Lewis-Sigler Institute for Integrative Genomics

Research output

Research output per year 1965 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024

• 2508 Article
• 208 Review article
• 129 Comment/debate
• 65 Conference contribution
• 167 More
  • 50 Chapter
  • 29 Editorial
  • 29 Short survey
  • 25 Letter
  • 17 Paper
  • 14 Conference article
  • 1 Book
  • 1 Foreword/postscript
  • 1 Innovation

Research output per year

Research output per year

Search results

• 2024

  DeST-OT: Alignment of Spatiotemporal Transcriptomics Data

  Halmos, P., Liu, X., Gold, J., Chen, F., Ding, L. & Raphael, B. J., 2024, Research in Computational Molecular Biology - 28th Annual International Conference, RECOMB 2024, Proceedings. Ma, J. (ed.). Springer Science and Business Media Deutschland GmbH, p. 434-437 4 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 14758 LNCS).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Transcriptomics 100%
  • Descendant Cell 100%
  • Plausibility 100%
  • Gene Expression 40%
  • Tissue Slice 40%

• Inferring Allele-Specific Copy Number Aberrations and Tumor Phylogeography from Spatially Resolved Transcriptomics

  Ma, C., Balaban, M., Liu, J., Chen, S., Ding, L. & Raphael, B. J., 2024, Research in Computational Molecular Biology - 28th Annual International Conference, RECOMB 2024, Proceedings. Ma, J. (ed.). Springer Science and Business Media Deutschland GmbH, p. 466-469 4 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 14758 LNCS).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Allele 100%
  • Transcriptomics 100%
  • Phylogeography 100%
  • Gene Expression 66%
  • Genetics 33%

• Mapping the Topography of Spatial Gene Expression with Interpretable Deep Learning

  Chitra, U., Arnold, B. J., Sarkar, H., Ma, C., Lopez-Darwin, S., Sanno, K. & Raphael, B. J., 2024, Research in Computational Molecular Biology - 28th Annual International Conference, RECOMB 2024, Proceedings. Ma, J. (ed.). Springer Science and Business Media Deutschland GmbH, p. 368-371 4 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 14758 LNCS).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Gene Expression 100%
  • Interpretable Deep Learning 50%
  • Spatial Markers 50%
  • Transcriptomics 20%
  • Marker Gene 20%

• Maximum Likelihood Inference of Time-Scaled Cell Lineage Trees with Mixed-Type Missing Data

  Mai, U., Chu, G. & Raphael, B. J., 2024, Research in Computational Molecular Biology - 28th Annual International Conference, RECOMB 2024, Proceedings. Ma, J. (ed.). Springer Science and Business Media Deutschland GmbH, p. 360-363 4 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 14758 LNCS).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Tree 100%
  • Cell Lineage 100%
  • Lineages 100%
  • Clustered Regularly Interspaced Short Palindromic Repeat 80%
  • Lineage Analysis 66%
• 2022

  A Maximum Parsimony Principle for Multichromosomal Complex Genome Rearrangements

  Simonaitis, P. & Raphael, B. J., Sep 1 2022, 22nd International Workshop on Algorithms in Bioinformatics, WABI 2022. Boucher, C. & Rahmann, S. (eds.). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 21. (Leibniz International Proceedings in Informatics, LIPIcs; vol. 242).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Chromothripsis 100%
  • Complex Rearrangement 100%
  • Human Genome 50%
  • Genome Sequencing 50%
  • Ill-posed Problem 33%
  1 Scopus citations

• Belayer: Modeling Discrete and Continuous Spatial Variation in Gene Expression from Spatially Resolved Transcriptomics

  Ma, C., Chitra, U., Zhang, S. & Raphael, B. J., 2022, Research in Computational Molecular Biology - 26th Annual International Conference, RECOMB 2022, Proceedings. Pe’er, I. (ed.). Springer Science and Business Media Deutschland GmbH, p. 372-373 2 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 13278 LNBI).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Gene Expression 100%
  • Transcriptomics 100%
  • Transcriptomics Technology 50%
  • Spatially Resolved Transcriptomics 50%

• Learning Probabilistic Protein-DNA Recognition Codes from DNA-Binding Specificities Using Structural Mappings

  Wetzel, J. L., Zhang, K. & Singh, M., 2022, Research in Computational Molecular Biology - 26th Annual International Conference, RECOMB 2022, Proceedings. Pe’er, I. (ed.). Springer Science and Business Media Deutschland GmbH, p. 363-365 3 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 13278 LNBI).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Recognition Code 100%
  • Protein-DNA Recognition 100%
  • Gene Control 100%

• NetMix2: Unifying Network Propagation and Altered Subnetworks

  Chitra, U., Park, T. Y. & Raphael, B. J., 2022, Research in Computational Molecular Biology - 26th Annual International Conference, RECOMB 2022, Proceedings. Pe’er, I. (ed.). Springer Science and Business Media Deutschland GmbH, p. 193-208 16 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 13278 LNBI).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Facilitated Diffusion 100%
  • Solution and Solubility 100%
  • Somatic Mutation 100%
  • Subnetwork 100%
  • Subnetwork Identification 33%
  1 Scopus citations
• 2021

  Intensity uniformity optimization in spatial-light-modulator-based multifocal microscope

  Amin, M. J., Petry, S., Yang, H. & Shaevitz, J. W., 2021, Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing XXVIII. Brown, T. G., Wilson, T. & Waller, L. (eds.). SPIE, 116490P. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 11649).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Uniformity Optimization 100%
  • Grid Search 66%
  • Grating Pattern 33%
  • Pixel Crosstalk 11%
  • Fixed Object 11%
• 2020

  Defining admissible rewards for high-confidence policy evaluation in batch reinforcement learning

  Prasad, N., Engelhardt, B. & Doshi-Velez, F., Feb 4 2020, ACM CHIL 2020 - Proceedings of the 2020 ACM Conference on Health, Inference, and Learning. Association for Computing Machinery, Inc, p. 1-9 9 p. (ACM CHIL 2020 - Proceedings of the 2020 ACM Conference on Health, Inference, and Learning).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  Open Access

  • Batch Reinforcement Learning 100%
  • Reinforcement Learning 100%
  • Real Application 50%
  • Reward Design 33%
  • Past Trajectories 33%
  1 Scopus citations

• Forced imbibition in stratified porous media

  Lu, N. B., Pahlavan, A. A., Browne, C. A., Amchin, D. B., Stone, H. A. & Datta, S. S., 2020, 2020 Virtual AIChE Annual Meeting. American Institute of Chemical Engineers, (AIChE Annual Meeting, Conference Proceedings; vol. 2020-November).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Imbibition 100%
  • Stratified Porous Media 100%
  • Forced Imbibition 100%
  • Energy Engineering 100%
  • Pore Space 100%

• Identifying Evolutionary Origins of Repeat Domains in Protein Families

  Aluru, C. & Singh, M., Sep 21 2020, Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, BCB 2020. Association for Computing Machinery, Inc, (Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, BCB 2020).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Domain Duplication 100%
  • Protein Family 100%
  • Tree 66%
  • Solution and Solubility 33%
  • Sequence Tree 25%
  1 Scopus citations

• Netmix: a network-structured mixture model for reduced-bias estimation of altered subnetworks

  Reyna, M. A., Chitra, U., Elyanow, R. & Raphael, B. J., 2020, Research in Computational Molecular Biology - 24th Annual International Conference, RECOMB 2020, Proceedings. Schwartz, R. (ed.). Springer, p. 169-185 17 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 12074 LNBI).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  Open Access

  • Microarrays 100%
  • Somatic Mutation 100%
  • Probability Distribution 100%
  • Gaussian Distribution 100%
  • RNA Sequencing 100%
  1 Scopus citations

• Single-cell tumor phylogeny inference with copy-number constrained mutation losses

  Satas, G., Zaccaria, S., Mon, G. & Raphael, B. J., 2020, Research in Computational Molecular Biology - 24th Annual International Conference, RECOMB 2020, Proceedings. Schwartz, R. (ed.). Springer, p. 273 1 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 12074 LNBI).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  Open Access

  • Evolutionary History 100%
  • Tumor 100%
  • Phylogenetic Tree Inference 100%
  • Tumor Cells 100%
  • Somatic mutation 100%
• 2019

  Design of an optofluidic device for the measurement of the elastic modulus of deformable particles

  Villone, M. M., Nunes, J. K., Li, Y., Stone, H. A. & Maffettone, P. L., 2019, Optical Methods for Inspection, Characterization, and Imaging of Biomaterials IV. Ferraro, P., Grilli, S., Ritsch-Marte, M., Ritsch-Marte, M. & Hitzenberger, C. K. (eds.). SPIE, 110600L. (Proceedings of SPIE - The International Society for Optical Engineering; vol. 11060).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  Open Access

  • Elastic Moduli 100%
  • Optofluidic Device 100%
  • Optical Imaging 50%
  • High-throughput Characterization 50%
  • Section Reduction 50%

• Random walks on hypergraphs with edge-dependent vertex weights

  Chitra, U. & Raphael, B. J., Jan 1 2019, 36th International Conference on Machine Learning, ICML 2019. International Machine Learning Society (IMLS), p. 2002-2011 10 p. (36th International Conference on Machine Learning, ICML 2019; vol. 2019-June).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Hypergraphs 100%
  • Edge 100%
  • Random Walk 100%
  • Edge-dependent Vertex Weights 100%
  • Spectral Theory 28%
  34 Scopus citations
• 2018

  Statistical Inference of Peroxisome Dynamics

  Galitzine, C., Beltran, P. M. J., Cristea, I. M. & Vitek, O., 2018, Research in Computational Molecular Biology - 22nd Annual International Conference, RECOMB 2018, Proceedings. Raphael, B. J. (ed.). Springer Verlag, p. 54-74 21 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10812 LNBI).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Statistical Inference 100%
  • Biochemical Model 100%
  • Peroxisome 100%
  • Dynamics 100%
  • Rate Parameter 100%
  1 Scopus citations
• 2017

  The copy-number tree mixture deconvolution problem and applications to multi-sample bulk sequencing tumor data

  Zaccaria, S., El-Kebir, M., Klau, G. W. & Raphael, B. J., 2017, Research in Computational Molecular Biology - 21st Annual International Conference, RECOMB 2017, Proceedings. Sahinalp, S. C. (ed.). Springer Verlag, p. 318-335 18 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10229 LNCS).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  Open Access

  • Bulk Sequencing 100%
  • Mixture Deconvolution 100%
  • Tree Species Mixture 100%
  • Volume 100%
  • Tree 100%
  13 Scopus citations

• Viscoelastic polymer jets induced by blister-actuated laser-induced forward transfer (BA-LIFT)

  Turkoz, E., Perazzo, A., Kim, H., Stone, H. A. & Arnold, C. B., 2017, The European Conference on Lasers and Electro-Optics, CLEO_Europe 2017. Optica Publishing Group (formerly OSA), (Optics InfoBase Conference Papers; vol. Part F82-CLEO_Europe 2017).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Laser-induced Forward Transfer 100%
  • Blister 100%
  • Viscoelastic Polymer 100%
  • Laser Induced Forward Transfer 100%
• 2016

  Hierarchical compound poisson factorization

  Basbug, M. E. & Engelhardt, B. E., 2016, 33rd International Conference on Machine Learning, ICML 2016. Weinberger, K. Q. & Balcan, M. F. (eds.). International Machine Learning Society (IMLS), p. 2665-2674 10 p. (33rd International Conference on Machine Learning, ICML 2016; vol. 4).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Poisson Factorization 100%
  • Behavior (Neuroscience) 100%
  • Epileptic Absence 100%
  • Poisson Structure 50%
  • Matrix Factorization Model 25%
  9 Scopus citations

• Regulatory principles governing tissue specificity of developmental enhancers

  Farley, E. K., Olson, K. M. & Levine, M. S., 2016, 21st Century Genetics Genes at Work, 2015. Grodzicker, T., Stillman, B. & Stewart, D. (eds.). Cold Spring Harbor Laboratory Press, p. 27-32 6 p. (Cold Spring Harbor Symposia on Quantitative Biology; vol. 80).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  Open Access

  • Tissue Specificity 100%
  • Enhancer Region 100%
  • Regulatory Principles 100%
  • Sequence Constraint 50%
  • Genomic Assay 50%
  18 Scopus citations

• Research in computational molecular biology: 20th annual conference, RECOMB 2016 Santa Monica, CA, USA, April 17–21, 2016 proceedings

  Singh, M., 2016, Research in Computational Molecular Biology - 20th Annual Conference, RECOMB 2016, Proceedings. Singh, M. (ed.). Springer Verlag, (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9649).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Annual Conference 100%
  • Computational Molecular Biology 100%
• 2015

  Coordinating Cell Cycle Remodeling with Transcriptional Activation at the Drosophila MBT

  Blythe, S. A. & Wieschaus, E. F., 2015, Current Topics in Developmental Biology: The Maternal-to-Zygotic Transition, 2015. Lipshitz, H. D. (ed.). Academic Press Inc., p. 113-148 36 p. (Current Topics in Developmental Biology; vol. 113).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Maternal-to-zygotic Transition 100%
  • Maternal to Zygotic Transition 75%
  • Major Change 33%
  • Zygotic Genome Activation 33%
  43 Scopus citations

• Observations of different oscillation modes and control of droplet sequence in alternating droplet generation

  Um, E., Kim, H., Jeong, J. & Stone, H. A., 2015, MicroTAS 2015 - 19th International Conference on Miniaturized Systems for Chemistry and Life Sciences. Chemical and Biological Microsystems Society, p. 1041-1043 3 p. (MicroTAS 2015 - 19th International Conference on Miniaturized Systems for Chemistry and Life Sciences).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Droplet Generation 100%
  • Oscillation Control 100%
  • Oscillation Mode 100%
  • Liquid 100%
  • Two-branch 33%
• 2014

  Deep supervised and convolutional generative stochastic network for protein secondary structure prediction

  Zhou, J. & Troyanskaya, O. G., 2014, 31st International Conference on Machine Learning, ICML 2014. International Machine Learning Society (IMLS), p. 1121-1129 9 p. (31st International Conference on Machine Learning, ICML 2014; vol. 2).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Generative Stochastic Networks 100%
  • Deep Supervised 100%
  • Depthwise Separable Convolution 100%
  • Protein Secondary Structure Prediction 100%
  • Deep Learning Methods 25%
  45 Scopus citations
• 2012

  Engineering flow cross-section via programmed pillars

  Amini, H., Masaeli, M., Sollier, E., Xie, Y., Ganapathysubramanian, B., Stone, H. A. & Di Carlo, D., 2012, Proceedings of the 16th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2012. Chemical and Biological Microsystems Society, p. 67-69 3 p. (Proceedings of the 16th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2012).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Flow-induced Deformation 100%
  • Single pillars 100%
  • Inertial Flow 100%
  • Fluid Stream 100%
  • Program Flow 100%

• Minimal reaction network for bistability in the MAPK signalling cascade

  Hadač, O., Schreiber, I., Přibyl, M. & Shvartsman, S. Y., 2012, AIChE 2012 - 2012 AIChE Annual Meeting, Conference Proceedings. (AIChE Annual Meeting, Conference Proceedings).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Mitogen-Activated Protein Kinase Kinase 100%
  • MAP Kinase Kinase Kinase 100%
  • Huang's Model 77%
  • Stoichiometric Network Analysis 77%

• Simultaneous acquisition of multiple focal planes for real time 3-D microscopy using ultra-high speed adaptive optics

  Duocastella, M., Sun, B., Stone, H. A. & Arnold, C. B., 2012, 2012 Conference on Lasers and Electro-Optics, CLEO 2012. IEEE Computer Society, 6326132. (2012 Conference on Lasers and Electro-Optics, CLEO 2012).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Adaptive Optics 100%
  • Microfabrication 100%
  • Focal Plane 100%
  • Simultaneous Acquisition 100%
• 2011

  Separation of magnetic beads in a microfluidic device - Modeling and experimentation

  Tsai, S. S. H., Wexler, J. S., Griffiths, I. M. & Stone, H. A., 2011, Fluids and Thermal Systems; Advances for Process Industries. PARTS A AND B ed. American Society of Mechanical Engineers (ASME), p. 615-616 2 p. (ASME 2011 International Mechanical Engineering Congress and Exposition, IMECE 2011; vol. 6, no. PARTS A AND B).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Magnetic Field 100%
  • Magnetic Properties 100%
  • Similar Systems 100%
  • Microfluidic System 100%
  • Device Modeling 100%

• Substrate-induced oscillatory activity of an enzyme regulated by multisite phosphorylation

  Liu, P., Kevrekidis, I. G. & Shvartsman, S. Y., 2011, Computing and Systems Technology Division - Core Programming Topic at the 2011 AIChE Annual Meeting. AIChE, p. 214-215 2 p. (Computing and Systems Technology Division - Core Programming Topic at the 2011 AIChE Annual Meeting; vol. 1).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Substrate-induced 100%
  • Enzyme 100%
• 2010

  Gene regulation by MAPK substrate competition

  Kim, Y., Paroush, Z., Jimenez, G. & Shvartsman, S. Y., 2010, 10AIChE - 2010 AIChE Annual Meeting, Conference Proceedings. (AIChE Annual Meeting, Conference Proceedings).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Gene Control 100%
  • Mitogen-Activated Protein Kinase 100%
  • MAPK Substrate 100%

• High-throughput end-on imaging of drosophila embryo for quantitative analysis of morphogens and signaling

  Chung, K., Kim, Y., Gong, E., Shvartsman, S. & Lu, H., 2010, 14th International Conference on Miniaturized Systems for Chemistry and Life Sciences 2010, MicroTAS 2010. p. 1676-1678 3 p. (14th International Conference on Miniaturized Systems for Chemistry and Life Sciences 2010, MicroTAS 2010; vol. 3).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Quantitative Technique 100%
  • Morphogen 100%
  • Dorsal-Ventral Patterning 50%
  • Standing 50%
  • Upright Position 50%
  3 Scopus citations

• Microfluidic magnetic multi-cell sorting

  Tsai, S. S. H. & Stone, H. A., 2010, ASME 2010 8th International Conference on Nanochannels, Microchannels, and Minichannels Collocated with 3rd Joint US-European Fluids Engineering Summer Meeting, ICNMM2010. PARTS A AND B ed. p. 875-876 2 p. (ASME 2010 8th International Conference on Nanochannels, Microchannels, and Minichannels Collocated with 3rd Joint US-European Fluids Engineering Summer Meeting, ICNMM2010; no. PARTS A AND B).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Permanent Magnet 100%
  • Magnetic Force 100%
  • Microfluidic Device 100%
  • Cell Multi 100%
  • Magnetic Polymer Beads 100%

• Origins of reduction in efficiency in microfluidic particle separation

  Lee, W., Amini, H., Stone, H. A. & Di Carlo, D., 2010, 14th International Conference on Miniaturized Systems for Chemistry and Life Sciences 2010, MicroTAS 2010. p. 381-383 3 p. (14th International Conference on Miniaturized Systems for Chemistry and Life Sciences 2010, MicroTAS 2010; vol. 1).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Microfluidics 100%
  • Particle Separation 100%
  • Flow Field 50%
  • High Concentration 50%
  • Channel Flow 50%
• 2008

  Development of laboratory and computational techniques for optimal and quantitative understanding of cellular metabolic networks

  Feng, X., Rabinowitz, J. & Rabitz, H., 2008, IPDPS Miami 2008 - Proceedings of the 22nd IEEE International Parallel and Distributed Processing Symposium, Program and CD-ROM. 4536416. (IPDPS Miami 2008 - Proceedings of the 22nd IEEE International Parallel and Distributed Processing Symposium, Program and CD-ROM).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Metabolite 100%
  • Metabolic Network 100%
  • Computational Technique 100%
  • Cell Metabolism 50%
  • Cell Culture 50%

• Systems-level analysis of epithelial patterning and morphogenesis: The control of cytoskeleton and adhesion proteins by signaling pathways

  Zartman, J., Yakoby, N., Kanodia, J. S. & Shvartsman, S. Y., 2008, AIChE100 - 2008 AIChE Annual Meeting, Conference Proceedings. (AIChE Annual Meeting, Conference Proceedings).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Epithelial Morphogenesis 100%
  • Signaling Pathway 100%
  • Cytoskeletal Proteins 100%
  • Epithelial Patterning 100%
  • System-level Analysis 100%

• The coordinated control of EGFR signaling by multiple feedback loops: An experimental and computational study in a developing tissue

  Zartman, J. J. & Shvartsman, S. Y., 2008, AIChE100 - 2008 AIChE Annual Meeting, Conference Proceedings. (AIChE Annual Meeting, Conference Proceedings).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Multiple Loops 100%
  • Epidermal Growth Factor Receptor 100%
• 2007

  Cellular-scale hydrodynamics

  Stone, H. A., 2007, Proceedings of the 11th International Conference on Miniaturized Systems for Chemistry and Life Sciences, uTAS 2007. Viovy, J.-L., Tabeling, P., Descroix, S. & Malaquin, L. (eds.). Chemical and Biological Microsystems Society, p. 38-40 3 p. (Proceedings of the 11th International Conference on Miniaturized Systems for Chemistry and Life Sciences, uTAS 2007).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Individual Cells 100%
  • Gas-liquid 100%
  • Liquid-liquid 100%
  • Cellular Scale 100%
  • Hydrodynamics 100%

• Scalable, dynamic analysis and visualization for genomic datasets

  Wallace, G., Hibbs, M., Dunham, M., Sealfon, R., Troyanskaya, O. G. & Li, K., 2007, Proceedings - 21st International Parallel and Distributed Processing Symposium, IPDPS 2007; Abstracts and CD-ROM. 4228257. (Proceedings - 21st International Parallel and Distributed Processing Symposium, IPDPS 2007; Abstracts and CD-ROM).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  Open Access

  • Princeton 100%
  • Dynamic Analysis 100%
  • Dynamic Visualization 100%
  • Genomic Datasets 100%
  • Data Visualization 100%

• Systems support for remote visualization of genomics applications over wide area networks

  Bongo, L. A., Wallace, G., Larsen, T., Li, K. & Troyanskaya, O. G., 2007, Distributed, High-Performance and Grid Computing in Computational Biology International Workshop, GCCB 2006, Proceedings. Springer Verlag, p. 157-174 18 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4360 LNBI).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Remote Visualization 100%
  • Remote Environment 50%
  • Bioinformatics Researcher 50%
  • Remote Desktop 33%
  • Collaborative Investigation 33%
• 2006

  A graphical model for predicting protein molecular function

  Engelhardt, B. E., Jordan, M. I. & Brenner, S. E., 2006, ACM International Conference Proceeding Series - Proceedings of the 23rd International Conference on Machine Learning, ICML 2006. p. 297-304 8 p. (ACM International Conference Proceeding Series; vol. 148).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Graphical Models 100%
  • Molecular Function 100%
  • Amino Acid Sequence 100%
  • Protein Function 100%
  • Peptide Sequence 100%
  3 Scopus citations

• A graphical model for predicting protein molecular function

  Engelhardt Martin, B., Jordan, M. I. & Brenner, S. E., 2006, ICML 2006 - Proceedings of the 23rd International Conference on Machine Learning. p. 297-304 8 p. (ICML 2006 - Proceedings of the 23rd International Conference on Machine Learning; vol. 2006).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Protein Function 100%
  • Peptide Sequence 100%
  • Protein Family 50%
  • Phylogenetic Tree 50%
  • Deaminase 50%
  8 Scopus citations

• Efficient representation as a design principle for neural coding and computation

  Bialek, W., De Ruyter Van Steveninck, R. R. & Tishby, N., 2006, Proceedings - 2006 IEEE International Symposium on Information Theory, ISIT 2006. p. 659-663 5 p. 4036045. (IEEE International Symposium on Information Theory - Proceedings).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  Open Access

  • Systems Model 100%
  • Sensory Input 100%
  • Neural Coding 100%
  • Internal Representation 33%
  • Sensory World 33%
  38 Scopus citations
• 2005

  A general methodology for integration of microarray data

  Huttenhower, C. & Troyanskaya, O., 2005, 2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts. p. 109 1 p. 1540561. (2005 IEEE Computational Systems Bioinformatics Conference, Workshops and Poster Abstracts).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Microarrays 100%
  • Microarray Data 100%

• Cell depletion in synthetic micro-thrombosis: On the enhanced FåHraeus effect

  Faivre, M., Abkarian, M., Bikraj, K. & Stone, H. A., Dec 1 2005, 05AIChE: 2005 AIChE Annual Meeting and Fall Showcase, Conference Proceedings. 1 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Cell Depletion 100%
  • Microthrombi 100%
  • Free Layer 100%
  • Cell-free Layer 66%
  • Cell Deformability 50%

• Dynamic scalable visualization for collaborative scientific applications

  Li, K., Hibbs, M., Wallace, G. & Troyanskaya, O. G., 2005, Proceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005. 1420140. (Proceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005; vol. 2005).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Data Visualization 100%
  • Scientific Application 100%
  • Scalable Visualization 100%
  • Software Development Tool 75%
  • Multi-cursor 50%
  5 Scopus citations

• Hydrodynamic dispersion in narrow microchannels: Shape matters!

  Ajdari, A., Bontoux, N. & Stone, H. A., Dec 1 2005, 05AIChE: 2005 AIChE Annual Meeting and Fall Showcase, Conference Proceedings. 1 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Hydrodynamics 100%
  • Microchannel 100%
  • Microchannel Shape 100%
  • Diffusive 50%
  • Cross Section 50%
• 2004

  Ambiguous model learning made unambiguous with 1/f priors

  Atwal, G. S. & Bialek, W., 2004, Advances in Neural Information Processing Systems 16 - Proceedings of the 2003 Conference, NIPS 2003. Neural information processing systems foundation, (Advances in Neural Information Processing Systems).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Time Constraints 100%
  • Model Learning 100%
  • Learning Model 100%
  • Bayesian 100%
  • Physical Systems 50%
  1 Scopus citations

• Geometric clustering using the Information Bottleneck method

  Still, S., Bialek, W. & Bottou, L., 2004, Advances in Neural Information Processing Systems 16 - Proceedings of the 2003 Conference, NIPS 2003. Neural information processing systems foundation, (Advances in Neural Information Processing Systems).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Data Point 100%
  • Initial Condition 100%
  • Geometrical Property 100%
  • K-Means 100%
  • Deterministic Annealing 100%
  18 Scopus citations

• Optimal manifold representation of data: An information theoretic approach

  Chigirev, D. & Bialek, W., 2004, Advances in Neural Information Processing Systems 16 - Proceedings of the 2003 Conference, NIPS 2003. Neural information processing systems foundation, (Advances in Neural Information Processing Systems).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Manifold 100%
  • Theoretic Approach 100%
  • Manifold Representation 100%
  • Probabilistic Maps 100%
  • Information Distortion 50%
  8 Scopus citations