Research Output 1961 2017

Conference contribution

Positive-Unlabeled Learning in the Face of Labeling Bias

Youngs, N., Shasha, D. & Bonneau, R. Jan 29 2016 Proceedings - 15th IEEE International Conference on Data Mining Workshop, ICDMW 2015. Institute of Electrical and Electronics Engineers Inc., p. 639-645 7 p. 7395727

Research output: ResearchConference contribution

Supervised learning
Learning algorithms

Text classification for automatic detection of e-cigarette use and use for smoking cessation from twitter: A feasibility pilot

Aphinyanaphongs, Y., Lulejian, A., Brown, D. P., Bonneau, R. & Krebs, P. 2016 Pacific Symposium on Biocomputing 2016, PSB 2016. World Scientific Publishing Co. Pte Ltd, p. 480-491 12 p.

Research output: ResearchConference contribution

Public health

An integrated model of multiple-condition ChIP-Seq data reveals predeterminants of Cdx2 binding

Mahony, S., Edwards, M. D., Mazzoni, E. O., Sherwood, R. I., Kakumanu, A., Morrison, C. A., Wichterle, H. & Gifford, D. K. 2014 Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Springer Verlag, Vol. 8394 LNBI, p. 175-176 2 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8394 LNBI)

Research output: ResearchConference contribution

Ellipses from triangles

Cicconet, M., Gunsalus, K., Geiger, D. & Werman, M. Jan 28 2014 2014 IEEE International Conference on Image Processing, ICIP 2014. Institute of Electrical and Electronics Engineers Inc., p. 3626-3630 5 p. 7025736

Research output: ResearchConference contribution

Linear algebra

Mirror symmetry histograms for capturing geometric properties in images

Cicconet, M., Geiger, D., Gunsalus, K. C. & Werman, M. Sep 24 2014 Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. IEEE Computer Society, p. 2981-2986 6 p. 6909777

Research output: ResearchConference contribution

Data structures

Shape statistics for cell division detection in time-lapse videos of early mouse embryo

Cicconet, M., Gunsalus, K., Geiger, D. & Werman, M. Jan 28 2014 2014 IEEE International Conference on Image Processing, ICIP 2014. Institute of Electrical and Electronics Engineers Inc., p. 3622-3625 4 p. 7025735

Research output: ResearchConference contribution

Hough transforms
Dynamic programming

Wavelet-based circular hough transform and its application in embryo development analysis

Cicconet, M., Geiger, D. & Gunsalus, K. 2013 VISAPP 2013 - Proceedings of the International Conference on Computer Vision Theory and Applications. Vol. 1, p. 669-674 6 p.

Research output: ResearchConference contribution

Hough transforms
Dynamic programming
Computer vision
Learning systems

Modeling host-pathogen interactions: Computational biology and bioinformatics for infectious disease research

McDermott, J. E., Braun, P., Bonneau, R. & Hyduke, D. R. 2012 Pacific Syposium on Biocomputing 2012, January 3-7, 2012, Honolulu, Hawaii. p. 283-286 4 p.

Research output: ResearchConference contribution


A blind deconvolution method for neural spike identification

Ekanadham, C., Tranchina, D. & Simoncelli, E. P. 2011 Advances in Neural Information Processing Systems 24: 25th Annual Conference on Neural Information Processing Systems 2011, NIPS 2011.

Research output: ResearchConference contribution

Electric potential
Systematic errors
Clustering algorithms

Sparse decomposition of transformation-invariant signals with continuous basis pursuit

Ekanadham, C., Tranchina, D. & Simoncelli, E. P. 2011 2011 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2011 - Proceedings. p. 4060-4063 4 p. 5947244

Research output: ResearchConference contribution

Convex optimization

Rapid and accurate developmental stage recognition of C. elegans from high-throughput image data

White, A. G., Cipriani, P. G., Kao, H. L., Lees, B., Geiger, D., Sontag, E., Gunsalus, K. C. & Piano, F. 2010 2010 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, CVPR 2010. p. 3089-3096 8 p. 5540065

Research output: ResearchConference contribution

Object recognition
Function evaluation
Image analysis

The inferelator 2.0: A scalable framework for reconstruction of dynamic regulatory network models

Madar, A., Greenfield, A., Ostrer, H., Vanden-Eijnden, E. & Bonneau, R. 2009 Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009. p. 5448-5451 4 p. 5334018

Research output: ResearchConference contribution

Ordinary differential equations
Kinetic parameters

Modeling gene regulation and spatial organization of sequence based motifs

Supper, J., Kampe, C. A., Wanke, D., Berendzen, K. W., Harter, K., Bonneau, R. & Zell, A. 2008 8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008. 4696696

Research output: ResearchConference contribution

Gene Regulatory Networks
Transcription Factors
Gene expression
Transcription factors

Systems biology via redescription and ontologies (III): Protein classification using malaria parasite's temporal transcriptomic profiles

Mitrofanova, A., Kleinberg, S., Carlton, J., Kasif, S. & Mishra, B. 2008 Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008. p. 278-283 6 p. 4684903

Research output: ResearchConference contribution

Systems Biology

Gemina: A web-based epidemiology and genomic metadata system designed to identify infectious agents

Schriml, L. M., Gussman, A., Phillippy, K., Angiuoli, S., Hari, K., Goates, A., Jain, R., Davidsen, T., Ganapathy, A., Ghedin, E., Salzberg, S., White, O. & Hall, N. 2007 Intelligence and Security Informatics: Biosurveillance - Second NSF Workshop, BioSurveillance 2007, Proceedings. Vol. 4506 LNCS, p. 228-229 2 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4506 LNCS)

Research output: ResearchConference contribution


UniPep: A database of human N-linked glycosylation sites and a resource for biomarker discovery

Bonneau, R. & al. 2006 54th ASMS Conference Proceedings.

Research output: ResearchConference contribution


Modelling the effect of diffuse light on canopy photosynthesis in controlled environments

Cavazzoni, J., Volk, T., Tubiello, F. & Monje, O. 2002 IV International Symposium on Models for Plant Growth and Control in Greenhoues: Modeling for the 21st Century - Agronomic and Greenhouse Crop Models. Vol. 593, p. 39-45 7 p. (Acta Horticulturae; vol. 593)

Research output: ResearchConference contribution

growth chambers
leaf angle

What is the best way to find binding site for a transcription factor?

Shasha, D., Benfey, P. N. & Birnbaum, K. 2001 Integrating the genome sequence, sequence variation and gene expression, September 28-30, 2001, Cold Spring Harbor, New York.

Research output: ResearchConference contribution


Crop growth and associated life support for a lunar farm

Volk, T. & Cullingford, H. 1992 Proceedings of the Second Conference on Lunar Bases and Space Activities of the 21st Century, Houston, TX, April 5-7, 1988. Mendell, W. W. (ed.). p. 525 (NASA Conference Publication 3166)

Research output: ResearchConference contribution


Neuropeptides as positive or negative neuronal growth regulatory factors: Effects of ACTH and Leu-enkephalin on cultured serotonergic neurons

Davila-Garcia, M. I. & Azmitia, E. C. 1990 Advances in Experimental Medicine and Biology. Vol. 265, p. 75-92 18 p.

Research output: ResearchConference contribution

Leucine Enkephalin
Serotonergic Neurons
Adrenocorticotropic Hormone
Intercellular Signaling Peptides and Proteins

Life sciences and space research XXIII: Natural and artificial ecosystems

MacElroy, R. D., Tibbitts, T. W. & Volk, T. 1989 Proceedings of the Topical Meeting of the COSPAR Interdisciplinary Scientific Commission F (Meetings F9, F10, F11 and F12) of the COSPAR Twenty-seventh Plenary Meeting, Espoo, Finland, July 18-29, 1988.

Research output: ResearchConference contribution



Peskin, C. S., McQueen, D. M., Fogelson, A. L., Tranchina, D., Lacker, H. M. & Novick, R. P. 1987 IEEE/Engineering in Medicine and Biology Society Annual Conference. IEEE, p. 1120-1122 3 p.

Research output: ResearchConference contribution

Mathematical models

Geographical, seasonal, and secular variations of the partial pressure of CO2 in surface waters of the North Atlantic Ocean: The results of the North Atlantic TTO Program

Takahashi, T., Chipman, D. & Volk, T. 1983 Proceedings: Carbon Dioxide Research Conference: Carbon Dioxide, Science and Consensus. US Department of Energy, p. 123-146

Research output: ResearchConference contribution