Health Data Lab

Contact: larsab@cs.uit.no

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Journal, conference, book, and workshop papers

  1. Louise Ludvigsen, Mads Perner, Bjørn-Richard Pedersen, Rafael Nozal Cañadas, Anders Sildnes, Nikita Shvetsov, Trygve Andersen, Lars Ailo Bongo, and Hilde Leikny Sommerseth. Automated Coding of Historical Danish Cause of Death Data Using String Similarity. Digital Humanities in the Nordic and Baltic Countries Publications 5, no. 1 (2023): 203-221.
  2. Pavitra Chauhan, Lars Ailo Bongo, and Edvard Pedersen. Ethical Challenges of Using Synthetic Data. In Proceedings of the AAAI Symposium Series, vol. 1, no. 1, pp. 133-134. 2023.
  3. Askar Mohsen, Kristian Svendsen, Lars Småbrekke, Lars Ailo Bongo, and Einar Holsbø. “Using machine learning methods to predict all-cause somatic hospital admissions and readmissions in adults: A systematic review”. Research in Social and Administrative Pharmacy 19, no. 7 (2023): 22-23.
  4. Maria Luz Gámiz, Fernando Navas-Gómez, Rafael Nozal-Cañadas, Rocío Raya-Miranda Unsupervised and supervised learning for the reliability analysis of complex systems Quality and Reliability Engineering International. doi: 10.1002/qre.3311 ; 2023.03.18
  5. Bjørn-Jostein Singstad, Antony M. Gitau, Markus Kreutzer Johnsen, Johan Ravn, Lars Ailo Bongo, and Henrik Schirmer. Phonocardiogram classification using 1-dimensional inception time convolutional neural networks. In 2022 Computing in Cardiology (CinC), vol. 498, pp. 1-4. IEEE, 2022.
  6. Mohsen Askar, Kristian Svendsen, Lars Smabrekke, and Lars Ailo Bongo. “Using network analysis modularity to represent health code systems in machine learning models.” In Pharmacoepidemiology and drug safety, vol. 31, pp. 121-121. 111 River St, Hoboken 07030-5774, NJ USA: Wiley, 2022.
  7. Dina Benedicte Stensen, Rafael Adolfo Nozal Cañadas, Lars Småbrekke, Karina Olsen, Christopher Sivert Nielsen, Kristian Svendsen, Anne Merethe Hanssen, Johanna Sollid, Gunnar Skov Simonsen, Lars Ailo Bongo, Anne-Sofie Furberg. Social network analysis of Staphylococcus aureus carriage in a general youth population. Int J Infect Dis. 2022 Oct; 123:200-209. doi: 10.1016/j.ijid.2022.08.018.
  8. Nikita Shvetsov, Morten Grønnesby, Edvard Pedersen, Kajsa Møllersen, Lill-Tove Rasmussen Busund, Ruth Schwienbacher, Lars Ailo Bongo, Thomas Karsten Kilvaer. A Pragmatic Machine Learning Approach to Quantify Tumor-Infiltrating Lymphocytes in Whole Slide Images. Cancers 2022, 14(12), 2974; https://doi.org/10.3390/cancers14122974.
  9. Bjørn-Richard Pedersen, Einar Holsbø, Trygve Andersen, Nikita Shvetsov, Johan Ravn, Hilde Leikny Sommerseth, Lars Ailo Bongo. Lessons Learned Developing and Using a Machine Learning Model to Automatically Transcribe 2.3 Million Handwritten Occupation Codes. Historical Life Course Studies 12 2022 (January):1-17. https://doi.org/10.51964/hlcs11331.
  10. María Luz Gámiz, Anton Kalén, Rafael Nozal Cañadas, Rocío Raya Miranda Statistical supervised learning with engineering data: a case study of low frequency noise measured on semiconductor devices. in The International Journal of Advanced Manufacturing Technology 2022.
  11. Vi Ngoc-Nha Tran, Alireza Shams, Sinan Ascioglu, Antal Martinecz, Jingyi Liang, Fabrizio Clarelli, Rafal Mostowy, Ted Cohen & Pia Abel zur Wiesch. vCOMBAT: a novel tool to create and visualize a computational model of bacterial antibiotic target-binding. BMC Bioinformatics 23, 22 (2022). https://doi.org/10.1186/s12859-021-04536-3
  12. Mohsen Askar, Rafael Nozal Cañadas, Kristian Svendsen. An introduction to network analysis for studies of medication use. in Research in Social and Administrative Pharmacy 2021.
  13. Alvaro Martinez Fernandez, Lars Ailo Bongo, Edvard Pedersen. GeneNet VR: Interactive visualization of large-scale biological networks using a standalone headset. Proc. of NIK 2021.
  14. Bjørn Fjukstad, Nikita Shvetsov, Therese H Nøst, Hege Bøvelstad, Till Halbach, Einar Holsbø, Knut Hansen, Eiliv Lund, Lars Ailo Bongo. Reproducible data management and analysis using R. Advancing systems epidemiology in cancer - exploring trajectories of gene expression. Universitetsforlaget. 2021.
  15. Jo Inge Arnes, Lars Ailo Bongo. Beauty of complex designs. Advancing systems epidemiology in cancer - exploring trajectories of gene expression. Universitetsforlaget. 2021.
  16. Einar Holsbø, Kajsa Møllersen. Woes of the Practicing Omics Researcher. Advancing systems epidemiology in cancer - exploring trajectories of gene expression. Universitetsforlaget. 2021.
  17. Maria Luz Gámiz, Rafael Nozal-Cañadas, Rocío Raya-Miranda. TTT-SiZer: A graphic tool for aging trends recognition. Reliability Engineering & System Safety. vol. 202, 2020, https://doi.org/10.1016/j.ress.2020.107010.
  18. Tengel Ekrem Skar, Einar Holsbø, Kristian Svendsen, Lars Ailo Bongo. Interactive exploration of population scale pharmacoepidemiology datasets, in Proc. of the 11th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics, Virtual Event. 2020.
  19. Einar Holsbø, Karina Standahl Olsen. Metastatic Breast Cancer and Pre-Diagnostic Blood Gene Expression Profiles—The Norwegian Women and Cancer (NOWAC) Post-Genome Cohort. Frontiers in oncology. 2020 Oct 15;10:2277.
  20. Einar Holsbø, Vittorio Perduca, Lars Ailo Bongo, Eiliv Lund, Etienne Birmelé, (2020). Predicting breast cancer metastasis from whole-blood transcriptomic measurements. BMC Research Notes, 13(1), 1-5.
  21. Mike Voets, Kajsa Møllersen, Lars Ailo Bongo. Reproduction study using public data of: Development and validation of a deep learning algorithm for detection of diabetic retinopathy in retinal fundus photographs. PLoS ONE 14(6): e0217541.
  22. Dong, C, Metzger, M, Holsbø, E, Perduca, V, Carbonnel, F. Systematic review with meta‐analysis: mortality in acute severe ulcerative colitis. Aliment Pharmacol Ther. 2019; 00: 1– 27.
  23. Cristina Jácome, Johan Ravn, Einar Holsbø, Juan Carlos Aviles-Solis, Hasse Melbye, Lars Ailo Bongo. Convolutional neural network for breathing phase detection in lung sounds. Sensors (Basel). 2019 Apr 15;19(8).
  24. Bjørn Fjukstad, Nina Angelvik, Morten Grønnesby, Maria Wulff Hauglann, Hedinn Gunhildrud, Fredrik Høisæther Rasch, Julianne Iversen, Margaret Dalseng, Lars Ailo Bongo. Teaching Electronics and Programming in Norwegian Schools Using the air:bit Sensor Kit. In Proceedings of the 2019 ACM Conference on Innovation and Technology in Computer Science Education. July 2019. Pages 374–380. https://doi.org/10.1145/3304221.3325527
  25. Jo Inge Arne, Randi Karlsen. Cloudless Friend-to-Friend Middleware for Smartphones. Communications in Computer and Information Science, vol 1118. Springer, Cham. 2018.
  26. Bjørn Fjukstad, Vanessa Dumeaux, Michael Hallett, Lars Ailo Bongo. Reproducible Data Analysis Pipelines for Precision Medicine. In Proceedings of the 27th Euromicro International Conference on Parallel, Distributed, and Network-Based Processing. 2019.
  27. Einar Holsbø, Vittorio Perduca. Shrinkage estimation of rate statistics. Case Studies in Business, Industry and Government Statistics. 2018; Volum 71.
  28. Kidane M. Tekle1, Sveinung Gundersen, Kjetil Klepper, Lars Ailo Bongo, Inge Alexander Raknes, Xiaxi Li, Wei Zhang, Christian Andreetta, Teshome Dagne Mulugeta, Matúš Kalaš, Morten B. Rye, Erik Hjerde, Jeevan Karloss Antony Samy, Ghislain Fornous, Abdulrahman Azab, Dag Inge Våge, Eivind Hovig, Nils Peder Willassen, Finn Drabløs, Ståle Nygård, Kjell Petersen, Inge Jonassen. Norwegian e-Infrastructure for Life Sciences (NeLS). F1000Research 2018, 7(ELIXIR):968 (doi: 10.12688/f1000research.15119.1).
  29. Yury Kiselev, Sigve Andersen, Charles Johannessen, Bjørn Fjukstad, Karina Standahl Olsen, Helge Stenvold, Samer Al-Saad, Tom Donnem, Elin Richardsen, Roy M. Bremnes & Lill-Tove Rasmussen Busund. Transcription factor pax6 as a novel prognostic factor and putative tumour suppressor in non-small cell lung cancer. Scientific reports, vol. 8, no. 1, p. 5059, 2018
  30. Inge Alexander Raknes, Lars Ailo Bongo. META-pipe Authorization service. F1000Research 2018, 7(ELIXIR):32 (doi: 10.12688/f1000research.13256.2).
  31. Bjørn Fjukstad, Nina Angelvik, Maria Wulff Hauglann, Joachim Sveia Knutsen, Morten Grønnesby, Hedinn Gunhildrud, Lars Ailo Bongo. Low-Cost Programmable Air Quality Sensor Kits in Science Education. In Proceedings of the 49th ACM Technical Symposium on Computer Science Education (SIGCSE ‘18). ACM, New York, NY, USA, 227-232. 2018.
  32. Aleksandr Agafonov, Kimmo Mattila, Cuong Duong Tuan, Lars Tiede, Inge Alexander Raknes, Lars Ailo Bongo. META-pipe cloud setup and execution. F1000Research 2017, 6(ELIXIR):2060(doi: 10.12688/f1000research.13204.1).
  33. Inge Alexander Raknes, Bjørn Fjukstad, Lars Ailo Bongo. nsroot: Minimalist Process Isolation Tool Implemented With Linux Namespaces. In Proceedings of NIK 2017.
  34. Bjørn Fjukstad, Lars Ailo Bongo. A review of scalable bioinformatics pipelines. Data Science and Engineering, 2(3), 2017
  35. Vanessa Dumeaux, Bjørn Fjukstad, Hans E. Fjosne, Jan-Ole Frantzen, Marit Muri Holmen, Enno Rodegerdts, Ellen Schlichting, Anne-Lise Børresen-Dale, Lars Ailo Bongo, Eiliv Lund, Michael Hallett. Interactions between the tumor and the blood systemic response of breast cancer patients. PLoS Computational Biology, 13(9), 2017.
  36. Bjørn Fjukstad, Vanessa Dumeaux, Karina Standahl Olsen, Michael Hallett, Eiliv Lund, Lars Ailo Bongo. [Building applications for interactive data exploration in systems biology] (http://www.biorxiv.org/content/biorxiv/early/2017/05/24/141630). in Proc. of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics. Pp 556-561. 2017.
  37. Petra ten Hoopen P, Robert D. Finn, Lars Ailo Bongo, Erwan Corre, Bruno Fosso, Folker Meyer, Alex Mitchell, Eric Pelletier, Graziano Pesole, Monica Santamaria, Nils Peder Willassen, and Guy Cochrane. The-metagenomic-data-life-cycle-standards-and-best”>The metagenomics data life-cycle: standards and best practices. GigaScience. 2017.
  38. Espen Mikal Robertsen, Hubert Denise, Alex Mitchell, Robert D. Finn, Lars Ailo Bongo, Nils Peder Willassen. ELIXIR pilot action: Marine metagenomics – towards a domain specific set of sustainable services. F1000Research. 2017.
  39. Edvard Pedersen, Lars Ailo Bongo. Large-scale Biological Meta-Database Management. Future Generation Computer Systems. Vol 67. Feb 2017.
  40. Nils Peder Willassen, Robert D. Finn, Guy Cochrane, Lars Ailo Bongo, Petra Ten Hoppen. Marine metagenomics infrastructure as driver for research and industrial innovation. In Proc. of ECCB. 2016.
  41. Edvard Pedersen, Lars Ailo Bongo. Big Biological Data Management. Book chapter in “Resource Management for Big Data Platforms and Applications”, Springer series on Computer Communications and Networks. 2016.
  42. Ove Kåven, Lars Ailo Bongo. MORTAL - Multiparadigm Optimizing Retargetable Transdisciplinary Abstraction Language. in Proc. of NIK 2015, Ålesund, Norway.
  43. Milan Mihajlovic, Lars Ailo Bongo, Raimondas Ciegis, Neki Frasheri, Dragi Kimovski, Peter Kropf, Svetozar Margenov, Maya Neytcheva, Thomas Rauber, Gudula Runger, Roman Trobec, Roel Wuyts, Roman Wyrzykowski, Jing Gong. Applications for ultrascale computing. Supercomputing Frontiers and Innovations v. 2, n. 1, June 2015. ISSN 2313-8734.
  44. Bjørn Fjukstad, Karina Standahl Olsen, Mie Jareid, Eiliv Lund, Lars Ailo Bongo. Kvik: three-tier data exploration tools for flexible analysis of genomic data in epidemiological studies. F1000Research 2015, 4:81.
  45. Lars Ailo Bongo, Edvard Pedersen, and Martin Ernstsen. Data-intensive computing infrastructure systems for unmodified biological data analysis pipelines. Lecture Notes in Bioinformatics, vol. 8623. Springer, 2015.
  46. Qian Zhu, Aaron K Wong, Arjun Krishnan, Miriam R Aure, Alicja Tadych, Ran Zhang, David C Corney, Casey S Greene, Lars A Bongo, Vessela N Kristensen, Moses Charikar, Kai Li, Olga G Troyanskaya. Targeted exploration and analysis of large cross-platform human transcriptomic compendia. Nature Methods. 12, 211–214. 2015.
  47. Edvard Pedersen, Inge Alexander Raknes, Martin Ernstsen, and Lars Ailo Bongo. Integrating Data-intensive Computing Systems with Biological Data Processing Frameworks. in Proc. of PDP 2015, IEEE. March 2015, Turku, Finland.
  48. Bjørn Fjukstad, Karina Standahl Olsen, Mie Jareid, Eiliv Lund, Lars Ailo Bongo. Kvik: Interactive exploration of genomic data from the NOWAC postgenome biobank. in Proc. of NIK 2014. November 2014, Fredrikstad, Norway.
  49. Giacomo Tartari, Lars Tiede, Einar Jakobsen Holsbø, Kenneth Knudsen, Inge Alexander Raknes, Bjørn Fjukstad, Nicolle Mode, John Markus Bjørndalen, Eiliv Lund, Lars Ailo Bongo. Mr. Clean: a tool for tracking and comparing the lineage of scientific visualization code. in Proc. of 2nd IEEE Working Conference on Software Visualization (VISSOFT 2014). September 2014, Victoria, Canada.
  50. Martin Ernstsen, Erik Kjærner-Semb, Nils P. Willassen, Lars Ailo Bongo. Mario: interactive tuning of biological analysis pipelines using iterative processing. in Proc. of 5th International Workshop on High Performance Bioinformatics and Biomedicine (HiBB). Springer LNCS, vol. 8805, 2014.
  51. Lars Ailo Bongo, Edvard Pedersen, and Martin Ernstsen. Data-intensive computing infrastructure systems for unmodified biological data analysis pipelines. in Proc. of CIBB 2014 – Eleventh International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics. June 2014, Cambridge, UK.
  52. Edvard Pedersen, Nils P. Willassen, Lars Ailo Bongo. Transparent incremental updates for Genomics Data Analysis Pipelines. in Proc. of HiBB 2013 – 4th Workshop on High Performance Bioinformatics and Biomedicine. Springer LNCS, vol 8374, 2014, pp 311-320.
  53. Christopher Park, Aaron Wong, Casey Greene, Jessica Rowland, Yuanfang Guan, Lars Ailo Bongo, Rebecca D. Burdine, Olga Troyanskaya. Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes. PLoS Computational Biology. vol 9(3), 2013.
  54. Otto Anshus, Tor-Magne Stien Hagen, Bård Fjukstad, Lars Ailo Bongo, Yong Liu, Lars Tiede. Nine Years of the Tromsø Display Wall. in POWERWALL: International Workshop on Interactive, Ultra-High-Resolution Displays, part of the ACM SIGCHI Conference on Human Factors in Computing Systems. 2013.
  55. Lars Ailo Bongo. Bulk Synchronous Visualization. in Proc. of the 2013 International Workshop on Programming Models and Applications for Multicores and Manycores. ACM, pp 21-30, Shenzhen, China, 2013.
  56. Edvard Pedersen, Nils Peder Willassen, Lars Ailo Bongo. GeStore – Incremental Computation for Metagenomic Pipelines. in Proceedings of NIK 2012. Tapir. pp. 251-254. Bodø, Norway, 2012.
  57. Lars Ailo Bongo. BSV - 1000 Window Visualization System. in Proceedings of NIK 2012. Tapir. pp. 251-254. Bodø, Norway.
  58. Aaron Wong, Christopher Park, Casey Greene, Lars Ailo Bongo, Yuanfang Guan, Olga Troyanskaya. IMP: A multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Research. vol 40, 2012.
  59. Terje André Johansen, Daniel Stødle, Lars Ailo Bongo. A Web Application Widget Library for Scalable Interactive Biological Data Visualization. in Proceedings of NIK 2011. Tapir. pp. 109-120. Tromsø, Norway.
  60. William Josephson, Lars Ailo Bongo, David Flynn, Kai Li. DFS: A File System for Virtualized Flash Storage. ACM TOS. Vol. 6, Issue 3. September 2010.
  61. William Josephson, Lars Ailo Bongo, David Flynn, Kai Li. DFS: A File System for Virtualized Flash Storage. Usenix; login. Vol. 35, Number 2. April 2010.
  62. William Josephson, Lars Ailo Bongo, David Flynn, Kai Li. DFS: A File System for Virtualized Flash Storage. in Proceedings of the 8th USENIX Conference on File and Storage Technologies (FAST ‘10). February 23–26, 2010.
  63. Lars Ailo Bongo, Grant Wallace, Tore Larsen, Kai Li, and Olga Troyanskaya. System Support for Remote Visualization of Genomics Applications over Wide Area Networks. in Proc. of The International Workshop on Distributed, High-Performance and Grid Computing in Computational Biology. Springer Lecture Notes in Bioinformatics 4360. Pp. 157-174. Eilat, Israel, 2007.
  64. Lars Ailo Bongo, Brian Vinter, Otto J. Anshus, Tore Larsen and John Markus Bjørndalen. Using Overdecomposition to Overlap Communication Latencies with Computation and Take Advantage of SMT Processors. in Proceedings of the 2006 International Conference on Parallel Processing Workshops. IEEE Computer Society. pp 239–247. Columbus, Ohio, USA. August. 2006.
  65. Lars Ailo Bongo, Otto J. Anshus and John Markus Bjørndalen. Low overhead high performance monitoring of collective communication. in Proceedings of the 2005 International Conference on Parallel Processing. IEEE Computer Society. pp 455–464. Oslo, Norway. June. 2005.
  66. Lars Ailo Bongo, Otto Anshus, John Markus Bjørndalen. Collective communication performance analysis within the communication system. in Proceedings of Euro-Par 2004. LNCS 3149, Springer 2004.
  67. Lars Ailo Bongo, Otto Anshus, John Markus Bjørndalen, Tore Larsen. Extending Collective Operations with Application Semantics for Improving Multi-cluster Performance. in Proceedings of Third International Workshop on Algorithms, Models and Tools for Parallel Computing on Heterogeneous Networks (HeteroPar04). IEEE Computer Society 2004.
  68. Otto Anshus, John Markus Bjørndalen, Lars Ailo Bongo. Experiences Parallelizing, Configuring, and Monitoring of Parallel Applications on Clusters. Parallel computing: Software Technology, Algorithms, Architectures and Applications. Elsevier 2004.
  69. Lars Ailo Bongo, Otto Anshus, John Markus Bjørndalen. EventSpace - Exposing and Observing Communication Behavior of Parallel Cluster Applications. in Proceedings of the 9th International Euro-Par Conference . Springer 2003.
  70. Lars Ailo Bongo, Otto Anshus, John Markus Bjørndalen. Using a Virtual Event Space to Understand Parallel Application Communication Behavior. in * Proc. of Norsk informatikkonferanse NIK’2003*. Tapir Akademisk Forlag 2003.
  71. John Markus Bjørndalen, Otto Anshus, Tore Larsen, Lars Ailo Bongo, Brian Vinter. Scalable Processing and Communication Performance in a Multi-Media Related Context. in Proceedings of the 28th EuroMicro Conference. 2002.

Preprints and reports

  1. Pavitra Chauhan, Mohsen Gamal Saad Askar, Bjørn Fjukstad, Lars Ailo Bongo, and Edvard Pedersen. Interoperable synthetic health data with SyntHIR to enable the development of CDSS tools. arXiv preprint arXiv:2308.02613 (2023).
  2. Per Niklas Waaler, Lars Ailo Bongo, Christina Rolandsen, and Geir F. Lorem. Simplifying and personalising health information with mobile apps: translating complex models into understandable visuals. medRxiv (2023): 2023-05.
  3. Bjørn-Richard Pedersen, Rigmor Katrine Johansen, Einar Holsbø, Hilde Sommerseth, and Lars Ailo Bongo. More efficient manual review of automatically transcribed tabular data. arXiv preprint arXiv:2306.16126 (2023).
  4. Masoud Tafavvoghi, Lars Ailo Bongo, Nikita Shvetsov, Lill-Tove Rasmussen Busund, and Kajsa Møllersen. Publicly available datasets of breast histopathology H&E whole-slide images: A systematic review. arXiv preprint arXiv:2306.01546 (2023).
  5. Per Niklas Waaler, Hasse Melbye, Henrik Schirmer, Markus Kreutzer Johnsen, Tom Dønnem, Johan Ravn, Stian Andersen, Anne Herefoss Davidsen, Juan Carlos Aviles-Solis, Michael Stylidis, Lars Ailo Bongo. Algorithm for Predicting Valvular Heart Disease from Heart Sounds in an Unselected Cohort. medRxiv 2022.11.28.22279153; doi: https://doi.org/10.1101/2022.11.28.22279153.
  6. Hasse Melbye, Johan Ravn, Mikolaj Pabiszczak, Lars Ailo Bongo, Juan Carlos Aviles Solis. Validity of deep learning algorithms for detecting wheezes and crackles from lung sound recordings in adults. medRxiv 2022.11.18.22282442; doi: https://doi.org/10.1101/2022.11.18.22282442
  7. Eiliv Lund, Marit Holden, Lill-Tove Rasmussen Busund, Igor Snapkov, Nikita Shvetsov, Lars Holden. Trajectories of gene expression, seasonal influenza, and within-host seasonal immunity: transfer value to covid-19. medRxiv 2022.03.01.22271679.
  8. Einar Holsbø, Vittorio Perduca, Lars Ailo Bongo, Eiliv Lund, Etienne Birmelé. Stratified time-course gene preselection shows a pre-diagnostic transcriptomic signal for metastasis in blood cells: a proof of concept from the NOWAC study. bioRxiv. 2018.
  9. Morten Grønnesby, Juan Carlos Aviles Solis, Einar Holsbø, Hasse Melbye, Lars Ailo Bongo. Feature Extraction for Machine Learning Based Crackle Detection in Lung Sounds from a Health Survey. arXiv, 2017.
  10. Hege Marie Bøvelstad, Einar Holsbø, Lars Ailo Bongo, and Eiliv Lund. A standard operating procedure for outlier removal in large-sample epidemiological transcriptomics datasets. biorXiv, 2017.
  11. Lars Ailo Bongo, Mikael Borg, Amelie Cornelis, Montserrat Gonzalez, Luis Gracia, Rob Hooft, Jarno Laitinen, Ilkka Lappalainen, Mikael Linden, Ludek Matyska, Steven Newhouse, Tommi Nyrönen, Michael Prochazka, Mirek Ruda, Harri Salminen, Christine Staiger, Tony Wildish. The ELIXIR Compute Platform: A Technical Services Roadmap for supporting Life Science Research in Europe. 2016.
  12. Espen Mikal Robertsen, Tim Kahlke, Inge Alexander Raknes, Edvard Pedersen, Erik Kjærner Semb, Martin Ernstsen, Lars Ailo Bongo, Nils Peder Willassen. META-pipe - Pipeline Annotation, Analysis and Visualization of Marine Metagenomic Sequence Data. ArXiv.org. 2016.
  13. Lars Ailo Bongo. The Longcut Wide Area Network Emulator: Design and Evaluation. IFI-UITØ Technical Report(53). 2005.
  14. Lars Ailo Bongo, Otto Anshus, John Markus Bjørndalen. Evaluating the Performance of the Allreduce Collective Operation on Clusters: Approach and Results. IFI-UITØ Technical Report(48). 2004.
  15. Lars Ailo Bongo, Otto Anshus, John Markus Bjørndalen. Performance Monitoring. A Report for the NOTUR Project Emerging Technologies: Cluster. 2003.
  16. Lars Ailo Bongo, Otto Anshus, John Markus Bjørndalen. Using a Virtual Event Space to Understand Parallel Application Communication Behavior. IFI-UITØ Technical Report(44). 2003.
  17. Espen S. Johnsen, Otto Anshus, John Markus Bjørndalen, Lars Ailo Bongo. Survey of execution monitoring tools for computer clusters. A Report for the NOTUR Project Emerging Technologies: Cluster. 2003.
  18. Espen S. Johnsen, Otto Anshus, John Markus Bjørndalen, Lars Ailo Bongo. Survey of optimizing techniques for parallel programs running on computer clusters. A Report for the NOTUR Project Emerging Technologies: Cluster. 2003.

Patents

  1. Analysing heart or respiratory-system sounds. UK patent application number 2212073.7.
  2. Assessing health of a heart valve. UK patent application number 2217512.9.

Theses

  1. Elias Estefano Gutierrez Riise. Improving automated underwater ship hull inspection through incremental learning & uncertainty quantification in deep learning models. Master’s thesis. Dept. of Computer Science, UiT The Arctic University of Norway. May 2023.
  2. Erling Devold. Through Space and Time. Master’s thesis. Dept. of Computer Science, UiT The Arctic University of Norway. May 2023.
  3. Mirza Aneeq Hassan Baig. Tram-tastic Cloud Computing. Master’s thesis. Dept. of Computer Science, UiT The Arctic University of Norway. May 2023.
  4. Simen Lund Kirkvik. Interactive visualizations of unstructured oceanographic data . Master’s thesis. Dept. of Computer Science, UiT The Arctic University of Norway. February 2023.
  5. Narae Park. Record linkage of Norwegian historical census data using machine learning. Master’s thesis. Dept. of Computer Science, UiT The Arctic University of Norway. August 2022.
  6. Mariel Ellingsen. First steps towards solving the café problem. Master’s thesis. Dept. of Computer Science, UiT The Arctic University of Norway. June 2022.
  7. Markus Tiller. End-to-end Trainable Ship Detection in SAR Images with Single Level Features. Master’s thesis. Dept. of Computer Science, UiT The Arctic University of Norway. June 2022.
  8. Michael Lau. Management of large geospatial datasets. Master’s thesis. Dept. of Computer Science, UiT The Arctic University of Norway. May 2022.
  9. Sidra Tahi. Can a code snippet portal contribute to greater learning outcomes in other fields of science and technology?. Master’s thesis. Dept. of Computer Science, UiT The Arctic University of Norway. June 2021.
  10. Anton Garri Fagerbakk. [Keeping Up with the Market: Extracting competencies from Norwegian job listings]. Master’s thesis. Dept. of Computer Science, UiT The Arctic University of Norway. May 2021.
  11. Alvaro Martinez Fernandez. GeneNet VR: Large biological networks in virtual teality using inexpensive hardware. Master’s thesis. Dept. of Computer Science, UiT The Arctic University of Norway. November 2020.
  12. Tengel Ekrem Skar. Scalable exploration of population-scale drug consumption data. Master’s thesis. Dept. of Computer Science, UiT The Arctic University of Norway. June 2019.
  13. Einar Holsbø. Small data: practical modeling issues in human-model -omic data. Ph. D. thesis. Dept. of Computer Science, UiT The Arctic University of Norway. February 2019.
  14. Bjørn Fjukstad. Toward Reproducible Analysis and Exploration of High-Throughput Biological Datasets. Ph. D. thesis. Dept. of Computer Science, UiT The Arctic University of Norway. January 2019.
  15. Tim Alexander Teige. Auto scaling framework, simulator, and algorithms for the META-pipe backend. Master’s thesis. Dept. of Computer Science, UiT The Arctic University of Norway. June 2018.
  16. Nina Angelvik. Data management platform for citizen science education projects. Master’s thesis. Dept. of Computer Science, UiT The Arctic University of Norway. May 2018.
  17. Mike Voets. Deep Learning: From Data Extraction to Large-Scale Analysis. Master’s thesis. Dept. of Computer Science, UiT The Arctic University of Norway. May 2018.
  18. Johan Fredrik Eggen Ravn. Detection of Wheezes and Breathing Phases using Deep Convolutional Neural Networks. Master’s thesis. Dept. of Computer Science, UiT The Arctic University of Norway. June 2017.
  19. Espen Mikal Robertsen. META-pipe – Distributed Pipeline Analysis of Marine Metagenomic Sequence Data. Ph. D. thesis. Dept. of Chemistry. UiT The Arctic University of Norway. February 2017.
  20. Edvard Pedersen. A Data Management Model For Large-Scale Bioinformatics Analysis. Ph. D. thesis. Dept. of Computer Science, UiT The Arctic University of Norway. September 2016.
  21. Jarl Fagerli. COMBUSTI/O. Abstractions facilitating parallel execution of programs implementing common I/O patterns in a pipelined fashion as workflows in Spark. Master’s thesis. Dept. of Computer Science, UiT The Arctic University of Norway. December 2015.
  22. Kenneth Knudsen. Freia: Exploring Biological Pathways Using Unity3D. Master thesis. Dept. of Computer Science, UiT The Arctic University of Norway. November 2015.
  23. Morten Grønnesby. Automated Lung Sound Analysis. Master’s thesis. Dept. of Computer Science. UiT The Arctic University of Norway. June 2016.
  24. Ove Kåven. Multiparadigm optimizing retargetable transdisciplinary abstraction language. Master thesis. Dept. of Computer Science, UiT The Arctic University of Norway. April 2015.
  25. Inge Alexander Raknes. Spark-SPELL: low-latency query-based search for gene expression compendia on cluster computers. Master thesis. Dept. of Computer Science,UiT The Arctic University of Norway. June 2014.
  26. Kenneth Knudsen. Amdex: automated meta-data extraction from KEGG pathways. Bachelor thesis. Dept. of Computer Science, UiT The Arctic University of Norwayø. June 2014.
  27. Bjørn Fjukstad. Kvik: interactive exploration of genomic data from the NOWAC postgenome biobank. Master thesis. Dept. of Computer Science, UiT The Arctic University of Norway. Mai 2014.
  28. Martin Ernstsen. Mario - A system for iterative and interactive processing of biological data. Master thesis. Dept. of Computer Science, University of Tromsø. December 2013.
  29. Edvard Pedersen. GeStore: incremental computation for metagenomic pipelines. Master thesis. Dept. of Computer Science, University of Tromsø. June 2012.
  30. Terje André Johansen. A scalable, interactive widget library for visualizing biological data. Master thesis. Dept. of Computer Science, University of Tromsø. June 2011.
  31. Daniel R. Barrett. Undergraduate thesis. Dept. of Computer Science. Princeton University.
  32. Torje Henriksen. Efficient intra-node Communication for Chip Multiprocessors. Master thesis. Dept. of Computer Science, University of Tromsø. October 2008.
  33. Espen S. Johnsen. Configuration of collective operations in LAM/MPI by use of scripting. Master thesis. Dept. of Computer Science, University of Tromsø. October 2008.
  34. Lars Ailo Bongo. Reducing the network latency and bandwidth requirements of distributed and parallel applications. PhD. Thesis. University of Tromsø. July 2007.

Project reports

  1. Markus Tiller. PointYOLOF: End-to-end Trainable Vessel Detection in SAR Images Captured by Satellites. Capstone Project. Dept. of Computer Science, Uit The Arctic University of Norway. December 2021.
  2. Tengel Skar. An efficient, interactive environment for Big Data exploration. Capstone Project. Dept. of Computer Science, University of Tromsø. December 2018.
  3. Tim Alexander Teige. Autoscaling framework and simulator for automatic META-pipe job scaling. Capstone Project. Dept. of Computer Science, University of Tromsø. December 2017.
  4. Johan Ravn. Wheeze Detection using Deep Convolutional Neural Network. Capstone Project. Dept. of Computer Science, UiT The Arctic University of Norway. December 2016.
  5. Frode Opdahl. Virtual reality. Capstone Project. Dept. of Computer Science, UiT The Arctic University of Norway. December 2016.
  6. Nina Angelvik. Low-cost portable air quality sensor kit and cloud service. Capstone Project. Dept. of Computer Science, UiT The Arctic University of Norway. December 2016.
  7. Morten Grønnesby. Pulmonary Crackle Detection Using Signal Processing and Machine Learning. Capstone Project. Dept. of Computer Science, UiT The Arctic University of Norway. December 2015.
  8. Jarl Fagerli. Big Data Facilitation and Management. Capstone Project. Dept. of Computer Science, UiT The Arctic University of Norway. December 2015.
  9. Inge Alexander Raknes. Data cleaning for biological data. Capstone Project. Dept. of Computer Science, University of Tromsø. December 2013.
  10. Bjørn Fjukstad. NOWAC Data Exploration. Capstone Project. Dept. of Computer Science, University of Tromsø. June 2013.
  11. Edvard Pedersen. Big data analysis for metagenomics. Capstone Project. Dept. of Computer Science, University of Tromsø. June 2013.

Abstracts and Posters

  1. Ross, Theodor Anton; Pöntinen, Anna Kaarina; Janice, Jessin ; Holsbø, Einar; Corander, Jukka; Hegstad, Kristin; Kampffmeyer, Michael. Leveraging machine learning for finding novel putative virulence factors in Enterococcus faecium. Poster. 6th Annual meeting National Graduate School in Infection Biology and Antimicrobials, 2022.
  2. Mathiesen, Ingeborg; Ross, Theodor Anton; Pöntinen, Anna Kaarina; Holsbø, Einar; Kampffmeyer, Michael; Johannessen, Mona; Hegstad, Kristin; Wagner, Theresa. Characterization of Putative Virulence Factors in Enterococcus faecium. Poster. 6th International Conference on Enterococci, 2023.
  3. Mehrdad Rakaee, Masoud Tafavvoghi, Elio Adib, Biagio Ricciuti, Joao Victor Machado Alessi, Alessio Cortellini, Claudia AM Fulgenzi et al. Artificial intelligence algorithm developed to predict immune checkpoint inhibitors efficacy in non–small-cell lung cancer. (2023): 9132-9132.
  4. Anders Sildnes, Kajsa Møllersen, Lill-Tove Rasmussen Busund, Vi-Ngoc-Nha Tran, Thomas K Kilvær and Lars Ailo Bongo. Detecting overfitting for very-large pathology images. Poster. Visual Intelligence days 28.10.23. Oslo, Norway
  5. Møllersen, Kajsa, Lars Ailo Bongo, and Masoud Tafavvoghi. Cancer detection for white urban Americans. NORA Annual Conference 2023 05.06. - 06.06.23, Tromsø, Norway.
  6. Asal Asgari, Helge Fredriksen and Ståle Haugset Nymo. Clustering clinical multivariate time-series with variable lengths and irregular sampling intervals. Poster at NORA Annual Conference 2023 05.06. - 06.06.23, Tromsø, Norway
  7. Anders Sildnes, Kajsa Møllersen, Lill-Tove Rasmussen Busund, Vi-Ngoc-Nha Tran, Thomas K Kilvær and Lars Ailo Bongo. Detecting overfitting for self-supervised learning with very-large pathology images. Poster. PRESIMAL 2023 14.05.23, Tromsø, Norway
  8. Rafael Adolfo Nozal Cañadas. Social network analysis of Staphylococcus aureus carriage in a general youth population. CANS day 23th of February 2023. Tromsø, Norway.
  9. Markus Tiller, Torgeir Brenn, Robert Jenssen, Lars Ailo Bongo. ShipPointYolo: End-to-end network for ship detection in SAR images. Poster. Visual Intelligence days. Oslo, 28.09.22
  10. Rigmor Katrine Johansen. GEN-Ethics: What do Norwegian women think of utilising genetic testing as part of breast cancer screening. 34th European conference on philosophy of medicine and health care. 24 – 27 august 2022. Warsaw, Poland.
  11. Markus Tiller. Lars Ailo Bongo. Robert Jenssen. Torgeir Brenn. End-to-end trainable ship detection in SAR images with single level features. Poster at NORA Annual Conference 2022. Stavanger, 9-10th of June, 2022.
  12. Helge Fredriksen, Arthur Schuchter. Segmentation of costa in 2d MRI scans utilizing the U-Net convolutional network architecture. Poster at Northern Light Deep Learning conference 10.01.22-12.01.22, Tromsø, Norway.
  13. Jarno Laitinen, Lars Ailo Bongo, Inge Alexander Raknes, Sampsa Hautaniemi. ELIXIR-FI Pouta scientific cloud services. Poster at the Elixir all-hands meeting. Berlin, Germany, June 2018.
  14. Terje Klemetsen, Inge A. Raknes, Juan Fu, Alexander Agafonov, Sudhagar V. Balasundaram, Giacomo Tartari, Espen Robertsen, Nils P. Willassen.Succession of the MAR-databases and marine metagenomics portal (MMP), coordination of marine sequenced data. Poster at the Elixir all-hands meeting. Berlin, Germany. June 2018.
  15. Nina Angelvik.Air pollution data analysis platform for computer science education projects. Poster at the 49th ACM Technical Symposium on Computer Science Education. Baltimore, USA, February 2018.
  16. Morten Grønnesby, Juan Carlos Aviles Solis, Einar Holsbø, Hasse Melbye, Lars Ailo Bongo. Machine Learning Based Crackle Detection (abstract). in Proc. of the 42nd annual conference of the International Lung Sound Association. September 2017.
  17. Johan Ravn, Juan Carlos Aviles Solis, Morten Grønnesby, Hasse Melbye, Lars Ailo Bongo. Detection of Wheezes and Breathing Phases Using Deep Convolutional Neural Networks (extended abstract).in Proc. of the 42nd annual conference of the International Lung Sound Association. September 2017.
  18. Bjørn Fjukstad, Vanessa Dumeaux, Michael Hallett, Lars Ailo Bongo. Reproducible Data Analysis Pipelines for Precision Medicine. Poster at the 6th Norwegian Cancer Symposium. Oslo, Norway, December 2017.
  19. Terje Klemetsen, et al. Novel Marine Reference Databases, The Marine Metagenomics Portal (MMP). Poster at the Elixir all-hands meeting. Rome, Italy. April 2017.
  20. Espen M. Robertsen, et al. META-pipe 2.0. Poster at the Elixir all-hands meeting. Rome, Italy. April 2017.
  21. Einar Holsbø. Predicting breast cancer metastasis from blood gene expression using time-to-diagnosis data to derive signature estimates. Poster presented at the 2017 Statistical Methods for Postgenomic Data workshop. London, UK. January 2017.
  22. Espen M. Robertsen, et al. Elixir Pilot Action: Marine metagenomics - towards user centric services. Poster at the Elixir all-hands meeting. Barcelona, Spain. March 2016.
  23. ELIXIR.NO team. ELIXIR.NO - The national technology platform for bioinformatics. Poster at NBS meeting. Tromsø, Norway. January 2016.
  24. Espen Mikal Robertsen, Edvard Pedersen, Martin Ernstsen, Tim Kalhke, Lars Ailo Bongo, Nils Peder Willassen. META-pipe – Pipeline annotation, analysis and visualization of metagenomic data. Poster at NBS meeting. Tromsø, Norway. January 2016.
  25. Karina Standahl Olsen, Einar Holsbø, Kamilla Rognmo, Sanda Krum-Hansen, Eiliv Lund. Stress related to a suspicious mammogram - potential transcriptomic effects. Norsk Epidemiologi, Supplement 2015; Volume 25.
  26. Bjørn Fjukstad, Karina Standahl Olsen, Mie Jareid, Eiliv Lund, Lars Ailo Bongo. Interactive omics data exploration in epidemiological studies. Norsk Epidemiologi, Supplement 2015; Volume 25.
  27. NeLS team. NeLS: Norwegian e-Infrastructure for Life Sciences. Poster at 2015 Galaxy Community Conference (GCC2015). Norwich, UK. July 2015.
  28. Espen M. Robertsen, et al. Elixir Pilot Action: Marine metagenomics - towards user centric services. Poster at the Elixir all-hands meeting. Hinxton, UK. March 2015.
  29. Giacomo Tartari, Lars Tiede, Einar Jakobsen Holsbø, Kenneth Knudsen, Inge Alexander Raknes, Bjørn Fjukstad, Nicolle Mode, John Markus Bjørndalen, Eiliv Lund, Lars Ailo Bongo. Mr. Clean: a tool for tracking and comparing the lineage of scientific visualization code. Poster at 2nd IEEE Working Conference on Software Visualization (VISSOFT 2014). September 2014, Victoria, Canada.
  30. Lars Ailo Bongo. Bulk Synchronous Visualization. Poster at the 2nd IEEE Symposium on Biological Data Visualization. Seattle, WA, USA. October 2012. (Extended abstract, Poster.
  31. Edvard Pedersen, Nils Peder Willassen, Lars Ailo Bongo. GeStore - Incremental Computations for Metagenomic Pipelines. Poster at Norsk Bioinformatikk Forum. Bergen, Norway. October 2012.
  32. Edvard Pedersen, Nils Peder Willassen, Lars Ailo Bongo. [GeStore - Incremental Computations for Metagenomic Pipelines]https://www.cs.uit.no/hdl/papers/gestore-poster.pdf). Poster at the 11th Annual Meeting on High Performance Computing and Infrastructure in Norway - NOTUR 2012. Tromsø, Norway. June 2012.
  33. Lars Ailo Bongo, Daniel Stødle, Grant Wallace, Tore Larsen, Kai Li and Olga Troyanskaya. System Support for Collaborative Genomics Visualizations. Poster at the 16th International Conference on Intelligent Systems for Molecular Biology. Toronto, Canada. July 2008.
  34. Lars Ailo Bongo. Dynamically adapting communication behavior of parallel applications. NOTUR gathering. Oslo, Norway. May 2003.