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Robert F. Murphy
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2020 – today
- 2024
- [j33]Huangqingbo Sun, Jiayi Li, Robert F. Murphy:
Expanding the coverage of spatial proteomics: a machine learning approach. Bioinform. 40(2) (2024) - 2023
- [j32]James C. Schaff, Anuradha Lakshminarayana, Robert F. Murphy, Frank T. Bergmann, Akira Funahashi, Devin P. Sullivan, Lucian P. Smith:
SBML level 3 package: spatial processes, version 1, release 1. J. Integr. Bioinform. 20(1) (2023) - [c46]Mingyu Feng, Neil T. Heffernan, Kelly Collins, Cristina Heffernan, Robert F. Murphy:
Implementing and Evaluating ASSISTments Online Math Homework Support At large Scale over Two Years: Findings and Lessons Learned. AIED 2023: 28-40 - 2022
- [j31]Huangqingbo Sun, Xuecong Fu, Serena Abraham, Shen Jin, Robert F. Murphy:
Improving and evaluating deep learning models of cellular organization. Bioinform. 38(23): 5299-5306 (2022) - 2021
- [j30]Huangqingbo Sun, Robert F. Murphy:
Evaluation of categorical matrix completion algorithms: toward improved active learning for drug discovery. Bioinform. 37(20): 3538-3545 (2021) - 2020
- [j29]Ying-Ying Xu, Hong-Bin Shen, Robert F. Murphy:
Learning complex subcellular distribution patterns of proteins via analysis of immunohistochemistry images. Bioinform. 36(6): 1908-1914 (2020) - [i2]Ligong Han, Robert F. Murphy, Deva Ramanan:
Learning Generative Models of Tissue Organization with Supervised GANs. CoRR abs/2004.00140 (2020)
2010 – 2019
- 2019
- [j28]Xiongtao Ruan, Robert F. Murphy:
Evaluation of methods for generative modeling of cell and nuclear shape. Bioinform. 35(14): 2475-2485 (2019) - [j27]Michael P. Snyder, Shin Lin, Amanda Posgai, Mark Atkinson, Aviv Regev, Jennifer Rood, Orit Rozenblatt-Rosen, Leslie Gaffney, Anna Hupalowska, Rahul Satija, Nils Gehlenborg, Jay Shendure, Julia Laskin, Pehr Harbury, Nicholas A. Nystrom, Jonathan C. Silverstein, Ziv Bar-Joseph, Kun Zhang, Katy Börner, Yiing Lin, Richard Conroy, Dena Procaccini, Ananda L. Roy, Ajay Pillai, Marishka Brown, Zorina S. Galis, Long Cai, Cole Trapnell, Dana Jackson, Garry P. Nolan, William James Greenleaf, Sylvia K. Plevritis, Sara Ahadi, Stephanie A. Nevins, Hayan Lee, Christian Martijn Schuerch, Sarah Black, Vishal Gautham Venkataraaman, Ed Esplin, Aaron Horning, Amir Bahmani, Xin Sun, Sanjay Jain, James S. Hagood, Gloria Pryhuber, Peter V. Kharchenko, Bernd Bodenmiller, Todd Brusko, Michael Clare-Salzler, Harry Nick, Kevin Otto, Clive Wasserfall, Marda Jorgensen, Maigan Brusko, Sergio Maffioletti, Richard M. Caprioli, Jeffrey M. Spraggins, Danielle Gutierrez, Nathan Heath Patterson, Elizabeth K. Neumann, Raymond Harris, Mark P. de Caestecker, Agnes B. Fogo, Raf Van de Plas, Ken Lau, Guo-Cheng Yuan, Qian Zhu, Ruben Dries, Peng Yin, Sinem K. Saka, Jocelyn Y. Kishi, Yu Wang, Isabel Goldaracena, Dong Hye Ye, Kristin E. Burnum-Johnson, Paul D. Piehowski, Charles Ansong, Ying Zhu, Tushar Desai, Jay Mulye, Peter Chou, Monica Nagendran, Sarah A. Teichmann, Benedict Paten, Robert F. Murphy, Jian Ma, Vladimir Yu. Kiselev, Carl Kingsford, Allyson Ricarte, Maria Keays, Sushma Anand Akoju, Matthew Ruffalo, Margaret Vella, Chuck McCallum, Leonard E. Cross, Samuel H. Friedman, Randy W. Heiland, Bruce William Herr II, Paul Macklin, Ellen M. Quardokus, Lisel Record, James P. Sluka, Griffin M. Weber, Philip D. Blood, Alexander Ropelewski, William Shirey, Robin M. Scibek, Paula M. Mabee, W. Christopher Lenhardt, Kimberly Robasky, Stavros Michailidis, John C. Marioni, Andrew Butler, Tim Stuart, Eyal Fisher, Shila Ghazanfar, Gökcen Eraslan, Tommaso Biancalani, Eeshit D. Vaishnav, Pothur Srinivas, Aaron Pawlyk, Salvatore Sechi, Elizabeth L. Wilder, James Anderson:
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nat. 574(7777): 187-192 (2019) - [j26]Timothy Majarian, Robert F. Murphy, Seema S. Lakdawala:
Learning the sequence of influenza A genome assembly during viral replication using point process models and fluorescence in situ hybridization. PLoS Comput. Biol. 15(1) (2019) - [c45]Jose Lugo-Martinez, Jörn Dengjel, Ziv Bar-Joseph, Robert F. Murphy:
Integration of Heterogeneous Experimental Data Improves Global Map of Human Protein Complexes. BCB 2019: 144-153 - 2018
- [c44]Ligong Han, Robert F. Murphy, Deva Ramanan:
Learning Generative Models of Tissue Organization with Supervised GANs. WACV 2018: 682-690 - 2017
- [j25]Xiongtao Ruan, Christoph Wülfing, Robert F. Murphy:
Image-based spatiotemporal causality inference for protein signaling networks. Bioinform. 33(14): i217-i224 (2017) - 2016
- [j24]Rory M. Donovan, José Juan Tapia, Devin P. Sullivan, James R. Faeder, Robert F. Murphy, Markus Dittrich, Daniel M. Zuckerman:
Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories. PLoS Comput. Biol. 12(2) (2016) - 2015
- [j23]Maja Temerinac-Ott, Armaghan W. Naik, Robert F. Murphy:
Deciding when to stop: efficient experimentation to learn to predict drug-target interactions. BMC Bioinform. 16: 213:1-213:10 (2015) - [j22]Gregory R. Johnson, Jieyue Li, Aabid Shariff, Gustavo K. Rohde, Robert F. Murphy:
Automated Learning of Subcellular Variation among Punctate Protein Patterns and a Generative Model of Their Relation to Microtubules. PLoS Comput. Biol. 11(12) (2015) - [c43]Devin P. Sullivan, Rohan Arepally, Robert F. Murphy, José Juan Tapia, James R. Faeder, Markus Dittrich, Jacob Czech:
Design Automation for Biological Models: A Pipeline that Incorporates Spatial and Molecular Complexity. ACM Great Lakes Symposium on VLSI 2015: 321-323 - [c42]Maja Temerinac-Ott, Armaghan W. Naik, Robert F. Murphy:
Deciding When to Stop: Efficient Experimentation to Learn to Predict Drug-Target Interactions (Extended Abstract). RECOMB 2015: 323-325 - [i1]Maja Temerinac-Ott, Armaghan W. Naik, Robert F. Murphy:
Deciding when to stop: Efficient stopping of active learning guided drug-target prediction. CoRR abs/1504.02406 (2015) - 2014
- [j21]Robert F. Murphy:
A new era in bioimage informatics. Bioinform. 30(10): 1353 (2014) - [j20]Joshua D. Kangas, Armaghan W. Naik, Robert F. Murphy:
Efficient discovery of responses of proteins to compounds using active learning. BMC Bioinform. 15: 143 (2014) - [c41]Mingyu Feng, Jeremy Roschelle, Robert F. Murphy, Neil T. Heffernan:
Using Analytics for Improving Implementation Fidelity in an Large Scale Efficacy Trial. ICLS 2014 - [c40]Mingyu Feng, Jeremy Roschelle, Neil T. Heffernan, Janet Fairman, Robert F. Murphy:
Implementation of an Intelligent Tutoring System for Online Homework Support in an Efficacy Trial. Intelligent Tutoring Systems 2014: 561-566 - 2013
- [j19]Luís Pedro Coelho, Joshua D. Kangas, Armaghan W. Naik, Elvira Osuna-Highley, Estelle Glory-Afshar, Margaret Fuhrman, Ramanuja Simha, Peter B. Berget, Jonathan W. Jarvik, Robert F. Murphy:
Determining the subcellular location of new proteins from microscope images using local features. Bioinform. 29(18): 2343-2349 (2013) - 2012
- [j18]Jieyue Li, Liang Xiong, Jeff G. Schneider, Robert F. Murphy:
Protein subcellular location pattern classification in cellular images using latent discriminative models. Bioinform. 28(12): 32-39 (2012) - [c39]Robert F. Murphy:
(3) The CellOrganizer project: An open source system to learn image-derived models of subcellular organization over time and space. BIBM 2012: 1-2 - 2011
- [j17]Charles Jackson, Estelle Glory-Afshar, Robert F. Murphy, Jelena Kovacevic:
Model building and intelligent acquisition with application to protein subcellular location classification. Bioinform. 27(13): 1854-1859 (2011) - [j16]Tien-ho Lin, Ziv Bar-Joseph, Robert F. Murphy:
Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs. J. Comput. Biol. 18(11): 1709-1722 (2011) - [j15]Tien-ho Lin, Robert F. Murphy, Ziv Bar-Joseph:
Discriminative Motif Finding for Predicting Protein Subcellular Localization. IEEE ACM Trans. Comput. Biol. Bioinform. 8(2): 441-451 (2011) - [c38]Aabid Shariff, Robert F. Murphy, Gustavo K. Rohde:
Automated estimation of microtubule model parameters from 3-D live cell microscopy images. ISBI 2011: 1330-1333 - [c37]Arvind Rao, Robert F. Murphy:
Determination of protein location diversity via analysis of immunohistochemical images from the Human Protein Atlas. ISBI 2011: 1727-1729 - [c36]Tien-ho Lin, Ziv Bar-Joseph, Robert F. Murphy:
Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs. RECOMB 2011: 204-221 - 2010
- [j14]Luís Pedro Coelho, Tao Peng, Robert F. Murphy:
Quantifying the distribution of probes between subcellular locations using unsupervised pattern unmixing. Bioinform. 26(12): 7-12 (2010) - [j13]Yanhua Hu, Elvira Osuna-Highley, Juchang Hua, Theodore Scott Nowicki, Robert Stolz, Camille McKayle, Robert F. Murphy:
Automated analysis of protein subcellular location in time series images. Bioinform. 26(13): 1630-1636 (2010) - [j12]Amr Ahmed, Andrew Arnold, Luís Pedro Coelho, Joshua D. Kangas, Abdul-Saboor Sheikh, Eric P. Xing, William W. Cohen, Robert F. Murphy:
Structured literature image finder: Parsing text and figures in biomedical literature. J. Web Semant. 8(2-3): 151-154 (2010) - [c35]Estelle Glory-Afshar, Elvira Osuna-Highley, Brian Granger, Robert F. Murphy:
A graphical model to determine the subcellular protein location in artificial tissues. ISBI 2010: 1037-1040
2000 – 2009
- 2009
- [j11]Charles Jackson, Robert F. Murphy, Jelena Kovacevic:
Intelligent Acquisition and Learning of Fluorescence Microscope Data Models. IEEE Trans. Image Process. 18(9): 2071-2084 (2009) - [c34]Robert F. Murphy, Chun-Nan Hsu, Loris Nanni:
Workshop summary: Automated interpretation and modelling of cell images. ICML 2009: 4 - [c33]Luís Pedro Coelho, Aabid Shariff, Robert F. Murphy:
Nuclear Segmentation in Microscope Cell Images: A Hand-Segmented Dataset and Comparison of Algorithms. ISBI 2009: 518-521 - [c32]Tao Peng, Wei Wang, Gustavo K. Rohde, Robert F. Murphy:
Instance-Based Generative Biological Shape Modeling. ISBI 2009: 690-693 - [c31]Justin Newberg, Jieyue Li, Arvind Rao, Fredrik Ponten, Mathias Uhlen, Emma Lundberg, Robert F. Murphy:
Automated Analysis of Human Protein Atlas Immunofluorescence Images. ISBI 2009: 1023-1026 - [c30]Amr Ahmed, Eric P. Xing, William W. Cohen, Robert F. Murphy:
Structured correspondence topic models for mining captioned figures in biological literature. KDD 2009: 39-48 - 2008
- [j10]Yuntao Qian, Robert F. Murphy:
Improved recognition of figures containing fluorescence microscope images in online journal articles using graphical models. Bioinform. 24(4): 569-576 (2008) - [j9]Shann-Ching Chen, Geoffrey J. Gordon, Robert F. Murphy:
Graphical Models for Structured Classification, with an Application to Interpreting Images of Protein Subcellular Location Patterns. J. Mach. Learn. Res. 9: 651-682 (2008) - [c29]Luís Pedro Coelho, Robert F. Murphy:
Identifying Subcellular Locations from Images of Unknown Resolution. BIRD 2008: 235-242 - [c28]Estelle Glory, Justin Newberg, Robert F. Murphy:
Automated comparison of protein subcellular location patterns between images of normal and cancerous tissues. ISBI 2008: 304-307 - [c27]Robert F. Murphy:
Automated proteome-wide determination of subcellular location using high throughput microscopy. ISBI 2008: 308-311 - [c26]Gustavo K. Rohde, Wei Wang, Tao Peng, Robert F. Murphy:
Deformation-based nonlinear dimension reduction: Applications to nuclear morphometry. ISBI 2008: 500-503 - [c25]Luís Pedro Coelho, Estelle Glory-Afshar, Joshua D. Kangas, Shannon Quinn, Aabid Shariff, Robert F. Murphy:
Principles of Bioimage Informatics: Focus on Machine Learning of Cell Patterns. BioLINK@ISMB/ECCB 2008: 8-18 - [c24]Luís Pedro Coelho, Amr Ahmed, Andrew Arnold, Joshua D. Kangas, Abdul-Saboor Sheikh, Eric P. Xing, William W. Cohen, Robert F. Murphy:
Structured Literature Image Finder: Extracting Information from Text and Images in Biomedical Literature. BioLINK@ISMB/ECCB 2008: 23-32 - [e1]Mourad Elloumi, Josef Küng, Michal Linial, Robert F. Murphy, Kristan Schneider, Cristian Toma:
Bioinformatics Research and Development, Second International Conference, BIRD 2008, Vienna, Austria, July 7-9, 2008, Proceedings. Communications in Computer and Information Science 13, Springer 2008, ISBN 978-3-540-70598-7 [contents] - 2007
- [j8]Amina Chebira, Yann Barbotin, Charles Jackson, Thomas E. Merryman, Gowri Srinivasa, Robert F. Murphy, Jelena Kovacevic:
A multiresolution approach to automated classification of protein subcellular location images. BMC Bioinform. 8 (2007) - [c23]Xiang Chen, Robert F. Murphy:
Interpretation of Protein Subcellular Location Patterns in 3D Images Across Cell Types and Resolutions. BIRD 2007: 328-342 - [c22]Charles Jackson, Robert F. Murphy, Jelena Kovacevic:
Efficient Acquisition and Learning of Fluorescence Microscope Data Models. ICIP (6) 2007: 245-248 - [c21]Robert F. Murphy:
Systematic Description of Subcellular Location for Integration with Proteomics Databases and Systems Biology Modeling. ISBI 2007: 1052-1055 - [c20]Juchang Hua, Orhan N. Ayasli, William W. Cohen, Robert F. Murphy:
Identifying Fluorescence Microscope Images in Online Journal Articles Using Both Image and Text Features. ISBI 2007: 1224-1227 - [c19]Shann-Ching Chen, Ting Zhao, Geoffrey J. Gordon, Robert F. Murphy:
Automated image analysis of protein localization in budding yeast. ISMB/ECCB (Supplement of Bioinformatics) 2007: 66-71 - [c18]Zhenzhen Kou, William W. Cohen, Robert F. Murphy:
A Stacked Graphical Model for Associating Sub-Images with Sub-Captions. Pacific Symposium on Biocomputing 2007: 257-268 - 2006
- [j7]Shann-Ching Chen, Robert F. Murphy:
A graphical model approach to automated classification of protein subcellular location patterns in multi-cell images. BMC Bioinform. 7: 90 (2006) - [j6]Jelena Kovacevic, Robert F. Murphy:
Molecular and cellular bioimaging [Guest editorial]. IEEE Signal Process. Mag. 23(3): 19 (2006) - [c17]Shann-Ching Chen, Ting Zhao, Geoffrey J. Gordon, Robert F. Murphy:
A Novel Graphical Model Approach to Segmenting Cell Images. CIBCB 2006: 1-8 - [c16]Shann-Ching Chen, Geoffrey J. Gordon, Robert F. Murphy:
A novel approximate inference approach to automated classification of protein subcellular location patterns in multi-cell images. ISBI 2006: 558-561 - [c15]Ting Zhao, Stalia Soto, Robert F. Murphy:
Improved comparison of protein subcellular location patterns. ISBI 2006: 562-565 - [c14]Lionel Coulot, Heather Kirschner, Amina Chebira, José M. F. Moura, Jelena Kovacevic, Elvira Garcia Osuna, Robert F. Murphy:
Topology preserving STACS segmentation of protein subcellular location images. ISBI 2006: 566-569 - [c13]Yanhua Hu, Jesus Carmona, Robert F. Murphy:
Application of temporal texture features to automated analysis of protein subcellular locations in time series fluorescence microscope images. ISBI 2006: 1028-1031 - 2005
- [j5]Ting Zhao, Meel Velliste, Michael V. Boland, Robert F. Murphy:
Object Type Recognition for Automated Analysis of Protein Subcellular Location. IEEE Trans. Image Process. 14(9): 1351-1359 (2005) - [c12]Thomas E. Merryman, Jelena Kovacevic, Elvira Garcia Osuna, Robert F. Murphy:
Adaptive Multirate Data Acquisition of 3D Cell Images. ICASSP (2) 2005: 133-136 - [c11]Zhenzhen Kou, William W. Cohen, Robert F. Murphy:
High-recall protein entity recognition using a dictionary. ISMB (Supplement of Bioinformatics) 2005: 266-273 - [c10]Robert F. Murphy, Christos Faloutsos:
Research issues in protein location image databases. SIGMOD Conference 2005: 966-967 - [p1]Kai Huang, Robert F. Murphy:
Data Mining Methods for a Systematics of Protein Subcellular Location. Data Mining in Bioinformatics 2005: 143-187 - 2004
- [j4]Kai Huang, Robert F. Murphy:
Boosting accuracy of automated classification of fluorescence microscope images for location proteomics. BMC Bioinform. 5: 78 (2004) - [j3]Ambuj K. Singh, B. S. Manjunath, Robert F. Murphy:
A Distributed Database for BioMolecular Images. SIGMOD Rec. 33(2): 65-71 (2004) - [c9]Robert F. Murphy:
Automated Interpretation of Subcellular Location Patterns. ISBI 2004: 53-56 - [c8]Kai Huang, Robert F. Murphy:
Automated Classification of Subcellular Patterns In Multicell Images Without Segmentation Into Single Cells. ISBI 2004: 1139-1142 - 2003
- [j2]Robert F. Murphy, Meel Velliste, Gregory Porreca:
Robust Numerical Features for Description and Classification of Subcellular Location Patterns in Fluorescence Microscope Images. J. VLSI Signal Process. 35(3): 311-321 (2003) - [c7]Zhenzhen Kou, William W. Cohen, Robert F. Murphy:
Extracting information from text and images for location proteomics. BIOKDD 2003: 2-9 - [c6]William W. Cohen, Richard C. Wang, Robert F. Murphy:
Understanding captions in biomedical publications. KDD 2003: 499-504 - 2002
- [c5]Kai Huang, Jennifer Lin, James A. Gajnak, Robert F. Murphy:
Image content-based retrieval and automated interpretation of fluorescence microscope images via the protein subcellular location image database. ISBI 2002: 325-328 - [c4]Meel Velliste, Robert F. Murphy:
Automated determination of protein subcellular locations from 3D fluorescence microscope images. ISBI 2002: 867-870 - [c3]Robert F. Murphy, Meel Velliste, Gregory Porreca:
Robust classification of subcellular location patterns in fluorescence microscope images. NNSP 2002: 67-76 - 2001
- [j1]Michael V. Boland, Robert F. Murphy:
A neural network classifier capable of recognizing the patterns of all major subcellular structures in fluorescence microscope images of HeLa cells. Bioinform. 17(12): 1213-1223 (2001) - [c2]Robert F. Murphy, Meel Velliste, Jie Yao, Gregory Porreca:
Searching Online Journals for Fluorescence Microscope Images Depicting Protein Subcellular Location Patterns. BIBE 2001: 119-128 - 2000
- [c1]Robert F. Murphy, Michael V. Boland, Meel Velliste:
Towards a Systematics for Protein Subcellular Location: Quantitative Description of Protein Localization Patterns and Automated Analysis of Fluorescence Microscope Images. ISMB 2000: 251-259
Coauthor Index
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last updated on 2024-10-07 21:23 CEST by the dblp team
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