Publications of Vebjorn Ljosa

Mark-Anthony Bray, Sigrun M Gustafsdottir, Mohammad H Rohban, Shantanu Singh, Vebjorn Ljosa, Katherine L Sokolnicki, Joshua A Bittker, Nicole E Bodycombe, Vlado Dančík, Thomas P Hasaka, Cindy S Hon, Melissa M Kemp, Kejie Li, Deepika Walpita, Mathias J Wawer, Todd R Golub, Stuart L Schreiber, Paul A Clemons, Alykhan F Shamji, and Anne E Carpenter:
“A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay,”
Gigascience, 2017, doi:10.1093/gigascience/giw014.
Abstract | Paper (PDF) | Publisher's page

David Dao, Adam N. Fraser, Jane Hung, Vebjorn Ljosa, Shantanu Singh, and Anne E. Carpenter:
“CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets,”
Bioinformatics, 32(20):3210–3212, 2016, doi:10.1093/bioinformatics/btw390.
Abstract | Paper (PDF) | Publisher's page

Shantanu Singh, Xiaoyun Wu, Vebjorn Ljosa, Mark-Anthony Bray, Federica Piccioni, David E. Root, John G. Doench, Jesse S. Boehm, and Anne E. Carpenter:
“Morphological Profiles of RNAi-Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects,”
PLoS One, 2015, doi:10.1371/journal.pone.0131370.
Abstract | Paper (PDF) | Publisher's page

Mathias J. Wawer, Kejie Li, Sigrun M. Gustafsdottir, Vebjorn Ljosa, Nicole E. Bodycombe, Melissa A. Marton, Katherine L. Sokolnicki, Mark-Anthony Bray, Melissa M. Kemp, Ellen Winchester, Bradley Taylor, George B. Grant, C. Suk-Yee Hon, Jeremy R. Duvall, J. Anthony Wilson, Joshua A. Bittker, Vlado Dančík, Rajiv Narayan, Aravind Subramanian, Wendy Winckler, Todd R. Golub, Anne E. Carpenter, Alykhan F. Shamji, Stuart L. Schreiber, and Paul E. Clemons:
“Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling,”
Proceedings of the National Academy of Sciences of the United States of America, vol. 111, no. 30, 2014, doi:10.1073/pnas.1410933111.
Abstract | Paper (PDF) | Publisher's page

Sigrun M. Gustafsdottir*, Vebjorn Ljosa*, Katherine L. Sokolnicki, J. Anthony Wilson, Deepika Walpita, Melissa M. Kemp, Kathleen Petri Seiler, Hyman A. Carrel, Todd R. Golub, Stuart L. Schreiber, Paul A. Clemons, Anne E. Carpenter, and Alykhan F. Shamji:
“Multiplex Cytological Profiling Assay to Measure Diverse Cellular States,”
PLoS One, 2014, doi:10.1371/journal.pone.0080999.
Abstract | Paper (PDF) | Publisher's page

Vebjorn Ljosa, Peter D. Caie, Rob ter Horst, Katherine L. Sokolnicki, Emma L. Jenkins, Sandeep Daya, Mark E. Roberts, Thouis R. Jones, Shantanu Singh, Auguste Genovesio, Paul A. Clemons, Neil O. Carragher, and Anne E. Carpenter:
“Comparison of methods for image-based profiling of cellular morphological responses to small-molecule treatment,”
Journal of Biomolecular Screening, 2013, doi:10.1177/1087057113503553.
Abstract | Paper (PDF) | Publisher's page

Vebjorn Ljosa, Katherine L. Sokolnicki, and Anne E. Carpenter:
“Annotated high-throughput microscopy image sets for validation,”
Nature Methods, 9(7), p. 637, 2012, doi:10.1038/nmeth.2083.
Paper (PDF) | Publisher's page

Carolina Wählby, Lee Kamentsky, Zihan H. Liu, Tammy Riklin-Raviv, Annie L. Conery, Eyleen J. O'Rourke, Katherine L. Sokolnicki, Orane Visvikis, Vebjorn Ljosa, Javier E. Irazoqui, Polina, Golland, Gary, Ruvkun, Frederick M. Ausubel, and Anne E. Carpenter:
“An image analysis toolbox for high-throughput C. elegans assays,”
Nature Methods, 9(7), p. 714–716, 2012, doi:10.1038/nmeth.1984.
Abstract | Paper (PDF) | Publisher's page

Lee Kamentsky, Thouis R. Jones, Adam Fraser, Mark-Anthony Bray, David J. Logan, Katherine L. Madden, Vebjorn Ljosa, Curtis Rueden, Kevin W. Eliceiri, and Anne E. Carpenter:
“Improved structure, function, and compatibility for CellProfiler: modular high-throughput image analysis software,”
Bioinformatics, 2011, doi:10.1093/bioinformatics/btr095.
Abstract | Paper (PDF) | Publisher's page

Tammy Riklin-Raviv, Vebjorn Ljosa, Annie L. Conery, Frederick M. Ausubel, Anne E. Carpenter, Polina Golland, and Carolina Wählby:
“Morphology-Guided Graph Search for Untangling Objects: C. elegans Analysis,”
in Proceedings of the 13th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), p. 634-641, 2010, doi:10.1007/978-3-642-15711-0_79.
Abstract | Paper (PDF) | Publisher's page

Carolina Wählby, Tammy Riklin-Raviv, Vebjorn Ljosa, Annie L. Conery, Polina Golland, Frederick M. Ausubel, and Anne E. Carpenter:
“Resolving clustered worms via probabilistic shape models,”
in Proceedings of the IEEE International Symposium on Biomedical Imaging (ISBI), p. 552–555, April, 2010, doi:10.1109/ISBI.2010.5490286.
Abstract | Paper (PDF) | Publisher's page

Vebjorn Ljosa and Anne E. Carpenter:
“Introduction to the Quantitative Analysis of Two-Dimensional Fluorescence Microscopy Images for Cell-Based Screening,”
PLoS Computational Biology, 5(12):e10000603, 2009, doi:10.1371/journal.pcbi.1000603.
Abstract | Paper (PDF) | Publisher's page

Vebjorn Ljosa, Piyush B. Gupta, Thouis R. Jones, Eric S. Lander, and Anne E. Carpenter:
“Large-scale learning of cellular phenotypes from images,”
in RECOMB Systems Biology, 2009.
Peer-reviewed abstract and talk
Paper (PDF) | Slides (PDF) | Movie

Arnab Bhattacharya and Vebjorn Ljosa:
“Image Management for Biological Data,”
in Encyclopedia of Database Systems, M. Tamer Özsu and Ling Liu, Eds., Springer, 2009, ISBN 978-0-387-35544-3 (print), ISBN 978-0-387-39940-9 (online), doi:10.1007/978-0-387-39940-9_629.
Publisher's page

Vebjorn Ljosa and Ambuj K. Singh:
“Probabilistic Querying and Mining of Biological Images,”
in Managing and Mining Uncertain Data, Charu C. Aggarwal, Ed., p. 461–482, Springer, February, 2009, ISBN 978-0-387-09689-6.
Abstract | Publisher's page

Vebjorn Ljosa and Anne E. Carpenter:
“High-throughput screens for fluorescent dye discovery,”
Trends in Biotechnology, 26(10), p. 527–530, 2008, doi:10.1016/j.tibtech.2008.06.008.
Abstract | Manuscript (PDF) | Publisher's page

Vebjorn Ljosa and Ambuj K. Singh:
“APLA: Indexing Arbitrary Probability Distributions,”
in Proceedings of the 23rd International Conference on Data Engineering (ICDE), p. 946-955, April, 2007, doi:10.1109/ICDE.2007.367940.
Abstract | Paper (PDF) | Publisher's page

Vebjorn Ljosa and Ambuj K. Singh:
“Probabilistic Segmentation and Analysis of Horizontal Cells,”
in Proceedings of the 2006 IEEE International Conference on Data Mining (ICDM), p. 980-985, December, 2006, doi:10.1109/ICDM.2006.129.
Abstract | Paper (PDF) | Slides (PDF) | Publisher's page | Software

Vebjorn Ljosa and Ambuj K. Singh:
“Probabilistic segmentation of horizontal cells,”
in Proceedings of the 2006 workshop on multiscale biological imaging, data mining & informatics (Bioimage Informatics), p. 39–40, September, 2006.
Abstract | Paper (PDF) | Software

Vebjorn Ljosa, Arnab Bhattacharya, and Ambuj K. Singh:
“LB-Index: A Multi-Resolution Index Structure for Images,”
in Proceedings of the 22nd International Conference on Data Engineering (ICDE), April, 2006, doi:10.1109/ICDE.2006.85.
Peer-reviewed short paper and Poster.
Paper (PDF) | Publisher's page | Data

Vebjorn Ljosa, Arnab Bhattacharya, and Ambuj K. Singh:
“Indexing Spatially Sensitive Distance Measures Using Multi-Resolution Lower Bounds,”
in Proceedings of the 10th International Conference on Extending Database Technology (EDBT), p. 865-883, March, 2006, doi:10.1007/11687238_51.
Abstract | Paper (PDF) | Slides (PDF) | Publisher's page | Data

Arnab Bhattacharya, Vebjorn Ljosa, Jia-Yu Pan, Mark R. Verardo, Hyungjeong Yang, Christos Faloutsos, and Ambuj K. Singh:
“ViVo: Visual vocabulary construction for mining biomedical images,”
in Proceedings of the Fifth IEEE International Conference on Data Mining (ICDM), p. 50–57, November, 2005, doi:10.1109/ICDM.2005.151.
Received one of five "best student paper" awards.
Abstract | Paper (PDF) | Publisher's page

Ambuj K. Singh, Arnab Bhattacharya, and Vebjorn Ljosa:
“Current challenges in bioimage database design,”
in Proceedings of the International Workshop on Bioimage Data Mining and Informatics, IEEE Computational Systems Bioinformatics Conference (CSB), p. 375–379, August, 2005, doi:10.1109/CSBW.2005.47.
Invited talk and abstract.
Abstract | Paper (PDF) | Publisher's page

Chao-I Chen, Xiaofang Lei, Vebjorn Ljosa, Thomas A. McCloskey, Chiou-Wei Tsai, S. Rao Jammalamadaka, Joel H. Rothman, and Ambuj K. Singh:
“A Bayesian approach toward analyzing the network of genes involved in C. elegans programmed cell death,”
West Coast Worm Meeting, 2004.
Peer-reviewed abstract, talk, and poster.
Abstract | Publisher's page

Tamer Kahveci, Vebjorn Ljosa, and Ambuj K. Singh:
“Speeding up whole-genome alignment by indexing frequency vectors,”
Bioinformatics, 20(13), p. 2122–2134, 2004, doi:10.1093/bioinformatics/bth212.
Abstract | Paper (PDF) | Publisher's page | Software

Last updated: 2018-10-29