View Scopus Subject Areas

2025

Abgrall, Remi; Barsukow, Wasilij; Klingenberg, Christian (2025). A Semi-discrete Active Flux Method for the Euler Equations on Cartesian Grids. Journal of Scientific Computing, 102(2):36.

2024

Melenk, J M; Sauter, Stefan A (2024). Wavenumber-Explicit hp-FEM Analysis for Maxwell’s Equations with Impedance Boundary Conditions. Foundations of Computational Mathematics, 24(6):1871-1939.

Gerbaldo, Felix Ezequiel; Sonder, Emanuel; Fischer, Vincent; Frei, Selina; Wang, Jiayi; Gapp, Katharina; Robinson, Mark D; Germain, Pierre-Luc (2024). On the identification of differentially-active transcription factors from ATAC-seq data. PLoS Computational Biology, 20(10):e1011971.

Micalizzi, Lorenzo; Ricchiuto, Mario; Abgrall, Remi (2024). Novel Well-Balanced Continuous Interior Penalty Stabilizations. Journal of Scientific Computing, 100(1):14.

Immer, Alexander; Stark, Stefan G; Jacob, Francis; Bonilla, Ximena; Thomas, Tinu; Kahles, André; Goetze, Sandra; Milani, Emanuela S; Wollscheid, Bernd; Aebersold, Rudolf; Ak, Melike; Al-Quaddoomi, Faisal S; Albert, Silvana I; Albinus, Jonas; Alborelli, Ilaria; Andani, Sonali; Attinger, Per-Olof; Bacac, Marina; Baumhoer, Daniel; Beck-Schimmer, Beatrice; Beerenwinkel, Niko; Beisel, Christian; Bernasconi, Lara; Bertolini, Anne; Bodenmiller, Bernd; Bonilla, Ximena; Bosshard, Lars; Calgua, Byron; Casanova, Ruben; et al; Pelkmans, Lucas (2024). Probabilistic pathway-based multimodal factor analysis. Bioinformatics, 40(Suppl 1):i189-i198.

Rigoux, Lionel; Stephan, Klaas E; Petzschner, Frederike H (2024). Beliefs, compulsive behavior and reduced confidence in control. PLoS Computational Biology, 20(6):e1012207.

Guazzini, Marco; Reisach, Alexander G; Weichwald, Sebastian; Seiler, Christof (2024). spillR: spillover compensation in mass cytometry data. Bioinformatics, 40(6):btae337.

Robinson, Mark D; Cai, Peiying; Emons, Martin; Gerber, Reto; Germain, Pierre-Luc; Gunz, Samuel; Luo, Siyuan; Moro, Giulia; Sonder, Emanuel; Sonrel, Anthony; Wang, Jiayi; Wissel, David; Mallona, Izaskun (2024). Ten simple rules for computational biologists collaborating with wet lab researchers. PLoS Computational Biology, 20(6):e1012174.

Narayanan, Manu; Aepli, Noëmi (2024). A Tulu Resource for Machine Translation. In: Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024), Turin, 20 May 2024 - 25 May 2024, 1756-1767.

Reich, David Robert; Deng, Shuwen; Björnsdóttir, Marina; Jäger, Lena A; Hollenstein, Nora (2024). Reading Does Not Equal Reading: Comparing, Simulating and Exploiting Reading Behavior Across Populations. In: Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024), Torino, 20 May 2024 - 25 May 2024.

Phaniraj, Nikhil; Brügger, Rahel K; Burkart, Judith M (2024). Marmosets mutually compensate for differences in rhythms when coordinating vigilance. PLoS Computational Biology, 20(5):e1012104.

Sovrano, Francesco; Ashley, Kevin; Brusilovsky, Peter Leonid; Vitali, Fabio (2024). How to Improve the Explanatory Power of an Intelligent Textbook: a Case Study in Legal Writing. International Journal of Artificial Intelligence in Education:online.

Holfeld, Aleš; Schuster, Dina; Sesterhenn, Fabian; Gillingham, Alison K; Stalder, Patrick; Haenseler, Walther; Barrio-Hernandez, Inigo; Ghosh, Dhiman; Vowles, Jane; Cowley, Sally A; Nagel, Luise; Khanppnavar, Basavraj; Serdiuk, Tetiana; Beltrao, Pedro; Korkhov, Volodymyr M; Munro, Sean; Riek, Roland; de Souza, Natalie; Picotti, Paola (2024). Systematic identification of structure-specific protein–protein interactions. Molecular Systems Biology, 20(6):651-675.

Wagner, Andreas (2024). Genotype sampling for deep-learning assisted experimental mapping of a combinatorially complete fitness landscape. Bioinformatics, 40(5):btae317.

Fidon, Lucas; Aertsen, Michael; Kofler, Florian; Bink, Andrea; David, Anna L; Deprest, Thomas; Emam, Doaa; Guffens, Frédéric; Jakab, András; Kasprian, Gregor; Kienast, Patric; Melbourne, Andrew; Menze, Bjoern; Mufti, Nada; Pogledic, Ivana; Prayer, Daniela; Stuempflen, Marlene; Van Elslander, Esther; Ourselin, Sébastien; Deprest, Jan; Vercauteren, Tom (2024). A Dempster-Shafer Approach to Trustworthy AI With Application to Fetal Brain MRI Segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence, 46(5):3784-3795.

Gnehm, Ann-Sophie; Clematide, Simon (2024). Mapping Work Task Descriptions from German Job Ads on the O*NET Work Activities Ontology. In: Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024), Torino, Italy, May 2024. ELRA and ICCL, 11049-11059.

Chodroff, Eleanor; Pažon, Blaž; Baker, Annie; Moran, Steven (2024). Phonetic Segmentation of the UCLA Phonetics Lab Archive. In: Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024), Torino, Italy, May 2024. ELRA and ICCL, 12724-12733.

Jiang, Zifan; Göhring, Anne; Moryossef, Amit; Sennrich, Rico; Ebling, Sarah (2024). SwissSLi: The Multi-parallel Sign Language Corpus for Switzerland. In: Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024), Turin, 20 May 2024 - 25 May 2024. ELRA and ICCL, 15448-15456.

Battisti, Alessia; Ebling, Sarah (2024). Automatic Annotation Elaboration as Feedback to Sign Language Learners. In: The 18th Linguistic Annotation Workshop (LAW-XVIII), St. Julian's, Malta, 22 March 2024.

Vamvas, Jannis; Aepli, Noëmi; Sennrich, Rico (2024). Modular Adaptation of Multilingual Encoders to Written Swiss German Dialect. In: Proceedings of the 1st Workshop on Modular and Open Multilingual NLP (MOOMIN 2024), St Julians, Malta, March 2024. Association for Computational Linguistics, 16-23.

Fromont, Lauren A; Moldes, Mauricio; Baudis, Michael; Brookes, Anthony J; Navarro, Arcadi; Rambla, Jordi (2024). Twelve quick tips for deploying a Beacon. PLoS Computational Biology, 20(3):e1011817.

Balázs, Zsolt; Gitchev, Todor; Ivanković, Ivna; Krauthammer, Michael (2024). Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis. Bioinformatics, 40(1):btae017.

Gubelmann, Reto (2024). Pragmatic norms are all you need – why the symbol grounding problem does not apply to LLMs. In: Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing, Miami, Florida, USA, 1 November 2024, 11663-11678.

Gehrig, Mathias; Muglikar, Manasi; Scaramuzza, Davide (2024). Dense Continuous-Time Optical Flow from Event Cameras. IEEE Transactions on Pattern Analysis and Machine Intelligence:1-12.

2023

Ni, Jingwei; Bingler, Julia; Colesanti Senni, Chiara; Kraus, Mathias; Gostlow, Glen; Schimanski, Tobias; Stammbach, Dominik; Ashraf Vaghefi, Saeid; Wang, Qian; Webersinke, Nicolas; Wekhof, Tobias; Yu, Tingyu; Leippold, Markus (2023). CHATREPORT: Democratizing Sustainability Disclosure Analysis through LLM-based Tools. In: The 2023 Conference on Empirical Methods in Natural Language Processing, Singapore, Singapore, 6 December 2023 - 10 December 2023. Association for Computational Linguistics, 21-51.

Schimanski, Tobias; Bingler, Julia; Kraus, Mathias; Hyslop, Camilla; Leippold, Markus (2023). ClimateBERT-NetZero: Detecting and Assessing Net Zero and Reduction Targets. In: The 2023 Conference on Empirical Methods in Natural Language Processing, Singapore, Singapore, 6 December 2023 - 10 December 2023. Association for Computational Linguistics, 15745-15756.

Rodríguez, Andrés C; D’Aronco, Stefano; Schindler, Konrad; Wegner, Jan Dirk (2023). Fine-Grained Species Recognition With Privileged Pooling: Better Sample Efficiency Through Supervised Attention. IEEE Transactions on Pattern Analysis and Machine Intelligence, 45(12):14575-14589.

Sauter, Stefan (2023). The inf-sup constant for hp-Crouzeix-Raviart triangular elements. Computers & Mathematics with Applications, 149:49-70.

Epp, Robert; Glück, Chaim; Binder, Nadine Felizitas; El Amki, Mohamad; Weber, Bruno; Wegener, Susanne; Jenny, Patrick; Schmid, Franca (2023). The role of leptomeningeal collaterals in redistributing blood flow during stroke. PLoS Computational Biology, 19(10):e1011496.

Rocchini, Duccio; Nowosad, Jakub; D’Introno, Rossella; Chieffallo, Ludovico; Bacaro, Giovanni; Gatti, Roberto Cazzolla; Foody, Giles M; Furrer, Reinhard; Gábor, Lukáš; Malavasi, Marco; Marcantonio, Matteo; Marchetto, Elisa; Moudrý, Vítězslav; Ricotta, Carlo; Šímová, Petra; Torresani, Michele; Thouverai, Elisa (2023). Scientific maps should reach everyone: The cblindplot R package to let colour blind people visualise spatial patterns. Ecological Informatics, 76:102045.

Gontier, Camille; Surace, Simone Carlo; Delvendahl, Igor; Müller, Martin; Pfister, Jean-Pascal (2023). Efficient sampling-based Bayesian Active Learning for synaptic characterization. PLoS Computational Biology, 19(8):e1011342.

Nassajian Mojarrad, Fatemeh; Han Veiga, Maria; Hesthaven, Jan S; Öffner, Philipp (2023). A new variable shape parameter strategy for RBF approximation using neural networks. Computers & Mathematics with Applications, 143:151-168.

Vargas-Rosales, Pablo Andrés; D'Addio, Alessio; Zhang, Yang; Caflisch, Amedeo (2023). Disrupting Dimeric β-Amyloid by Electric Fields. ACS Physical Chemistry Au, 3(5):456-466.

Adde, Antoine; Rey, Pierre-Louis; Fopp, Fabian; Petitpierre, Blaise; Schweiger, Anna K; Broennimann, Olivier; Lehmann, Anthony; Zimmermann, Niklaus E; Altermatt, Florian; Pellissier, Loïc; Guisan, Antoine (2023). Too many candidates: Embedded covariate selection procedure for species distribution modelling with the covsel R package. Ecological Informatics, 75:102080.

Zhang, Kunyang; Fenner, Kathrin (2023). enviRule: an end-to-end system for automatic extraction of reaction patterns from environmental contaminant biotransformation pathways. Bioinformatics, 39(7):btad407.

Goldzycher, Janis (2023). CL-UZH at SemEval-2023 Task 10: Sexism Detection through Incremental Fine-Tuning and Multi-Task Learning with Label Descriptions. In: Proceedings of the 17th International Workshop on Semantic Evaluation (SemEval-2023), Toronto, Canada, 13 July 2023 - 14 July 2023. Association for Computational Linguistics, 1562-1572.

Michail, Andrianos; Konstantinou, Stefanos; Clematide, Simon (2023). UZH_CLyp at SemEval-2023 Task 9: Head-First Fine-Tuning and ChatGPT Data Generation for Cross-Lingual Learning in Tweet Intimacy Prediction. In: Proceedings of the 17th International Workshop on Semantic Evaluation (SemEval-2023), Toronto, Canada, 13 July 2023 - 14 July 2023. Association for Computational Linguistics, 1021-1029.

De Sterck, Hans; Shu, Chi-Wang; Abgrall, Remi (2023). Correction to: Enhancing Reproducibility of Research Papers in SISC, JSC and JCP. Journal of Scientific Computing, 95(3):86.

De Sterck, Hans; Shu, Chi-Wang; Abgrall, Remi (2023). Enhancing Reproducibility of Research Papers in SISC, JSC and JCP. Journal of Scientific Computing, 95(3):77.

Han, Chao; English, Gwendolyn; Saal, Hannes P; Indiveri, Giacomo; Gilra, Aditya; von der Behrens, Wolfger; Vasilaki, Eleni (2023). Modelling novelty detection in the thalamocortical loop. PLoS Computational Biology, 19(5):e1009616.

Zhang, Biao; Haddow, Barry; Sennrich, Rico (2023). Efficient CTC Regularization via Coarse Labels for End-to-End Speech Translation. In: Proceedings of the 17th Conference of the European Chapter of the Association for Computational Linguistics, Dubrovnik, Croatia, 2 May 2023 - 6 May 2023. Association for Computational Linguistics, 2264-2276.

Jiang, Zifan; Moryossef, Amit; Müller, Mathias; Ebling, Sarah (2023). Machine Translation between Spoken Languages and Signed Languages Represented in SignWriting. In: Findings of the Association for Computational Linguistics: EACL 2023, Dubrovnik, Croatia, May 2023. Association for Computational Linguistics, 1706-1724.

Winata, Genta Indra; Aji, Alham Fikri; Cahyawijaya, Samuel; Mahendra, Rahmad; Koto, Fajri; Romadhony, Ade; Kurniawan, Kemal; Moeljadi, David; Prasojo, Radityo Eko; Fung, Pascale; Baldwin, Timothy; Lau, Jey Han; Sennrich, Rico; Ruder, Sebastian (2023). NusaX: Multilingual Parallel Sentiment Dataset for 10 Indonesian Local Languages. In: Proceedings of the 17th Conference of the European Chapter of the Association for Computational Linguistics, Dubrovnik, Croatia, 2 May 2023 - 6 May 2023. Association for Computational Linguistics, 815-834.

Stawarczyk, Bogna; Roos, Malgorzata (2023). Establishing effective cross-disciplinary collaboration: Combining simple rules for reproducible computational research, a good data management plan, and good research practice. PLoS Computational Biology, 19(4):e1011052.

Michel, Sixtine; Torlo, Davide; Ricchiuto, Mario; Abgrall, Remi (2023). Spectral Analysis of High Order Continuous FEM for Hyperbolic PDEs on Triangular Meshes: Influence of Approximation, Stabilization, and Time-Stepping. Journal of Scientific Computing, 94(3):49.

Rügamer, David; Baumann, Philipp F M; Kneib, Thomas; Hothorn, Torsten (2023). Probabilistic time series forecasts with autoregressive transformation models. Statistics and Computing, 33:37.

Reveilhac, Maud; Morselli, Davide (2023). Integrating surveys and social media to better understand the dynamics of public opinion. Computational Communication Research, 5(1):1.

Niklaus, Joel; Matoshi, Veton; Rani, Pooja; Galassi, Andrea; Stürmer, Matthias; Chalkidis, Ilias (2023). LEXTREME: A Multi-Lingual and Multi-Task Benchmark for the Legal Domain. In: The 2023 Conference on Empirical Methods in Natural Language Processing, Singapore, Singapore, 6 December 2023 - 10 December 2023. Association for Computational Linguistics, 3016-3054.

Rohanian, Morteza; Nooralahzadeh, Farhad; Rohanian, Omid; Clifton, David; Krauthammer, Michael (2023). Disfluent Cues for Enhanced Speech Understanding in Large Language Models. In: Empirical Methods in Natural Language Processing (EMNLP), Singapore, 2023, 3676-3684.

2022

Leippold, Markus; Hershcovich, Daniel; Bingler, Julia Anna; Kraus, Mathias; Webersinke, Nicolas (2022). Towards Climate Awareness in NLP Research. In: Empirical Methods in Natural Language Processing (EMNLP), Abu Dhabi, 7 December 2022 - 11 December 2022. Association for Computational Linguistics, 2480-2494.

Hu, Xiaobin; Ren, Wenqi; Yang, Jiaolong; Cao, Xiaochun; Wipf, David P; Menze, Bjoern; Tong, Xin; Zha, Hongbin (2022). Face Restoration via Plug-and-Play 3D Facial Priors. IEEE Transactions on Pattern Analysis and Machine Intelligence, 44(12):8910-8926.

Katircioglu, Isinsu; Rhodin, Helge; Constantin, Victor; Spörri, Jörg; Salzmann, Mathieu; Fua, Pascal (2022). Self-supervised Human Detection and Segmentation via Background Inpainting. IEEE Transactions on Pattern Analysis and Machine Intelligence, 44(12):9574-9588.

Hartmann, Maximilian C; Schott, Moritz; Dsouza, Alishiba; Metz, Yannick; Volpi, Michele; Purves, Ross S (2022). A text and image analysis workflow using citizen science data to extract relevant social media records: Combining red kite observations from Flickr, eBird and iNaturalist. Ecological Informatics, 71:101782.

Kerstjens, Stan; Michel, Gabriela; Douglas, Rodney J (2022). Constructive connectomics: How neuronal axons get from here to there using gene-expression maps derived from their family trees. PLoS Computational Biology, 18(8):e1010382.

Batzilla, Alina; Lu, Junyan; Kivioja, Jarno; Putzker, Kerstin; Lewis, Joe; Zenz, Thorsten; Huber, Wolfgang (2022). Inferring tumor-specific cancer dependencies through integrating ex vivo drug response assays and drug-protein profiling. PLoS Computational Biology, 18(8):e1010438.

Fan, Bowen; Klatt, Juliane; Moor, Michael M; Daniels, Latasha A; Swiss Pediatric Sepsis Study; Sanchez-Pinto, Lazaro N; Agyeman, Philipp K A; Schlapbach, Luregn J; Borgwardt, Karsten M (2022). Prediction of recovery from multiple organ dysfunction syndrome in pediatric sepsis patients. Bioinformatics, 38(Suppl 1):i101-i108.

Bertolini, Anne; Prummer, Michael; Tuncel, M A; Menzel, Ulrike; Rosano-González, María Lourdes; Kuipers, Jack; Stekhoven, Daniel Johannes; Tumor Profiler consortium; Beerenwinkel, Niko; Singer, Franziska (2022). scAmpi—A versatile pipeline for single-cell RNA-seq analysis from basics to clinics. PLoS Computational Biology, 18(6):e1010097.

Hediger, Simon; Michel, Loris; Näf, Jeffrey (2022). On the use of random forest for two-sample testing. Computational Statistics & Data Analysis, 170:107435.

Schwab, Simon; Janiaud, Perrine; Dayan, Michael; Amrhein, Valentin; Panczak, Radoslaw; Palagi, Patricia M; Hemkens, Lars G; Ramon, Meike; Rothen, Nicolas; Senn, Stephen; Furrer, Eva; Held, Leonhard (2022). Ten simple rules for good research practice. PLoS Computational Biology, 18(6):e1010139.

Righelli, Dario; Weber, Lukas M; Crowell, Helena L; Pardo, Brenda; Collado-Torres, Leonardo; Ghazanfar, Shila; Lun, Aaron T L; Hicks, Stephanie C; Risso, Davide (2022). SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor. Bioinformatics, 38(11):3128-3131.

Kew, Tannon; Volk, Martin (2022). Improving Specificity in Review Response Generation with Data-Driven Data Filtering. In: Proceedings of the Fifth Workshop on e-Commerce and NLP (ECNLP 5), Dublin, Ireland, 26 May 2022, Association for Computational Linguistics.

Soutschek, Michael; Gross, Fridolin; Schratt, Gerhard; Germain, Pierre-Luc (2022). scanMiR: a biochemically based toolkit for versatile and efficient microRNA target prediction. Bioinformatics, 38(9):2466-2473.

Munglani, Gautam; Vogler, Hannes; Grossniklaus, Ueli (2022). Fast and flexible processing of large FRET image stacks using the FRET-IBRA toolkit. PLoS Computational Biology, 18(4):1009242.

Cheng, Rongshan; Wang, Huizhi; Dimitriou, Dimitris; Jiang, Ziang; Cheng, Cheng-Kung; Tsai, Tsung-Yuan (2022). Central femoral tunnel placement can reduce stress and strain around bone tunnels and graft more than anteromedial femoral tunnel in anterior cruciate ligament reconstruction. International Journal for Numerical Methods in Biomedical Engineering, 38(5):e3590.

Carstensen, C; Sauter, Stefan (2022). Critical functions and inf-sup stability of Crouzeix-Raviart elements. Computers & Mathematics with Applications, 108:12-23.

Bacigaluppi, Paola; Carlier, Julien; Pelanti, Marica; Congedo, Pietro Marco; Abgrall, Remi (2022). Assessment of a non-conservative four-equation multiphase system with phase transition. Journal of Scientific Computing, 90(1):28.

Li, Chunchun; Günther, Manuel; Dhamija, Akshay Raj; Cruz, Steve; Jafarzadeh, Mohsen; Ahmad, Touqeer; Boult, Terrance E (2022). Agglomerative Clustering with Threshold Optimization via Extreme Value Theory. Algorithms, 15(5):170.

2021

Michel, Sixtine; Torlo, Davide; Ricchiuto, Mario; Abgrall, Remi (2021). Spectral analysis of continuous FEM for hyperbolic PDEs: Influence of approximation, stabilization, and time-stepping. Journal of Scientific Computing, 89(2):31.

López Bernal, Sergio; Perez Martins, Daniel; Huertas Celdran, Alberto (2021). Towards the mitigation of distributed denial-of-service cyberbioattacks in bacteria-based biosensing systems. Digital Signal Processing, 118:46498.

Balakrishna, Suraj; Salazar-Vizcaya, Luisa; Schmidt, Axel J; Kachalov, Viacheslav; Kusejko, Katharina; Thurnheer, Maria Christine; Roth, Jan A; Nicca, Dunja; Cavassini, Matthias; Battegay, Manuel; Schmid, Patrick; Bernasconi, Enos; Günthard, Huldrych F; Rauch, Andri; Kouyos, Roger D; Swiss HIV Cohort Study (2021). Assessing the drivers of syphilis among men who have sex with men in Switzerland reveals a key impact of screening frequency: A modelling study. PLoS Computational Biology, 17(10):e1009529.

Posada-Céspedes, Susana; Van Zyl, Gert; Montazeri, Hesam; Kuipers, Jack; Rhee, Soo-Yon; Kouyos, Roger; Günthard, Huldrych F; Beerenwinkel, Niko (2021). Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C. PLoS Computational Biology, 17(9):e1008363.

Wang, Craig; Furrer, Reinhard (2021). Combining heterogeneous spatial datasets with process-based spatial fusion models: A unifying framework. Computational Statistics & Data Analysis, 161:107240.

Sinisi, S; Alimguzhin, V; Mancini, T; Tronci, E; Leeners, B (2021). Complete populations of virtual patients for in silico clinical trials. Oxford University Studies in the Enlightenment, 36(22-23):5465-5472.

Miraki, Mojdeh; Sohrabi, Hormoz; Fatehi, Parviz; Kneubühler, Mathias (2021). Individual tree crown delineation from high-resolution UAV images in broadleaf forest. Ecological Informatics, 61:101207.

Glaubitz, Jan; Le Mélédo, Elise; Öffner, Philipp (2021). Towards stable radial basis function methods for linear advection problems. Computers & Mathematics with Applications, 85:84-97.

Han Veiga, Maria; Öffner, Philipp; Torlo, Davide (2021). DeC and ADER: Similarities, Differences and a Unified Framework. Journal of Scientific Computing, 87(2):2.

Tepekule, Burcu; Hauser, Anthony; Kachalov, Viacheslav N; Andresen, Sara; Scheier, Thomas; Schreiber, Peter W; Günthard, Huldrych F; Kouyos, Roger D (2021). Assessing the potential impact of transmission during prolonged viral shedding on the effect of lockdown relaxation on COVID-19. PLoS Computational Biology, 17:e1008609.

Kachalov, Viacheslav N; Nguyen, Huyen; Balakrishna, Suraj; Salazar-Vizcaya, Luisa; Sommerstein, Rami; Kuster, Stefan P; Hauser, Anthony; Abel Zur Wiesch, Pia; Klein, Eili; Kouyos, Roger D (2021). Identifying the drivers of multidrug-resistant Klebsiella pneumoniae at a European level. PLoS Computational Biology, 17:e1008446.

Posada-Céspedes, Susana; Seifert, David; Topolsky, Ivan; Jablonski, Kim Philipp; Metzner, Karin J; Beerenwinkel, Niko (2021). V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data. Bioinformatics, 37(12):1673-1680.

Moura, Rita; Borges, Margarida; Vila Pouca, Maria C P; Oliveira, Dulce A; Parente, Marco P L; Kimmich, Nina; Mascarenhas, Teresa; Natal, Renato M (2021). A numerical study on fetal head molding during labor. International Journal for Numerical Methods in Biomedical Engineering, 37(1):e3411.

Bojar, Ondřej; Macháček, Dominik; Sagar, Sangeet; Smrž, Otakar; Kratochvíl, Jonáš; Polák, Peter; Ansari, Ebrahim; Mahmoudi, Mohammad; Kumar, Rishu; Franceschini, Dario; Canton, Chiara; Simonini, Ivan; Nguyen, Thai-Son; Schneider, Felix; Stüker, Sebastian; Waibel, Alex; Haddow, Barry; Sennrich, Rico; Williams, Philip (2021). ELITR Multilingual Live Subtitling: Demo and Strategy. In: Proceedings of the 16th Conference of the European Chapter of the Association for Computational Linguistics: System Demonstrations, Online, 1 April 2021, ACL Anthology.

Draws, Tim; Rieger, Alisa; Inel, Oana; Gadiraju, Ujwal; Tintarev, Nava (2021). A Checklist to Combat Cognitive Biases in Crowdsourcing. In: Proceedings of the Ninth AAAI Conference on Human Computation and Crowdsourcing, HCOMP 2021, Virtual, 14 November 2021 - 18 November 2021. AAAI} Press, 48-59.

Barsukow, Wasilij (2021). The active flux scheme for nonlinear problems. Journal of Scientific Computing, 86:3.

Melenk, Jens Markus; Sauter, Stefan A (2021). Wavenumber-explicit hp-FEM analysis for Maxwell’s equations with transparent boundary conditions. Foundations of Computational Mathematics, 21:145-241.

2020

Stark, Stefan G; Ficek, Joanna; Locatello, Francesco; Bonilla, Ximena; Chevrier, Stéphane; Singer, Franziska; Tumor Profiler Consortium; Rätsch, Gunnar; Lehmann, Kjong-Van (2020). SCIM: universal single-cell matching with unpaired feature sets. Bioinformatics, 36(Supp.):i919-i927.

San Roman, Magdalena; Wagner, Andreas (2020). Acetate and glycerol are not uniquely suited for the evolution of cross-feeding in E. coli. PLoS Computational Biology, 16(11):e1008433.

Abgrall, Rémi; Nordström, Jan; Öffner, Philipp; Tokareva, Svetlana (2020). Analysis of the SBP-SAT stabilization for finite element methods part I: Linear problems. Journal of Scientific Computing, 85(2):43.

Schmutzer, Michael; Wagner, Andreas (2020). Gene expression noise can promote the fixation of beneficial mutations in fluctuating environments. PLoS Computational Biology, 16(10):e1007727.

Henco, Lara; Diaconescu, Andreea O; Lahnakoski, Juha M; Brandi, Marie-Luise; Hörmann, Sophia; Hennings, Johannes; Hasan, Alkomiet; Papazova, Irina; Strube, Wolfgang; Bolis, Dimitris; Schilbach, Leonhard; Mathys, Christoph (2020). Aberrant computational mechanisms of social learning and decision-making in schizophrenia and borderline personality disorder. PLoS Computational Biology, 16(9):e1008162.

Sinisi, Stefano; Alimguzhin, Vadim; Mancini, Toni; Tronci, Enrico; Mari, Federico; Leeners, Brigitte (2020). Optimal Personalised Treatment Computation through In Silico Clinical Trials on Patient Digital Twins. Fundamenta Informaticae, 174(3-4):283-310.

Eling, Nils; Damond, Nicolas; Hoch, Tobias; Bodenmiller, Bernd (2020). Cytomapper: an R/bioconductor package for visualisation of highly multiplexed imaging data. bioRxiv 287516, Cold Spring Harbor Laboratory.

Schweizer, Gabriel; Wagner, Andreas (2020). Genotype networks of 80 quantitative Arabidopsis thaliana phenotypes reveal phenotypic evolvability despite pervasive epistasis. PLoS Computational Biology, 16(8):e1008082.

Sturrock, Peter; Scholkmann, Felix (2020). The RONO (Rank-Order-Normalization) Procedure for Power-Spectrum Analysis of Datasets with Non-Normal Distributions. Algorithms, 13(7):157.

Bouvel, Mathilde; Mishna, Marni; Nicaud, Cyril (2020). Some families of trees arising in permutation analysis. Electronic Journal of Combinatorics, 27(2):P2.20.

Fagerholm, Erik D; Foulkes, W M C; Gallero-Salas, Yasir; Helmchen, Fritjof; Friston, Karl J; Moran, Rosalyn J; Leech, Robert (2020). Conservation laws by virtue of scale symmetries in neural systems. PLoS Computational Biology, 16(5):e1007865.

Albert, Michael; Bouvel, Mathilde; Féray, Valentin (2020). Two first-order logics of permutations. Journal of Combinatorial Theory, Series A, 171:105158.

Numminen, Elina; Laine, Anna-Liisa (2020). The spread of a wild plant pathogen is driven by the road network. PLoS Computational Biology, 16(3):e1007703.

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.

Kovaltsuk, Aleksandr; Raybould, Matthew I J; Wong, Wing Ki; Marks, Claire; Kelm, Sebastian; Snowden, James; Trück, Johannes; Deane, Charlotte M (2020). Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice. PLoS Computational Biology, 16(2):e1007636.

Hothorn, Torsten (2020). Transformation boosting machines. Statistics and Computing, 30(1):141-152.

Lang, Brian M; Kuipers, Jack; Misselwitz, Benjamin; Beerenwinkel, Niko (2020). Predicting colorectal cancer risk from adenoma detection via a two-type branching process model. PLoS Computational Biology, 16(2):e1007552.

O'Connor, Brian; Bojinski, Stephan; Roeoesli, Claudia; Schaepman, Michael E (2020). Monitoring global changes in biodiversity and climate essential as ecological crisis intensifies. Ecological Informatics, 55:101033.

2019

Grosskurth, Elmar D; Bach, Dominik R; Economides, Marcos; Huys, Quentin J M; Holper, Lisa (2019). No substantial change in the balance between model-free and model-based control via training on the two-step task. PLoS Computational Biology, 15(11):e1007443.

Yu, Xiaoquan; Li, Xiang-Yi (2019). Applications of WKB and Fokker–Planck Methods in Analyzing Population Extinction Driven by Weak Demographic Fluctuations. Bulletin of Mathematical Biology, 81(11):4840-4855.

Schmid, Franca; Barrett, Matthew J P; Obrist, Dominik; Weber, Bruno; Jenny, Patrick (2019). Red blood cells stabilize flow in brain microvascular networks. PLoS Computational Biology, 15(8):e1007231.

Koppe, Georgia; Toutounji, Hazem; Kirsch, Peter; Lis, Stefanie; Durstewitz, Daniel (2019). Identifying nonlinear dynamical systems via generative recurrent neural networks with applications to fMRI. PLoS Computational Biology, 15(8):e1007263.

Laaber, Christoph (2019). Continuous Software Performance Assessment: Detecting Performance Problems of Software Libraries on Every Build. In: The 28th ACM SIGSOFT International Symposium on Software Testing and Analysis, Beijing, China, 15 August 2019 - 19 August 2019, ACM Press.

Moor, Dmitry (2019). Data markets with dynamic arrival of buyers and sellers. In: The 14th Workshop on the Economics of Networks, Systems and Computation, Phoenix, Arizona, 28 July 2019. ACM Press, 1-6.

Libby, Eric; Hébert-Dufresne, Laurent; Hosseini, Sayed-Rzgar; Wagner, Andreas (2019). Syntrophy emerges spontaneously in complex metabolic systems. PLoS Computational Biology, 15(7):e1007169.

Grano, Giovanni (2019). A New Dimension of Test Quality: Assessing and Generating Higher Quality Unit Test Cases. In: Proceedings of the 28th ACM SIGSOFT International Symposium on Software Testing and Analysis, Beijing, 17 July 2019 - 20 July 2019. ACM, 419-423.

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.

Hauser, Anthony; Kusejko, Katharina; Johnson, Leigh F; Wandeler, Gilles; Riou, Julien; Goldstein, Fardo; Egger, Matthias; Kouyos, Roger D (2019). Bridging the gap between HIV epidemiology and antiretroviral resistance evolution: Modelling the spread of resistance in South Africa. PLoS Computational Biology, 15(6):e1007083.

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.

Solinas, Sergio M G; Edelmann, Elke; Leßmann, Volkmar; Migliore, Michele (2019). A kinetic model for Brain-Derived Neurotrophic Factor mediated spike timing-dependent LTP. PLoS Computational Biology, 15(4):e1006975.

Bouckaert, Remco; Vaughan, Timothy G; Barido-Sottani, Joëlle; Duchêne, Sebastián; Fourment, Mathieu; Gavryushkina, Alexandra; Heled, Joseph; Jones, Graham; Kühnert, Denise; De Maio, Nicola; Matschiner, Michael; Mendes, Fábio K; Müller, Nicola F; Ogilvie, Huw A; du Plessis, Louis; Popinga, Alex; Rambaut, Andrew; Rasmussen, David; Siveroni, Igor; Suchard, Marc A; Wu, Chieh-Hsi; Xie, Dong; Zhang, Chi; Stadler, Tanja; Drummond, Alexei J (2019). BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis. PLoS Computational Biology, 15(4):e1006650.

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

Miladinović, Đorđe; Muheim, Christine; Bauer, Stefan; Spinnler, Andrea; Noain, Daniela; Bandarabadi, Mojtaba; Gallusser, Benjamin; Krummenacher, Gabriel; Baumann, Christian; Adamantidis, Antoine; Brown, Steven A; Buhmann, Joachim M (2019). SPINDLE: End-to-end learning from EEG/EMG to extrapolate animal sleep scoring across experimental settings, labs and species. PLoS Computational Biology, 15(4):e1006968.

Vinckier, Fabien; Rigoux, Lionel; Kurniawan, Irma T; Hu, Chen; Bourgeois-Gironde, Sacha; Daunizeau, Jean; Pessiglione, Mathias (2019). Sour grapes and sweet victories: How actions shape preferences. PLoS Computational Biology, 15:e1006499.

2018

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.

Vassallo, Carmine; Palomba, Fabio; Bacchelli, Alberto; Gall, Harald C (2018). Continuous code quality: are we (really) doing that? In: ASE '18: 33rd ACM/IEEE International Conference on Automated Software Engineering, Montpellier France, 3 October 2018 - 7 October 2018. ACM, 790-795.

Kovalenko, Vladimir; Palomba, Fabio; Bacchelli, Alberto (2018). Mining file histories: should we consider branches? In: ASE '18: 33rd ACM/IEEE International Conference on Automated Software Engineering, Montpellier France, 3 October 2018 - 7 October 2018. ACM, 202-213.

Scalabrino, Simone; Grano, Giovanni; Di Nucci, Dario; Guerra, Michele; De Lucia, Andrea; Gall, Harald C; Oliveto, Rocco (2018). OCELOT"" A Search-Based Test Data Generation Tool for C. In: Proceedings of the 33rd IEEE/ACM International Conference on Automated Software Engineering, Montpellier, France, 3 September 2018 - 7 September 2018, IEEE.

Tiberi, Simone; Walsh, Mark; Cavallaro, Massimo; Hebenstreit, Daniel; Finkenstädt, Bärbel (2018). Bayesian inference on stochastic gene transcription from flow cytometry data. Bioinformatics, 34(17):i647-i655.

Katthagen, Teresa; Mathys, Christoph; Deserno, Lorenz; Walter, Henrik; Kathmann, Norbert; Heinz, Andreas; Schlagenhauf, Florian (2018). Modeling subjective relevance in schizophrenia and its relation to aberrant salience. PLoS Computational Biology, 14(8):e1006319.

Tzovara, Athina; Korn, Christoph W; Bach, Dominik R (2018). Human Pavlovian fear conditioning conforms to probabilistic learning. PLoS Computational Biology, 14(8):e1006243.

San Roman, Magdalena; Wagner, Andreas (2018). An enormous potential for niche construction through bacterial cross-feeding in a homogeneous environment. PLoS Computational Biology, 14(7):e1006340.

Voita, Elena; Serdyukov, Pavel; Sennrich, Rico; Titov, Ivan (2018). Context-Aware Neural Machine Translation Learns Anaphora Resolution. In: Proceedings of the 56th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers), Melbourne, 15 July 2018 - 20 July 2018. Association for Computational Linguistics, 1264-1274.

Muller, Lorenz K; Martel, Julien N P; Indiveri, Giacomo (2018). Kernelized Synaptic Weight Matrices. In: International Conference on Machine Learning 2018, Stockholm, 10 July 2018 - 15 July 2018. International Conference on Machine Learning, 3651-3660.

Schwab, Patrick; Keller, Emanuela; Muroi, Carl; Mack, David J; Strässle, Christian; Karlen, Walter (2018). Not to Cry Wolf: Distantly Supervised Multitask Learning in Critical Care. In: 35 th International Conference on Machine Learning, Stockholm, Sweden, 10 July 2018 - 15 July 2018, International Conference on Machine Learning.

Martin, Mike; Weibel, Robert; Röcke, Christina; Boker, Steven M (2018). Semantic Activity Analytics for Healthy Aging: Challenges and Opportunities. IEEE Pervasive Computing, 17(3):73-77.

Quaglino, A; Pezzuto, S; Koutsourelakis, P S; Auricchio, A; Krause, R (2018). Fast uncertainty quantification of activation sequences in patient-specific cardiac electrophysiology meeting clinical time constraints. International Journal for Numerical Methods in Biomedical Engineering, 34(7):e2985.

Radom, Filip; Plückthun, Andreas; Paci, Emanuele (2018). Assessment of ab initio models of protein complexes by molecular dynamics. PLoS Computational Biology, 14(6):e1006182.

Nguyen, Anh; Rothacher, Yannick; Lenggenhager, Bigna; Brugger, Peter; Kunz, Andreas (2018). Individual Differences and Impact of Gender on Curvature Redirection Thresholds. In: SAP, 18. Proceedings of the 15th ACM Symposium on Applied Perception. New York, NY, USA: ACM, 5:1-5:4.

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.

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

2017

Gallego, Guillermo; Lund, Jon E A; Müggler, Elias; Rebecq, Henri; Delbruck, Tobi; Scaramuzza, Davide (2017). Event-based, 6-DOF Camera Tracking from Photometric Depth Maps. IEEE Transactions on Pattern Analysis and Machine Intelligence, 1(1):1-10.

Muir, Dylan R; Molina-Luna, Patricia; Roth, Morgane M; Helmchen, Fritjof; Kampa, Björn M (2017). Specific excitatory connectivity for feature integration in mouse primary visual cortex. PLoS Computational Biology, 13(12):e1005888.

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

Ashcroft, Peter; Manz, Markus G; Bonhoeffer, Sebastian (2017). Clonal dominance and transplantation dynamics in hematopoietic stem cell compartments. PLoS Computational Biology, 13(10):e1005803.

Kotelnikova, Ekaterina; Kiani, Narsis A; Abad, Elena; Martinez-Lapiscina, Elena H; Andorra, Magi; Zubizarreta, Irati; Pulido-Valdeolivas, Irene; Pertsovskaya, Inna; Alexopoulos, Leonidas G; Olsson, Tomas; Martin, Roland; Paul, Friedemann; Tegnér, Jesper; Garcia-Ojalvo, Jordi; Villoslada, Pablo (2017). Dynamics and heterogeneity of brain damage in multiple sclerosis. PLoS Computational Biology, 13(10):e1005757.

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.

Matias Rodrigues, João F; 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.

Neil, D; Lee, J-H; Delbruck, T; Liu, S-C (2017). Delta networks for optimized recurrent network computation. In: 34th International Conference on Machine Learning 2017, Sydney, 6 August 2017 - 11 August 2017, Proceedings of the 34th International Conference on Machine Learning.

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.

Hauser, Tobias U; Moutoussis, Michael; Iannaccone, Reto; Brem, Silvia; Walitza, Susanne; Drechsler, Renate; Dayan, Peter; Dolan, Raymond J (2017). Increased decision thresholds enhance information gathering performance in juvenile Obsessive-Compulsive Disorder (OCD). PLoS Computational Biology, 13(4):e1005440.

Gauvrit, Nicolas; Zenil, Hector; Soler-Toscano, Fernando; Delahaye, Jean-Paul; Brugger, Peter (2017). Human behavioral complexity peaks at age 25. PLoS Computational Biology, 13(4):e1005408.

Rasmussen, David A; Kouyos, Roger; Günthard, Huldrych F; Stadler, Tanja (2017). Phylodynamics on local sexual contact networks. PLoS Computational Biology, 13(3):e1005448.

Gorgolewski, Krzysztof J; Alfaro-Almagro, Fidel; Auer, Tibor; Bellec, Pierre; Capotă, Mihai; Chakravarty, M Mallar; Churchill, Nathan W; Cohen, Alexander Li; Craddock, R Cameron; Devenyi, Gabriel A; Eklund, Anders; Esteban, Oscar; Flandin, Guillaume; Ghosh, Satrajit S; Guntupalli, J Swaroop; Jenkinson, Mark; Keshavan, Anisha; Kiar, Gregory; Liem, Franziskus; Raamana, Pradeep Reddy; Raffelt, David; Steele, Christopher J; Quirion, Pierre-Olivier; Smith, Robert E; Strother, Stephen C; Varoquaux, Gaël; Wang, Yida; Yarkoni, Tal; Poldrack, Russell A (2017). BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods. PLoS Computational Biology, 13(3):e1005209.

Fortuna, Miguel A; Zaman, Luis; Ofria, Charles; Wagner, Andreas (2017). The genotype-phenotype map of an evolving digital organism. PLoS Computational Biology, 13(2):e1005414.

Grano, Giovanni; Di Sorbo, Andrea; Mercaldo, Francesco; Visaggio, Corrado A; Canfora, Gerardo; Panichella, Sebastiano (2017). Android Apps and User Feedback: A Dataset for Software Evolution and Quality Improvement. In: Proceedings of the 2Nd ACM SIGSOFT International Workshop on App Market Analytics, Paderborn, Germany, 1 January 2017. ACM, 8-11.

Rigoli, Francesco; Mathys, Christoph; Friston, Karl J; Dolan, Raymond J (2017). A unifying Bayesian account of contextual effects in value-based choice. PLoS Computational Biology, 13(10):e1005769.

Schmid, Franca; Tsai, Philbert S; Kleinfeld, David; Jenny, Patrick; Weber, Bruno (2017). Depth-dependent flow and pressure characteristics in cortical microvascular networks. PLoS Computational Biology, 13(2):e1005392.

Gallego, Guillermo; Lund, Jon E A; Mueggler, Elias; Rebecq, Henri; Delbruck, Tobi; Scaramuzza, Davide (2017). Event-based, 6-DOF camera tracking from photometric depth maps. IEEE Transactions on Pattern Analysis and Machine Intelligence, PP(99):n/a.

Arcadu, Filippo; Vogel, Jakob; Stampanoni, Marco; Marone, Federica (2017). Improving Analytical Tomographic Reconstructions Through Consistency Conditions. Fundamenta Informaticae, 155(4):341-361.

Devaine, Marie; Daunizeau, Jean (2017). Learning about and from others' prudence, impatience or laziness: The computational bases of attitude alignment. PLoS Computational Biology, 13(3):e1005422.

Castellví, Quim; Sánchez-Velázquez, Patricia; Moll, Xavier; Berjano, Enrique; Andaluz, Anna; Burdío, Fernando; Bijnens, Bart; Ivorra, Antoni (2017). Modeling liver electrical conductivity during hypertonic injection. International Journal for Numerical Methods in Biomedical Engineering, 34(1):e2904.

Courty, Nicolas; Flamary, Rémi; Tuia, Devis; Rakotomamonjy, Alain (2017). Optimal transport for domain adaptation. IEEE Transactions on Pattern Analysis and Machine Intelligence, 39(9):1853-1865.

Aponte, Eduardo A; Schöbi, Dario; Stephan, Klaas E; Heinzle, Jakob (2017). The Stochastic Early Reaction, Inhibition, and late Action (SERIA) model for antisaccades. PLoS Computational Biology, 13(8):e1005692.

2016

di Biase, Marco; Bruntink, Magiel; Bacchelli, Alberto (2016). A Security Perspective on Code Review: The Case of Chromium. In: 2016 IEEE 16th International Working Conference on Source Code Analysis and Manipulation, Raleigh, NC, USA, 2 November 2016 - 3 November 2016. IEEE, 21-30.

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.

Cohen, Daniel C; Costa, Armindo; Farber, Michael S; Kappeler, Thomas (2016). Correction to our article “Topology of random 2-complexes” published in DCG 47 (2012), pp. 117–149. Discrete & Computational Geometry, 56(2):502-503.

Cito, Jürgen; Rubin, Julia; Stanley-Marbell, Phillip; Rinard, Martin (2016). Battery-Aware Transformations in Mobile Applications. In: ASE'16: ACM/IEEE International Conference on Automated Software Engineering, Singapore, Singapore, 3 September 2016 - 7 September 2016. ACM Digital library, 702-707.

Panichella, Annibale; Alexandru, Carol V; Panichella, Sebastiano; Bacchelli, Alberto; Gall, Harald C (2016). A search-based training algorithm for cost-aware defect prediction. In: GECCO '16: Genetic and Evolutionary Computation Conference, Denver, USA, 20 July 2016 - 24 July 2016. ACM Digital library, 1077-1084.

Tang, Li-Ying; Li, Sheng-Nan; Lin, Jian-Hong; Guo, Qiang; Liu, Jian-Guo (2016). Community structure detection based on the neighbor node degree information. International Journal of Modern Physics C, 27(04):1650046.

Cadosch, Dominique; Abel zur Wiesch, Pia; Kouyos, Roger; Bonhoeffer, Sebastian (2016). The Role of Adherence and Retreatment in De Novo Emergence of MDR-TB. PLoS Computational Biology, 12(3):e1004749.

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.

Hofner, Benjamin; Kneib, Thomas; Hothorn, Torsten (2016). A unified framework of constrained regression. Statistics and Computing, 26(1-2):1-14.

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.

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.

2015

Bach, Dominik R (2015). Anxiety-like behavioural inhibition is normative under environmental threat-reward correlations. PLoS Computational Biology, 11(12):e1004646.

Cito, Jürgen; Leitner, Philipp; Gall, Harald C; Dadashi, Aryan; Keller, Anne; Roth, Andreas (2015). Runtime Metric Meets Developer - Building Better Cloud Applications Using Feedback. In: Proceedings of the 2015 ACM International Symposium on New Ideas, New Paradigms, and Reflections on Programming & Software (Onward! 2015), Pittsburgh, Pennsylvania, United States, 25 October 2015 - 30 October 2015, ACM.

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, s.n..

Brandtner, Martin; Leitner, Philipp; Gall, Harald C (2015). Intent, Tests, and Release Dependencies: Pragmatic Recipes for Source Code Integration. In: Proceedings of the 15th IEEE International Working Conference on Source Code Analysis and Manipulation (SCAM), Bremen, Germany, 27 September 2015 - 28 September 2015, s.n..

Klenner, Manfred (2015). Verb-centered Sentiment Inference with Description Logics. In: 6th Workshop on Computational Approaches to Subjectivity, Sentiment & Social Media Analysis, Lissabon, 17 September 2015 - 21 September 2015. s.n., 134-140.

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.

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

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

Korn, Christoph W; Bach, Dominik R (2015). Maintaining homeostasis by decision-making. PLoS Computational Biology, 11(5):e1004301.

Panichella, Sebastiano; Arnaoudova, Venera; Di Penta, Massimiliano; Antoniol, Giuliano (2015). Would static analysis tools help developers with code reviews? In: 2015 IEEE 22nd International Conference on Software Analysis, Evolution and Reengineering (SANER), Montreal, QC, Canada, 2 April 2015 - 6 April 2015. IEEE, 161-170.

Siebourg-Polster, Juliane; Mudrak, Daria; Emmenlauer, Mario; Rämö, Pauli; Dehio, Christoph; Greber, Urs; Fröhlich, Holger; Beerenwinkel, Niko (2015). NEMix: Single-cell Nested Effects Models for Probabilistic Pathway Stimulation. PLoS Computational Biology, 11(4):e1004078.

Brandtner, Martin; Müller, Sebastian C; Leitner, Philipp; Gall, Harald C (2015). SQA-Profiles: Rule-based Activity Profiles for Continuous Integration Environments. In: 22nd IEEE International Conference on Software Analysis, Evolution, and Reengineering, Montréal, Canada, 2 March 2015 - 6 March 2015. IEEE, 301-310.

Wang, Fang; Cao, Kun; Wu, Yi; Patzke, Greta R; Zhou, Ying (2015). Electronic and optical properties of N-doped Bi2O3 polymorphs for visible light-induced photocatalysis. Journal of Molecular Modeling, 21(3):2596-2604.

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.

Vayena, Effy; Salathé, Marcel; Madoff, Lawrence C; Brownstein, John S (2015). Ethical challenges of big data in public health. PLoS Computational Biology, 11(2):e1003904.

Krajbich, Ian; Hare, Todd A; Bartling, Björn; Morishima, Yosuke; Fehr, Ernst (2015). A common mechanism underlying food choice and social decisions. PLoS Computational Biology, 11(10):e1004371.

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.

Rutishauser, Ueli; Slotine, Jean-Jaques; Douglas, Rodney (2015). Computation in cynamically bounded asymmetric systems. PLoS Computational Biology, 11(1):e1004039.

Hosseini, Sayed-Rzgar; Barve, Aditya; Wagner, Andreas (2015). Exhaustive analysis of a genotype space comprising 1015 central carbon metabolisms reveals an organization conducive to metabolic innovation. PLoS Computational Biology, 11(8):e1004329.

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.

Sinnott, Richard O; Bayliss, Christopher; Bromage, Andrew; Galang, Gerson; Grazioli, Guido; Greenwood, Philip; Macaulay, Angus; Morandini, Luca; Nogoorani, Ghazal; Nino-Ruiz, Marcos; Tomko, Martin; Pettit, Christopher; Sarwar, Muhammad; Stimson, Robert; Voorsluys, William; Widjaja, Ivo (2015). The Australia urban research gateway. Concurrency and Computation: Practice & Experience, 27(2):358-375.

2014

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.

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.

Volk, Martin; Clematide, Simon (2014). Detecting Code-Switching in a Multilingual Alpine Heritage Corpus. In: Proceedings of the First Workshop on Computational Approaches to Code Switching, Doha, Qatar, 25 October 2014. Association for Computational Linguistics, 24-33.

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.

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.

Stankevicius, Aistis; Huys, Quentin J M; Kalra, Aditi; Seriès, Peggy (2014). Optimism as a prior belief about the probability of future reward. PLoS Computational Biology, 10(5):e1003605.

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

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.

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.

Hapfelmeier, Alexander; Hothorn, Torsten; Ulm, Kurt; Strobl, Carolin (2014). A new variable importance measure for random forests with missing data. Statistics and Computing, 24(1):21-34.

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

Bauer, Roman; Zubler, Frédéric; Pfister, Sabina; Hauri, Andreas; Pfeiffer, Michael; Muir, Dylan R; Douglas, Rodney J (2014). Developmental self-construction and -configuration of functional neocortical neuronal networks. PLoS Computational Biology, 10(12):e1003994.

Kollmorgen, Sepp; Hahnloser, Richard H R (2014). Dynamic alignment models for neural coding. PLoS Computational Biology, 10(3):e1003508.

Schmidt, Thomas S B; Matias Rodrigues, João F; von Mering, Christian (2014). Ecological consistency of SSU rRNA-based operational taxonomic units at a global scale. PLoS Computational Biology, 10(4):e1003594.

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

Diaconescu, Andreea O; Mathys, Christoph; Weber, Lilian A E; Daunizeau, Jean; Kasper, Lars; Lomakina, Ekaterina I; Fehr, Ernst; Stephan, Klaas E (2014). Inferring on the intentions of others by hierarchical bayesian learning. PLoS Computational Biology, 10(9):e1003810.

Tronci, E; Mancini, T; Salvo, I; Sinsi, S; Mari, F; Melatti, I; Massini, A; Davì, F; Dierkes, T; Ehrig, R; Röblitz, S; Leeners, B; Krüger, T H C; Egli, M; Ille, F (2014). Patient-specific models from inter-patient biological models and clinical records. In: Proceedings of the 14th Conference on Formal Methods in Computer-Aided Design, Lausanne, 2014. FMCAD Inc, 207-214.

Althaus, Christian L; Joos, Beda; Perelson, Alan S; Günthard, Huldrych F (2014). Quantifying the turnover of transcriptional subclasses of HIV-1-infected cells. PLoS Computational Biology, 10(10):e1003871.

Sunnaker, M; Zamora-Sillero, E; de Lomana, A Lopez Garcia; 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.

2013

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

Mancini, Maurizio; Hofmann, Jennifer; Platt, Tracey; Volpe, Gualtiero; Varni, Giovanna; Glowinski, Donald; Ruch, Willibald; Camurri, Antonio (2013). Towards automated full body detection of laughter driven by human expert annotation. In: Humaine Association Conference on Affective Computing and Intelligent Interaction, Geneva, 2 September 2013 - 5 September 2013. IEEE Computer Society, 757-762.

Payne, Joshua L; Wagner, Andreas (2013). Constraint and contingency in multifunctional gene regulatory circuits. PLoS Computational Biology, 9(6):e1003071.

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

Bank, Randolph E; Parsania, Asieh; Sauter, Stefan (2013). Saturation estimates for hp-finite element methods. Computing and Visualization in Science, 16(5):195-217.

Lieder, Falk; Stephan, Klaas E; Daunizeau, Jean; Garrido, Marta I; Friston, Karl J (2013). A neurocomputational model of the mismatch negativity. PLoS Computational Biology, 9(11):e1003288.

Nessler, B; Pfeiffer, M; Büsing, L; Maass, W (2013). Bayesian computation emerges in generic cortical microcircuits through spike-timing-dependent plasticity. PLoS Computational Biology, 9(4):e1003037.

Censi, Andrea; Scaramuzza, Davide (2013). Calibration by correlation using metric embedding from non-metric similarities. IEEE Transactions on Pattern Analysis and Machine Intelligence, 35(10):2357-2370.

Käser, Tanja; Busetto, Alberto Giovanni; Solenthaler, Barbara; Baschera, Gian-Marco; Kohn, Juliane; Kucian, Karin; Aster, Michael; Gross, Markus (2013). Modelling and optimizing mathematics learning in children. International Journal of Artificial Intelligence in Education, 23(1-4):115-135.

Lieder, Falk; Daunizeau, Jean; Garrido, Marta I; Friston, Karl J; Stephan, Klaas E (2013). Modelling trial-by-trial changes in the mismatch negativity. PLoS Computational Biology, 9(2):e1002911.

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.

Zubler, Frederic; Hauri, Andreas; Pfister, Sabina; Bauer, Roman; Anderson, John C; Whatley, Adrian M; Douglas, Rodney J (2013). Simulating cortical development as a self constructing process: A novel multi-scale approach combining molecular and physical aspects. PLoS Computational Biology, 9(8):e1003173.

Beerenwinkel, Niko; Montazeri, Hesam; Schuhmacher, Heike; Knupfer, Patrick; von Wyl, Viktor; Furrer, Hansjakob; Battegay, Manuel; Hirschel, Bernard; Cavassini, Matthias; Vernazza, Pietro; Bernasconi, Enos; Yerly, Sabine; Böni, Jürg; Klimkait, Thomas; Cellerai, Cristina; Günthard, Huldrych F (2013). The individualized genetic barrier predicts treatment response in a large cohort of HIV-1 infected patients. PLoS Computational Biology, 9(8):e1003203.

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.

2012

Collier, Nigel; Tran, Mai-Vu; Le, Hoang-Quynh; Oellrich, Anika; Kawazoe, Ai; Hall-May, Martin; Rebholz-Schuhmann, Dietrich (2012). A hybrid approach to finding phenotype candidates in genetic texts. In: 24th International Conference on Computational Linguistics (COLING 2012), Mumbai, India, 10 December 2012 - 14 December 2012.

Perony, Nicolas; Tessone, Claudio J; König, Barbara; Schweitzer, Frank (2012). How Random Is Social Behaviour? Disentangling Social Complexity through the Study of a Wild House Mouse Population. PLoS Computational Biology, 8(11):e1002786.

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

Avella Gonzalez, Oscar J; van Aerde, Karlijn I; van Elburg, Ronald A J; Poil, Simon-Shlomo; Mansvelder, Huibert D; Linkenkaer-Hansen, Klaus; van Pelt, Jaap; van Ooyen, Arjen (2012). External drive to inhibitory cells induces alternating episodes of high- and low-amplitude oscillations. PLoS Computational Biology, 8(8):e1002666.

Matias Rodrigues, João F; Rankin, Daniel J; Rossetti, Valentina; Wagner, Andreas; Bagheri, Homayoun C (2012). Differences in cell division rates drive the evolution of terminal and differentiation in microbes. PLoS Computational Biology, 8(4):e1002468.

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.

Kuhn, Christoph (2012). An information-carrying and knowledge-producing molecular machine. A Monte-Carlo simulation. Journal of Molecular Modeling, 18(2):607-609.

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.

Bender, Emily M; Schikowski, Robert; Bickel, Balthasar (2012). Deriving a lexicon for a precision grammar from language documentation resources: a case study of Chintang. In: Kay, M; Boitet, C. Proceedings of the 24th International Conference on Computational Linguistics (COLING). Mumbai: Association for Computational Linguistics, 247-262.

Friston, K J; Shiner, T; FitzGerald, T; Galea, J M; Adams, R; Brown, H; Dolan, R J; Moran, R; Stephan, K E; Bestmann, S (2012). Dopamine, affordance and active inference. PLoS Computational Biology, 8(1):e1002327.

Leventhal, Gabriel E; Kouyos, Roger; Stadler, Tanja; von Wyl, Viktor; Yerly, Sabine; Böni, Jürg; Cellerai, Cristina; Klimkait, Thomas; Günthard, Huldrych F; Bonhoeffer, Sebastian (2012). Inferring epidemic contact structure from phylogenetic trees. PLoS Computational Biology, 8(3):e1002413.

Sennrich, Rico (2012). Perplexity minimization for translation model domain adaptation in statistical machine translation. In: Proceedings of the 13th Conference of the European Chapter of the Association for Computational Linguistics, Avignon, France, April 2012 - 2012. Association For Computational Linguistics, 539-549.

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.

Jol, Stefan J; Kümmel, Anne; Terzer, Marco; Stelling, Jörg; Heinemann, Matthias (2012). System-Level Insights into Yeast Metabolism by Thermodynamic Analysis of Elementary Flux Modes. PLoS Computational Biology, 8(3):e1002415.

Cohen, D; Costa, A; Farber, M; Kappeler, T (2012). Topology of random 2-complexes. Discrete & Computational Geometry, 47(1):117-149.

2011

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.

Hecht, Fabio V; Bocek, Thomas; Stiller, Burkhard (2011). B-Tracker: Improving load balancing and efficiency in distributed P2P trackers. In: IEEE P2P 2011, Kyoto, Japan, 31 August 2011. IEEE Computer Society, 310-313.

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.

Sabanés Bové, D; Held, L (2011). Bayesian fractional polynomials. Statistics and Computing, 21(3):309-324.

Schilling, S; Willecke, M; Aegerter-Wilmsen, T; Cirpka, O A; Basler, K; von Mering, C (2011). Cell-sorting at the a/p boundary in the Drosophila wing primordium: a computational model to consolidate observed non-local effects of hh signaling. PLoS Computational Biology, 7(4):e1002025.

Augsten, Nikolaus; Barbosa, Denilson; Böhlen, Michael; Palpanas, Themis (2011). Efficient top-k approximate subtree matching in small memory. IEEE Transactions on Knowledge & Data Engineering, 23(8):1123-1137.

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

Brodersen, Kay H; Schofield, Thomas M; Leff, Alexander P; Ong, Cheng S; Lomakina, Ekaterina I; Buhmann, Joachim M; Stephan, Klaas E (2011). Generative embedding for model-based classification of FMRI data. PLoS Computational Biology, 7(6):e1002079.

Chumbley, J R; Flandin, G; Bach, D R; Daunizeau, Jean; Fehr, Ernst; Dolan, R J; Friston, K J (2011). Learning and generalization under ambiguity: An fMRI Study. PLoS Computational Biology, 8(1):e1002346.

Daunizeau, Jean; Preuschoff, Kerstin; Friston, Karl; Stephan, Klaas E (2011). Optimizing experimental design for comparing models of brain function. PLoS Computational Biology, 7(11):e1002280.

Delgado-Eckert, Edgar; Ojosnegros, Samuel; Beerenwinkel, Niko (2011). The Evolution of Virulence in RNA Viruses under a Competition–Colonization Trade-Off. Bulletin of Mathematical Biology, 73(8):1881-1908.

Huang, D; Caflisch, A (2011). The free energy landscape of small molecule unbinding. PLoS Computational Biology, 7(2):e1002002.

2010

Müller, Christian L; Sbalzarini, Ivo F (2010). Gaussian Adaptation as a unifying framework for continuous black-box optimization and adaptive Monte Carlo sampling. In: 2010 IEEE Congress on Evolutionary Computation (CEC), Barcelona, Spain, 18 July 2010 - 23 July 2010, 1-8.

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.

Türker, C; Akal, F; Joho, D; Panse, C; Barkow-Oesterreicher, S; Rehrauer, H; Schlapbach, R (2010). B-Fabric: the Swiss Army Knife for life sciences. In: Proceedings of the 13th International Conference on Extending Database Technology, Lausanne, Switzerland, 22 March 2010 - 26 March 2010, 717-720.

Penny, W D; Stephan, K E; Daunizeau, J; Rosa, M J; Friston, K J; Schofield, T M; Leff, A P (2010). Comparing families of dynamic causal models. PLoS Computational Biology, 6(3):e1000709.

Romero-Isart, N; Oliva, B; Vašák, M (2010). Influence of NH-S gamma bonding interactions on the structure and dynamics of metallothioneins. Journal of Molecular Modeling, 16(3):387-394.

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.

Espinosa-Soto, C; Wagner, A (2010). Specialization can drive the evolution of modularity. PLoS Computational Biology, 6(3):e1000719.

2009

Gazzola, M; Burckhardt, C J; Bayati, B; Engelke, M; Greber, U F; Koumoutsakos, P (2009). A stochastic model for microtubule motors describes the in vivo cytoplasmic transport of human adenovirus. PLoS Computational Biology, 5(12):e1000623.

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

Stoiber, R; Glinz, M (2009). Modeling and managing tacit product line requirements knowledge. In: 2nd International Workshop on Managing Requirements Engineering Knowledge (MaRK'09), Atlanta, GA, USA, 1 September 2009.

Kietz, J-U; Serban, F; Bernstein, A; Fischer, S (2009). Towards cooperative planning of data mining workflows. In: Proc of the ECML/PKDD09 Workshop on Third Generation Data Mining: Towards Service-oriented Knowledge Discovery (SoKD-09), Bled, Slovenia, September 2009.

Zimmermann, Thomas; Nagappan, Nachiappan; Gall, Harald; Giger, Emanuel; Murphy, Brendan (2009). Cross-project defect prediction: a large scale experiment on data vs. domain vs. process. In: 7th Joint Meeting of the European Software Engineering Conference and the ACM SIGSOFT Symposium on the Foundations of Software Engineering, Amsterdam, The Netherlands, 24 August 2009 - 28 August 2009. ACM, 91-100.

Knab, Patrick; Pinzger, Martin; Gall, Harald (2009). Smart views for analyzing problem reports: tool demo. In: 7th joint meeting of the European Software Engineering Conference and the ACM SIGSOFT Symposium on the Foundations of Software Engineering, Amsterdam, 24 August 2009 - 28 August 2009. ACM, 289-290.

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

Bird, C; Bachmann, A; Aune, E; Duffy, J; Bernstein, A; Filkov, V; Devanbu, P (2009). Fair and balanced? Bias in bug-fix datasets. In: ESEC/FSE '09: Proceedings of the 7th joint meeting of the European software engineering conference and the ACM SIGSOFT symposium on The foundations of software engineering on European software engineering conference and foundations of software engineering, Amsterdam, The Netherlands, August 2009, 121-130.

Bachmann, A; Bernstein, A (2009). Software process data quality and characteristics - a historical view on open and closed source projects. In: IWPSE-Evol'09: Proceedings of the joint international and annual ERCIM workshops on Principles of software evolution (IWPSE) and software evolution (Evol) workshops, Amsterdam, The Netherlands, August 2009, 119-128.

Miao, Y; Diaz-Gutierrez, P; Pajarola, R; Gopi, M; Feng, J (2009). Shape isophotic error metric controllable re-sampling for point-sampled surfaces. In: IEEE International Conference of Shape Modeling and Applications, Beijing, China, 26 June 2009 - 28 June 2009, 28-35.

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

Taliun, Andrej; Böhlen, Michael Hanspeter; Mazeika, Arturas (2009). CORE: Nonparametric Clustering of Large Numeric Databases. In: SDM 2009: Proceedings of the SIAM International Conference on Data Mining, Sparks, Nevada, USA, 30 April 2009 - 2 May 2009. SIAM (Society for Industrial and Applied Mathematics), 14-25.

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.

Hafner, M; Koeppl, H; Hasler, M; Wagner, A (2009). 'Glocal' robustness analysis and model discrimination for circadian oscillators. PLoS Computational Biology, 5(10):e1000534.

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

Liehr, F; Preusser, T; Rumpf, M; Sauter, S; Schwen, L O (2009). Composite finite elements for 3D image based computing. Computing and Visualization in Science, 12(4):171-188.

Matias Rodrigues, J F; Wagner, A (2009). Evolutionary plasticity and innovations in complex metabolic reaction networks. PLoS Computational Biology, 5(12):e1000613.

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.

Frühwirth-Schnatter, S; Frühwirth, R; Held, L; Rue, H (2009). Improved auxiliary mixture sampling for hierarchical models of non-Gaussian data. Statistics and Computing, 19(4):479-492.

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

Kiebel, S J; von Kriegstein, K; Daunizeau, J; Friston, K J (2009). Recognizing sequences of sequences. PLoS Computational Biology, 5(8):e1000464.

Cöltekin, Arzu (2009). Space-variant image coding for stereoscopic media. In: IEEE. 2009 Picture Coding Symposium (PCS). Los Alamitos, CA: Institute of Electrical and Electronics Engineers ( IEEE ), 1-4.

Furrer, R; Sain, S R (2009). Spatial model fitting for large datasets with applications to climate and microarray problems. Statistics and Computing, 19(2):113-128.

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

2008

Schiller, Eryk; Starzetz, Paul; Rousseau, Franck; Duda, Andrzej (2008). Binary waypoint geographical routing in wireless mesh networks. In: 11th International Symposium on Modeling, Analysis and Simulation of Wireless and Mobile Systems, Vancouver, British Columbia, Canada, 27 November 2008 - 1 December 2008. ACM Press, 252-259.

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.

Bisson, William H; Westera, Gerrit; Schubiger, P Augustus; Scapozza, Leonardo (2008). Homology modeling and dynamics of the extracellular domain of rat and human neuronal nicotinic acetylcholine receptor subtypes α4β2 and α7. Journal of Molecular Modeling, 14(10):891-899.

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.

Banjai, L; Börm, S; Sauter, S (2008). FEM for elliptic eigenvalue problems: how coarse can the coarsest mesh be chosen? An experimental study. Computing and Visualization in Science, 11(4-6):363-372.

De Lellis, P; Di Bernardo, M; Sorrentino, F; Tierno, A (2008). Adaptive synchronization of complex networks. International Journal of Computer Mathematics, 85(8):1189-1218.

Kern, A; Heid, C; Steeb, W H; Stoop, N; Stoop, R (2008). Biophysical parameters modification could overcome essential hearing gaps. PLoS Computational Biology, 4(8):e1000161.

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.

Panchaphongsaphak, Bundit; Riener, Robert; Brygg, Ullmer; Burgkart, Rainer; Ravi, Nishkam (2008). The Hacking Tradition. IEEE Pervasive Computing, 7(3):70-71.

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.

Zambon, M (2008). An example of coisotropic submanifolds C1-close to a given coisotropic submanifold. Differential Geometry and its Applications, 26(6):635-637.

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

Bertoin, Jean (2008). Two-parameter Poisson-Dirichlet measures and reversible exchangeable fragmentation-coalescence processes. Combinatorics, Probability & Computing, 17(3):329-337.

2007

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.

Bernstein, Abraham; Ekanayake, Jayalath; Pinzger, Martin (2007). Improving defect prediction using temporal features and non linear models. In: Proceedings of the International Workshop on Principles of Software Evolution, Cavtat, Croatia, 1 September 2007. IEEE Computer Society, 11-18.

Uwate, Y; Nishio, Y; Stoop, R (2007). Scale-rule selection of affordable neural network for chaotic time series learning. In: European Conference on Circuit Theory and Design (ECCTD) 2007, Sevilla, Spain, 26 August 2007 - 30 August 2007. Proceedings of European Conference on Circuit Theory and Design (ECCTD) 2007, 811-814.

Schneider, G; Kaljurand, K; Rinaldi, Fabio; Kuhn, T (2007). Pro3Gres parser in the CoNLL domain adaptation shared task. In: ACL Conference, Workshop on Computational Natural Language Learning (CoNLL-XI) Shared Task, Prague, June 2007, 1161-1165.

Fisher, J; Piterman, N; Hajnal, A; Henzinger, T A (2007). Predictive modeling of signaling crosstalk during C. elegans vulval development. PLoS Computational Biology, 3(5):e92.

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.

Bächtold, M (2007). Ricci flat metrics with bidimensional null orbits and non-integrable orthogonal distribution. Differential Geometry and its Applications, 25(2):167-176.

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

Kumar, S; Stephan, K E; Warren, J D; Friston, K J; Griffiths, T D (2007). Hierarchical processing of auditory objects in humans. PLoS Computational Biology, 3(6):e100.

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.

Hackbusch, W; Kress, W; Sauter, S A (2007). Sparse convolution quadrature for time domain boundary integral formulations of the wave equation by cutoff and panel-clustering. In: Schanz, M; Steinbach, O. Boundary element analysis. Berlin: Springer, 113-134.

Weber, A P; Hahnloser, Richard H R (2007). Spike correlations in a songbird agree with a simple Markov population model. PLoS Computational Biology, 3(12):e249.

2006

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

Arratia, R; Barbour, A D; Tavaré, S (2006). A tale of three couplings: Poisson-Dirichlet and GEM approximations for random permutations. Combinatorics, Probability & Computing, 15(1-2):31-62.

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 A (2006). Coarsening of boundary-element spaces. Computing, 77(3):253-273.

Sauter, S A; 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.

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.

Wu, Y; Price, B; Isenegger, D; Fischlin, A; Allgöwer, B; Nüesch, D (2006). Real-time 4D visualization of migratory insect dynamics within an integrated spatiotemporal system. Ecological Informatics, 1(2):179-187.

2005

Barone-Adesi, Giovanni; Rasmussen, Henrik; Ravanelli, Claudia (2005). An option pricing formula for the GARCH diffusion model. Computational Statistics & Data Analysis, 49(2):287-310.

Barbour, A D; Granovsky, B (2005). Random combinatorial structures: the convergent case. Journal of Combinatorial Theory, Series A, 109(2):203-220.

Bernstein, Abraham; Provost, Foster; Hill, Shawndra (2005). Toward intelligent assistance for a data mining process: an ontology-based approach for cost-sensitive classification. IEEE Transactions on Knowledge and Data Engineering, 17(4):503-518.

2004

Babuska, I; Sauter, Stefan A (2004). Efficient solution of lattice equations by the recovery method. I. Scalar elliptic problems. Computing and Visualization in Science, 7(3-4):113-119.

2003

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.

Feuchter, D; Heppner, I; Sauter, S A; Wittum, G (2003). Bridging the gap between geometric and algebraic multi-grid methods. Computing and Visualization in Science, 6(1):1-13.

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

2002

Butler, R W; Paolella, Marc S (2002). Calculating the density and distribution function for the singly and doubly noncentral F. Statistics and Computing, 12(1):9-16.

2001

Baudis, Michael; Cleary, Michael L (2001). Progenetix.net: an online repository for molecular cytogenetic aberration data. Bioinformatics, 17(12):1228-1229.

Chipot, M; Elfanni, A (2001). Some remarks on nonuniqueness of minimizers for discrete minimization problems. Journal of Applied Analysis, 7(2):191-208.

2000

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

1999

Constantin, A (1999). Nonlinear alternative: application to an integral equation. Journal of Applied Analysis, 5(1):119-123.

Eichelsbacher, Peter; Roos, Malgorzata (1999). Compound poisson approximation for dissociated random variables via Stein's method. Combinatorics, Probability & Computing, 8(4):335-346.

Arratia, R; Barbour, A D; Tavaré, S (1999). On Poisson-Dirichlet limits for random decomposable combinatorial structures. Combinatorics, Probability & Computing, 8(3):193-208.

Cakir, I; Chryssaphinou, O; Månsson, M (1999). On a conjecture by Eriksson concerning overlap in strings. Combinatorics, Probability & Computing, 8(5):429-440.

Arratia, R; Barbour, A D; Tavaré, S (1999). The Poisson-Dirichlet distribution and the scale-invariant Poisson process. Combinatorics, Probability & Computing, 8(5):407-416.

Hummel, C; Schroeder, Viktor (1999). Tits geometry of cocompact real-analytic Hadamard manifolds of dimension 4. Differential Geometry and its Applications, 11(2):129-143.

1998

Smarandache, R; Rosenthal, J (1998). A state space approach for constructing MDS rate 1/n convolutional codes. In: 1998 Information Theory Workshop. Piscataway, NJ: IEEE, 116-117.

1997

Barbour, A D; Godbole, A; Qian, J (1997). Imperfections in random tournaments. Combinatorics, Probability & Computing, 6(1):1-15.

1995

Stark, D (1995). First occurrence in pairs of long words: a Penney-ante conjecture of Pevzner. Combinatorics, Probability & Computing, 4(3):279-285.

Chipot, M (1995). The use of Young measures for constructing minimizing sequences in the calculus of variations. Journal of Applied Analysis, 1(1):71-81.

1994

Barbour, A D; Tavaré, S (1994). A rate for the Erdős-Turán law. Combinatorics, Probability & Computing, 3(2):167-176.

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

1993

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

1989

Barbour, A D; Karoński, Michal; Ruciński, Andrzej (1989). A central limit theorem for decomposable random variables with applications to random graphs. Journal of Combinatorial Theory. Series B, 47(2):125-145.