.A. Boncz (Peter)

Wiskundigen kijken kat uit de boom miljoenenclaim - de Volkskrant Magazine Article

B. Koren (Barry)

Online monitoring van bosbranden - Technisch Weekblad Magazine Article

S. Manegold (Stefan)

Software helpt bij redigeren video - Automatisering Gids Magazine Article

R.L. Guimarães (Rodrigo Laiola), P.S. César Garcia (Pablo Santiago) and D.C.A. Bulterman (Dick)

Kwantumcomputers: razendsnel rekenn op de kleinste deeltjes - Tweakers Magazine Article

H.M. Buhrman (Harry)

Navraag: Paul Klint - Folia Magazine Article

P. Klint (Paul)

CWI-software maakt persoonlijke video - Computable Magazine Article

R.L. Guimarães (Rodrigo Laiola), P.S. César Garcia (Pablo Santiago) and D.C.A. Bulterman (Dick)

Uncertainty-Aware Visualization of Fish Populations (Demo) Lecture

E.M.A.L. Beauxis-Aussalet (Emmanuelle) and L. Hardman (Lynda)

Bridging the Web and Digital Publishing Lecture

M. Gylling and I. Herman (Ivan)

Forbidden minor characterizations for low-rank optimal solutions to semidefinite programs over the elliptope Article

M. Eisenberg-Nagy (Marianna), M. Laurent (Monique) and A. Varvitsiotis (Antonios)

Optimization over polynomials: Selected topics In Proceedings

M. Laurent (Monique)

Optimization over polynomials: Selected topics Lecture

M. Laurent (Monique)

A medium-grain method for fast 2D bipartitioning of sparse matrices In Proceedings

D.M. Pelt (Daniël) and R.H. Bisseling (Rob)

Finding Lightweight Opportunities for Parallelism in .NET C# Master Thesis

R. Bos

How accurately do Java profilers predict runtime performance bottlenecks? Master Thesis

P. Klijn

Coupling as a trade-off in an Enterprise Service Bus Master Thesis

A. van der Veek

Static, Lightweight Includes Resolution for PHP In Proceedings

M.A. Hills (Mark), P. Klint (Paul) and J.J. Vinju (Jurgen)

3D Frequency-Domain Seismic Inversion with Controlled Sloppiness. Article

T. van Leeuwen (Tristan) and F.J. Herrmann (Felix)

Social networks with competing products Article

K.R. Apt (Krzysztof) and V. Markakis (Vangelis)

Selfishness level of strategic games Article

K.R. Apt (Krzysztof) and G. Schäfer (Guido)

Practice-Oriented Optimization of Distribution Network Planning Using Metaheuristic Algorithms In Proceedings

M.O.W. Grond, N.H. Luong (Hoang), J. Morren (Johan), P.A.N. Bosman (Peter), J.G. Slootweg (Han) and J.A. La Poutré (Han)

Efficiency enhancements for evolutionary capacity planning in distribution grids In Proceedings

N.H. Luong (Hoang), M.O.W. Grond, J.A. La Poutré (Han) and P.A.N. Bosman (Peter)

The influence of interactivity patterns on the Quality of Experience in multi-party video-mediated conversations under symmetric delay conditions In Proceedings

M.R. Schmitt (Marwin), S.N.B. Gunkel (Simon), P.S. César Garcia (Pablo Santiago) and D.C.A. Bulterman (Dick)

Secure Identification and QKD in the Bounded-Quantum-Storage Model Article

I.B. Damgård (Ivan), S. Fehr (Serge), L. Salvail (Louis) and C. Schaffner (Christian)

On the Conditional Rényi Entropy Article

S. Fehr (Serge) and S. Berens (Stefan)

Performing Arts and Technology: Toward Connected Shared Experiences Lecture

P.S. César Garcia (Pablo Santiago)

Interaction Design for Online Video and Television Lecture

D. Geerts (David) and P.S. César Garcia (Pablo Santiago)

Uniform Signaling for Timeline Alignment Standard

H.M. Stokking (Hans), E. Thomas, R. Koenen, A.J. Jansen (Jack) and P.S. César Garcia (Pablo Santiago)

Interacting with third-party content: is a second screen enough? In Proceedings

D.C.A. Bulterman (Dick)

Interacting with Third-Party Content: Is a Secondary Screen Enough Lecture

D.C.A. Bulterman (Dick)