Research Output

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2018

A single pressure pulse-actuated 3D-printed microfluidic tip for high throughput dispensing of C. elegans worms

Chaturvedi, N., Baban, N. S., Sofela, S. O., Orozaliev, A., Giakoumidis, N., Kim, J., Gunsalus, K. C. & Song, Y. A., Jan 1 2018, 22nd International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2018. Chemical and Biological Microsystems Society, p. 1557-1559 3 p. (22nd International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2018; vol. 3).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2016

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. Wu, X., Tuzhilin, A., Xiong, H., Dy, J. G., Aggarwal, C., Zhou, Z-H. & Cui, P. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 639-645 7 p. 7395727. (Proceedings - 15th IEEE International Conference on Data Mining Workshop, ICDMW 2015).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2014

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: Chapter in Book/Report/Conference proceedingConference 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. (2014 IEEE International Conference on Image Processing, ICIP 2014).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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. (Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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. (2014 IEEE International Conference on Image Processing, ICIP 2014).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2013

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. p. 669-674 6 p. (VISAPP 2013 - Proceedings of the International Conference on Computer Vision Theory and Applications; vol. 1).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2012

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: Chapter in Book/Report/Conference proceedingConference contribution

Simultaneous reconstruction of multiple signaling pathways via the prize-collecting steiner forest problem

Tuncbag, N., Braunstein, A., Pagnani, A., Huang, S. S. C., Chayes, J., Borgs, C., Zecchina, R. & Fraenkel, E., 2012, Research in Computational Molecular Biology - 16th Annual International Conference, RECOMB 2012, Proceedings. p. 287-301 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 7262 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2011

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. (Advances in Neural Information Processing Systems 24: 25th Annual Conference on Neural Information Processing Systems 2011, NIPS 2011).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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. (ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2010

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. (Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2009

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. IEEE Computer Society, p. 5448-5451 4 p. 5334018. (Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2008

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. (8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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. (Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2007

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. 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: Chapter in Book/Report/Conference proceedingConference contribution

2006

Identification of over-represented combinations of transcription factor binding sites in sets of co-expressed genes

Huang, S. S., Fulton, D. L., Arenillas, D. J., Perco, P., Ho Sui, S. J., Mortimer, J. R. & Wasserman, W. W., 2006, Proceedings of the 4th Asia-Pacific Bioinformatics Conference, APBC 2006. p. 247-256 10 p. (Series on Advances in Bioinformatics and Computational Biology; vol. 3).

Research output: Chapter in Book/Report/Conference proceedingConference 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: Chapter in Book/Report/Conference proceedingConference contribution

2002

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. International Society for Horticultural Science, p. 39-45 7 p. (Acta Horticulturae; vol. 593).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2001

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: Chapter in Book/Report/Conference proceedingConference contribution

1992

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: Chapter in Book/Report/Conference proceedingConference contribution

1990

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. p. 75-92 18 p. (Advances in Experimental Medicine and Biology; vol. 265).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1989

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: Chapter in Book/Report/Conference proceedingConference contribution

1987

MATHEMATICAL MODELS IN PHYSIOLOGY.

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: Chapter in Book/Report/Conference proceedingConference contribution

1983

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: Chapter in Book/Report/Conference proceedingConference contribution